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| Status |
Public on Dec 01, 2019 |
| Title |
DBSCC1 |
| Sample type |
SRA |
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| Source name |
colonic epithelium
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| Organism |
Homo sapiens |
| Characteristics |
strain: HT-29/B6-GR/MR
tissue: colonic epithelium
cell type: colonic epithelium from cell culture
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| 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.
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
A006850028_106646_S45_L002
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| 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
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| Submission date |
Nov 30, 2019 |
| Last update date |
Dec 02, 2019 |
| Contact name |
Oliver Nagel |
| Organization name |
Charité - Universitätsmedizin Berlin
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| Department |
Department of Gastroenterology, Rheumatology and Infectious Diseases
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| Lab |
Institute of Clinical Physiology/Nutritional Medicine
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| Street address |
Hindenburgdamm 30
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| City |
Berlin |
| ZIP/Postal code |
12203 |
| Country |
Germany |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE141217 |
Campylobacter concisus Impairs sodium absorption in colonic epithelium via ENaC dysfunction and claudin-8 disruption |
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| Relations |
| BioSample |
SAMN13431021 |
| SRA |
SRX7246448 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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