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| Status |
Public on Jun 03, 2015 |
| Title |
ECMB09_a8_N2-embryo_IgG-IP |
| Sample type |
SRA |
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| Source name |
mixed stage embryos
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
genotype: wild type
developmental stage: embryo
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| Treatment protocol |
Embryos were cross-linked with 2% formaldehyde for 30 min. Cross-linked embryos were resuspended in 1 ml of FA Buffer (150 mM NaCl, 50 mM HEPES-KOH (pH 7.6), 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM DTT, protease inhibitor cocktail) for every 1 gram of embryos. This mixture was frozen in small droplets in liquid nitrogen.
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| Growth protocol |
Wild-type N2 worms were grown at 20°C on NG agar plates with concentrated HB101 bacteria. For DC-mutant embryos, 10 ml of packed synchronous sdc-2(y93) L1 worms were placed onto 10 cm RNAi plates (NG agar with 1 mM IPTG and 100 mg/ml Carbenicillin) seeded with 2-3 ml of concentrated HT115 (DE3) bacteria carrying the Ahringer feeding library plasmid expressing the coding region of sdc-2. The RNAi plates were incubated at 25°C overnight before L1s were added. Mixed-stage embryos were harvested from gravid hermaphrodites.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The frozen embryos were ground under liquid nitrogen by mortar and pestle. Chromatin was sheared by the Covaris S2 (20% duty factor, power level 8, 200 cycles per burst) for a total of 30 min processing time (60 sec ON, 45 sec OFF, 30 cycles). To perform the ChIP reactions, extract containing approximately 2 mg of protein was incubated in a microfuge tube with 5 ug of anti-SDC-3 or random IgG antibodies overnight at 4°C. A 25 ul bed volume of protein A sepharose beads was added to the ChIP for 2 hr. ChIPs were washed for 5 min at room temperature twice with FA Buffer (150 mM NaCl), once with FA Buffer (1 M NaCl), once with FA Buffer (500 mM NaCl), once with TEL buffer (10 mM Tris-HCl (pH 8.0), 250 mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA), and twice with TE Buffer. Protein and DNA were eluted twice with 1% SDS, 250 mM NaCl, 1mM EDTA at 65°C for 15 min.
Sequencing libraries were prepared as published in Zhong et al. (2010) with minor changes: sequencing adapters were as described in Lefrancois et al. (2009) and adapters were ligated using NEB Quick Ligation Kit (M2200).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
50 base single end Illumina sequences were sorted by the bar code in the first 4 or 6 sequenced bases, then bar codes were removed
alignment to reference C. elegans genome WS230 with BOWTIE
pileup files were made using SamTools
the number of reads at each base was normalized by the total number of reads per million, then the average normalized read value for 50 bp windows was calculated and formatted into gff3
Genome_build: WS230
Supplementary_files_format_and_content: the processed data only contains reads for chromosome X
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| Submission date |
Jul 18, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara J. Meyer |
| E-mail(s) |
bjmeyer@berkeley.edu
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| Phone |
510 643 5583
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| Organization name |
HHMI/UCB
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| Department |
MCB
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| Lab |
Meyer
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| Street address |
16 Barker Hall #3204
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| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
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| Platform ID |
GPL13657 |
| Series (2) |
| GSE59597 |
Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation [ChIP-Seq] |
| GSE59716 |
Condensin-Driven Remodeling of X-Chromosome Topology during Dosage Compensation |
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| Relations |
| BioSample |
SAMN02927654 |
| SRA |
SRX657408 |
| 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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