|
| Status |
Public on May 09, 2017 |
| Title |
SDC3 N2 MxEmb rep1 ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
whole worms
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: mixed embryo
antibody target: SDC-3
antibody (vendor, catalog#, lot#): Covance, Jason Lieb JL00002
antibody antigen: 1067-1340aa
antibody (host, clone): Rabbit, polyclonal
matching input: EE4 input N2 MxEmb ChIP-seq
|
| 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.
|
| Growth protocol |
Embryos were isolated by bleaching gravid adults grown on plates at 20C.
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
SDC3_N2_MxEmb_MACS141_e5_average.bw
SDC3_N2_MxEmb_MACS141_e10_peaks.bed
|
| Data processing |
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.0.1 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 1.4.2 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 1.4.2 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 2.0.12 using default parameters, specifying first strand alignment.
Resultant RNA-seq bam files were converted to sam files using samtools version 1.2. 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 1.4.2, normalized according to the genome-wide mean coverage and the 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 1.4.2 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.
|
| |
|
| Submission date |
Oct 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sarah Elizabeth Albritton |
| E-mail(s) |
sarahea283@gmail.com
|
| Organization name |
New York University
|
| Department |
Biology
|
| Lab |
Ercan
|
| Street address |
100 Washington Square East
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL9269 |
| Series (1) |
| GSE87741 |
Cooperation between a hierarchical set of recruitment sites specifically targets the C. elegans dosage compensation complex to the X chromosomes. |
|
| Relations |
| BioSample |
SAMN05879046 |
| SRA |
SRX2228852 |
