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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 |
|
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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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 |