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| Status |
Public on Feb 08, 2019 |
| Title |
H3K4me1 ChIP-Seq rbbp-5(-) |
| Sample type |
SRA |
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| Source name |
late C. elegans embryos rbbp-5(-)
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| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole embryo
genotype: rbbp-5(-)
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| Growth protocol |
A synchronised population of adult worms were grown on a dish (245x245 mm) and embryos harvested by bleaching of young adults
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were fixed with 2% formaldehyde for 30 min and quenched with 0.1 M Tris pH7.5. Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction antibody was first incubated overnight at 4 C then Protein A agarose beads were incubated overnight at 4 C. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by Qiaquick (Qiagen) extraction.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
chip antibody: anti-H3K4me1 (AM39297)
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| Data processing |
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the C. elegans genome (ce6) using the BWA algorithm (v0.6.1, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v1.4.2) with a cutoff of pvalue = 1E-7. --- or e.g.: Peak calling was done with the SICER script (SICER v1.1; FDR 1E-10, gap=600).
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: ce6
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)
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| Submission date |
Feb 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Gino Bernard Poulin |
| E-mail(s) |
[email protected]
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| Phone |
+44 (0)161 275 5694
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| Organization name |
University of Manchester
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| Street address |
Michael Smith Building, C2257 Oxford Road
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| City |
Manchester |
| ZIP/Postal code |
M13 9PT |
| Country |
United Kingdom |
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| Platform ID |
GPL19757 |
| Series (1) |
| GSE94639 |
WDR-5 prevents global and chromosomal accumulation of methyl marks at H3K4 |
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| Relations |
| BioSample |
SAMN06310440 |
| SRA |
SRX2543058 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2479984_03_0133_003KManch_RBBP5_H3K4me1_ce6_i78_dmnorm_signal.bw |
8.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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