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| Status |
Public on Jun 07, 2023 |
| Title |
CD 5, scRNAseq, sigma |
| Sample type |
SRA |
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| Source name |
sigma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: sigma
gender: Male
disease state: Crohn’s disease
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
10x Genomics
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| 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
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| Submission date |
Oct 03, 2022 |
| Last update date |
Jun 07, 2023 |
| Contact name |
Azucena Salas |
| E-mail(s) |
asalas1@recerca.clinic.cat
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| Organization name |
IDIBAPS
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| Department |
Gastroenterology
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| Street address |
Rosselló, 149-153
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| City |
Barcelona |
| ZIP/Postal code |
08036 |
| Country |
Spain |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE214695 |
IBD single cell data from colonic mucosa |
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| Relations |
| BioSample |
SAMN31138552 |
| SRA |
SRX17781802 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6614364_CD-5_barcodes.tsv.gz |
20.0 Mb |
(ftp)(http) |
TSV |
| GSM6614364_CD-5_features.tsv.gz |
297.6 Kb |
(ftp)(http) |
TSV |
| GSM6614364_CD-5_matrix.mtx.gz |
15.0 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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