|
| Status |
Public on Jul 03, 2017 |
| Title |
Naked DNA |
| Sample type |
SRA |
| |
|
| Source name |
Husk
|
| Organism |
Zea mays |
| Characteristics |
line: B73
developmental stage: stage silk emerging 2-5 cm
tissue: inner layer husk
|
| Growth protocol |
Plants grown till stage V2 (Abendroth et al 2011) or till flowering (ears with emerging silks, before pollination) in greenhouse, 16h of light per day. Temperature above 22°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNase I digestion of the chromatin and DNase I digestion of gDNA (naked DNA)
Library constructed with the Ovation Ultralow DR Multiplex kit (NuGEN)
|
| |
|
| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Basecalls performed using Illumina’s real-time analysis software (RTA).
Quality filtering of ChIP-seq reads were done using FastX Toolkit and PRINSEQ (Q20).
ChIP-seq reads were aligned to the AGPv3 genome assembly using BWA
Non-uniquely mapped reads were filtered out using samtools (MAPQ20)
Peaks were called using MACS2 (-q 0.001, -broad)
Genome_build: AGPv3
Supplementary_files_format_and_content: bed files were generated using MACS2; bigwig files were converted from wig output from MACS2 using wigToBigWig tool (SPMR)
|
| |
|
| Submission date |
Jan 30, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Johan Zicola |
| E-mail(s) |
johan.zicola@gmail.com
|
| Organization name |
Max Planck Institute for Plant Breeding Research
|
| Department |
Plant Developmental Biology
|
| Lab |
Turck
|
| Street address |
Carl-von-Linné
|
| City |
Cologne |
| ZIP/Postal code |
50829 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE94291 |
Genome-wide chromatin accessibility profiling in maize using DNase-seq on two different tissues: inner stem tissue of V2 seedlings and husk |
|
| Relations |
| BioSample |
SAMN06282444 |
| SRA |
SRX2528146 |
