|
| Status |
Public on Mar 15, 2017 |
| Title |
Input R2 |
| Sample type |
SRA |
| |
|
| Source name |
13d-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: 35S::MYC-bZIP28
treatment: treated at 42C for 1h
tissue: seedlings
developmental stage: 13 day old
ecotype: Col-0
|
| Treatment protocol |
13-day-old seedlings of 35S::MYC-bZIP28 plants were subjected to heat stress (42 0C for 1 hour). The stressed materials and non-stressed controls were fixed with 1% Formaldehyde solution for 2 times, 10 min each time, then glycine was added to a concentration of 0.125M to stop the reaction.
|
| Growth protocol |
Seeds were sow directly on 1/2 MS medium (with 1.2% sucrose and 0.7% agar, PH5.7) and stratified at 4 0C for two days, then transferred to illumination incubator with stable condition (22 0C, 16/8 h day/night photoperiod).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Protein A agarose beads (Millipore) with MYC antibody (Sigma) were used to precipitate the DNA.
The ChIP-DNA and input-DNA libraries were constructed and sequenced with Illumina HiSeq3000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Input DNA
|
| Data processing |
Raw reads were preprocessed to remove adapters, as well as to filter out low-quality and short (<50bp) reads.
Processed reads were aligned against the Arabidopsis thaliana reference genome using Bowtie (version 2.2.3), with only uniquely aligned reads retained and duplication redundancy removed.
Peak-calling were performed using MACS (version 1.4.2) (Zhang et al., 2008), and between-sample differential bindings were evaluated using MAnorm (Shao et al., 2012).
Significant peak regions were defined as those showing >2-fold increase in binding strength (as measured by normalized M values) in the heat-stressed samples compared with controls, and with p-values <0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files, read coverage across genomic regions
|
| |
|
| Submission date |
Jan 27, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hongxing Yang |
| E-mail(s) |
yanghx81@gmail.com
|
| Organization name |
Shanghai Chenshan Botanical Garden
|
| Street address |
3888 Chenhua Rd, Songjiang District
|
| City |
Shanghai |
| State/province |
- |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL21179 |
| Series (1) |
| GSE94146 |
Tissue-Specific Transcriptomics Reveals Role of the Unfolded Protein Response in Maintaining Fertility upon Heat Stress in Arabidopsis - ChIP-Seq |
|
| Relations |
| BioSample |
SAMN06276667 |
| SRA |
SRX2523225 |
