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Sample GSM4785457 Query DataSets for GSM4785457
Status Public on Dec 01, 2021
Title d7_KO_423
Sample type SRA
 
Source name Intestinal epithelial cells
Organism Mus musculus
Characteristics genotype: Hk2dIEC
day of experiment: Day 7
strain: C57BL/6
Treatment protocol For DSS-induced colitis we used 10 to 12 weeks old male mice. Both genotypes were co-housed throughout the entire experiment. To induce colitis, mice received 1,5% (w/v) dextran sodium sulfate in autoclaved tap water.
Growth protocol All animal experiments were approved by the local animal safety review board of the federal ministry of Schleswig Holstein and conducted according to national and international laws and policies (V 312-72241.121-33 (95-8/11) and V242-62324/2016 (97-8/16)). Specific-pathogen free (SPF) animals were housed in the Central Animal Facility (ZTH) of the University Hospital Schleswig Holstein (UKSH, Kiel, Germany). To create the Hk2∆IEC mouse line, we crossed commercially available mice carrying a floxed Hk2 allele (EMMA #02074, 45) with mice expressing the CRE recombinase under the control of the Villin promoter. As controls we used littermate Hk2fl/fl mice, referred to as WT mice. All mice were kept under a 12-h light cycle and fed gamma-irradiated diet ad libitum. Mice were killed by cervical dislocation prior to removing tissues for histological and molecular analyses. For basal phenotyping we used 9 to 11 and 86 to 92 weeks old mice.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was measured using a NanoDrop ND-1000 spectrophotometer (PeqLab Biotechnologie). Total RNA was extracted as described from isolated IECs from Hk2∆IEC and littermate control mice under untreated conditions and after administering DSS for 3 or 7 days.
RNA libraries were prepared using TruSeq stranded mRNA Kit (Illumina) according to manufacturer’s instructions. All samples were sequenced using an Illumina NovaSeq 6000 sequencer (Illumina, San Diego,CA) with an average of 23 million paired-end reads (2x 50 bp) at IKMB NGS core facilities.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore
The filtered reads were mapped to the mouse genome (GRCm38) using STAR aligner
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene expression counts in tabular format
 
Submission date Sep 16, 2020
Last update date Dec 01, 2021
Contact name Neha Mishra
E-mail(s) n.mishra@ikmb.uni-kiel.de
Organization name Institute of Clinical Molecular Biology
Lab Cell biology Lab
Street address Rosalind-Franklin-Str. 12
City Kiel
ZIP/Postal code 24105
Country Germany
 
Platform ID GPL24247
Series (1)
GSE158026 Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis
Relations
BioSample SAMN16179008
SRA SRX9132017

Supplementary file Size Download File type/resource
GSM4785457_I10118-L1_S26_L001_R1_001Aligned.sortedByCoord.out_gene.featureCounts.txt.gz 3.4 Mb (ftp)(http) TXT
GSM4785457_I10118-L1_S26_L002_R1_001Aligned.sortedByCoord.out_gene.featureCounts.txt.gz 3.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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