|
| Status |
Public on Mar 29, 2021 |
| Title |
IgG Cut&Run |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Retina
developmental time point: embryonic day 14
strain: C57Bl6/J
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cut&Run experiements were perfored as described in Skene and Henikoff, 2018 with DNA extracted using the Qiagen Nucleotide Romval Kit.
Libraries were prepared using Manufacturer's protocols using the KAPA HyperPrep Kit (Roche)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Cut&Run sequencing
|
| Data processing |
Library strategy: Cut&Run
Bowtie2 v2.3.5 alignment onto the mm10 genome assembly. Samtools was used to filter out low quality (<30 MAPQ score) reads. Duplicate reads were removed using Picard v2.0.1 MarkDuplicates
MACS2 v2.2.7.1 was used to call peaks. High confidence peaks were annotated based on overlapping peaks between replicates, called using bedtools.
Genome_build: mm10
Supplementary_files_format_and_content: peak calls
|
| |
|
| Submission date |
Aug 24, 2020 |
| Last update date |
Mar 29, 2021 |
| Contact name |
Brian Clark |
| Organization name |
Washington University
|
| Department |
Ophthalmology and Visual Sciences
|
| Lab |
Clark
|
| Street address |
660 S Euclid Ave; Campus Box #8096
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE156756 |
Atoh7-independent specification of retinal ganglion cell identity |
|
| Relations |
| BioSample |
SAMN15893768 |
| SRA |
SRX8998610 |
