|
Status |
Public on Apr 29, 2021 |
Title |
HiChIP-K27-Root-rep2 |
Sample type |
SRA |
|
|
Source name |
HiChIP K27 Root rep2
|
Organism |
Arabidopsis thaliana |
Characteristics |
genotype: Col0
|
Growth protocol |
Hi-ChIP experiments were performed on shoots and roots of 14 day-old-seedlings
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Hi-ChIP experiments were performed using the same procedure as in Concia et al., 2020 with either anti-H3K9ac (Millipore 07–352) or anti-H3K27me3 (Millipore 07–449). Libraries were performed using Tn5 transposase using the same procedure as in Concia et al., 2020. Hi-ChIP libraries
|
|
|
Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
Trimmomatic-0.38 to remove Illumina sequencing adapters. The 5′ and 3′ ends with a quality score below 5 (Phred+33) were trimmed and reads shorter than 30 bp after trimming were dropped. The trimmed files were then processed with HiC-Pro v2.11.1 (Servant et al., 2015). The reads were aligned using Bowtie2 onto the TAIR10 assembly with default settings, except for the parameter “--score-min L, -0.6, -0.8”. Genome_build: TAIR10
|
|
|
Submission date |
Jul 31, 2020 |
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 |
SAMN15689634 |
SRA |
SRX8860828 |