|
| Status |
Public on Mar 16, 2020 |
| Title |
s678 SMXL6HA_ChIPSeq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
whole seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: smxl6/7/8 pSMXL6:SMXL6-HA
age: two weeks
tissue: whole seedlings
chip antibody: anti-HA polyclonal antibody (Sigma, H6908)
|
| Growth protocol |
Arabidopsis seeds were surface sterilized, vernalized at 4 ºC for 2-4 days, germinated and grown on the 0.5× Murashige and Skoog (MS) medium containing 1.0% sucrose and 0.7% agar under a long day photoperiod (16-h light, 8-h dark cycle) with a light intensity of 60-80 μE m−2 sec−1 at 21 ºC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Two-week-old seedlings were frozen and ground into powder in liquid nitrogen, then fixed in formaldehyde solution to cross-link protein-DNA complexes. The protein-DNA complexes were extracted from nuclei, underwent subsequent sonication, and immune precipitation with an anti-HA polyclonal antibody.
DNA libraries were prepared for sequencing according to Illumina's instructions accompanying the NextflexTM Rapid DNA-seq Kit (Bioo Scientific, 5144-02).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
pSMXL6:SMXL6-HA transgenic line
processed data file: s678_SMXL6HA_Rep2_vs_s678_Rep2_peaks.bed
|
| Data processing |
All ChIP-seq reads were mapped to the Arabidopsis genome TAIR10 using BWA (version 0.7.10-r789) software with default parameters.
Duplicated reads and reads with low mapping quality were discarded using SAMtools (version 0.1.19-44428cd) with default parameters.
Peaks for SMXL6-HA were identified by the model-based analysis software (MACS version 1.4.2) in comparison with smxl6/7/8 with the parameters '--mfold=10, 30' and fold enrichment equal or larger than 2 using DNA enriched from the smxl6/7/8 mutant as a control.
Genome_build: Arabidopsis genome TAIR10
Supplementary_files_format_and_content: wig, bed files
|
| |
|
| Submission date |
Nov 19, 2019 |
| Last update date |
Mar 16, 2020 |
| Contact name |
Jiayang Li |
| E-mail(s) |
jyli@genetics.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology, CAS
|
| Street address |
West Beichen Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE140705 |
Genome-wide maps of SMXL6 binding sites in Arabidopsis seedlings [pSMXL6:SMXL6-HA] |
|
| Relations |
| BioSample |
SAMN13332771 |
| SRA |
SRX7187015 |
