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Sample GSM6596310 Query DataSets for GSM6596310
Status Public on Sep 24, 2022
Title P0.5 lens epithelium, WGBS, rep1
Sample type SRA
 
Source name lens
Organism Mus musculus
Characteristics tissue: lens
cell type: embryonic lens epithelium
genotype: CD1
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 Bisulfite-Seq
Library source genomic
Library selection RANDOM
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 SAMN30955032
SRA SRX17664612

Supplementary file Size Download File type/resource
GSM6596310_AC-P0-5-epi-6_TAAGGCGA-TCTACTCT_H2JFWCCX2_L005_001.R1_val_1_bismark_bt2_pe.deduplicated.filterFillIn.sorted_ucscChrNames.bw 264.7 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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