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| Status |
Public on Feb 26, 2017 |
| Title |
chdC-null 0H rep1 |
| Sample type |
SRA |
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| Source name |
Dictyostelium
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| Organism |
Dictyostelium discoideum |
| Characteristics |
development stage: Growing
cell type: chdC-null
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| Treatment protocol |
Cells were developed on nitrocellulose filters until they reached loose-mound stage of development (10H for Ax2, 12H for ChdC null cells)
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| Growth protocol |
Cells were grown axenicly in HL5 + glucose media (Formedium)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 1 x 109 cells were washed in 100 mM sorbitol and resuspended in 400 ml digestion buffer [100 mM sorbitol, 50 mM NaCl, 10 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 1 mM CaCl2, 1 mM 2-mercaptoethanol, 0.5 mM spermidine, 0.1% Nonidet P40] and transferred to a 1.5 ml microcentrifuge tube containing MNase (USB/Affymetrix) at a final concentration of 800 U/ml; incubation was at 37o C for 2 min. Digestion was stopped by addition of 40 ml stop buffer [5% SDS, 250 mM EDTA (pH 8.4)], followed by phenol/chlorophorm extraction of DNA. RNase A treatment was at 37o C for 30 min. The DNA was re-extracted with phenol/chloroform and precipitated with sodium acetate and 100% ethanol. Control digests used 10 mg of previously extracted undigested ‘naked’ DNA suspended in digestion buffer at 20o C for 30 sec. Three independent replicates for each sample were pooled, and separated on a 1.5% agarose gel. The 50-1000 bp gel region was extracted and libraries prepared with the Illumina paired-end kit.
Liibraries prepared with the Illumina paired-end kit
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using CASAVA version 1.7
Paired-end reads were aligned using bowtie version 0.12.7 to the chromosomes 1-6 of the Ax4 dictyostelium genome masking the duplicated region on chromosome 2 (nucleotides 3,015,984 to 3,768,555) and gene models from dictybase.org
Paired reads mapping with an isize of 150bp (+/- 20%) were selected as providing nucleosome position data
The centerpoint between the two paired reads was defined as the nucleosome dyad, the nucleosome dyads were then calculated genome wide in the resulting processed .sgr file.
Genome_build: Ax4_May2009
Supplementary_files_format_and_content: sgr
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| Submission date |
Jun 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
James Platt |
| Organization name |
University of Oxford
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| Street address |
Roosevelt Drive
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| City |
Oxfors |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
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| Platform ID |
GPL15643 |
| Series (1) |
| GSE70122 |
Regulation of nucleosome positioning by a CHD Type III chromatin remodeller and its relationship to developmental gene expression in Dictyostelium [MNase-seq] |
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| Relations |
| BioSample |
SAMN03785392 |
| SRA |
SRX1068238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1717317_ChdC-0H_36bp_Part150_10_rep1.sgr.gz |
9.4 Mb |
(ftp)(http) |
SGR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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