 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 24, 2022 |
| Title |
P1 lens fiber, H3.3 ChIP-seq, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
lens
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lens
cell type: newborn lens fiber
genotype: CD1
antibody: H3.3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
WGBS: genomic DNA was isolated from all samples using QIAamp DNA Mini Kits (Cat. ID 51304) followed by isopropanol precipitation (-80C, one hour incubation).
Histone 3.3 ChIP-seq: Mouse lenses from P0.5 CD1 mice (Charles River) were micro dissected into epithelium and fiber as previously described (Zhao et al. Epigenetics & Chromatin (2019). 150 lenses were used per sample duplicate (total 300 lenses) and stored at -80C prior to the use. Preparation of samples for ChIP-seq was provided by ActiveMotif (Carlsbad, CA, USA).
WGBS: identical to GEO sample GSM2772524.
Histone 3.3 ChIP-seq: Immunoprecipitation was performed on 12 µg chromatin from microdissected lens cells with 5 µl anti-H3.3 antibody (Millipore, cat. # 17-10245), n=2 biological replicates, at ActiveMotif.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
WGBS data were aligned and methylation called with Bismark and bowtie2
histone 3.3 ChIP-seq was aligned to the mm10 mouse genome using BWA
histone 3.3 profiles were calculated as bigWigs using deeptools (bamCoverage)
histone 3.3 peaks were called using SICER2
Assembly: mm10
Supplementary files format and content: bigWig, bed
|
| |
|
| Submission date |
Sep 21, 2022 |
| Last update date |
Sep 24, 2022 |
| Contact name |
William Chang |
| E-mail(s) |
william.chang@einsteinmed.edu, williamkurtischang@gmail.com
|
| Phone |
4107331644
|
| Organization name |
Albert Einstein College of Medicine
|
| Department |
Ophthalmology
|
| Lab |
Cvekl
|
| Street address |
1301 Morris Park Ave
|
| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE213901 |
Whole-genome bisulfite sequencing and histone 3.3 ChIP-seq of microdissected developing mouse lens |
|
| Relations |
| BioSample |
SAMN30955023 |
| SRA |
SRX17664621 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6596319_4_0BKS_01NDEinstein_Fiber-2_H3.3_mm10_i67-W200-G600-FDR0.01-island.bed.gz |
304.6 Kb |
(ftp)(http) |
BED |
| GSM6596319_4_0BKS_01NDEinstein_Fiber-2_H3.3_mm10_i67_uniqnorm_signal.bw |
164.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
