|
| Status |
Public on Sep 07, 2017 |
| Title |
H3_kyp_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype: kyp6
antibody: anti-H3 cat. no. H9289 (Sigma)
biological replicate: 1
demultiplexbarcode: GCTG
|
| Growth protocol |
Leaves number 5-6th were harvested from 5-week-old plants grown under short day conditions (8 h light).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native Chromatin Immunoprecipitation (N-ChIP) was performed following a slightly modified procedure of (Mahrez et al. 2016).
Libraries were generated using the Ovation Ultralow Library System (NuGEN, San Carlos, USA) following the manufacturer's protocol using 1 ng of starting material previously sonicated for 25 cycles (30 sec ON, 30 sec OFF at high power) using a Bioruptor (Diagenode).
Sequencing was performed on an Illumina HiSeq2000 in 50-bp single-end mode.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
coverageNormSize_H3_kyp.bw
|
| Data processing |
Quality control was done with an in-house R script
Demultiplexing and adapter trimmng was done with reaper (EMBL-EBI)
Clean reads of the replicates were merged and mapped to Arabidopsis TAIR10 genome using Bowtie2
SAM file output from bowtie was converted to BAM format using SAMTOOLS (version 1.4) and imported into R.
Identical reads present more than 15 times were considered as PCR artifacts and filtered out using the filterDuplReads function from package HtSeqTools
ChIP-seq coverage was calculated using the coverage function from R
Normalization of the coverage to identical sequencing depth
Subsequent analysis were performed in R. The used gene models were from TAIR10 gff annotation file
Genome_build: TAIR10
Supplementary_files_format_and_content: BigWig files of coverage
|
| |
|
| Submission date |
Sep 07, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Minerva Susana Trejo Arellano |
| E-mail(s) |
Minerva.Trejo-Arellano@jic.ac.uk
|
| Organization name |
SLU
|
| Department |
Plant Biology
|
| Lab |
Lars Hennig's Lab
|
| Street address |
Almas Allé 5
|
| City |
Uppsala |
| State/province |
Uppsala |
| ZIP/Postal code |
75007 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE86498 |
H3K23me1 is an evolutionary conserved histone modification associated with CG DNA methylation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN05735456 |
| SRA |
SRX2143557 |
