|
| Status |
Public on May 29, 2024 |
| Title |
Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide+/+ C57BL/6J, biol rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreas
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Pancreas
strain: C57BL/6J
cell type: Hand-picked pancreatic islets
Sex: Female
genotype: Ide+/+
treatment: 2-weeks high-fat diet
age at_treatment_initiation: 10 weeks-old
|
| Treatment protocol |
10-weeks-old female Ide-/- and Ide+/+ C57BL/6J mice were fed with a high-fat diet for 2 weeks (D12492. Rodent Diet With 60 kcal% Fat, Brogaarden, Denmark).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of high-quality total RNA sample (RIN>6.5) was used for the construction of sequencing libraries.
RNA-seq libraries for RNA-seq were prepared using NEBNext low input RNA library prep kit (NEB) according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequence reads were mapped to GRCm38 from Ensembl release 101 using STAR v.2.7.1a with the following parameters : --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
Read count were performed using RSEM v1.3.1) with the AlignedtoTranscriptome bam files from STAR
Supplementary files format and content: tab-delimited text files including RSEM expected count, FPKM and TPM values for each sample
|
| |
|
| Submission date |
Jul 08, 2022 |
| Last update date |
May 29, 2024 |
| Contact name |
François-Xavier MAUVAIS |
| E-mail(s) |
francois-xavier.mauvais@inserm.fr
|
| Organization name |
INSERM
|
| Department |
U1151
|
| Lab |
van Endert
|
| Street address |
160 rue de Vaugirard
|
| City |
Paris |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE207797 |
Effect of depletion of IDE on gene expression in adult pancreatic islets during a metabolic stress |
|
| Relations |
| BioSample |
SAMN29613460 |
| SRA |
SRX16101786 |
