|
| Status |
Public on Dec 01, 2021 |
| Title |
d3_WT_487 |
| Sample type |
SRA |
| |
|
| Source name |
Intestinal epithelial cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Hk2 flox/flox
day of experiment: Day 3
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 |
SAMN16179005 |
| SRA |
SRX9132020 |
