|
| Status |
Public on May 01, 2024 |
| Title |
AT1, LB1, sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung, adult Hopx-EGFP
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung, adult Hopx-EGFP
cell type: Alveolar type 1 cell
chip antibody: LB1 (abcam, ab16048)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Target cells were FACS sorted and were crosslinked by 1% formaldehyde for 10 min. Glycine was then added to quench aldehyde. The cell pellets were stored at -80°C until library preparation.
Crude nuclei were isolated and were sonicated by using a Covaris S220 sonicator. LB1 antibodies (Abcam, ab16048) were added and the mixture was incubated 4°C overnight. Libraries were prepared with NEBNext Ultra II DNA library prep kit (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were aligned to mm10 using bwa (parameters ‘-q 5 -l 32 -k 2’). Duplicates were removed with Picard tools, and the samples were downsampled to 43 million (AT1) or 48.8 million (AT2) reads using samtools.
Assembly: mm10
Supplementary files format and content: bigWig
|
| |
|
| Submission date |
May 05, 2022 |
| Last update date |
May 01, 2024 |
| Contact name |
Michael Patrick Morley |
| E-mail(s) |
mmorley@pennmedicine.upenn.edu
|
| Phone |
215-898-2026
|
| Organization name |
Perelman School of Medicine at the University of Pennsylvania
|
| Department |
Penn Cardiovascular Institute
|
| Street address |
3400 Civic Center Blvd, Bldg 421
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE202318 |
Lamin B1 ChIP-seq analysis of alveolar type 1 and type 2 cells. |
| GSE202319 |
Mechanotransduction mediated by cyclical respiratory motion maintains lung alveolar epithelial cell fate |
|
| Relations |
| BioSample |
SAMN28102481 |
| SRA |
SRX15165925 |
