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| Status |
Public on Jul 01, 2020 |
| Title |
Whole seedlings, bZIP68-FLAG.CHIP.rep1 |
| Sample type |
SRA |
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| Source name |
bZIP68-FLAG.CHIP
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole seedlings
age: 8-day-old
genotype: bZIP68-FLAG
chip antibody: FLAG antibody (Sigma Aldrich, F1804)
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| Growth protocol |
Arabidopsis seedlings were growth on 1/2 MS plates containing 3% sucrose and 0.8% agar for 8 days under 16h light/ 8h dark condition(with light 125 umoles/m2 seg )
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Three gram of bZIP68-FLAG or GFP-FLAG seedling per sample was cross-linked with 1% formaldehyde for 10 min, and then incubated with 0.125 M glycine (final concentration) for an extra 5 min. Chromatin extraction and immunoprecipitation was carried out according to the protocol from Joseph Ecker lab (Song et al., 2016). DNA-Protein complexes were pulled down using FLAG antibody (Sigma Aldrich, F1804) which has been bound to Pierce™ ChIP-grade Protein A/G Magnetic Beads (ThermoFisher, 26162). The immune complexes were treated with NaCl, RNase A, proteinase K and 65 degree heating for de-crosslinking. Finally, DNAs were purified using ChIP DNA Clean & Concentrator™ kit (ZYMO research, D5205). Illumina sequencing libraries preparation was carried out according to the manufacturer’s manual (CWBIO, CW2585S, NGS Fast DNA Library Prep Set for Illumina). The libraries were sent to Novogene company (Tianjin, China) and sequenced using the Illumina HiSEQ1500 platform.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
Supplementary_Tables_S1_S2.BZIP68_CHIPSeq_peaks_v4.xlsx
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| Data processing |
The reference genome sequence used for analyzing the ChIP-Seq data and motif finding was the Arabidopsis thaliana TAIR10 database. Enriched peak regions were identified using MACS-1.4.3 (Feng et al., 2012) with default parameters (-g 1.2e8 -p 1e-5 -w --space 50 -m 10,30 -s 49). Chipseeker (Yu et al., 2015) was applied to calculate average profiles of ChIP peaks binding to TSS regions, perform enrichment analysis, and peak annotation.
Genome_build: A. thaliana Ensemble 41 (TAIR10)
Supplementary_files_format_and_content: 20190704.bzip.counts.xlsx, Supplementary_Tables_S1_S2.BZIP68_CHIPSeq_peaks_v4.xlsx
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| Submission date |
Jul 06, 2019 |
| Last update date |
Jul 01, 2020 |
| Contact name |
Huan ZHONG |
| E-mail(s) |
zhdorothy5@gmail.com
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| Phone |
91493987
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| Organization name |
HKBU
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| Department |
BIOLOGY
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| Street address |
T1012 CHA CHI-MING SCIENCE TOWER
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| City |
HONG KONG |
| State/province |
HONG KONG |
| ZIP/Postal code |
00000 |
| Country |
Hong Kong |
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| Platform ID |
GPL19080 |
| Series (1) |
| GSE133900 |
Redox-sensitive bZIP68 plays a role in balancing stress tolerance with growth in Arabidopsis |
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| Relations |
| BioSample |
SAMN12226102 |
| SRA |
SRX6410178 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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