|
| Status |
Public on Jul 01, 2013 |
| Title |
AG-GFP (AP1-GR ap1 cal) ChIPseq replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Inflorescence
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: AG-GFP AP1-GR ap1 cal
developmental stage: 4 days after Dexamethasone treatment (early-intermediate floral stage ~ stage 4-5 flowers)
chip antibody: Anti-GFP AB290 (Abcam)
chip antibody manufacturer: Abcam
tissue: Inflorescence
genetic background: Ler-0
|
| Treatment protocol |
For all experiments, ~4 week-old plants were used. For the experiments using the FIS (35S:AP1-GR ap1-1 cal-1 plants), flower development was induced using a solution containing 10 μM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol and 0.015% (v/v) Silwet L-77 (De Sangosse) – as described in Wellmer F, et al. (2006) Genome-Wide Analysis of Gene Expression during Early Arabidopsis Flower Development. PLoS Genetics 2(7):e117.
|
| Growth protocol |
Plants were grown on a soil:vermiculite:perlite (3:1:1) mixture at 20 degrees under constant illumination with cool white fluorescent light
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP was performed using a modified version of previously described protocols (Gomez-Mena C, de Folter S, Costa MM, Angenent GC, & Sablowski R (2005); Development 132(3):429-438 + Kaufmann K, et al. (2010), Nat Protoc 5(3):457-472.) Library preparation was performed as described in the instructions of the Illumina ChIP-Seq DNA Sample Prep Kit (IP-102-1001), whereby the adapter-oligo dilution used was 1:30 in water, the gel for DNA purification was run at low voltage (20V for > 6hrs) and gel-extraction step performed twice.
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| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
First ChIP-Seq replicate generated on an Illumina GAIIx machine running data collection SCS2.9/RTA1.9 software
|
| Data processing |
For each dataset, alignment was performed using the SOAPv2 short read alignment program and subsequent peak calling using the CSAR package as implemented in the Bioconductor project.
Main method: Arabidopsis genomic sequences were downloaded from TAIR (www.arabidopsis.org; files ‘TAIR10_chr1.fas’ - ‘TAIR10_chr5.fas’). Short read alignments were performed using the SOAP2 software with default settings. Data were read into R using the CSAR package. and functionality provided by various Bioconductor packages (including the IRanges v1.12.5 and GenomicRanges v1.6.4 packages) was used for data handling operations.
Peak calling was performed using the CSAR package that included a normalization and a test based on the Poisson distribution, and enriched regions were identified at a False Discovery Rate (FDR)<0.001 (with five rounds of permutations for each dataset, resulting in >600,000 permutations). Default parameters were used. Only peak regions with stretches of >50 bp were retained.
Peaks were associated with genes located in the vicinity using CSAR functionality, whereby a peak had to reside in a genomic region ranging from 3 kb upstream of a gene’s transcriptional start position to 1 kb downstream of its transcriptional end position. Gene range definitions were downloaded from TAIR (file TAIR10_GFF3_genes.gff).
Genome_build: TAIR10
Supplementary_files_format_and_content: csv formatted files, 1) file containing peak definitions (chromosome, peak start, peak end, peak position and maximal Poisson-based enrichment score) and putative direct target genes and 2) lists of putative direct target genes according to TAIR v10 genome build. The position of significantly enriched region(s) with respect to the corresponding gene is indicated by dividing the gene region into different segments (as indicated) and the maximum peak scores within these segments are shown. A value of 0 indicates that no significantly enriched peak region was detected within a given segment.
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| |
|
| Submission date |
Apr 10, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Pat Ryan |
| E-mail(s) |
pat.ryan12@gmail.com
|
| Organization name |
TCD
|
| Street address |
College Green
|
| City |
Dublin |
| ZIP/Postal code |
na |
| Country |
Ireland |
| |
|
| Platform ID |
GPL11221 |
| Series (2) |
| GSE45938 |
Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUS (ChIP) |
| GSE45939 |
Control of Reproductive Floral Organ Identity Specification in Arabidopsis by the C Function Regulator AGAMOUS |
|
| Relations |
| SRA |
SRX263743 |
| BioSample |
SAMN02028858 |
