|
| Status |
Public on Nov 03, 2017 |
| Title |
Input DNA of replicate 2 (GBY-1) |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis pistil/silique stage 12-16
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col/Ler
genotype: pFUL:FUL-GFP ful-1
tissue: pistil/silique
developmental stage: stage 12-16
antibody: none, input control
|
| Treatment protocol |
Sample collection was laborious and tissue was harvested throughout the day. No specific treatment was applied.
|
| Growth protocol |
The plants were grown on soil at 22 °C under long day condition (16 h light, 8 h dark).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed according to a previously published protocol (Kaufmann et al., Nature Protocols, 2010) using a GFP antibody. Approximately 1 g of pistils/siliques were used for each biological replicate. The input sample was used as negative control.
Libraries were prepared using the Illumina protocol for preparation of ChIP-SEQ libraries with modifications described in Kaufmann et al., Nature Protocols 2010
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
GAPipeline-1.4.0
Alignment: Sequence reads were obtained and mapped to the Arabidopsis thaliana genome using the SOAP mapping software (soap.genomics.org.cn/). All reads mapping with two or fewer mismatches at unique positions were retained. Iteratively, one base was discarded form the 3`end of the nonmapped reads until the reads were uniquelly mapped or fell bellow a minimum length of 30 bp
Peaks were detected using CSAR
Genome_build: Arabidopsis TAIR9
Supplementary_files_format_and_content: Location of peaks and their associated score enrichment are reported in the processed data
|
| |
|
| Submission date |
Mar 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marian Bemer |
| E-mail(s) |
marian.bemer@wur.nl
|
| Organization name |
Wageningen University
|
| Department |
Molecular Biology
|
| Street address |
Droevendaalsesteeg 1
|
| City |
Wageningen |
| ZIP/Postal code |
6708 PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL9302 |
| Series (2) |
| GSE79554 |
Targets of FRUITFULL in the pistil/silique [ChIP-Seq] |
| GSE79555 |
Expression profiling and identification of targets of FRUITFULL in the Arabidopsis pistil/silique |
|
| Relations |
| BioSample |
SAMN04577543 |
| SRA |
SRX1658532 |
