 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 06, 2020 |
| Title |
ChIP-seq.CCE-KO_LSD1_C |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: mESC CCE
strain: 129/Sv
antibody: LSD1, Cell Signaling Tech #2184, clone C69G12
genotype: Zmym2KO
|
| Growth protocol |
Feeder-free mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated plates under standard conditions: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 50 U/mL Penicillin/Streptomycin).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed with SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Tech. #9005) following the standard protocol.
About 4 million cells were used for each ChIP experiment, with two antibodies of LSD1 (Cell Signaling Tech. #2184, clone C69G12; and Abcam, ab17721). Massively parallel sequencing was performed with the Illumina HiSeq4000 according to the manufacturer’s protocol, and paired-end 150 bp-length reads were produced.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the mouse genome (NCBI build 37, mm9) using the bowtie2 (v2.3.4) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
ChIP-seq peaks were determined by the MACS program (v.2.0.10), using input as the control data, and all other parameters followed the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of MACS called peaks.
|
| |
|
| Submission date |
Dec 18, 2019 |
| Last update date |
Feb 06, 2020 |
| Contact name |
Jianlong Wang |
| Organization name |
Columbia University Irving Medical Center
|
| Department |
Department of Medicine
|
| Lab |
Jianlong Wang
|
| Street address |
650 W. 168th St.
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (2) |
| GSE119820 |
DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state |
| GSE142280 |
DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state [LSD1 ChIP-seq] |
|
| Relations |
| BioSample |
SAMN13624306 |
| SRA |
SRX7409687 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4224368_EKO_Lsd1_C.bed.gz |
280.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
