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| Status |
Public on Jan 09, 2018 |
| Title |
4C_D0_DKO_Car2SE |
| Sample type |
SRA |
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| Source name |
E14, mouse embryonic stem cell line
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| Organism |
Mus musculus |
| Characteristics |
genotype: Mll3/4 double knock out
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| Growth protocol |
Mouse embryonic stem cell lines E14 and Mll3/4 double knockout were cultured in mouse ES cell media: DMEM 85%, 15% fetal bovine serum (Hyclone), penicillin/streptomycin, 1× non-essential amino acids (Gibco), 1× GlutaMax, 1000 U/ml LIF (Millipore), 0.4 mM β-mercaptoethanol. Mouse ES cells were initially cultured on 0.1% gelatin-coated petridish with CF-1 irradiated mouse embryonic fibroblasts (GlobalStem) and were passaged twice on 0.1% gelatin-coated feeder-free plates before harvesting.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq: Cells were lysed in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (details see Yan et al). Hi-C and 4C-seq: Briefly, 2 million cells were cross-linked with 1% formaldehyde for 10min at RT and reaction was quenched using 125 mM of Glycine for 5 min at RT. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n.
All libraries were constructed using standard illumina TruSeq LT library prep.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
4C, DKO, D0, Car2 super-enhancer
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| Data processing |
Library strategy: 4C-seq
base-calling use bcl2fastq version 2.17
alignment was performed using bowtie for ChIP-seq, bwa for Hi-C, Tophat for RNA-seq, 4cseqpipe for 4C-seq
Genome_build: mm9
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| Submission date |
Mar 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Yan |
| E-mail(s) |
jian.yan618@gmail.com
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| Organization name |
City University of Hong Kong
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| Department |
Biomedical Sciences
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| Lab |
Jian Yan
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| Street address |
83 Tat Chee Ave
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| City |
Kowloon |
| ZIP/Postal code |
999077 |
| Country |
Hong Kong |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE74055 |
Histone H3 lysine 4 monomethylation modulates longrange chromatin interactions at enhancers |
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| Relations |
| BioSample |
SAMN04590681 |
| SRA |
SRX1670256 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2099886_3.nearcis.norm.median.scales.txt.gz |
63.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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