|
| Status |
Public on Oct 14, 2020 |
| Title |
RML957_KO2 |
| Sample type |
SRA |
| |
|
| Source name |
12 month old Cdk1 Liv-/- whole liver
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Cdk1 Liv-/-
sample type: Whole liver
age: 12 months
|
| Treatment protocol |
Cdk1 Liv-/- mice were generated crossing Cdk1 flox/flox to Albumin-Cre mice.
|
| Growth protocol |
Mice were fed ad libitum with standard diet under 12 hour light/dark cycle in specific pathogen-free (SPF) conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated by first homogenizing liver tissue or pelleted hepatocytes in TRIzol reagent, and upon phase separation step, aqueous portion was transferred to columns and extracted as per PureLink RNA Mini Kit, with rDNase treatment on column
Library was prepared using TruSeq Stranded mRNA Library Prep (Illumina) according to manufacturer's instructions. RNA-Seq, single-end, 75bp read length
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
sample name:
RML957
|
| Data processing |
The gene and isoform expression levels from the RNASeq reads were quantified using the RSEM software version 1.2.31
The GTF file for the mm10 genome was used to prepare reference STAR genome index files
Fragments Per Kilobase of transcript per Million mapped (FPKM) were quantified using the "rsem-calculate-expression" function with "--star" as the sequence alignment program. Inputs were single-end read files.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited matrix file with FPKM values for every gene and every sample
|
| |
|
| Submission date |
Oct 13, 2020 |
| Last update date |
Oct 20, 2020 |
| Contact name |
Jin Rong Ow |
| E-mail(s) |
owjr@imcb.a-star.edu.sg
|
| Phone |
(+65) 65869516
|
| Organization name |
A*STAR
|
| Department |
Institute of Molecular and Cell Biology
|
| Street address |
61 Biopolis Drive
|
| City |
Singapore |
| State/province |
Singapore |
| ZIP/Postal code |
138673 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE159498 |
Remodelling of whole-body lipid metabolism and a diabetic-like phenotype caused by loss of hepatic CDK1 and hepatocyte division |
|
| Relations |
| BioSample |
SAMN16432411 |
| SRA |
SRX9288306 |
