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| Status |
Public on Apr 04, 2019 |
| Title |
DLS396_CEH-60_3F10_IP |
| Sample type |
SRA |
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| Source name |
Whole animals
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: DLS396
developmental stage: Day 1 adults
genotype: ceh-60(rhd116); gaIs285
chip antibody: anti-HA (3F10, Sigma-Aldrich, 11867423001)
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| Growth protocol |
C. elegans L1 animals were synchronized by egg prep and grown at 20°C on E. coli OP50 for ~72 hours until they reached day 1 of adulthood.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Animals were harvested in M9 buffer, washed, and ground to a find powder with a mortar and pestle in liquid Nitrogen. Whole animal lysates were crosslinked with 2% formaldehyde for 30 minutes, and the genomic DNA was sheared using a Bioruptor Plus (Diagenode). The resulting chromatin was immunoprecipitated with anti-HA or anti-GFP antibodies.
ChIP-Seq libraries were prepared for sequencing using the KAPA Hyper Prep Kit (Kapa Biosystems) according to the manufacturer’s instructions.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
The adapter-trimmed ChIP-Seq reads were mapped to the WS260 genome with bowtie2 using the default parameters.
Low quality reads (view -bS -q 10) and duplicate reads (rmdup -s) were removed using the SAMtools package (Li et al., Bioinformatics, 2009).
ChIP-Seq peaks were identified from the filtered sequencing read files using MACS2 (Zhang et al., Genome Biology, 2008) with the following parameters: -g ce --nomodel --extsize 175 --SPMR --keep-dup all -q 0.01.
ChIP-Seq enrichment calculations were performed using the bamCompare module within the deepTools suite (Ramirez et al., Nucleic Acids Research, 2016). The enrichment was calculated for 10 bp bins as the log2 ratio relative to input (--extendReads 175 --scaleFactorsMethod readCount).
Genome_build: WS260
Supplementary_files_format_and_content: BigWig ChIP enrichment files were generated from the processed alignment files using the bamCompare module within the deepTools suite (Ramirez et al., Nucleic Acids Research, 2016). The ChIP enrichment was calculated for 10 bp bins as the log2 ratio relative to input (--extendReads 175 --scaleFactorsMethod readCount).
Supplementary_files_format_and_content: NarrowPeak files were generated from the processed alignment files using MACS2 (Zhang et al., Genome Biology, 2008) with the following parameters: -g ce --nomodel --extsize 175 --SPMR --keep-dup all -q 0.01.
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| Submission date |
Apr 11, 2018 |
| Last update date |
Apr 04, 2019 |
| Contact name |
Robert Houston Dowen |
| E-mail(s) |
dowen@email.unc.edu
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Cell Biology and Physiology
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| Lab |
133 N. Medical Drive
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| Street address |
321 Fordham Hall, CB7100
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7100 |
| Country |
USA |
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| Platform ID |
GPL22765 |
| Series (2) |
| GSE112979 |
Genome-wide occupancy of the CEH-60 and UNC-62 Transcription Factors in Caenorhabditis elegans |
| GSE112981 |
Analysis of the transcription factor CEH-60 in Caenorhabditis elegans development |
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| Relations |
| BioSample |
SAMN08915692 |
| SRA |
SRX3923761 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3092620_DLS396_3F10_IP_enrichment.bw |
58.2 Mb |
(ftp)(http) |
BW |
| GSM3092620_DLS396_3F10_IP_peaks.narrowPeak.gz |
229.4 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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