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Status |
Public on Apr 12, 2016 |
Title |
Agg_H3K27ac_ChIPSeq |
Sample type |
SRA |
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Source name |
Aggregative stage cells
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Organism |
Capsaspora owczarzaki |
Characteristics |
stage/cell type: Aggregative strain: ATCC 30864 chip antibody: anti-H3K27Ac (#07-360, Millipore)
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Growth protocol |
Capsaspora strain ATCC30864 cells were grown axenically in 5 ml flasks with ATCC medium 1034 (modified PYNFH medium) in an incubator at 23¼C
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Extracted molecule |
genomic DNA |
Extraction protocol |
For ChIP-seq: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature (RT). Crosslinking was quenched with 0.125 M glycine for 5 min RT. Pelleted cells were lysed in Lysis buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40, plus protease inhibitors and 0.5 mM DTT), incubated on ice for 10 minutes and centrifuged at 8000xg 10 min to pellet the nuclei. Nuclei were resuspended in Lysis buffer II (1%SDS, 10 mM EDTA, 50 mM tris ClH pH 8.1 plus protease inhibitors), incubated on ice for 10 min and sonicated for 15 min (15 cycles, each one 30sec “on”, 30 sec “off”) in a Bioruptor (Diagenode, Seraing, Belgium) in order to generate 200bp fragments. For ChIP-seq: Libraries of immunoprecipitated and input DNA were prepared using the NEBNext DNA sample prep reagent Set 1 kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer's protocol. For ATAC-seq: Fresh nuclei were obtained using Lysis Buffer I (10 mM HEPES.KOH pH 7.9, 1.5 mM MgCl2, 10 mM KCl, 0.2 % NP40) For ATAC: Fresh nuclei incubated 30min at 37ºC with Tn5 transposases from the Nextera DNA Library Prep Kit (Illumina, San Diego, CA)
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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 |
Genome mapping using Bowtie v1.1.1 with -v 1 -m 1 parameters. Remove duplicates using samtools v1.1 For ChIP-seq: Peak calling using MACS2 with parameters --nomodel, --shiftsize 100 and a q-value threshold of 0.01; except for H3K36me3 samples, for which additionally used --broad parameter and a q-value threshold of 0.05. Corrected by genome mappability. For ATAC-seq: Peak calling using MACS2 with parameters -q 0.001 --extsize 40 --call-summits --nomodel Genome_build: Capsaspora genome v2 (Broad Institute) Supplementary_files_format_and_content: Peak BED files from MACS2 peak calling
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Submission date |
Jul 21, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Arnau Sebe-Pedros |
E-mail(s) |
arnau.sebe@crg.es
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Organization name |
Centre for Genomic Regulation
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Department |
Systems Biology
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Lab |
Sebe-Pedros lab
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Street address |
Dr. Aiguader 88
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City |
Barcelona |
ZIP/Postal code |
08003 |
Country |
Spain |
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Platform ID |
GPL20718 |
Series (1) |
GSE71131 |
The dynamic regulatory genome of Capsaspora owczarzaki and the origin of animal multicellularity |
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Relations |
BioSample |
SAMN03891605 |
SRA |
SRX1113426 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1827965_A27A_MACS2_peaks.narrowPeak.gz |
290.7 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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