|
| Status |
Public on Oct 02, 2019 |
| Title |
H3K4me3_NST7 |
| Sample type |
SRA |
| |
|
| Source name |
immature wrapped leaf
|
| Organism |
Zea mays |
| Characteristics |
cultivar: B73
tissue: immature wrapped leaf
growth condition: control + recovery 7days
antibody: H3K4me3 (Active Motif, Cat. 39159)
|
| Treatment protocol |
Stresses were applied for 10 days: control plants (NS) were watered with 75% of disposable water at 0.1dS/m salt concentration; drought-stressed plants (WS) with 25% of disposable water at 0.1dS/m salt concentration.
|
| Growth protocol |
Maize plants were grown in greenhouse until V5-V6 leaf stage with normal watering
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin was purified from frozen tisses, sonicated and immuno-precipitated with antibody.
Ovation Ultralow Library System kit (Nugen) for Illumina sequencing
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
processed data file:
H3K4me3_rawcounts.txt
|
| Data processing |
base-calling and demultiplexing with Illumina CASAVA 1.8
manual trimming of 5 bp at the 3’ end
mapping with bowtie2, allowing at most 3 substitutions per read and no indels
Genes significantly enriched for a ChIP-Seq with respect to the WC control or between two conditions were identified by multiple 2 x 2 χ2 tests
Genome_build: RefGen ZmB73 Assembly AGPv4 + Zea_mays.AGPv4.34.gtf Gramene annotation
Supplementary_files_format_and_content: tab-delimited matrix with raw read counts for each gene in each sample/antibody. For H3K27me3 the gene boundaries are from TSS to TTS. For H3K4me3 and H3K9ac gene boundaries are from 0bp to +1000bp with respect to the TSS.
|
| |
|
| Submission date |
Mar 07, 2019 |
| Last update date |
Oct 02, 2019 |
| Contact name |
Federico Zambelli |
| Organization name |
University of Milan
|
| Department |
Department of Biosciences
|
| Street address |
Via Giovanni Celoria 26
|
| City |
Milano |
| ZIP/Postal code |
20133 |
| Country |
Italy |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE128002 |
Response to extended drought stress and recovery involve epigenetic control of stress adaptation and flowering regulation in Zea mays |
|
| Relations |
| BioSample |
SAMN11082614 |
| SRA |
SRX5492098 |
