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Sample GSM6614362 Query DataSets for GSM6614362
Status Public on Jun 07, 2023
Title CD 3, scRNAseq, descending colon
Sample type SRA
 
Source name descending colon
Organism Homo sapiens
Characteristics tissue: descending colon
gender: Female
disease state: Crohn’s disease
Extracted molecule total RNA
Extraction protocol Biopsies (n=4-6 per patient) were taken from involved areas of the colon of UC and CD patients with signs of endoscopic activity, placed immediately in cold Hank’s Balanced Salt Solution (HBSS) (Gibco, MA, USA) and kept at 4º until processing (<1 h). Colonic biopsies from non-IBD controls were collected from the sigmoid colon and processed in the same way. Freshly collected biopsies were washed with HBSS/DTT (Roche, Spain) 5mM for 15 min and then washed in complete medium (CM) (RPMI 1640 medium (Lonza, MD, USA) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Biosera, France), 100U/ml penicillin, 100 U/ml streptomycin and 250 ng/ml amphotericin B (Lonza), 10µg/ml gentamicin sulfate (Lonza) and 1,5mM Hepes (Lonza) for 10 minutes. Both incubations were performed at room temperature in a platform rocker. Biopsies were chopped with scalpel and placed into tubes containing 500 μl of Digestion Solution (CM + Liberase TM (0.5 Wünsch units/ml) (Roche, Spain) + DNase I (10 μg/mL) (Roche, Spain) and incubated on a shaking platform for 1h at 250 RPM at 37ºC. After incubation biopsies were filtered through a 50-μm cell strainer (CellTrics, Sysmex, USA), washed with Dulbecco’s Phosphate Buffered Saline (PBS; Gibco, USA) and resuspended in RPMI (Roswell Park Memorial Institute) medium supplemented with 0.05% of Bovine fetal serum (BSA) at a concentration of ~500.000-1·106 cells/mL (Veny et al, JCC 2020).
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description 10x Genomics
Data processing The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38 p10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Oct 03, 2022
Last update date Jun 07, 2023
Contact name Azucena Salas
E-mail(s) asalas1@recerca.clinic.cat
Organization name IDIBAPS
Department Gastroenterology
Street address Rosselló, 149-153
City Barcelona
ZIP/Postal code 08036
Country Spain
 
Platform ID GPL18573
Series (1)
GSE214695 IBD single cell data from colonic mucosa
Relations
BioSample SAMN31138554
SRA SRX17781800

Supplementary file Size Download File type/resource
GSM6614362_CD-3_barcodes.tsv.gz 20.0 Mb (ftp)(http) TSV
GSM6614362_CD-3_features.tsv.gz 297.6 Kb (ftp)(http) TSV
GSM6614362_CD-3_matrix.mtx.gz 41.6 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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