|
| Status |
Public on Feb 26, 2024 |
| Title |
E17_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
Oct-GFP+ prospermatogonia
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E17.5
cell type: Oct-GFP+ prospermatogonia
chip antibody: H3K4me3 (Cell Signaling Technology, 9751)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly sorted cells were bound to concanavalin A-coated magenetic beads and wash and permeabilize using C&R Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, with 1x Roche complete protease inhibitor EDTA Free) with 0.05% Digitonin and 2 mM EDTA
CUT&RUN libraries were prepared using KAPA HyperPrep Kit and was ammplified using KAPA HiFi Hot Start Ready mix. All of DNA that was recovered following Phenol:Chloroform extraction was used as input.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
CUT&RUN reads were trimmed using TrimGalore with default parameters
CUT&RUN reads were aligned to mm10 using Bowtie2 version 2.5.0 with parameters: --N, 1 -sensitive -local
Low quality read (QMAP <= 10) and non-primary alignments were removed using SAMtools version 1.16.1 with parameters: view -q 10 -F 256
Duplicated reads were removed using SAMtool rmdup and mitochondrial reads were removed using grep function. Blacklisted regions were removed usign BEDtools version 2.27.1
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were prepared using deepTools version 3.5.1 with function bamCoverage and parameters -bs 1 --normalizeUsing CPM
Assembly: mm10
Supplementary files format and content: bigWig (normalized to counts per 10 million), narrowPeak (except for IgG sample), bedGraph (normalized to counts per million spike in sacCer3 reads)
Library strategy: CUT&RUN
|
| |
|
| Submission date |
Feb 03, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Rexxi Diptya Prasasya |
| E-mail(s) |
rexxi.prasasya@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Bartolomei Lab
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE224458 |
TET1 catalytic activity is required for reprogrammign of imprinting control regions and the patterning of sperm-specific hypomethylated regions [CUT&RUN] |
| GSE224459 |
TET1 catalytic activity is required for reprogrammign of imprinting control regions and the patterning of sperm-specific hypomethylated regions |
|
| Relations |
| BioSample |
SAMN33053833 |
| SRA |
SRX19275007 |
