|
| Status |
Public on Nov 03, 2021 |
| Title |
SA2017_138 |
| Sample type |
SRA |
| |
|
| Source name |
PDGFRa+ (CD140+) FBs
|
| Organism |
Mus musculus |
| Characteristics |
cell population: PDGFRa+ (CD140+) alveolar fibroblasts
treatment: Room Air
age: P4
|
| Treatment protocol |
MACS-sorted PDGFRa+ (CD140+) FBs from either RA or O2 PN4, PN7, and PN10 mouse lungs were prepared for bulk RNA-seq and used to determine changes to lung fibroblast populaton.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using trizol according to manufacturer’s instructions
RNAseq: Libraries were prepared with Illumina RNA PolyA selection
NextEra XT DNA Library Preparation Kit with 15-20 million reads
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
P4-Room Air2
|
| Data processing |
FASTQ files were aligned using Bowtie2 to mouse reference genome mm10.
RNAseq Normalized gene expressions were generated using Cufflinks.
RNAseq Gene counts were obtained using Bioconductor’s GenomicAlignment.
DeSeq was used to analyze the RNAseq raw gene counts and calculate differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: text file of RNA raw counts
|
| |
|
| Submission date |
Apr 09, 2021 |
| Last update date |
Nov 03, 2021 |
| Contact name |
John M. Snowball |
| E-mail(s) |
snowballdbs@yahoo.com
|
| Phone |
8594090321
|
| Organization name |
Cincinnati Childrens Hospital
|
| Department |
Pulmonary Research
|
| Lab |
Whitsett
|
| Street address |
3333 Burnet Ave
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE171812 |
Maladaptive functional changes in alveolar fibroblasts due to perinatal hyperoxia impair epithelial differentiation |
|
| Relations |
| BioSample |
SAMN18687147 |
| SRA |
SRX10567317 |
