|
| Status |
Public on Apr 04, 2016 |
| Title |
vDG_WTETF2_2 (eRRBS) |
| Sample type |
SRA |
| |
|
| Source name |
Ventral Dentate Gyrus
|
| Organism |
Mus musculus |
| Characteristics |
gender: Male
strain: Swiss Webster
maternal genotype: WT
grandmaternal genotype: WT
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 |
SAMN03651346 |
| SRA |
SRX1022738 |
