|
| Status |
Public on Nov 08, 2023 |
| Title |
ChIP-seq_p14_rhom_ip1 |
| Sample type |
SRA |
| |
|
| Source name |
Retina
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Retina
strain: C57BL/6
genotype: CrxR90W/W
developmental stage: Post-natal day 14
chip antibody: anti-CRX
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Pooled nuclear extracts from 6 retinae were cross-linked with formaldehyde prior to immunoprecipitation with anti-CRX antibody. Input controls were generated with normal rabbit IgG. The libraries were prepared following the standard ChIP-seq protocol (Schmidt et al., 2014)
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
For each sample, reads from two sequencing lanes were first concatenated and trimmed with Trim Galore (v0.6.1).
The trimmed reads were then mapped to the mm10 genome using Bowtie2 (v 2.3.4.1) with parameters -X 2000 --very-sensitive.
Only uniquely mapped and properly paired reads were retained with samtools (v1.9) with parameters -f 0x2 -q 30.
Mitochondria reads were removed with samtools (v1.9). Duplicated reads were marked and removed with Picard (v2.21.4).
Last, reads mapped to the mm10 blacklist regions were removed by bedtools (v2.27.1) by intersect -v.
Assembly: mm10
Supplementary files format and content: bigWig files generated with deeptools (v3.0.0). Scores represent CPM values at 10bp binsize.
Supplementary files format and content: narrowPeak files generated by MACS2 (v2.1.1.20160309) callpeak with default parameters
|
| |
|
| Submission date |
Jan 24, 2023 |
| Last update date |
Nov 08, 2023 |
| Contact name |
Shiming Chen |
| E-mail(s) |
[email protected]
|
| Phone |
314-747-4351
|
| Organization name |
Washington University in St Louis
|
| Department |
Department of Ophthalmology & Visual Sciences
|
| Lab |
Shiming Chen, Ph.D.
|
| Street address |
517 South Euclid Avenue
|
| City |
Saint Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE223657 |
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms [ChIP-seq] |
| GSE223659 |
Missense mutations in CRX homeodomain cause dominant retinopathies through two distinct mechanisms |
|
| Relations |
| BioSample |
SAMN32901343 |
| SRA |
SRX19164888 |
