|
| Status |
Public on Sep 30, 2016 |
| Title |
T1_H3K4me3_ChIPSeq |
| Sample type |
SRA |
| |
|
| Source name |
root tip
|
| Organism |
Gossypium hirsutum |
| Characteristics |
tissue: root tip
age: 18h root bourgeon
chip antibody: H3K4me3(Upstate/07-473)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Each biological replication 5g root tips were used for ChIP
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
T1_H3K4me3_wiggle.tar.gz
|
| Data processing |
Illumina CASAVA_v1.8.2 software used for basecalling.
Low-quality reads in the raw ChIP-seq data were examined using SOAPnuke_v1.5.0 and eliminated, and the high-quality reads were mapped onto the Gossypium hirsutum genome (Gossypium_hirsutum_v1.1) and assembled using SOAP2
peaks were called using MACS version 1.4.2 with the following setting: CallingParameter:macs14-s 49-g2500000000-p1e-5-w --space50-m 10,30
Genome_build: Gossypium hirsutum genome (Gossypium_hirsutum_v1.1)
Supplementary_files_format_and_content: wig files were generated using MACS version 1.4.2
|
| |
|
| Submission date |
Jun 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Dewei Zheng |
| E-mail(s) |
[email protected]
|
| Phone |
15005160205
|
| Organization name |
Nanjing Agricultural University
|
| Department |
State Key Laboratory of Crop Genetics and Germplasm Enhancement
|
| Lab |
Polyploid and Epigenetics Lab
|
| Street address |
1 Weigang Road
|
| City |
Nanjing |
| State/province |
Jiangsu Province |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL19231 |
| Series (2) |
| GSE83371 |
Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton |
| GSE83372 |
Histone modifications define expression bias of homoeologous genomes in allotetraploid cotton |
|
| Relations |
| BioSample |
SAMN05251166 |
| SRA |
SRX1846413 |
