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| Status |
Public on Oct 17, 2022 |
| Title |
db24_gWAT_vehicle_RNAseq |
| Sample type |
SRA |
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| Source name |
gWAT
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| Organism |
Mus musculus |
| Characteristics |
tissue: gWAT
genotype: db/db
treatment: vehicle (0.9% NaCl) daily for 6 weeks
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| Treatment protocol |
Mice homozygous for the leptin receptor (BKS.Cg-Dock7m +/+ Leprdb/J, JAX #000642 thereafter referred to as db/db) and the respective lean control animals (db/+) were treated starting at 4 weeks of age with either GSK-LSD1 (500 ug/kg/mouse, Sigma SML1072) or vehicle (0.9% NaCl) daily via intraperitoneal injections. Gonadial WAT was harvested after 6 weeks of treatment.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated in Trizol from homogenized tissue and purified using RNeasy columns and Rnase free Dnase digestion according to the manufacturer’s instructions (QIAGEN).
For mRNA-seq library preparation, total RNA was assessed for quality using an Agilent Tapestation 4200, and samples with an RNA Integrity Number (RIN) greater than 8.0 were used to generate RNA sequencing libraries using the Illumina® Stranded mRNA Prep (Illumina, San Diego, CA). For each sample, 500 ng of RNA was processed following manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
mRNA-seq reads were mapped to the NCBI37/mm9 (mouse) genome by STAR (STAR-STAR_2.4.0f1, --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5), excluding reads mapping to multiple loci. Reads with exact matches were used to determine RPKM by Cufflinks (cufflinks v2.2.1,-p 6 -G $gtf_file --max-bundle-frags 1000000000).
mRNA-seq: Cuffdiff was used to assess expression differences for all pairwise comparisons, with P < 0.01 considered significant. Genes with mean RPKM > 1 in at least one experimental group were considered to be expressed, and all non-expressed genes were excluded from downstream analyses.
Assembly: mm9
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| Submission date |
Aug 08, 2022 |
| Last update date |
Oct 17, 2022 |
| Contact name |
Matthew Wortham |
| E-mail(s) |
mwortham@ucsd.edu
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| Phone |
8582460588
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| Organization name |
University of California, San Diego
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| Lab |
Maike Sander
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| Street address |
2880 Torrey Pines Scenic Drive, Sanford Consortium for Regenerative Medicine, Room 3102
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE210761 |
Systemic LSD1 inhibition prevents aberrant remodeling of metabolism in obesity |
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| Relations |
| BioSample |
SAMN30196627 |
| SRA |
SRX16983182 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6436800_db24_gWAT_vehicle_RNAseq_1_S9_L001_R1_001.fastq.gz.bam.fpkm_tracking.gz |
642.8 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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