|
| Status |
Public on Jan 09, 2022 |
| Title |
panH3_HU-_ChIP-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: By4741
antibody: Histone H3, C-terminal antibody(pAB)
vendor/catalog#: Active Motif 39163
treatment: None
|
| Treatment protocol |
HU group cells are treated with 200mM hydroxurea (Sigma) for 2 hours
|
| Growth protocol |
BY4741 strain yeast cells were grown in YPD media to mid-log phase (OD600<1.0)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mid-log phase cells are utilized in chromatin immunoprecipitation (ChIP) experiments as described before (Kuo,M.H. 1999) with the following minor modifications. Sonication is performed for 6x10 cycles with Diagenode Bioruptor. ChIP washes are performed at 4oC. ChIP elution buffer contains 1.0% SDS, 10 mM Tris, 1 mM EDTA, pH 8.0. Crosslinking is reversed overnight at 65oC. The eluted DNA is purified with Invitrogen PureLink PCR Purification Kit.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit. (Part# 11257047)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
Images generated by the Illumina sequencer were initially processed using the the Illumina pipeline
Read alignment was done using BWA 0.5.9-r16 using the UCSC SacCer1 reference genome. Only unique alignments with no mismatches were kept.
Tags were shifted 100bp in the 3' direction and binned into 150bp windows.
The H3T45p and panH3 smples were normalized using the DESeq normalization procedure [PMID: 20979621], and differential enrichments were calculated.
Windows with significant H3T45p enrichment over panH3 were called as peaks (FDR adj p-value < 0.1)
Genome_build: SacCer1
Supplementary_files_format_and_content: Bedgraph files contain binned tag counts or normalized differential (H3T45p-panH3) tag counts. Bed files contain coordinates of significantly enriched windows (H3T45p over panH3).
|
| |
|
| Submission date |
Jan 24, 2013 |
| Last update date |
Jan 09, 2022 |
| Contact name |
Stephen Aurelien Hoang |
| Organization name |
HemoShear Therapeutics
|
| Street address |
501 Locust Ave, Suite 301
|
| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22902 |
| Country |
USA |
| |
|
| Platform ID |
GPL9377 |
| Series (1) |
| GSE43737 |
The Replication Kinase Cdc7 Marks Histones to Regulate Biosynthesis Genes |
|
| Relations |
| SRA |
SRX219975 |
| BioSample |
SAMN01902596 |
