|
| Status |
Public on Dec 15, 2017 |
| Title |
RNA-Seq AMPK-KO rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblast cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: mouse embryonic fibroblast cells
genotype: AMPK-/-
|
| Growth protocol |
The WT and AMPKa DKO MEFs were cultured in DMEM with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy mini kit (Qiagen, Cat#74104) according to the manufacturer's instructions.
1 ug of total RNA was used to construct the libraries using Illumina True-seq RNA sample preparation kit (RS-122-2001). Samples were sequenced using Illumina HiSeq2000 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b with default parameters. Refseq transcripts were supplied in GTF format file.
featureCounts v1.5.1 was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by edgeR.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample
|
| |
|
| Submission date |
Apr 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Kexin Xu |
| Organization name |
UT Health Science Center at San Antonio
|
| Department |
Molecular Medicine
|
| Street address |
7703 Floyd Curl, MC 8257
|
| City |
San Antonio |
| State/province |
Texas |
| ZIP/Postal code |
78229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE97735 |
Expression profiling of AMPK-regulated genes in mouse embryonic fibroblast cells |
| GSE97736 |
Phosphorylation of EZH2 by AMPK Suppresses PRC2 Methyltransferase Activity and Oncogenic Function |
|
| Relations |
| BioSample |
SAMN06718677 |
| SRA |
SRX2734510 |
