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Status |
Public on Jan 08, 2019 |
Title |
H4panAc CB428 emb rep2 ChIP-seq |
Sample type |
SRA |
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Source name |
whole worms
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Organism |
Caenorhabditis elegans |
Characteristics |
strain: CB428 developmental stage: mixed embryo antibody target: H4panAc chip antibody (vendor, cat#, lot#): Lake Placid Biologicals, AR-0109-50 antibody antigen: Peptide containing the amino terminal region of tetrahymena histone variant hv1 acetylated at multiple lysines antibody (host, clone): Rabbit, polyclonal matching input: LW145_input_CB428_emb
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Treatment protocol |
Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.
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Growth protocol |
Embryos were isolated by bleaching gravid adults grown on plates at 20C.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP. Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Description |
H4panAc_CB428_Emb_LW132_LW135_average.bw H4panAc_CB428_emb_LW132_LW135_final_peaks.bed
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Data processing |
Basecalls were performed using CASAVA version 1.8. ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.2.0 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments. Peaks were called using MACS version 1.4.3 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5) Genome coverage was estimated using MACS version 1.4.3 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1) Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage. Replicates were merged by averaging coverage at each base position. To determine a set of final peaks, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set. RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.1.1 using default parameters, specifying first strand alignment. Resultant RNA-seq bam files were converted to sam files using samtools version 1.6. Sam files were used to generate count data using htseq-cout version 0.6.1. Genome_build: WS220 Supplementary_files_format_and_content: BigWig files were generated by converting wiggle files using the UCSC wigToBigWig utility. Wiggle files were generated using MACS version 1.4.3, normalized according to the genome-wide mean coverage and then input subtracted. Scores represent the average coverage of each replicate at each base position. Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.3 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value. Supplementary_files_format_and_content: Counts files were generated using Htseq-counts version 0.6.1.
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Submission date |
Nov 16, 2018 |
Last update date |
Jan 08, 2019 |
Contact name |
Lena Annika Street |
E-mail(s) |
las821@nyu.edu
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Organization name |
New York University
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Department |
Biology
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Lab |
Sevinc Ercan
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Street address |
100 Washington Square East
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City |
New York City |
State/province |
NY |
ZIP/Postal code |
10003 |
Country |
USA |
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Platform ID |
GPL18245 |
Series (1) |
GSE122639 |
Binding of an X-specific condensin correlates with a reduction in active histone modifications at gene regulatory elements |
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Relations |
BioSample |
SAMN10437619 |
SRA |
SRX5020752 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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