|
| Status |
Public on May 13, 2019 |
| Title |
P0.5 fiber rep2 |
| Sample type |
SRA |
| |
|
| Source name |
lens fiber
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD1
tissue: lens
developmental stage: P0.5
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
After cell dissociation using freshly microdissected lens epithelium and fiber, the nuclei were extracted using cell lysis buffer
The ATAC-seq libraries were prepared using standard ATAC-seq protocols as described by Buenrostro JD et al 2013 Nature Methods
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Adapters were trimmed using trim-galore (v 0.4.1)
Trimmed reads were then mapped to mm10 using Bowtie2 (v2.3.3.1)
Reads with low mapping quality, mapped to mitochondrial or found duplicated were removed using SAMtools (v1.2) and picard (v 2.1.1)
MACS2 (2.1. 0) was used for peak calling
Genome_build: mm10
Supplementary_files_format_and_content: Narrowpeak files for each pooled sample
|
| |
|
| Submission date |
Dec 29, 2018 |
| Last update date |
May 13, 2019 |
| Contact name |
Ales Cvekl |
| E-mail(s) |
ales.cvekl@einstein.yu.edu
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
The Departments Ophthalmology and Visual Sciences, Genetics
|
| Lab |
Dr. Cvekl's lab
|
| Street address |
1300 Morris Park Avenue, Ullman 123
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE124497 |
Profiling of chromatin accessibility and identification of general cis-regulatory mechanisms that control two ocular lens differentiation pathways |
|
| Relations |
| BioSample |
SAMN10662546 |
| SRA |
SRX5190079 |
