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Sample GSM828041 Query DataSets for GSM828041
Status Public on Feb 15, 2012
Title F1r_RNA_Seq
Sample type SRA
 
Source name Frontal cortex
Organism Mus musculus
Characteristics strain: Cast/EiJ x 129X1/SvJ
tissue: frontal cortex
Growth protocol The crosses of the two mouse strains 129x1/SvJ (129) and Cast/EiJ (Cast) were performed at Jackson Laboratories (http://jaxmice.jax.org/) and the male mice F1 offspring and males of each of the two parental strains were shipped to investigator laboratories at 8 to 9 weeks of age.
Extracted molecule total RNA
Extraction protocol The frontal cortex from the F1 crosses of the two mouse lines was dissected and the RNA was isolated followed by two DNAseI treatments to remove DNA contaminant. The presence of DNA in the RNA was tested using quantitative PCR and probes designed to span exons. The quality of the RNA was determined by the Agilent 2100 Bioanalyzer prior to the construction of the libraries. RNA was treated with RiboMinus (Invitrogen, Carlsbad CA) to remove the ribosomal RNA. The methods for the preparation of the libraries are outlined in the Whole Transcriptome library preparation for SOLiD sequencing protocol (https://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_065852.pdf). Briefly, RNA depleted of ribosomal RNA was fragmented using RNAseIII. Purified RNA was hybridized and ligated to primers then converted to cDNA using reverse transcriptase. The cDNA was size selected to contain 50 to 150 bp inserts then purified and amplified prior to sequencing. Libraries were constructed with RNA from three independent mice (3 biological replicates) for each of the experimental crosses. Sequencing was performed at EdgeBio (http://www.edgebio.com/) and the data from the 3 mice for each experimental cross line were combined given the high correlation between each of the libraries (R >0.98).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model AB SOLiD System
 
Data processing Sequencing reads for the RNA-Seq reads were mapped using Novoalign (Novocraft, Malaysia) . Novoalign permits gapped alignment by allowing more than two mismatches per read (up to 8 for high quality base calls on single end reads and 16 on paired-end reads)
 
Submission date Nov 03, 2011
Last update date May 15, 2019
Contact name Wei Xie
E-mail(s) xiewei@ucsd.edu
Organization name UCSD
Street address 9500 Gilman Dr. CMM East, Room 2071
City San Diego
ZIP/Postal code 92093
Country USA
 
Platform ID GPL10010
Series (2)
GSE33468 Base-resolution analyses of parent-of-origin and sequence dependent allele specific DNA methylation in the mouse genome (RNA-seq)
GSE33722 Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation
Relations
SRA SRX107380
BioSample SAMN00760469
Named Annotation GSM828041_F1r_RNA_Seq_129.bed.gz
Named Annotation GSM828041_F1r_RNA_Seq_Cast.bed.gz
Named Annotation GSM828041_F1r_RNA_Seq_total.bed.gz

Supplementary file Size Download File type/resource
GSM828041_F1r_RNA_Seq_129.bed.gz 32.2 Mb (ftp)(http) BED
GSM828041_F1r_RNA_Seq_Cast.bed.gz 24.9 Mb (ftp)(http) BED
GSM828041_F1r_RNA_Seq_total.bed.gz 382.0 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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