|
| Status |
Public on Feb 15, 2012 |
| Title |
F1i_RNA_Seq |
| Sample type |
SRA |
| |
|
| Source name |
Frontal cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129X1/SvJ x Cast/EiJ
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 |
SRX107379 |
| BioSample |
SAMN00760468 |
| Named Annotation |
GSM828040_F1i_RNA_Seq_129.bed.gz |
| Named Annotation |
GSM828040_F1i_RNA_Seq_Cast.bed.gz |
| Named Annotation |
GSM828040_F1i_RNA_Seq_total.bed.gz |
