 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 09, 2018 |
| Title |
ChIP_D2_5_E14_input |
| Sample type |
SRA |
| |
|
| Source name |
E14, mouse embryonic stem cell line
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
cell line: E14
antibody: input
|
| 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.
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
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
|
| |
|
| Submission date |
Mar 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian Yan |
| E-mail(s) |
jian.yan618@gmail.com
|
| Organization name |
City University of Hong Kong
|
| Department |
Biomedical Sciences
|
| Lab |
Jian Yan
|
| Street address |
83 Tat Chee Ave
|
| City |
Kowloon |
| ZIP/Postal code |
999077 |
| Country |
Hong Kong |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE74055 |
Histone H3 lysine 4 monomethylation modulates longrange chromatin interactions at enhancers |
|
| Relations |
| BioSample |
SAMN04590591 |
| SRA |
SRX1670196 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2099826_ChIP_D2_5_E14_input.bw |
56.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
|
|
|
|
 |
