|
| Status |
Public on Nov 03, 2022 |
| Title |
Tfam_deficient lung_rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lung
time: Embryonic lung
developmental stage: 14.5 dpc
genotype: Tfamf/f; ShhCre/+
state: mutant sample
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embronic lungs were collected, snap freezed in liquid nitrogen, and RNAs were extracted with the RNeasy Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
Tfam_ShhCre_14.5dpc
|
| Data processing |
remove adaptor with 'trim_galore'
align the reading to genome with 'Hisat2'
sort the SAM file and convert it to BAM file
create table counts with 'featurecounts'
generate DEG table with DeSeq2 in R
Assembly: mm10
Supplementary files format and content: csv file include log2 fold change and p value
|
| |
|
| Submission date |
Sep 12, 2022 |
| Last update date |
Nov 03, 2022 |
| Contact name |
Pao-Tien Chuang |
| Organization name |
University of California, San Francisco
|
| Street address |
555 Mission Bay Blvd. South
|
| City |
San Francisco |
| ZIP/Postal code |
CA 94158-3118 |
| Country |
USA |
| |
|
| Platform ID |
GPL23479 |
| Series (1) |
| GSE213202 |
mTORC1 signaling facilitates differential stem cell differentiation to shape the developing murine lung and is associated with mitochondrial capacity |
|
| Relations |
| BioSample |
SAMN30812416 |
| SRA |
SRX17536831 |
