SRX22369530 iDisc_D0_GEX-1 SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417195 Day 0 iDiscoid (iPSCs) iDisc_D0_GEX-1 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369531 iDisc_D0_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417195 Day 0 iDiscoid (iPSCs) iDisc_D0_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369532 iDisc_D3_GEX SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417196 Day 3 iDiscoid iDisc_D3_GEX RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369533 iDisc_D3_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417196 Day 3 iDiscoid iDisc_D3_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369534 iDisc_D4-1_GEX-1 SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417197 Day 4 iDiscoid 1 iDisc_D4-1_GEX-1 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369535 iDisc_D4-1_GEX-2 SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417197 Day 4 iDiscoid 1 iDisc_D4-1_GEX-2 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369536 iDisc_D4-1_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417197 Day 4 iDiscoid 1 iDisc_D4-1_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369537 iDisc_D4-2_GEX-1 SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417198 Day 4 iDiscoid 2 iDisc_D4-2_GEX-1 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369538 iDisc_D4-2_GEX-2 SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417198 Day 4 iDiscoid 2 iDisc_D4-2_GEX-2 RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369539 iDisc_D4-2_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417198 Day 4 iDiscoid 2 iDisc_D4-2_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369540 iDisc_D5_GEX SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417199 Day 5 iDiscoid iDisc_D5_GEX RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369541 iDisc_D5_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417199 Day 5 iDiscoid iDisc_D5_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369542 iDisc_D0.5_GEX SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417200 Day 0.5 iDiscoid iDisc_D0.5_GEX RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369543 iDisc_D21_GEX SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417201 Day 21 iDiscoid iDisc_D21_GEX RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369544 iDisc_D21_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417201 Day 21 iDiscoid iDisc_D21_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369545 iDisc_D0.5_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417200 Day 0.5 iDiscoid iDisc_D0.5_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369546 iDisc_D1_GEX SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417202 Day 1 iDiscoid iDisc_D1_GEX RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369547 iDisc_D1_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417202 Day 1 iDiscoid iDisc_D1_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369548 iDisc_D1.5_GEX SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417203 Day 1.5 iDiscoid iDisc_D1.5_GEX RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369549 iDisc_D1.5_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417203 Day 1.5 iDiscoid iDisc_D1.5_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369550 iDisc_D2_GEX SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417204 Day 2 iDiscoid iDisc_D2_GEX RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000 SRX22369551 iDisc_D2_CellPlex SRP470196 bp0 Samples were prepared as described by the 10x Genomics Cell Multiplexing Oligo Labeling for Single Cell RNA Sequencing Protocols for cells with >80% viability. Cells were labeled with CellPlex Multiplexing Solution from 10x genomics with a sample-unique oligo barcode for multiplexing with other samples. Following a final counting and viability analysis, cells and 10x Genomics reagents were loaded into the single cell cassette, with a target of 25000 single cells for analysis, accounting for predicted cell loss and doublets resulting from multiplexing as laid out in the user guide for the Chromium Single-Cell 3 Reagent Kit (10x Genomics). After generation of GEMs, the cDNA library was prepared by Pitt Single Cell Core staff following the appropriate steps determined by the 10x Genomics user guide. Libraries were sent to the UPMC Genome Center for sequencing by a NovaSeq S4-200 for an intended read depth of 100,000 reads per cell with 150 bp paired end reads. Our downstream analysis from the sequencing data yielded between 40k-150k mean reads per cell in different samples. The 10x Genomics CellRanger pipeline was used to align reads to the reference genome (GRCh38.84) appended with transgene sequences, to assign reads to individual cells, and to estimate gene expression based on UMI counts. BAM files were created from the multiplexed fastq files, and these BAM files were converted back to Fastq files via the "bamtofastq" function in CellRanger. SRS19417204 Day 2 iDiscoid iDisc_D2_CellPlex RNA-Seq TRANSCRIPTOMIC SINGLE CELL RANDOM Illumina NovaSeq 6000