|
| Status |
Public on Apr 05, 2016 |
| Title |
input_Col_sdg8_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
genotype: sdg8-2
antibody: none
biological replicate: 1
demultiplexbarcode: CAGATC
|
| Growth protocol |
Leaf number six of plants grown for 35 days under short day conditions (8 h light) was harvested at zeitgeber time ZT=7 and used for nuclei isolation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native Chromatin Immunoprecipitation (N-ChIP) was performed following a slightly modified procedure of (Bernatavichute et al, 2008). Cross-linked chromatin immunoprecipitation (X-ChIP) assays were performed as described (Exner et al, 2009).
Libraries were generated using the Microplex Library Preparation kit (Diagenode) following the manufacturer's protocol using 1 ng of starting material.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Chrosslinked Chromatin
coverageNormSize_input_Col_sdg8.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 25 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 |
Nov 09, 2015 |
| 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) |
| GSE74841 |
H3K36ac is an evolutionary conserved histone modification that marks active genes in plants |
|
| Relations |
| BioSample |
SAMN04254428 |
| SRA |
SRX1426139 |
