|
| Status |
Public on Mar 20, 2024 |
| Title |
WT69, chew diet, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: C57BL/6
genotype: WT
treatment: Chew diet
time: 10 weeks
|
| Growth protocol |
Control or ACOX1-LKO mice were feeding with chew diet in room temperature for 10 weeks.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Liver RNA was isolated using PureLinkRNA kit from Invitrogen.
RNA-seq libraries were indexed, pooled according to library kit manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected
Assembly: mm10
Supplementary files format and content: space delimited text files include RPKM value for each feature and sample.
|
| |
|
| Submission date |
Mar 21, 2023 |
| Last update date |
Mar 20, 2024 |
| Contact name |
Irfan Lodhi |
| Organization name |
Washington University School of Medicine
|
| Department |
Endocrinology, Metabolism and Lipid Research
|
| Lab |
LodhiLab
|
| Street address |
660 S. Euclid Ave.
|
| City |
St. Louis |
| State/province |
MISSOURI |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE227896 |
Gene expression in liver from WT/ACOX1 liver specific knockout mice |
|
| Relations |
| BioSample |
SAMN33846745 |
| SRA |
SRX19743803 |
