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Sample GSM2673315 Query DataSets for GSM2673315
Status Public on Dec 25, 2022
Title A49 H3K9me3 ChIP-seq rep2
Sample type SRA
Source name ES Cell
Organism Mus musculus
Characteristics cell type: ESC
genotype: Terc knockout
strain: C57BL/6
chip antibody: H3K9me3 (ab8898, Abcam)
Growth protocol The embryonic stem cells were cultured on feeder in medium consisted of knock-out DMEM (Invitrogen) containing 20% FBS (HyClone), 1,000 U/ml mouse leukemia inhibitory factor (LIF; ESG1107, Millipore), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM L-glutamine, penicillin (100 U/ml) and streptomycin (100 μg/ml). For the culture of ESCs, the medium was changed daily, and cells were routinely passaged every two days.
Extracted molecule genomic DNA
Extraction protocol For ChIP-seq, ES cells were first fixed with 1% paraformaldehyde, and then lysed and sonicated to achieve the majority of DNA fragments at 100-1000 bp. DNA fragments were then enriched by immunoprecipitation with the H3K9me3 antibody (Abcam, ab8898). The immunoprecipitated material was eluted from the beads by heating for 30 min at 68 °C. Then, samples were incubated with Proteinase K at 42 °C for 2 h followed by 67 °C for 6 h to reverse the crosslinks. The samples were extracted with phenol:chloroform:isoamyl alcohol followed by chloroform, ethanol precipitation, and resuspension in TE buffer.
For ChIP-seq, libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
Data processing Raw Chip-Seq reads were aligned to mouse genome (mm10) by BOWTIE2 with parameter “--local -k 1”. This setting would ensure if one more equivalent best alignment is found, only one of those hits will be reported randomly. Therefore, instead of excluding reads from repetitive elements, multiple hits reads will be evenly distributed over highly similar repeat elements across genome. The peaks of H3K9me3 were called using DFilter (v1.5) with setting “ks=20 -lpval=3 –nonzero”.
genome build: mm10
processed data files format and content: bedgraph file generated using Bedtools
Submission date Jun 19, 2017
Last update date Dec 25, 2022
Contact name Xinyi Lu
Organization name Nankai University
Street address 94 Weijin Road
City Tianjin
ZIP/Postal code 300071
Country China
Platform ID GPL21273
Series (2)
GSE100168 Telomeres suppress the activity of retrotransposons in pluripotent stem cells [exp1]
GSE118027 Telomeres suppress the activity of retrotransposons in pluripotent stem cells
BioSample SAMN07252376
SRA SRX2931289

Supplementary file Size Download File type/resource
GSM2673315_A49-H3K9me3.rep2_nor.bedgraph.gz 222.1 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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