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| Status |
Public on Apr 14, 2024 |
| Title |
H3.3G34R_H3K4me1_ChIP |
| Sample type |
SRA |
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| Source name |
NE-4C
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| Organism |
Mus musculus |
| Characteristics |
tissue: Neural stem cell line established from cerebral vesicles of 9-day-old mouse embryos lacking a functional p53 gene
genotype: NE-4C H3,3A KO,H3.3G34R-HA
antibody: Active Motif 39297
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.1% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
base_calling: CASAVA package (Illumina v1.7)
alignment: bowtie (version 1.0.0)
peak_calling: macs14 (version 1.4)
Genome_build: mm9
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| Submission date |
Jun 13, 2017 |
| Last update date |
Apr 14, 2024 |
| Contact name |
Yang Shi |
| E-mail(s) |
yshi@hms.harvard.edu
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| Organization name |
Fudan university
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| Street address |
NO. 138, Yi-Xue-Yuan Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE99979 |
Recognition of a pediatric glioblastoma-associated histone mutation by chromatin reader ZMYND8 promotes tumorigenesis |
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| Relations |
| BioSample |
SAMN07225378 |
| SRA |
SRX2914323 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2666923_H3.3G34R_H3K4me1_peaks.bed.gz |
909.0 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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