|
| Status |
Public on Jan 01, 2015 |
| Title |
Control_pooled |
| Sample type |
SRA |
| |
|
| Source name |
pooled Control
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
developmental stage: adult
cell sorting: Lin-/CD326+/CD24-intermediate cells
genotype: tetOCre/Mst1-flx/flx;Mst2-flx/flx
|
| Treatment protocol |
Adult mice were maintained on doxycycline food (625 mg/kg; Harlan Teklad) for 16 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lin-/CD326+/CD24-intermediate cells were isolated by fluorescence cell sorting to enrich for non-ciliated, secretory airway epithelial cells. Total RNA from Lin-/CD326+/CD24-intermediate cells of control (n=4) and Mst1/2 D/D (n=4) mice was extraced using a RNeasy Micro kit (Qiagen). Genotype matched samples were pooled and analyzed by RNA-seq to identify transcriptional changes following deletion of Mst1 and Mst2 from mature lung.
Sequencing library was constructed using the Nextera XT DNA Sample Preparation Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
pooled RNA from 4 independent mice
|
| Data processing |
Sequences were aligned to the reference genome with TopHat
Sample were independently processed with Cufflinks to generate an initial transcriptome.
Cuffmerge was used to merge the transcriptomes into a single reference and annotate known genes and extend partial transcripts. This common transcriptome was used in a second pass with Cufflinks to quantify transcripts.
Genome_build: mm9
Supplementary_files_format_and_content: Tables include raw counts and FPKM values
|
| |
|
| Submission date |
Sep 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Lange |
| E-mail(s) |
[email protected]
|
| Organization name |
Cincinnati Children's Hospital Reseach Foundation
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE61627 |
RNA-seq analysis of Mst1/2 deleted bronchiolar epithelial cells from adult mouse lungs |
| GSE61628 |
Mst1/2-Yap in lung epithelial progenitor cells |
|
| Relations |
| BioSample |
SAMN03075535 |
| SRA |
SRX708094 |
