|
| Status |
Public on Mar 11, 2021 |
| Title |
ATAC-seq_P3 Lung CD45-depleted |
| Sample type |
SRA |
| |
|
| Source name |
P3 Atac
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
tissue: lung
age: P3
Sex: female
strain: CD-1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2. Genome_build: mm10 or hGRC38
Genome_build: mm10 or hGRC38
Supplementary_files_format_and_content: H5 matrix: contains the UMI counts per feature (gene or peak). BAM: alignment data. Singlecell: file is the Cellranger Cell annotation file. Fragments: a BED-like tabular file, where each line represents a unique ATAC-seq fragment captured by the assay.
|
| |
|
| Submission date |
Apr 29, 2020 |
| Last update date |
Mar 11, 2021 |
| Contact name |
Michael Patrick Morley |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17021 |
| Series (1) |
| GSE149563 |
The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung |
|
| Relations |
| BioSample |
SAMN14770600 |
| SRA |
SRX8202419 |
