|
| Status |
Public on Apr 25, 2013 |
| Title |
mRNAs from WildType Embryo Day11.5 |
| Sample type |
SRA |
| |
|
| Source name |
WildType Day11.5
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6
tissue: Whole Embryo
development stage: Day11.5
genotype/variation: wild type
|
| Treatment protocol |
Total RNA are extracted using TRIZOL.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina Library Preparation Protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The 3' adapter sequences (5'-TCGTATGCCGTCTTCTGCTTG-3') were removed from the small RNA samples and length of >= 17 nucleotides were retained for our further study. The RNA-seq samples were first mapped to the transcriptome generated by combining mRNA information from Refseq, UCSC, Ensembl, Vega and MGI. The unaligned reads then mapped directly to the mm9/NCBIM37 build. A maximum of 2 mismatches were allowed while mapping. A maximum of 10 multiple mapping was allowed while aligning to transcriptome but only unique alignment was considered while mapping directly to genome. We use Bowtie program for our alignment. Cufflinks program was used to estimate the expression of genes and transcripts.
|
| |
|
| Submission date |
Nov 04, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Kazuko Nishikura |
| Organization name |
The Wistar Institute
|
| Department |
Gene Expression & Regulation
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE33473 |
Small RNA analysis of wildtype Mouse embryo and Adar1 null mouse embryo at E11.0 and E11.5 together with mRNA-seq results of E11.5 |
| GSE43192 |
ADAR1 forms a complex with Dicer to promote microRNA processing and RNA-induced gene silencing |
|
| Relations |
| SRA |
SRX104340 |
| BioSample |
SAMN00750147 |
