SRX12683997 GSM5632809 SRP342094 SRS10634998 GSM5632809 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632809 GSM5632809 GEO Accession GSM5632809 SRX12683998 GSM5632810 SRP342094 SRS10634999 GSM5632810 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632810 GSM5632810 GEO Accession GSM5632810 SRX12683999 GSM5632811 SRP342094 SRS10635000 GSM5632811 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632811 GSM5632811 GEO Accession GSM5632811 SRX12684000 GSM5632812 SRP342094 SRS10635001 GSM5632812 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632812 GSM5632812 GEO Accession GSM5632812 SRX12684001 GSM5632813 SRP342094 SRS10635002 GSM5632813 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632813 GSM5632813 GEO Accession GSM5632813 SRX12684002 GSM5632814 SRP342094 SRS10635003 GSM5632814 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632814 GSM5632814 GEO Accession GSM5632814 SRX12684003 GSM5632815 SRP342094 SRS10635004 GSM5632815 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632815 GSM5632815 GEO Accession GSM5632815 SRX12684004 GSM5632816 SRP342094 SRS10635005 GSM5632816 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632816 GSM5632816 GEO Accession GSM5632816 SRX12684005 GSM5632817 SRP342094 SRS10635006 GSM5632817 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632817 GSM5632817 GEO Accession GSM5632817 SRX12684006 GSM5632818 SRP342094 SRS10635007 GSM5632818 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632818 GSM5632818 GEO Accession GSM5632818 SRX12684007 GSM5632819 SRP342094 SRS10635008 GSM5632819 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632819 GSM5632819 GEO Accession GSM5632819 SRX12684008 GSM5632820 SRP342094 SRS10635009 GSM5632820 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632820 GSM5632820 GEO Accession GSM5632820 SRX12684009 GSM5632821 SRP342094 SRS10635010 GSM5632821 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632821 GSM5632821 GEO Accession GSM5632821 SRX12684010 GSM5632822 SRP342094 SRS10635011 GSM5632822 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632822 GSM5632822 GEO Accession GSM5632822 SRX12684011 GSM5632823 SRP342094 SRS10635012 GSM5632823 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632823 GSM5632823 GEO Accession GSM5632823 SRX12684012 GSM5632824 SRP342094 SRS10635013 GSM5632824 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632824 GSM5632824 GEO Accession GSM5632824 SRX12684013 GSM5632825 SRP342094 SRS10635014 GSM5632825 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632825 GSM5632825 GEO Accession GSM5632825 SRX12684014 GSM5632826 SRP342094 SRS10635015 GSM5632826 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632826 GSM5632826 GEO Accession GSM5632826 SRX12684015 GSM5632827 SRP342094 SRS10635016 GSM5632827 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632827 GSM5632827 GEO Accession GSM5632827 SRX12684016 GSM5632828 SRP342094 SRS10635017 GSM5632828 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632828 GSM5632828 GEO Accession GSM5632828 SRX12684017 GSM5632829 SRP342094 SRS10635018 GSM5632829 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632829 GSM5632829 GEO Accession GSM5632829 SRX12684018 GSM5632830 SRP342094 SRS10635019 GSM5632830 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632830 GSM5632830 GEO Accession GSM5632830 SRX12684019 GSM5632831 SRP342094 SRS10635020 GSM5632831 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632831 GSM5632831 GEO Accession GSM5632831 SRX12684020 GSM5632832 SRP342094 SRS10635021 GSM5632832 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632832 GSM5632832 GEO Accession GSM5632832 SRX12684021 GSM5632833 SRP342094 SRS10635022 GSM5632833 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632833 GSM5632833 GEO Accession GSM5632833 SRX12684022 GSM5632834 SRP342094 SRS10635023 GSM5632834 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632834 GSM5632834 GEO Accession GSM5632834 SRX12684023 GSM5632835 SRP342094 SRS10635024 GSM5632835 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632835 GSM5632835 GEO Accession GSM5632835 SRX12684024 GSM5632836 SRP342094 SRS10635025 GSM5632836 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632836 GSM5632836 GEO Accession GSM5632836 SRX12684025 GSM5632837 SRP342094 SRS10635026 GSM5632837 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632837 GSM5632837 GEO Accession GSM5632837 SRX12684026 GSM5632838 SRP342094 SRS10635027 GSM5632838 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632838 GSM5632838 GEO Accession GSM5632838 SRX12684027 GSM5632839 SRP342094 SRS10635028 GSM5632839 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632839 GSM5632839 GEO Accession GSM5632839 SRX12684028 GSM5632840 SRP342094 SRS10635029 GSM5632840 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632840 GSM5632840 GEO Accession GSM5632840 SRX12684029 GSM5632841 SRP342094 SRS10635030 GSM5632841 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632841 GSM5632841 GEO Accession GSM5632841 SRX12684030 GSM5632842 SRP342094 SRS10635031 GSM5632842 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632842 GSM5632842 GEO Accession GSM5632842 SRX12684031 GSM5632843 SRP342094 SRS10635032 GSM5632843 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632843 GSM5632843 GEO Accession GSM5632843 SRX12684032 GSM5632844 SRP342094 SRS10635033 GSM5632844 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632844 GSM5632844 GEO Accession GSM5632844 SRX12684033 GSM5632845 SRP342094 SRS10635034 GSM5632845 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632845 GSM5632845 GEO Accession GSM5632845 SRX12684034 GSM5632846 SRP342094 SRS10635035 GSM5632846 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632846 GSM5632846 GEO Accession GSM5632846 SRX12684035 GSM5632847 SRP342094 SRS10635036 GSM5632847 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632847 GSM5632847 GEO Accession GSM5632847 SRX12684036 GSM5632848 SRP342094 SRS10635037 GSM5632848 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632848 GSM5632848 GEO Accession GSM5632848 SRX12684037 GSM5632849 SRP342094 SRS10635038 GSM5632849 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632849 GSM5632849 GEO Accession GSM5632849 SRX12684038 GSM5632850 SRP342094 SRS10635039 GSM5632850 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632850 GSM5632850 GEO Accession GSM5632850 SRX12684039 GSM5632851 SRP342094 SRS10635040 GSM5632851 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632851 GSM5632851 GEO Accession GSM5632851 SRX12684040 GSM5632852 SRP342094 SRS10635041 GSM5632852 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632852 GSM5632852 GEO Accession GSM5632852 SRX12684041 GSM5632853 SRP342094 SRS10635042 GSM5632853 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632853 GSM5632853 GEO Accession GSM5632853 SRX12684042 GSM5632854 SRP342094 SRS10635043 GSM5632854 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632854 GSM5632854 GEO Accession GSM5632854 SRX12684043 GSM5632855 SRP342094 SRS10635044 GSM5632855 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632855 GSM5632855 GEO Accession GSM5632855 SRX12684044 GSM5632856 SRP342094 SRS10635045 GSM5632856 RNA-Seq TRANSCRIPTOMIC cDNA RNA from FROZ samples was isolated using homogenization and RNAzol® RT (cat #RN 190; Molecular Research Center, Cincinnati, OH) followed by purification using a RNeasy MinElute column (Qiagen, GmbH, Hilden, Germany). RNA purity and concentration were assessed by Agilent Bioanalyzer (RNA 6000 Pico Kit cat #5067-1514 or Nano Kit 5067-1529; Agilent Technologies GmbH, Berlin, Germany), NanoDrop™-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA) and Qubit fluorometer (RNA BR Assay Kit cat #Q10210 or HS Assay Kit cat #Q32852; ThermoFisher Scientific, Waltham, MA). For FFPE samples, excess paraffin was removed and the tissue was transferred into lysis buffer, melted in mineral oil to remove remaining paraffin, and lysed. RNA within the lysate is annealed to a matched pair of detector oligos, with each pair of detector oligos targeting a single transcript within the mouse genome. Libraries were prepared as described in Trejo et al. (2019) (https://doi.org/10.1371/journal.pone.0212031). FROZ RNA or FFPE lysate was processed in annealing buffer with detector oligos (DOs), probes that have high selectivity for 21,451 Mus musculus target genes (Whole Genome Mouse Assay, BioSpyder Technologies; Carlsbad, CA). After oligo ligation, a nuclease mixture was added to digest unbound or erroneously bound DOs. A final ligase mix was added to facilitate addition of a single primer pair. The ligases were deactivated with heat and the probes were amplified by PCR, which added sample specific barcodes that flank the target sequence and are inserted into the standard Illumina adaptors. PCR-amplified and barcoded samples were then pooled into a single library, purified and sequenced. TempO-Seq RNA samples were sequenced on the Illumina HiSeq 2500 platform with 50-bp single-end reads to a target read depth of 5 million. Overly abundant transcripts were attenuated equally across all samples to save sequencing reads. Targeted RNA-seq Illumina HiSeq 2500 gds 305632856 GSM5632856 GEO Accession GSM5632856