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Sample GSM2433080 Query DataSets for GSM2433080
Status Public on Jan 24, 2017
Title Input-rep1
Sample type SRA
 
Source name epididymal WAT
Organism Mus musculus
Characteristics strain: C57BL/6J
tissue: adipose
Growth protocol Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).
Extracted molecule total RNA
Extraction protocol TRAP was performed as previously described (Long et al., Cell Metab 2014) with modifications. Adipose tissues were homogenized and processed to immunoprecipitation using anti-GFP antibody. Immunoprecipitates were washed and subjected to RNA extraction using Qiagen Micro RNeasy kit according to the manufacturer’s instructions. For input RNA, 5% of homogenates were mixed with TRIzol and processed according to the manufacturer’s instructions to extract total RNA. Isolated RNA was quantified by Qubit, and RNA integrity was analyzed by Agilent Bioanalyzer.
Extracted RNA (100ng) was processed for ribosomal RNA removal using the Epicentre rRNA depletion kit according to the manufacturer’s instructions. Ribosomal RNA-depleted RNA was subsequently used to generate paired-end sequencing libraries using the Illumina RNA TruSeq Library Kit according to the manufacturer’s instructions. Quantity and quality of RNA-Seq libraries were analyzed by Qubit and Agilent Bioanalyzer, respectively, and the libraries were pooled at a final concentration of 12pM and sequenced by HiSeq2500
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing RNA-seq data were aligned using TopHat2 (Trapnell et al., 2009) to the mm9 mouse genome.
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were assigned to transcripts, normalized and quantified using featureCounts (Liao et al., 2014) and EdgeR (Robinson et al., 2010).
Low expressed genes (log2 CPM <1) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥0.5 and log2 false discovery rate (FDR)≤0.25
Gene set enrichment analysis was performed using RDAVIDWebService (Fresno and Fernandez, 2013) and GOstats (Falcon and Gentleman, 2007).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts for each sample
 
Submission date Dec 19, 2016
Last update date May 15, 2019
Contact name Evan Rosen
E-mail(s) erosen@bidmc.harvard.edu
Organization name Beth Israel Deconess Medical Center
Department Endocrinology
Lab Rosen Lab
Street address 3 Blackfan Cir
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL17021
Series (1)
GSE92590 Simultaneous transcriptional and epigenomic profiling from specific cell types within heterogeneous tissues in vivo
Relations
BioSample SAMN06166485
SRA SRX2436349

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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