|
| 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 (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) 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 |
| 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 |
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 |
|
| Relations |
| SRA |
SRX120198 |
| BioSample |
SAMN00790676 |
