|
| Status |
Public on Nov 01, 2014 |
| Title |
Msx1-2 (d-d) KO - LCM RNA-Seq - Stroma |
| Sample type |
SRA |
| |
|
| Source name |
uterus (stroma cells)
|
| Organism |
Mus musculus |
| Characteristics |
strain: Msx1^d/d/Msx2^d/d
genotype: Knockout (d/d)
tissue: uterus
cell type: Stroma
|
| Treatment protocol |
Extracted on day 4 of pregnancy after mating with vasectomized male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Laser capture microdissection of indicated cell type onto CapSure HS LCM caps, extracted with Arcturus PicoPure kit following manufacturers instructions
TruSeq Stranded Total RNA Sample Prep kit with Ribo-Zero Deplete treatment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Laser capture microdissected
|
| Data processing |
Illumina Casava v1.8.2 software was used for basecalling.
Sequenced reads were mapped to the UCSC mouse mm9 genome using tophat v2.0.5.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.0.2 package, following a protocol from "Trapnell C. et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocol, 2012 Mar 1;7(3):562-78.".
Genome_build: mm9
Supplementary_files_format_and_content: text files with RPKM with statistics for identifying differentially expressed genes
|
| |
|
| Submission date |
May 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
SK Dey |
| Phone |
513-803-1158
|
| Organization name |
Cincinnati Children's Hospital
|
| Department |
Reproductive Sciences
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnti |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE57680 |
RNA-sequencing of luminal epithelium and stroma cells isolated by LCM from pseudopregnant day 4 Msx1/Msx2 knockout and control uteri |
|
| Relations |
| BioSample |
SAMN02777845 |
| SRA |
SRX542652 |
