|
| Status |
Public on Feb 13, 2018 |
| Title |
FUL IM, input |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence-like meristems
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Ler/Col F2
genotype/variation: pFUL:FUL-GFP 35S:AP1-GR ap1-1 cal-1
developmental stage: uninduced IM of plants
tissue: inflorescence meristem
chip antibody: none
|
| Treatment protocol |
No treatment
|
| Growth protocol |
All plants were grown on rock-wool at 21°C under long day conditions (16 h light, 8 h dark).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq experiments were performed following a previously published protocol (van Mourik et al 2015. Book Chapter. Methods in Molecular Biology: Plant Functional Genomics. 1284:93-1210.). ChIP-seq experiment input samples were used as negative controls. For each tissue two biological replicates and one input sample were sequencing on the Illumina HiSeq.
ChIP-seq libraries as well as control libraries that were based on “input” DNA were prepared using ThruPLEX DNA-seq kit (RUBICON GENOMICS, USA) following the manufacturer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file:
|
| Data processing |
Reads were then mapped to the A.thaliana genome (TAIR10) using Bowtie (version 1.1.2) with parameters “--threads 8 -n 2 -m 3 -k 1 --best --chunkmbs 256 -q”.
Redundant reads were removed using Picard tools (v2.60; http://broadinstitute.github.io/picard/). Peak-calling was performed using MACS2 (version 2.1.0). Duplicated reads were not considered (--keep-dup=1) during peak calling in order to achieve a better specificity
The "--mfold" parameter was set as "2-20" to build the model.
Peaks across replicates with an IDR ≤ 0.05 (https://sites.google.com/site/anshulkundaje/projects/idr) were retained.
Wiggle tracks were generated by DeepTools with the command “bamCoverage”; read coverage was normalized as RPKM (Reads Per Kilobase per Million reads).
The above processing pipeline was implemented in (Chen and Kaufmann 2017, Methods in Molecular Biology (Clifton, NJ) 1629, 239-269)
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Dec 22, 2017 |
| Last update date |
Feb 17, 2022 |
| Contact name |
Dijun Chen |
| E-mail(s) |
chendijun2012@gmail.com
|
| Phone |
030-2093 49744
|
| Organization name |
Humboldt University
|
| Department |
Plant Cell and Molecular Biology
|
| Lab |
Prof. Kaufmann
|
| Street address |
Philippstr. 13 (House 22)
|
| City |
Berlin |
| ZIP/Postal code |
10115 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE108455 |
Genome-wide mapping of binding sites of the MADS domain protein FRUITFULL in Arabidopis thaliana |
|
| Relations |
| BioSample |
SAMN08226873 |
| SRA |
SRX3505416 |
