|
| Status |
Public on Aug 08, 2021 |
| Title |
Acini-cKO-3 |
| Sample type |
SRA |
| |
|
| Source name |
primary acinar cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
genotype: ERRgamma -/-
tissue: Pancreas
cell type: primary acinar cells
|
| Growth protocol |
Primary acinar cells were maintained in Waymouth's media supplemented with 2.5 % FBS, 1% Penicillin-Streptomycin mixture (PS), 0.25 mg/ml of trypsin inhibitor, and 25 ng/ml of recombinant human Epidermal Growth Factor (EGF).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using Trizol reagent (Invitrogen).
500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015.96) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2.
Read count extraction and normalization were performed using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts.
|
| |
|
| Submission date |
Aug 05, 2021 |
| Last update date |
Aug 09, 2021 |
| Contact name |
Jinhyuk Choi |
| E-mail(s) |
jinhyuk@kaist.ac.kr
|
| Organization name |
KAIST
|
| Street address |
291, Daehak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE181529 |
Quantitative analysis of ERR gamma conditional knock-out (cKO) acinar cell transcriptome |
|
| Relations |
| BioSample |
SAMN20593968 |
| SRA |
SRX11657273 |
