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| Status |
Public on Feb 23, 2021 |
| Title |
normal IEL sample from colectomy patient donor 7420 |
| Sample type |
SRA |
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| Source name |
normal IEL sample from colectomy patient donor
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| Organism |
Homo sapiens |
| Characteristics |
subject id: donor 7420
disease status: Normal
compartment: IEL
cell type: T cells
sorting: CD3+, CD19-
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
T cells were sorted from processed IEL and LP as CD45+, lymphocyte gate, singlets, alive CD3+ CD19- expression.
Using the Chromium Single Cell 3′ Reagent Kit v3 User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
H_ZF-Unknown_N-7420-2
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| Data processing |
Processing was performed with the 10X Chromium cellranger pipeline version 2.0.2 using default settings
Genome_build: Genome_build: GRCm38.1.2.0
Supplementary_files_format_and_content: tar.gz of Filtered feature-barcode matrix with raw counts for each sample
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| Submission date |
Sep 04, 2020 |
| Last update date |
Feb 25, 2021 |
| Contact name |
Ramya Gamini |
| Organization name |
Pfizer Inc.,
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| Street address |
1 Portland st
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| City |
Cambrdge |
| State/province |
MA |
| ZIP/Postal code |
02139139 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE157477 |
ScRNAseq of human IEL and LPL T lymphocytes |
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| Relations |
| BioSample |
SAMN16058278 |
| SRA |
SRX9075309 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4766845_N-7420-2_filtered_gene_bc_matrices.tar.gz |
26.6 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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