NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4412286 Query DataSets for GSM4412286
Status Public on Jun 10, 2021
Title iWAT, KO_LFD_6
Sample type SRA
 
Source name iWAT
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: female
tissue: subcutaneous inguinal white adipose tissue
diet: low fat diet
genotype: knock out
Treatment protocol wild type vs knockout mice fed with high fat diet vs low fat diet
Growth protocol 6 months old, group caged, female mice fed with high fat vs low fat diet for 15 weeks. Ad libitum access to water. 12h dark and 12h light cyckles in air conditioned facility. Research Diets Inc. low fat diet(10.5% fat) - D12328; high fat diet(58% fat) - D12331
Extracted molecule total RNA
Extraction protocol total RNA was isolated by Rneasy Lipid Tissue Kit (Qiagen) - cat. No. 74804
Illumina TruSeq Stranded Total RNA Gold kit
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Align to Mouse mm9 assembly with STAR v2.5.3.a
Filter for properly paired, unique alignments
Remove reads in blacklisted regions
Convert to bigWig
Pseudo-align reads with Salmon 0.13.1 and Ensembl 67 transcripts
Genome_build: mm9
Supplementary_files_format_and_content: bigWig coverage files per strand, TPM gene expresion file
 
Submission date Mar 16, 2020
Last update date Jun 10, 2021
Contact name Shaun Michael Webb
E-mail(s) shaun.webb@ed.ac.uk
Organization name University of Edinburgh
Department Wellcome Trust Centre for Cell Biology
Lab Bioinformatics Core Facility
Street address 2.21 Swann Building, Kings Buildings
City Edinburgh
ZIP/Postal code EH9 3JR
Country United Kingdom
 
Platform ID GPL24247
Series (1)
GSE147016 RNA-seq analysis of subcutaneus inguinal adipose tissue from Tmem120a fat specific knockout mice (females)
Relations
BioSample SAMN14381478
SRA SRX7917310

Supplementary file Size Download File type/resource
GSM4412286_ko_lfd_6.uniq.bl.f.bw 115.3 Mb (ftp)(http) BW
GSM4412286_ko_lfd_6.uniq.bl.r.bw 110.2 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap