|
| Status |
Public on Sep 25, 2024 |
| Title |
Pancreas, Caerulein treated 5H, 7w of age, mouse 1 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
cell line: C57BL/6JRj
treatment: Caerulein 5H
|
| Treatment protocol |
To induce tissue injury in the pancreas, the cholecystokinin analogue caerulein (C9026; Sigma-Aldrich) was administered through intraperitoneal injections every hour for 4 hours at a concentration of 125ug/kg body weight.
|
| Growth protocol |
All animal experiments described were approved by the University of Copenhagen’s ethical committee. All animal experiments were performed in accordance with the Danish Animal Welfare Act and FELASA. Attention has been paid to the ARRIVE guidelines, recommendations, and policy. C57BL/6JRj mice used in this project were purchased from Janvier Labs (Le Genest-Saint-Isle, France), and animals were fed a laboratory chow diet and had free access to water. Mice were genotyped at weaning.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Based on the commercial protocol, the pancreatic tissue’s RNA was extracted using RNeasy Mini Kit (Qiagen #74106). Pancreatic tissue is added to 2 mL of RLT buffer (with 2-Mercaptoethanol, 1:100) and homogenised using a homogeniser (IKA, T10 basic). Homogenizer was washed between the samples with MilliQ water and 70% ethanol to avoid cross-contamination. After tissues were homogenised, 1 volume (2 mL) of 70% ethanol was added. Next, RNeasy Spin columns were loaded with 700μL of the sample and centrifuged for 30 seconds at maximum speed (>13.000rpm). All collected flow-through was discarded. This step was repeated several times. From here, the instructors´ protocol was followed. The extracted RNA’s concentration and sample quality were measured using a spectrophotometer (DeNovix, DS-11).
For RNA library preparation the mRNA is enriched by poly(A) capture. RNA is then fragmented by enzyme digestion (or Covaris). cDNA reverse transcription is followed by RNA library preparation. After a library quality control, sequencing is performed using the Illumina NovaSeq 6000 platform, pair-end 150 bp sequencing strategy (short-reads), with a depth of the recommended 20 million read pair per sample. Following data quality control, bioinformatic analysis is performed. Gene set enrichment analysis was performed using the open source GSEA software46
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
recommended 20 million read pair per sample
A_5HvsY_5H_deg.tsv
Y_5HvsY_control_deg.tsv
gene_count.tsv
gene_fpkm.tsv
Y_5H_1
|
| Data processing |
Mapping to the mouse genome was performed using hisat2 software 2.0.5
Reads with adapter contamination were removed. Reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) were removed. Reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read were removed.
Quantifications perfomed using Featurecounts 1.5.0-p3
Assembly: mm10
Supplementary files format and content: Tab-delimited tsv file includes raw counts for each sample
Supplementary files format and content: Tab-delimited tsv file includes fpkm values for each sample
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| |
|
| Submission date |
May 24, 2024 |
| Last update date |
Sep 25, 2024 |
| Contact name |
Luis Arnes |
| E-mail(s) |
luis.arnes@bric.ku.dk
|
| Phone |
93509271
|
| Organization name |
Biotech Research & Innovation Centre
|
| Street address |
Ole Maaløes Vej 5
|
| City |
Copenhagen |
| ZIP/Postal code |
DK-2200 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE268278 |
Age-related decline in pancreas regeneration is associated with an increased proinflammatory response to injury |
|
| Relations |
| BioSample |
SAMN41522825 |
| SRA |
SRX24681759 |
