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| Status |
Public on Mar 30, 2017 |
| Title |
ChIPseq_Spt5-WT_I_input |
| Sample type |
SRA |
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| Source name |
ChIPseq_Spt5-WT, input
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| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: FWP10
growth_medium: EMM
spike_in: 2.5% S. cerevisiae chromatin
demultiplex_code: GTCTAC
spt5_gene_status: wild type
chip antibody: none
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| Treatment protocol |
Spt5 depletion experiments were performed by adding NAA (0.5mM in DMSO, napthaleneacetic acid, Sigma, N0640) and thiamine (100nM, thiamine hydrochloride, Sigma, T4625), to cells grown to a density of 10^7 cells/ml (O.D.600 ~ 0.5). Cultures were incubated with shaking at 30°C for 4.5 hours.
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| Growth protocol |
S. pombe strains were grown in EMM complete media at 30°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were prepared as described in (PMID:24100010)
ChIP-seq libraries were prepared as described in (PMID:24100010). For the spike-in control, S. cerevisiae chromatin was added to S. pombe chromatin before immunoprecipitation with the relevant antibodies. S. cerevisiae chromatin corresponding to 2.5% of S. pombe chromatin, as estimated by Bradford assay (Bio-Rad), was used. Libraries were sequenced on the Illumina HiSeq platform at the Tufts University Core Facility.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Strain_FWP10_genotype_WT
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| Data processing |
Mapping using Bowtie2 first to S. pombe and then S. cerevisiae genomes.
WIG density tracks produced by SPP software functions select.informative.tags, remove.local.tag.anomalies, and get.smoothed.tag.density. The latter function was used with parameters control.tags=input (for ChIP), bandwidth=25,step=10,tag.shift = cross-correlation profile peak. Input samples were not background-subtracted.
Genome_build: S. pombe ASM294v2, S. cerevisiae R64-1-1
Supplementary_files_format_and_content: bedGraph track files for S. pombe tag-shifted density, sampled every 10bp, library-size-normalized, background-subtracted if ChIP-samples.
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| Submission date |
Aug 03, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
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| Phone |
617-432-7373
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| Organization name |
Harvard Medical School
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| Department |
Center for Biomedical Informatics
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| Street address |
10 Shattuck St
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL17225 |
| Series (2) |
| GSE85127 |
Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [ChIP-seq_round1] |
| GSE85182 |
Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription |
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| Relations |
| BioSample |
SAMN05507137 |
| SRA |
SRX1996836 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2258073_ChIPseq_Spt5-WT_I_input.bedGraph.gz |
16.4 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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