GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM876616 Query DataSets for GSM876616
Status Public on Feb 04, 2013
Title 5HT1A knock-out offspring of knock-out mother
Sample type SRA
Source name ventral dentate granule cell
Organism Mus musculus
Characteristics strain: Swiss Webster
tissue: hippocampus
genotype/variation: 5HT1A knock-out offspring of knock-out 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 ( Alignments were performed using GobyWeb ( and the LAST aligner (parameters: -d 108 -e 120 –s 150) ( against the mm9 mouse reference genome.
Genome Build:
GYACOIP-miklos-rrbs-Sample_5ht1a_koko-all.bedGraph: mm9
Submission date Feb 16, 2012
Last update date May 15, 2019
Contact name Miklos Toth
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
SRA SRX120196
BioSample SAMN00790674

Supplementary file Size Download File type/resource
GSM876616_GYACOIP-miklos-rrbs-Sample_5ht1a_koko-all.bedGraph.gz 24.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap