|
| Status |
Public on Mar 30, 2016 |
| Title |
RNAseq_prePHX_KO_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
frozen pre-hepatectomy liver tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/B6 and 129 mix
tissue: liver
age: postnatal day 90
genotype: Arid1a Fl/Fl; Alb-cre
|
| Treatment protocol |
The mice were performed for two thirds partial hepatectomy and 40 hours later sack mice.Liver tissues were collected and frozen in -80.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen liver tissues RNA was harvested using Trizol reagent and the Qiagen miRNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina or Nugen library protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequence reads were aligned to mouse genome version mm9(pre-phx) and mm10(post-phx) using TopHat.
The number of reads aligned to RefSeq annotated genes' exons were counted and further normalized to be of unit RPKM (number of reads per kilo base pair per million total reads)
Differential gene expression analyses were performed using edgeR.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: text file of gene RPKM values
|
| |
|
| Submission date |
Jan 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuxu Sun |
| Organization name |
shanghai jiao tong university
|
| Department |
school of medicine
|
| Street address |
227 south chongqing road
|
| City |
shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE76926 |
RNA-seq transcriptonal profiling in partial hepatectomy liver tissues in Arid1a WT and liver specific KO mice. |
| GSE76935 |
Suppression of SWI/SNF component Arid1a promotes mammalian regeneration through chromatin remodeling |
|
| Relations |
| BioSample |
SAMN04417786 |
| SRA |
SRX1532680 |
