|
Status |
Public on Aug 08, 2021 |
Title |
Acini-cKO-2 |
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.
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|
|
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 |
SAMN20593967 |
SRA |
SRX11657272 |