|
| Status |
Public on Mar 30, 2017 |
| Title |
ChIP-seq_Spt5-V5-IAA17_noTreat_Spt5_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Strain_FWP485_genotype_Spt5-V5-IAA17
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
growth_medium: EMM
spike_in: 10% S. cerevisiae chromatin
demultiplex_code: CTTGTAT
spt5_gene_status: nmt81-Spt5-V5-IAA17
antibody: anti-V5
antibody_target: Spt5
replicate: 1
|
| 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.
|
| Growth protocol |
S. pombe strains were grown in EMM complete media at 30°C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were prepared as described in (PMID:24100010)
ChIP-seq libraires 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 10% of S. pombe chromatin, as estimated by Bradford assay (Bio-Rad), was used. Libraries were sequenced on the Illumina NextSeq 500 platform at the Harvard Bauer Core facility.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Demultiplexing, 5' barcode removal, and 3' trimming of initial 75bp sequence to 60bp resulted in the attached FASTQs.
Alignment using Bowtie 1.1.1 (parameter -m 1 for unique mapping) to a concatenated S. pombe and S. cerevisiae genome.
Split resulting BAMs by organism, then counted reads to produce ratios for spike-in normalization.
Determined cross-correlations via SPP which recommended tag shift of ~180bp for all ChIP samples.
bedGraph track files produced for S. pombe of 180bp tag-shifted density with bandwidth 20, sampled every 10bp, spike-in-normalized.
Genome_build: S. pombe ASM294v2 concatenated to S. cerevisiae R64-1-1
Supplementary_files_format_and_content: bedGraph track files for S. pombe tag-shifted density with bandwidth 20, sampled every 10bp, spike-in-normalized.
|
| |
|
| Submission date |
Jan 18, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL20584 |
| Series (2) |
| GSE85182 |
Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription |
| GSE93803 |
Genome-wide analyses reveal widespread roles for Spt5 in sense and antisense transcription [ChIP-seq_round2] |
|
| Relations |
| BioSample |
SAMN06239076 |
| SRA |
SRX2501573 |
