|
| Status |
Public on Sep 12, 2019 |
| Title |
CTCF_ChIP_Seq_Rnase_Treatment |
| Sample type |
SRA |
| |
|
| Source name |
E14Tga2
|
| Organism |
Mus musculus |
| Characteristics |
genotype: embryonic stem cells
antibody: Anti-CTCF antibody - ChIP Grade, ab70303
|
| Treatment protocol |
Nuclei were permeabilized with 0.05% Tween-20 in PBS for 10 min at 4C, washed once and resuspended in PBS and finally incubated with RNase A (1 mg/ml) or a mock reaction for 30 minutes
|
| Growth protocol |
E14Tga2 ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% Formaldehyde. Nuclei were isolated and chromatin was fragmented. Chromatin immunoprecipitation (ChIP) was performed and the libraries were prepared using the eluted DNA from ChIP
Kapa Library Prep Kit following the manufacturer’s instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing files were aligned against the mouse reference genome (GRCm38/mm10) using Bowtie2 (version 2.3.4.1) (parameters: -N 1 -k 1 -q -x). Ambiguous reads were filtered to use uniquely mapped reads in the downstream analysis. PCR duplicates were removed using Picard-tools (version 1.88). MACS version 2.0.10 was used to call narrow peaks (parameters: -g 1.87e9 --qvalue 0.01).
supplementary_files_format_and_content:bigWigs or peaks called by MACS on bed format
Genome_build: mm10
|
| |
|
| Submission date |
Jan 24, 2019 |
| Last update date |
Oct 04, 2019 |
| Contact name |
Ricardo Saldana-Meyer |
| Organization name |
NYUMC - HHMI
|
| Department |
Biochemistry and Molecular Pharmacology
|
| Lab |
211
|
| Street address |
522 First Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE125595 |
RNA interactions are essential for proper CTCF function |
|
| Relations |
| BioSample |
SAMN10819196 |
| SRA |
SRX5292076 |
