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Sample GSM1679442 Query DataSets for GSM1679442
Status Public on Apr 04, 2016
Title vDG_ETF2_1 (eRRBS)
Sample type SRA
Source name Ventral Dentate Gyrus
Organism Mus musculus
Characteristics gender: Male
strain: Swiss Webster
maternal genotype: 5HT1A-/+
grandmaternal genotype: 5HT1A-/+
generation: F2
tissue: vDG
Extracted molecule genomic DNA
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 Bisulfite-Seq
Library source genomic
Library selection Reduced Representation
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 ( 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
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
BioSample SAMN03651347
SRA SRX1022739

Supplementary file Size Download File type/resource
GSM1679442_5HT1A_ET_WTH_F2_1.wig.gz 12.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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