|
| Status |
Public on Jun 21, 2013 |
| Title |
RPC128-FLAG IP_Normal Growth_Replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
Log-phase cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
antibody: ANTI-FLAG M2 Affinity Gel (Sigma)
|
| Treatment protocol |
Cells fixed with 1% HCHO and quenched with 0.125M Glycine.
|
| Growth protocol |
RPC128-FLAG strain grown up to A600~0.8 in YEP medium at 30C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as described earlier(Arimbasseri A.G and Bhargava P, Mol. Cell. Biol. April 2008 vol. 28 no. 8 2598-2607). Libraries for ChIP sequencing were constructed according to the Illumina ChIP Seq library protocol. Briefly, DNA was subjected to a series of enzymatic reactions that repair frayed ends, phosphorylate the fragments, add a single nucleotide A overhang and ligate adaptors (Illumina ChIP Seq Library preparation kit. lot# 6961486 ). The libraries were enriched using PCR, cleaned using Agencourt Ampure XP beads (Beckman Coulter) and size selected using a 2 % Low melting agarose gel. The prepared libraries were quantified using Nanodrop Spectrophotometer and validated for quality by running an aliquot on High Sensitivity Bioanalyzer Chip (Agilent).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Reads with phred score < 20 on 80% of the bases were filtered out with FASTX toolkit V0.0.13
Reads aligned to yeast genome using Bowtie 0.12.8 allowing unique alignments with 3 mismatches and taking the best stratum.
Reads are extended to ChIP fragment size (180bp)
Read coverage at each position in the genome is scaled to 1 million and normalized to total number of reads in the library.
Coverage at each base is bundled as .bedGraph files.
Genome_build: sacCer3
Supplementary_files_format_and_content: BEDGRAPH
|
| |
|
| Submission date |
Jul 23, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Yatendra Kumar |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
MRC Human Genetics Unit, The University Of Edinburgh
|
| Department |
MRC HGU
|
| Lab |
Wendy Bickmore
|
| Street address |
Crewe Road south
|
| City |
Edinburgh |
| ZIP/Postal code |
Eh42xu |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL9377 |
| Series (1) |
| GSE39566 |
Genome wide profiling of RNA polymerase III in Saccharomyces cerevisiae |
|
| Relations |
| SRA |
SRX170677 |
| BioSample |
SAMN01093682 |
