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Sample GSM879225 Query DataSets for GSM879225
Status Public on Aug 21, 2012
Title Control R1
Sample type SRA
Source name Ventral Tegmental Area
Organism Mus musculus
Characteristics tissue: Ventral Tegmental Area
stress: Unstressed control
exposure time: 10 days
strain: C57BL/6J
gender: male
Treatment protocol C57BL/6J male mice were exposed to either emotional stress, physical stress, or control for 10 days. 24 hr later, VTA punches were taken.
Extracted molecule total RNA
Extraction protocol Total RNA is isolated by using Trizol reagent (Invitrogen, California) following the product instructions. Four micrograms of total RNA is then used for mRNA library construction with the Illumina mRNA sample prep kit (cat#RS-100-0801). In brief, the poly-A containing mRNA is purified using poly-T oligo-attached magnetic beads. The mRNA is then fragmented into small pieces and converted into cDNA. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products are then gel purified and enriched with PCR to create the final cDNA libraries.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Adapter sequences (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) were removed from RNA-seq data using Fastx tool. They were then processed using the Cufflinks (v1.0.3) pipeline to determine gene expression levels and detect differential genes.
The three *.diff files are differential gene lists from comparison between the three treatment conditions and control.
Genome Build:
C1.fpkm_tracking: mm9
Submission date Feb 22, 2012
Last update date May 15, 2019
Contact name Li Shen
Organization name Icahn School of Medicine at Mount Sinai
Department Neuroscience
Lab Shen
Street address 1425 Madison Ave
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platform ID GPL13112
Series (1)
GSE36005 High throughput sequencing of the mouse transcriptome within the VTA following exposure to emotional stress.
SRA SRX121679
BioSample SAMN00791652

Supplementary file Size Download File type/resource
GSM879225_C1.fpkm_tracking.gz 1.1 Mb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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