|
| Status |
Public on Dec 11, 2020 |
| Title |
hf2_atm_frac_neg |
| Sample type |
SRA |
| |
|
| Source name |
ATMs-HFD
|
| Organism |
Mus musculus |
| Characteristics |
treatment: high fat, high sucrose diet-Research Diets (cat# D12492)
genotype: Cx3Cr1-GFP/WT mouse line
strain: C57BL/6
tissue: adipose
cell type: macrophage, frac_neg
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using microRNA isolation kit (Qiagen) according to manufacturer’s instructions.
The library preparation and sequencing were performed at the Genome Technology Access Center (GTAC) at Washington University School of Medicine.
Briefly, the total cellular RNA was also prepared for RNA sequencing with the Clonetech SMARTer kit according to manufacturer’s protocols, ligated with adapters
and unique molecular indexes for each sample for every read, and then sequenced on one single-end 50bp lane on an Illumina HiSeq 3000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNA-seq reads demultiplexed with Illumina’s bcl2fastq2 and
were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 2.0.4b (Dobin et al., 2013).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5 (Liao et al., 2014).
Genome_build: Mus musculus Ensembl release 76 top-level assembly
Supplementary_files_format_and_content: Xls file that includes raw count data for each sample.
|
| |
|
| Submission date |
Dec 10, 2020 |
| Last update date |
Dec 12, 2020 |
| Contact name |
Maxim N. Artyomov |
| E-mail(s) |
martyomov@pathology.wustl.edu
|
| Organization name |
Washington University in St.Louis
|
| Department |
Immunology&Pathology
|
| Street address |
660 S. Euclid Avenue, Campus Box 8118
|
| City |
St.Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE163003 |
Macrophage heterogenity in liver and adipose during obesity |
|
| Relations |
| BioSample |
SAMN17053376 |
| SRA |
SRX9670983 |
