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| Status |
Public on Feb 06, 2020 |
| Title |
ChIP-seq.CCE-WT_LSD1_A |
| Sample type |
SRA |
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| Source name |
Embryonic stem cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: mESC CCE
strain: 129/Sv
antibody: LSD1, Abcam, ab17721
genotype: WT
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| 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).
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| 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.
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| Submission date |
Dec 18, 2019 |
| Last update date |
Feb 06, 2020 |
| Contact name |
Jianlong Wang |
| Organization name |
Columbia University Irving Medical Center
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| Department |
Department of Medicine
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| Lab |
Jianlong Wang
|
| Street address |
650 W. 168th St.
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| 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] |
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| Relations |
| BioSample |
SAMN13624267 |
| SRA |
SRX7409683 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4224364_ECCE_Lsd1_A.bed.gz |
328.3 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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