|
| Status |
Public on Apr 29, 2021 |
| Title |
clf_Input_S4 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: clf mutant
antibody: input
|
| Growth protocol |
ChIPseq assays were performed on shoot or root of 14‐day‐old seedlings
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were then generated using 10ng of DNA and NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Trimmomatic-0.38: Minimum length of 36 bp; Mean Phred quality > 30; Leading and trailing bases removal with base quality <5. The reads were mapped onto the TAIR10 assembly using Bowtie2 with mismatch permission of 1 bp. MACS2 for peaks detection were set as follows: Number of duplicate reads at a location:1; mfold of 5:50; q-value cutoff: 0.05; extsize 200; broad peak
Genome_build: TAIR10
Supplementary_files_format_and_content: BIGWIG
|
| |
|
| Submission date |
Feb 19, 2021 |
| Last update date |
Apr 29, 2021 |
| Contact name |
Sanchari Sircar |
| E-mail(s) |
sancharisircar24@gmail.com
|
| Organization name |
IPS2
|
| Lab |
Chromosome Dynamics
|
| Street address |
Batiment 630 Rue Noetzlin
|
| City |
Orsay |
| ZIP/Postal code |
75015 |
| Country |
France |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE155502 |
Polycomb-dependent differential chromatin compartmentalization determines gene co-regulation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN17998768 |
| SRA |
SRX10133722 |
