|
| Status |
Public on Dec 31, 2013 |
| Title |
29CHIP_IPsample |
| Sample type |
SRA |
| |
|
| Source name |
Seed
|
| Organism |
Oryza sativa |
| Characteristics |
seed development stage: 9 Days after pollination seed
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of chromatin was done as per proctocol mentioned in Haring et al's paper- Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization, Plant Methods 2007, 3:11.
Library construction was done according to Illumina's protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
immunoprecipitated chromatin
|
| Data processing |
Reads were aligned to MSU RGAP Release 6.1 - Unified Rice Pseudomolecules version, using CLCBIO (defalt paprameters) and the resultant bam files were imported in Avadis NGS for analysis
Aligned reads were filtered using Quality threshold >= 30 Alignment score threshold >= 90
Peaks detected using MACS Algorithm. Treatment Sample: 29CHIP_IPsample mapping Control Sample: 29CHIP_Input mapping; Algorithm: Model-based Analysis for ChIP-Seq Parameters: Read Length (bp) = 36; Average Fragment Length (bp) = 350; Effective Genome Size (bp) = 3.33712896E8; p-value Cutoff = 9.999999747378752E-6; Enrichment Factor = 10
Peaks were also detected using MACS Algorithm. Treatment Sample: 29CHIP_IPsample mapping Control Sample: 29CHIP_mock mapping; Algorithm: Model-based Analysis for ChIP-Seq Parameters: Read Length (bp) = 36; Average Fragment Length (bp) = 350; Effective Genome Size (bp) = 3.33712896E8; p-value Cutoff = 9.999999747378752E-6; Enrichment Factor = 2
The peak regions satisfying both the above criteria were shortlisted and annotated with Genic parts, e.g. Upstream (2kb), 5"UTR, Exonic, Intronic, 3'UTR, Downstream (2 kb)
Genome_build: genome build: MSU RGAP Release 6.1 - Unified Rice Pseudomolecules version
Supplementary_files_format_and_content: Unique peaks (378) were idenfied by mapping the summit to a specific genic part
|
| |
|
| Submission date |
Nov 09, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Sanjay Kapoor |
| E-mail(s) |
saraswati.nayar@gmail.com
|
| Organization name |
University of Delhi, South Campus
|
| Department |
Department of Plant Molecular Biology
|
| Street address |
Benito Huarez MArg
|
| City |
New Delhi |
| ZIP/Postal code |
110021 |
| Country |
India |
| |
|
| Platform ID |
GPL9147 |
| Series (1) |
| GSE42201 |
Chromatin immunoprecipitation of MADS29 to find the cis regulatory regions and targets of this transcription factor |
|
| Relations |
| SRA |
SRX204117 |
| BioSample |
SAMN01805343 |
