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Sample GSM7881826 Query DataSets for GSM7881826
Status Public on Aug 02, 2024
Title pouch_cdp5, scRNA-seq
Sample type SRA
 
Source name pouch
Organism Homo sapiens
Characteristics tissue: pouch
condition: cdp
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
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description counts.txt.gz
metadata.txt
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
 
Submission date Nov 03, 2023
Last update date Aug 02, 2024
Contact name Khai Nguyen
E-mail(s) k.m.nguyen@wustl.edu
Organization name Washington University in St. Louis
Department Pathology & Immunology
Lab Marco Colonna
Street address 425 South Euclid Ave, 8107, 8th floor BJCIH,
City Saint Louis
State/province MO
ZIP/Postal code 63112
Country USA
 
Platform ID GPL24676
Series (1)
GSE246987 Mucosal Single-Cell Profiling of Crohn's-Like Disease of the Pouch Reveals Unique Pathogenesis and Therapeutic Targets

Supplementary file Size Download File type/resource
GSM7881826_CDP_Pouch5_barcodes.tsv.gz 30.1 Kb (ftp)(http) TSV
GSM7881826_CDP_Pouch5_features.tsv.gz 325.6 Kb (ftp)(http) TSV
GSM7881826_CDP_Pouch5_matrix.mtx.gz 29.0 Mb (ftp)(http) MTX
Raw data not provided for this record

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