|
| Status |
Public on Jul 23, 2023 |
| Title |
DTPCRep2 [input] |
| Sample type |
SRA |
| |
|
| Source name |
leaf tissue
|
| Organism |
Panicum virgatum |
| Characteristics |
developmental stage: E3
tissue: leaf
treatment: Input
|
| Treatment protocol |
The control and drought treated plants were arranged in one growth chamber and palnts with drought and heat treatment in a separate chamber
|
| Growth protocol |
The ramets of lowland ecotype Alamo, AP13 genotype of switcghrass were transplanted in 3GP nursery pots and later transferred to the green house for optimum conditions at the Samuel Roberts Noble Foundation in Ardmore, Oklahoma.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-DNA was extracted from Proteinase-K digested samples by phenol-chloroform extraction and ethanol precipitation using glycogen.
100 ng of purified DNA was used to generate the ChIP-Seq library using Illumina HiSeq using manusfacturer instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Robert Nobel Foundation
|
| Data processing |
The libraries were sequenced on Illumina HiSeq 2500 platform with 101 bp paired-end reads.
Read quality was assessed using FastQC (v 0.11.2) for all samples and quality trimming was done using cutadapt (v 1.13)
Histone modification peaks were detected using SICER (v 1.1)
Genome_build: The quality trimmed reads were mapped against the bowtie2-indexed Panicum virgatum reference genome (v4.1) using bowtie2 (v 2.3.1)
Supplementary_files_format_and_content: BigWig files were generated using deeptools
|
| |
|
| Submission date |
Feb 07, 2022 |
| Last update date |
Jul 23, 2023 |
| Contact name |
Shaojun Xie |
| E-mail(s) |
[email protected]
|
| Phone |
7657140672
|
| Organization name |
Purdue University
|
| Street address |
3135 Decatur Street
|
| City |
WEST LAFAYETTE |
| State/province |
Indiana |
| ZIP/Postal code |
47906 |
| Country |
USA |
| |
|
| Platform ID |
GPL31915 |
| Series (1) |
| GSE196295 |
ChIP-Seq analysis of switchgrass transcriptome in response to single drought and combinations of drought and heat stress |
|
| Relations |
| BioSample |
SAMN25710582 |
| SRA |
SRX14083537 |
