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Sample GSM1679448 Query DataSets for GSM1679448
Status Public on Apr 04, 2016
Title vDG_F2_1 (RNAseq)
Sample type SRA
 
Source name Ventral Dentate Gyrus
Organism Mus musculus
Characteristics gender: Male
strain: Swiss Webster
maternal genotype: WT
grandmaternal genotype: 5HT1A-/+
generation: F2
tissue: vDG
Extracted molecule polyA RNA
Extraction protocol Following sacrifice animal brains were frozen, cryosectioned and microdissected. DNA was collected using Qiagen DNeasy Blood and tissue extraction kit (cat# 69582). RNA was harvested using Qiagen RNeasy mini kit (cat# 74106). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Replicate 1
Data processing Illumina Casava1.8.2 software used for basecalling.
Alignment: DNA samples were aligned to the mm9 genome using Bismark software as part of an in-house pipeline (PMID 22737091). RNA fragments were mapped to the mosue genome using TopHat version 2.0.2 (http://tophat.cbcb.umd.edu) with bowtie version 1.0.0 against mm9 and annotated with NCBIM37 coding transcripts
DNA methylation analysis was performed using MethylKit software (PMID 23034086). RNA samples were counted using Htseq-count -m -intersection-strict and analysis was performed using tagwise dispersion and default parameters in edgeR (PMCID: PMC2796818).
Genome_build: mm9
Supplementary_files_format_and_content: DNA files are in the wig format. RNA files are the raw counts per gene as processed by Htseq-count.
 
Submission date May 11, 2015
Last update date May 15, 2019
Contact name Shifra Liba Klein
E-mail(s) slk2002@med.cornell.edu
Organization name Weill Cornell
Department Pharmacology
Lab Toth
Street address 1300 York Avenue
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platform ID GPL13112
Series (1)
GSE68713 Propogation of anxiety-traits through the maternal line via parallel and segregated gametic and non-gametic epigenetic mechanisms
Relations
BioSample SAMN03651353
SRA SRX1022745

Supplementary file Size Download File type/resource
GSM1679448_F2_1.gn_counts.txt.gz 134.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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