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Status |
Public on Aug 02, 2024 |
Title |
ileum_cdp4, scBCR-seq |
Sample type |
SRA |
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Source name |
ileum
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Organism |
Homo sapiens |
Characteristics |
tissue: ileum condition: cdp
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Extracted molecule |
total RNA |
Extraction protocol |
Live nucleated cells were sort-purified from mucosal cell suspensions as 7AAD-, MHC-I+ singlets. Sorted cells were sequenced using 10X Genomics platform with chemistry version 2 at the Genome Technology Access Center at Washington University
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Library strategy |
OTHER |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
counts.txt.gz
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Data processing |
Sample demultiplexing, barcode processing, and single-cell counting was performed using Cell Ranger suite. The Seurat R package (v4.0.4) was used for downstream analyses. Broad quality control was performed with cutoffs of < 15% mitochondrial content, > 200 and < 6000 unique features. Doublet removal was performed using DoubletFinder (v2.0.3). Samples from different batches were integrated using Seurat’s FindIntegrationAnchors and reciprocal principal component analysis (rPCA), and regressed on percentage of mitochondrial genes. Counts were normalized using SCTransform. Assembly: GRch38 Supplementary files format and content: scRNA-seq: count.txt (aggregated scRNA-seq matrix) and metadata.txt. In count.txt, sample column "1" corresponds to metadata.txt 1st sample row (AAACCTGAGACCCACC-1_1), sample column "2" corresponds to metadata.txt 2nd sample row (AAACCTGAGATATGGT-1_1), and so on. Supplementary files format and content: scTCR-seq: filtered_contig_annotations_vdj_t.csv Supplementary files format and content: scBCR-seq: filtered_contig_annotations_vdj_b.csv Library strategy: scBCR-seq
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Submission date |
Nov 03, 2023 |
Last update date |
Aug 02, 2024 |
Contact name |
Khai Nguyen |
E-mail(s) |
k.m.nguyen@wustl.edu
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Organization name |
Washington University in St. Louis
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Department |
Pathology & Immunology
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Lab |
Marco Colonna
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Street address |
425 South Euclid Ave, 8107, 8th floor BJCIH,
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City |
Saint Louis |
State/province |
MO |
ZIP/Postal code |
63112 |
Country |
USA |
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Platform ID |
GPL24676 |
Series (1) |
GSE246987 |
Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets |
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Supplementary file |
Size |
Download |
File type/resource |
GSM7881864_CDP_ileum4_filtered_contig_annotations_vdj_b.csv.gz |
235.9 Kb |
(ftp)(http) |
CSV |
Raw data not provided for this record |
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