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Status |
Public on Mar 16, 2020 |
Title |
s678 SMXL6HA_ChIPSeq_Rep1 |
Sample type |
SRA |
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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).
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
pSMXL6:SMXL6-HA transgenic line processed data file: s678_SMXL6HA_Rep1_vs_s678_Rep1_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
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|
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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 |
SAMN13332773 |
SRA |
SRX7187013 |