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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 25, 2022 |
| Title |
N33 Input ChIP-seq rep2 |
| Sample type |
SRA |
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| Source name |
ES Cell
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| Organism |
Mus musculus |
| Characteristics |
cell type: ESC
genotype: wildtype
strain: C57BL/6
chip antibody: none
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| 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
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| Submission date |
Jun 19, 2017 |
| Last update date |
Dec 25, 2022 |
| Contact name |
Xinyi Lu |
| E-mail(s) |
rnagenomics@foxmail.com
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| Organization name |
Nankai University
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| Street address |
94 Weijin Road
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| City |
Tianjin |
| ZIP/Postal code |
300071 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN07252386 |
| SRA |
SRX2931293 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2673319_N33-input.rep2_nor.bedgraph.gz |
72.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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