|
| Status |
Public on Mar 16, 2012 |
| Title |
E10.5_forelimb_mRNA_seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic forelimb bud, RNA-Seq
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: forelimb bud
developmental stage: gestational day E10.5
sequencing run type: Single-end 35
|
| Treatment protocol |
Pregnant mothers were euthanized, and embryos were removed and placed in cold PBS. Forelimb and hindlimb buds were individually removed with forceps.
|
| Growth protocol |
Normal mouse gestation to day 10.5.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the RNeasy kit (Qiagen).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
polyA-selected RNA
|
| Data processing |
RNA-Seq alignments and counts: RNA-Seq reads were aligned with bowtie (0.12.3) to the mouse genome (mm9) retaining only uniquely mapped reads ( command: bowtie -m 1 -B 1 --solexa1.3-quals --sam --sam-nohead ~/GENOME/mm9/dna/mm9_nh+splice30). Bowtie output was converted to tophatSAM format for use with Cufflinks for calculation of gene expression (RPKM).
|
| |
|
| Submission date |
Jul 13, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Justin Cotney |
| E-mail(s) |
cotneyj@chop.edu
|
| Organization name |
Children's Hospital of Philadelphia
|
| Department |
Surgery
|
| Lab |
Cotney Lab
|
| Street address |
3501 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE30641 |
Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb. |
|
| Relations |
| SRA |
SRX083280 |
| BioSample |
SAMN00668319 |
| Named Annotation |
GSM759869_E10.5_forelimb_mRNA_seq_rep2.bw |
