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Sample GSM6090503 Query DataSets for GSM6090503
Status Public on Oct 18, 2022
Title GCA7
Sample type SRA
 
Source name Terminal ileal biopsies
Organism Homo sapiens
Characteristics gender: Female
race: African American
age: 18
disease status: Not IBD
time point: Screening/Baseline
tissue: Ileal biopsies
Extracted molecule total RNA
Extraction protocol Terminal ieal biopsies collected were first minced with micro-scissors on ice in HBSS buffer containing 2mM EDTA without Ca2+/Mg2+. The minced pieces were vortexed gently and allowed to settle for 2 min on ice. The supernatant containing some of the loosely associated immune cells and other single cells released by the mincing process (primarily lamina propria) were removed and the sedimented minced tissue pieces were digested on ice with B. licheniformis protease for 30 minutes. Samples were periodically vortexed gently and placed back on ice during enzymatic digestion. For each patient sample, the supernatant fraction was mixed with the enzyme digested fraction 1 : 1 for non-inflamed mucosa, and 1 : 4 for inflamed mucosa (minimizing overloading with immune cells) before being passed through a 40- and then 20-µm filter, washed and finally resuspended at the appropriate cell density for loading onto the 10X Chromium Controller (~1000-1200 cells/µL). 
Tissue derived single cells were loaded onto the 10X Chromium Controller targeting 10,000 cells. Single cell capture, barcoding, GEM-RT, clean-up, cDNA amplification and library construction were performed according to the manufacturers’ instructions using Chromium Single Cell A Chip Kit (cat no: PN-1000152) and Chromium 5' Library & Gel Bead Kit (v1 chemistry; cat no: PN-1000006). Final library pools were sequenced in four batches on Illumina’s Novaseq6000 instrument at Georgia Tech Genomics Core or Yerkes Genomic Core with a targeted sequencing depth of 50,000 reads/cell.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Single cell 5' chemistry
10x Genomics
Data processing The demultiplexing, barcoded processing and gene counting were made using the Cell Ranger software v6 (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/6.0/)
Assembly: Human reference GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date May 02, 2022
Last update date Oct 18, 2022
Contact name Suresh Venkateswaran
E-mail(s) svenk30@emory.edu
Organization name Emory University
Department Pediatrics
Street address 1760 Haygood Drive, HSRB, Room No: E-250
City Atlanta
State/province Georgia
ZIP/Postal code 30322
Country USA
 
Platform ID GPL24676
Series (1)
GSE202052 Assessing Cellular and Transcriptional diversity of IIeal Mucosa amongst Treatment Naïve and Treated Crohn’s disease
Relations
BioSample SAMN28041213
SRA SRX15110552

Supplementary file Size Download File type/resource
GSM6090503_GCA7_barcodes.tsv.gz 19.7 Kb (ftp)(http) TSV
GSM6090503_GCA7_features.tsv.gz 325.6 Kb (ftp)(http) TSV
GSM6090503_GCA7_matrix.mtx.gz 11.1 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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