|
| Status |
Public on May 30, 2018 |
| Title |
NP_control_NS_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia 0
age: 5 weeks
antibody: Anti-GFP (Abcam, ab290)
treatment: no stress
|
| Treatment protocol |
Plants were subjected to heat stress treatment at 37C for 30 minutes with relative humidity of 86% to maintain the vapour pressure deficit (VPD) at 1 kilo pascal.
|
| Growth protocol |
Arabidopsis thaliana Col-0 ecotype plants were grown in a controlled environment at the following conditions: 8/16 hours light/dark cycles, temperature 23C, relative humidity 60%, light intensity of 120 micro mole / meter second
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Plants were crosslinked in 1% formaldehyde solution using the vacuum infiltration method, nuclei were isolated then lysed, extracted chromatin was sheared using sonication, DNA-HSFA1b complexes were captured using antibodies specific to the tag proteins. DNA-HSFA1b-antibody complexes were then purified using protein A-sepharose beads.
Libraries were constructed using Illumina TruSeq ChIP-seq library preparation kit at The Genome Analysis Centre (TGAC, Norwich, UK)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
native_no_stress_summits.bed, native_no_stress_peaks.xls, native_no_stress_peaks.narrowPeak
|
| Data processing |
Basecalls performed using CASAVA version 1.8.2
Illumina adapters and low quality as well as overrepresnted illumina TruSeq primer sequences were trimmed from fastq files using in-house made programs
Quality-trimmed ChIP-seq reads were aligned to the Arabidopsis thaliana genome (TAIR10) using the aligner GSNAP with the following options -t 6 -A sam -m 0.01 -d Arabidopsis_thaliana
Conversion of SAM files to BAM followed by filtering unmapped reads, sorting and indexing were performed using samtools
peaks were called using MACS2 with the following settings: -f BAMPE -g 1.2e8 -q 0.05 -B –trackline
Genome_build: TAIR10
Supplementary_files_format_and_content: BED files containing ChIP-seq narrow peaks and peak summits, excel spreadsheet files containing all peaks with p-values, q-values, and fold enrichments
|
| |
|
| Submission date |
Aug 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Philip M Mullineaux |
| E-mail(s) |
mullin@essex.ac.uk
|
| Phone |
+44 (0) 1206 872118
|
| Organization name |
University of Essex
|
| Department |
Environmental and Plant Bioscience Research Group
|
| Lab |
5.36
|
| Street address |
Wivenhoe Park
|
| City |
Colchester |
| State/province |
Essex |
| ZIP/Postal code |
CO4 3SQ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE85651 |
Genome-wide mapping of the Arabidopsis thaliana heat shock transcription factor A1b binding sites under non-stress and heat stress conditions [ChIP-seq] |
| GSE85655 |
Genome-wide mapping of the Arabidopsis thaliana heat shock transcription factor A1b binding sites under non-stress and heat stress conditions |
|
| Relations |
| BioSample |
SAMN05578494 |
| SRA |
SRX2024340 |
