|
| Status |
Public on Jul 03, 2017 |
| Title |
H3K9ac_ChIP_V2_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
V2 inner stem tissue
|
| Organism |
Zea mays |
| Characteristics |
line: B73
tissue: inner stem tissue V2 seedling
antibody: H3K9ac (ab10812)
|
| Treatment protocol |
V2 Seedlings were dissected to extract the inner stem: the outer leaves, including sheath, and also exposed leaf blades were removed. Soft husk leaves were obtained after longitudinal section of the ear including husk, removal of the ear tissue as well as the lignified most external husk leaves layers.
|
| Growth protocol |
B73 maize plants were grown till stage V2 (Abendroth et al 2011) or till flowering (ears with emerging silks, before pollination) in greenhouse (16h of light per day, average temperature = 23°C)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Plant tissues were fixed with formaldehyde (3%) followed by nuclei extraction, sonication and Immunoprecipitation with H3K9ac antibody (ab10812). Immunoprecipitated DNA was recovered by decrosslinking and purified on column.
Libraries were prepared according to KAPA Hyperprep kit (KK8500) instructions, using illumina Trueseq indexed adapters.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
H3K9ac_ist.bed
H3K9ac_ist.bw
|
| 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 AGPv4 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: AGPv4.32
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: 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 |
Maike Stam |
| Organization name |
University of Amsterdam
|
| Department |
Swammerdam Institute for Life Sciences
|
| Street address |
Science Park 904
|
| City |
Amsterdam |
| ZIP/Postal code |
1098XH |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL17628 |
| Series (2) |
| GSE94251 |
Genome-wide identification of H3K9ac enriched regions in inner stem tissue of V2 seedlings and husks (maize B73) [ChIP-Seq] |
| GSE94254 |
Inner stem tissue of V2 seedlings and husks (maize B73) |
|
| Relations |
| BioSample |
SAMN06279474 |
| SRA |
SRX2527279 |
