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| Status |
Public on Nov 29, 2014 |
| Title |
input1.3_4 |
| Sample type |
SRA |
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| Source name |
BY4741
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
stress: diamide
time: 4 min
antibody: na
experimental_batch: 1.3
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| Treatment protocol |
final concentration of 1.5 mM diamide
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| Growth protocol |
400 mL wild-type strain (BY4741) cells were grown in YPD medium to mid-log phase (OD600=0.55) with 220 rpm shaking at 30°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Formaldehyde was quenched by 125mM glycine. Cell pellets were then harvested, washed by water, and subjected to beads-beating, MNase digestion, and chromatin immunoprecipitation protocol as previously described in Liu et al (2005)
As described in Blecher-Gonen R et al 2013 (PMID 23429716)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1000 |
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| Data processing |
library-strategy: MNase-ChIP-Seq
mapping to S. cerevisiae S288C (release 64) using bowtie2.X with default settings
Read extension to 100bp and summation per bp in genome
Nucleosom calling after smoothing based on local minima/maxima pairs
Maximal level from every time points/Antibodies was collected per nucleosome (window size of 150bp)
each nuc/antibody/time was normalized to its respective input (there are 9 experimental batches) - see CSV file, in log2 ratio to input
failed sequencing libraries were linearly interpolated given adjacent time points
Genome_build: sacCer3
Supplementary_files_format_and_content: bigWig files containing bp-resolution data after extension of reads and summation; nucs_normed.csv.gz file contains all data, assigned to nucleosomes and normalized to respective input (log2 ratio). First 7 columns describe nucleosome - "nuc_id" is an ordinal number, "chr" is the chromsome number, "center" is the chromsome coordinate of the nucleosome center, "coverage (RPM)" is the reads per million assigned to the nucleosome in the input track from which it was called, "gene" is the gene name in the corresponding locus (where applicable), "acc" is the gene accession number (where applicable), and "gene_pos" is the nucleosome position of the nucleosome within the transcribing unit, i.e. -1, +1,+2, etc.
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| Submission date |
Sep 30, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alon Appleboim |
| Organization name |
Hebrew University of Jerusalem
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| Department |
Life Sciences
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| Lab |
Nir Friedman
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| Street address |
Hebrew University
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| City |
Jerusalem |
| ZIP/Postal code |
9190501 |
| Country |
Israel |
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| Platform ID |
GPL17582 |
| Series (1) |
| GSE61888 |
High resolution chromatin dynamics during a yeast stress response |
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| Relations |
| BioSample |
SAMN03084586 |
| SRA |
SRX717538 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1516581_input1.3_tp2_4.bw |
18.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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