|
| Status |
Public on Dec 13, 2016 |
| Title |
Control_1 |
| Sample type |
SRA |
| |
|
| Source name |
Control
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed C57BL/6 and Swiss Webster
age: E11.5 (47-48 somites)
tissue: forelimb
genotype/variation: control
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequences were trimmed to 100bp and aligned to mm10 using tophat (v 2.0.10) and bowtie (v 2.1.0) with parameters --b2-sensitive
Cufflinks/2.1.1 was used to assemble sequences to mm10, merge to assembled sequences and carryout differential expression analysis.
Differential expression data was analyzed using cummeRbund in R.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs. Supplemental table reports differentially expressed genes.
|
| |
|
| Submission date |
Mar 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael A Dyer |
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
DNB
|
| Street address |
262 Danny Thomas
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE79487 |
RNA sequencing of E11.5 Control and Prmt5cKO forelimbs |
|
| Relations |
| BioSample |
SAMN04572218 |
| SRA |
SRX1653057 |
