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| Status |
Public on Sep 24, 2022 |
| Title |
P1 lens epithelium, H3.3 ChIP-seq, rep2 |
| Sample type |
SRA |
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| Source name |
lens
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| Organism |
Mus musculus |
| Characteristics |
tissue: lens
cell type: newborn lens epithelium
genotype: CD1
antibody: H3.3
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| 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
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| Phone |
4107331644
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| Organization name |
Albert Einstein College of Medicine
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| Department |
Ophthalmology
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| Lab |
Cvekl
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| Street address |
1301 Morris Park Ave
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| City |
Bronx |
| State/province |
NY |
| ZIP/Postal code |
10461 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE213901 |
Whole-genome bisulfite sequencing and histone 3.3 ChIP-seq of microdissected developing mouse lens |
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| Relations |
| BioSample |
SAMN30955025 |
| SRA |
SRX17664619 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6596317_2_0BKQ_01NDEinstein_Epi-2_H3.3_mm10_i59-W200-G600-FDR0.01-island.bed.gz |
120.9 Kb |
(ftp)(http) |
BED |
| GSM6596317_2_0BKQ_01NDEinstein_Epi-2_H3.3_mm10_i59_uniqnorm_signal.bw |
168.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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