GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM876034 Query DataSets for GSM876034
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 total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA, USA). RNA concentration was measured using NanoDrop ND-1000 (Thermo Scientific, Wilmington, DE, USA). Following isolation total RNA integrity was checked using Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). RNA was purified using magnetic beads and fragmented using divalent cations at high temperature. cDNA library construction was carried out following the Illumina recommended sample preparation guide (Document 10004898 Rev. D) (Illumina, San Diego, CA, USA). Briefly, the cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Then RNaseH removed a strand of mRNA and a replacement strand synthesized to generate double-strand cDNA. The overhangs resulting from fragmentation were converted into blunt ends using T4 DNA polymerase and E. coli DNA polymerase I Klenow fragment. An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment (3' to 5' exo minus). Adapters were ligated to the DNA fragments, and the ligation products purified on a 2% TAE agarose gel. Size selection for 200bp ±25bp fragments was carried out. The Adapter-cDNA Fragments were amplified for 15 cycles of PCR. The library was validated by checking the size, purity, and concentration of the library constructs on an Invitrogen Qubit Fluorometer using Quant-IT dsDNA HS Assay Kit and Agilent Technologies 2100 Bioanalyzer using High Sensitivity DNA Kit. The libraries were sequenced on the Illumina GAIIx (one sample per lane) using a single end protocol for 42 cycles.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing Fastq reads were converted to Goby compact-read files ( Alignments were perfomred with GobyWeb ( and the bwa aligner. Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.
Genome Build:
ZQPDKUJ-5HT1A-KO-WTHet-s7-all.wig: NCBI37.55
Submission date Feb 15, 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 GPL11002
Series (2)
GSE35838 Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus [RNA-Seq]
GSE35856 Maternal Influence on Exonic CpG Island Methylation in the Developing Hippocampus
SRA SRX120198
BioSample SAMN00790676

Supplementary file Size Download File type/resource
GSM876034_ZQPDKUJ-5HT1A-KO-WTHet-s7-all.wig.gz 16.7 Mb (ftp)(http) WIG
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