|
| Status |
Public on Feb 04, 2013 |
| Title |
wild type offspring of heterozygote mother |
| Sample type |
SRA |
| |
|
| Source name |
ventral dentate granule cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: Swiss Webster
tissue: hippocampus
genotype/variation: wild type offspring of heterozygote mother
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protocol was performed as described in (Ref 1). Briefly, 50ng of DNA was digested with MspI restriction enzyme. This was followed by end repair and ligation of paired end illumina sequencing adaptors fully methylated at all cytosines. Size selection for library sizes of 150-400 bp was perfomed followed by a single round of bisulfite treatment using the EZ DNA Methylation Kit (Zymo Research). PCR amplification using Illumina PCR PE1.0 and 2.0 was followed by product isolation using AMPure XP beads per manufacturer’s recommended protocol (Agencort). Quality control was performed using quantitation on a Qubit 2.0 fluorometer (Invitrogen) and library visualization using a Quant-iT dsDNA HS Assay Kit for (Agilent 2100 Bioanalyzer). The amplified libraries were sequenced using a 50bp single end read run on a HiSeq2000 per manufacturer’s recommended protocol. Image capture, analysis and base calling was performed using Illumina’s CASAVA 1.7. References: 1 Altuna Akalin and Francine E. Garrett-Bakelman, Matthias Kormaksson, Jennifer Busuttil, Lu Zhang, Irina Khrebtukova, Peter JM Valk, Bob Löwenberg, Ruud Delwel, Hugo F Fernandez, Elisabeth Paietta, Martin S Tallman, Gary P. Schroth, Christopher E. Mason, Ari Melnick and Maria E. Figueroa. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in Acute Myeloid Leukemia. Under review.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Bisulfite treated, MspI digestion
|
| Data processing |
RRBS data was received as FASTQ files from the core facility and converted to Goby compact read files (http://goby.campagnelab.org). Alignments were performed using GobyWeb (http://gobyweb.campagnelab.org) and the LAST aligner (parameters: -d 108 -e 120 –s 150) (http://last.cbrc.jp/) against the mm9 mouse reference genome.
Genome Build:
PLKIQUC-miklos-rrbs-Sample_5ht1a_wth-all.bedGraph: mm9
|
| |
|
| Submission date |
Feb 16, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Miklos Toth |
| E-mail(s) |
[email protected]
|
| Organization name |
Weill Cornell Medical College
|
| Department |
Department of Pharmacology
|
| Lab |
Toth Lab
|
| Street address |
1300 York Ave. Room W-506
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE35854 |
Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus [Bisulfite-Seq] |
| GSE35856 |
Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus |
|
| Relations |
| SRA |
SRX120194 |
| BioSample |
SAMN00790672 |
