|
| Status |
Public on Sep 06, 2023 |
| Title |
Primary AT2_KO3 |
| Sample type |
SRA |
| |
|
| Source name |
Murine primary ATII cells
|
| Organism |
Mus musculus |
| Characteristics |
p300 knockout: p300 knockout
treatment: PBS
|
| Treatment protocol |
Before administration of bleomycin, 8-week-old mice were injected with 10 mg/kg tamoxifen to delete p300 gene in ATII cells. Mice were intratracheally injected with PBS or 4 mg/kg bleomycin.
|
| Growth protocol |
The mice were housed in a specific pathogen-free animal facility, with a controlled temperature and humidity under conditions of a 12-h light/12-h dark cycle. To generate a conditional p300 null allele, LoxP sites were inserted into the flanking regions of the p300 gene on exon 9.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were sacrificed, and the lungs were perfused and harvested. Dissociated lung cells were stained with CD74 and Ep-CAM antibodies. Primary ATII cells were sorted by using Flow cytometry. Total RNA was isolated using Trizol reagent. Total RNA was isolated using Trizol reagent (Invitrogen). RNA quality was as sessed by Agilent 2100 bioanaly zer using the RNA 6000 Nano Chip and RNA quantification was performed using ND-2000 Spectrophotometer.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Dec 03, 2021 |
| Last update date |
Sep 06, 2023 |
| Contact name |
Soo Yeon Lee |
| E-mail(s) |
lovesylxo@yuhs.ac
|
| Organization name |
Yonsei university
|
| Street address |
yonsei-ro 50-1
|
| City |
Seoul |
| ZIP/Postal code |
03722 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE190157 |
RNA quantitative sequencing in bleomycin-treated p300 knockout primary ATII cells |
|
| Relations |
| BioSample |
SAMN23610908 |
| SRA |
SRX13309058 |
