|
| Status |
Public on Mar 13, 2020 |
| Title |
ChIP-seq_Col-0_air_H3K4me3 |
| Sample type |
SRA |
| |
|
| Source name |
histone modification
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: etiolated seedlings
genotype: Col-0
antibodies: H3K4me3 (EMD Millipore, 04-745)
|
| Treatment protocol |
no treatment or 4 hours of JA treatment
|
| Growth protocol |
etiolated seedlings
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Sample 2
Wig file contains:
SICER comparison Sample 2 vs Sample 2
|
| Data processing |
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
ChIP-seq peak identification with SICER 1.1 with the following setting: redundancy threshold (1), window size (200), fragment size (100), effective genome fraction (0.8), gap size (600), FDR (0.01)
Genome_build: TAIR10
Supplementary_files_format_and_content: wig files with SICER output
|
| |
|
| Submission date |
Jun 27, 2019 |
| Last update date |
Mar 14, 2020 |
| Contact name |
Joseph R Ecker |
| E-mail(s) |
ecker@salk.edu
|
| Phone |
8584534100
|
| Organization name |
HHMI-Salk-Institute
|
| Department |
Genomic Analysis Laboratory
|
| Lab |
Ecker lab
|
| Street address |
10010 North Torrey Pines Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE133408 |
The jasmonate-response genome regulatory program is defined by the direct targets of transcription factors MYC2 and MYC3, chromatin modification and gene expression changes |
|
| Relations |
| BioSample |
SAMN12147612 |
| SRA |
SRX6370134 |
