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Sample GSM5504626 Query DataSets for GSM5504626
Status Public on Aug 08, 2021
Title Acini-cKO-1
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
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
BioSample SAMN20593966
SRA SRX11657271

Supplementary file Size Download File type/resource
GSM5504626_Acini-KO-1.txt.gz 146.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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