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Sample GSM4197422 Query DataSets for GSM4197422
Status Public on Dec 01, 2019
Title DBSCC2
Sample type SRA
Source name colonic epithelium
Organism Homo sapiens
Characteristics strain: HT-29/B6-GR/MR
tissue: colonic epithelium
cell type: colonic epithelium from cell culture
Treatment protocol The cells were incubated with 10% hormone-free FCS (h-f FCS; Sigma-Aldrich, St. Louis, MO, USA) for 24 hours and stimulated with DBA (a combination of dexamethasone (D, 50 nM; Sigma-Aldrich, St. Louis, MO, USA), sodium butyrate (B,2 mM; Merck-Schuchardt, Hohenbrunn, Germany) and aldosterone (A, 3 nM; Sigma-Aldrich, St. Louis, MO, USA)) for four days. Three days following DBA stimulation, the cell monolayers were washed and incubated with heat-inactivated 10% h-f FCS without any antibiotic supplements for 24 hours.
Growth protocol Fresh HT-29/B6-GR/MR cells were cultured in RPMI medium (Sigma Aldrich, St. Louis, MO, USA) for one week at 37°C in humidified atmosphere (95% air / 5% CO2). RPMI media were supplemented with 10% fetal calf serum (FCS; Gibco Carlsbad, CA, USA), 1% penicillin/streptomycin (Gibco, Carlsbad, CA, USA), 500 IU/mL G418 (Merck Millipore, Billerica, MA, USA) and 200 μg/mL hygromycin B (Biochrom GmbH, Berlin, Germany). After one week, the trypsinized cells were seeded on Millicell PCF filters of 3 μm pore size (Merck Millipore, Billerica, MA, USA) and cultured for 7-10 days. Experiments were performed when the cell monolayers reached a transepithelial electrical resistance (TER) of 1500-2100 Ω * cmˆ2.
Extracted molecule total RNA
Extraction protocol Total RNA was obtained from HT-29/B6-GR/MR cells using mirVanaTM miRNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA).
RNA sequencing was performed by the TrueSeq Stranded Total RNA method.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description A006850028_106648_S46_L002
Data processing Basecalling was performed using CASAVA version 1.8.
STAR aligner version 2.7.1a in two pass mode was used to map and sort the reads against the human genome GRCh38 release 97.
featureCounts function of Bioconductor package Rsubread was used to count reads on gene level
Genome_build: GRCh38
Supplementary_files_format_and_content: CSV file containing raw read counts of features (genes) of all samples
Submission date Nov 30, 2019
Last update date Dec 02, 2019
Contact name Oliver Nagel
Organization name Charité - Universitätsmedizin Berlin
Department Department of Gastroenterology, Rheumatology and Infectious Diseases
Lab Institute of Clinical Physiology/Nutritional Medicine
Street address Hindenburgdamm 30
City Berlin
ZIP/Postal code 12203
Country Germany
Platform ID GPL24676
Series (1)
GSE141217 Campylobacter concisus Impairs sodium absorption in colonic epithelium via ENaC dysfunction and claudin-8 disruption
BioSample SAMN13431020
SRA SRX7246449

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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