|
Status |
Public on Apr 04, 2016 |
Title |
vDG_F2_2 (eRRBS) |
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 |
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 2
|
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 |
SAMN03651342 |
SRA |
SRX1022734 |