|
| Status |
Public on May 15, 2019 |
| Title |
SPT6LΔSH2-GFP spt6l IP rep2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
age: 10 days
ecotype: Col-0
chip antibody: anti-GFP (ab290, abcam)
|
| Treatment protocol |
10 µM flavopiridol or DMSO was sprayed on 10 days old seedlings for 1h
|
| Growth protocol |
Plants were grown on half strength of Murashige and Skoog (½ MS) medium (0.5XMS salts, 1.5% [w/v] sucrose, and 0.8% agar [pH 5.8]) or soil under 16h/8h light/dark cycle at 23°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed as previously described (Chen et al., 2017) with some modifications. Five grams of 10-day-old Arabidopsis seedlings grown on ½ MS medium were collected. Protein A Dynabeads (Invitrogen) was pre-incubated with antibody (5 µL for 50 µL beads) at 4 degree in a rotor at least 6h. After removing excess or unbound antibodies, the pre-cleaned chromatins (cleaned by incubating with Dynabeads alone) were add into antibody bound Dynabeads.
NEBNext® Ultra™ DNA Library Prep Kit (E7370S)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
The reads were aligned to the TAIR10 assembly using the Bowtie2 program with default settings.
unmapped reads and PCR duplicates were removed by using Samtools (verion1.7)
peaks were called by using MACS2 program with following setting: -g 135000000, -broad, and -broad-cutoff 0.01
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files were generated by using bamCoverage (deeptools2) with following settings: -bs 10 --effectiveGenomeSize 135000000 --normalizeUsing RPGC --ignoreDuplicates -e 300 --samFlagExclude 1796
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
May 15, 2019 |
| Contact name |
Chen Chen |
| E-mail(s) |
chenchen101@scbg.ac.cn
|
| Organization name |
South China Botanical Garden, Chinese Academy of Science
|
| Lab |
Dr. Chen Chen
|
| Street address |
723 Xinke Rd.
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510650 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE108673 |
RNA polymerase II-Independent Recruitment of SPT6L at Transcription Start Sites in Arabidopsis |
|
| Relations |
| BioSample |
SAMN10618993 |
| SRA |
SRX5169069 |
