SRX18360140 GSM6753357_r1 SRP409417 PRJNA904693 SRS15846774 GSM6753357 GSM6753357 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360141 GSM6753358_r1 SRP409417 PRJNA904693 SRS15846775 GSM6753358 GSM6753358 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360142 GSM6753359_r1 SRP409417 PRJNA904693 SRS15846776 GSM6753359 GSM6753359 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360143 GSM6753360_r1 SRP409417 PRJNA904693 SRS15846777 GSM6753360 GSM6753360 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360144 GSM6753361_r1 SRP409417 PRJNA904693 SRS15846778 GSM6753361 GSM6753361 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360145 GSM6753362_r1 SRP409417 PRJNA904693 SRS15846779 GSM6753362 GSM6753362 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360146 GSM6753363_r1 SRP409417 PRJNA904693 SRS15846780 GSM6753363 GSM6753363 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360147 GSM6753364_r1 SRP409417 PRJNA904693 SRS15846781 GSM6753364 GSM6753364 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360148 GSM6753365_r1 SRP409417 PRJNA904693 SRS15846782 GSM6753365 GSM6753365 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360149 GSM6753366_r1 SRP409417 PRJNA904693 SRS15846783 GSM6753366 GSM6753366 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360150 GSM6753367_r1 SRP409417 PRJNA904693 SRS15846784 GSM6753367 GSM6753367 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360151 GSM6753368_r1 SRP409417 PRJNA904693 SRS15846785 GSM6753368 GSM6753368 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360152 GSM6753369_r1 SRP409417 PRJNA904693 SRS15846786 GSM6753369 GSM6753369 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360153 GSM6753370_r1 SRP409417 PRJNA904693 SRS15846787 GSM6753370 GSM6753370 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360154 GSM6753371_r1 SRP409417 PRJNA904693 SRS15846788 GSM6753371 GSM6753371 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360155 GSM6753372_r1 SRP409417 PRJNA904693 SRS15846789 GSM6753372 GSM6753372 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360156 GSM6753373_r1 SRP409417 PRJNA904693 SRS15846790 GSM6753373 GSM6753373 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500 SRX18360157 GSM6753374_r1 SRP409417 PRJNA904693 SRS15846791 GSM6753374 GSM6753374 RNA-Seq TRANSCRIPTOMIC cDNA Fifteen FFPE sections of 4 μm thickness from each sample were stored in tubes prior to RNA extraction, as previously described 16,36. Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Illumina, San Diego, CA, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorom-eter (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method, as previously described 15,37. We recently demonstrated that MACE al-lows sequencing of FFPE samples with high accuracy, even after more than 10 years of storage 18. Briefly, 18 barcoded libraries comprising unique molecule identifiers were se-quenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers. NextSeq 500