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Status |
Public on Oct 18, 2022 |
Title |
GCA7 |
Sample type |
SRA |
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Source name |
Terminal ileal biopsies
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Organism |
Homo sapiens |
Characteristics |
gender: Female race: African American age: 18 disease status: Not IBD time point: Screening/Baseline tissue: Ileal biopsies
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic single cell |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
Single cell 5' chemistry 10x Genomics
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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
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Submission date |
May 02, 2022 |
Last update date |
Oct 18, 2022 |
Contact name |
Suresh Venkateswaran |
E-mail(s) |
svenk30@emory.edu
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Organization name |
Emory University
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Department |
Pediatrics
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Street address |
1760 Haygood Drive, HSRB, Room No: E-250
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City |
Atlanta |
State/province |
Georgia |
ZIP/Postal code |
30322 |
Country |
USA |
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Platform ID |
GPL24676 |
Series (1) |
GSE202052 |
Assessing Cellular and Transcriptional diversity of IIeal Mucosa amongst Treatment Naïve and Treated Crohn’s disease |
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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 Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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