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| Status |
Public on Jan 14, 2018 |
| Title |
Rpb3 ChIP-Exo HS12 replicate2 |
| Sample type |
SRA |
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| Source name |
in vivo
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
chip antibody: Rpb3-TAP
cell description: GRF88, MATa his4-38, S288C background
strain: BY4741
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| Treatment protocol |
For ChIP-exo, cells were crosslinked with formaldehyde to a final concentration of 1.0%.For PIP seq 100 mMKmNO4 added.
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| Growth protocol |
For ChIP-exo, cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-exo, lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
ChIP-exo libraries were prepared for sequencing using standard SOLiD & Illumina protocols with a minor modification; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/
ChIP-exo, PIP-seq
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Replicate 2
RPB3_extract_tag_occupancy.csv
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| Data processing |
For single end reads from HiSeq, basecalls were performed using CASAVA version 1.7 and for paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
ChIP-exo reads were aligned to Saccer3 genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Supplementary_files_format_and_content: gff, gene track peak calls using (smoothing 5bp, exclusion 10bp)
Supplementary_files_format_and_content: txt, peak pair calls filtered for significance over background
Supplementary_files_format_and_content: csv, extraction of PIP-seq, ChIP-exo tag count(or ratio to NoTag) in TSS
Supplementary_files_format_and_content: tab, tag extraction from 5' end of uniquely mapped sequencing reads, tab-delimited
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| Submission date |
May 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Bongsoo Park |
| E-mail(s) |
[email protected]
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| Phone |
814-441-3861
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| Organization name |
Penn State University
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| Street address |
453 North Frear Building
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| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE98573 |
Widespread and precise epigenomic reprogramming in response to heat shock |
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| Relations |
| BioSample |
SAMN06893058 |
| SRA |
SRX2785895 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2601030_51839sacCer3.tab.gz |
357.5 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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