|
| Status |
Public on May 10, 2021 |
| Title |
hhp1_rnaseq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
treatment: untreated
genotype: hhp1 T-DNA insertion line
|
| Treatment protocol |
untreated
|
| Growth protocol |
Arabidopsis seeds were sown on 1/2 MS medium plates plates under a long-day photoperiod with 16 h of light at 24 °C and 8 h of darkness at 22 °C, and 12-day-old seedlings were harvested for RNA-seq and ChIP-seq experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq: seedling samples were harvested and frozen immediately in liquid nitrogen and total RNA was extracted with TRIzol reagent (Invitrogen). For ChIP-seq: histone-DNA complexes were isolated with anti-acetylated Histone H3 antibody .
Both of the RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
gene_hhp1_vs_WT_exp.txt
TE_hhp1_vs_WT_exp.txt
|
| Data processing |
RNA-seq: Illumina CASAVA software was used for basecalling
RNA-seq: sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
RNA-seq: clean reads were mapped to the TAIR10 Arabidopsis genome using TopHat v 2.0.12 program with parameter --b2-very-sensitive
RNA-seq: the differentially expressed genes and TEs were identified using “Cuffdiff” program of Cufflinks v 2.2.1 , which uses the normalized RNA-seq fragment counts to measure the relative abundances of the genes
ChIP-seq: Illumina CASAVA software was used for basecalling
ChIP-seq: sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
ChIP-seq: clean reads were mapped to the TAIR10 Arabidopsis genome using Bowtie v2.4.1 with default parameters
ChIP-seq: PCR duplicates were removed by Sambamba v 0.6.6 program
ChIP-seq: peaks were called using MACS2 v 2.1.1.20160309 program with parameters -g 1.2e8 -B -q 0.05
ChIP-seq: differentially enriched peaks were determined by DiffBind R package in Bioconductor
ChIP-seq: the read count falling in each gene region which used for generating RPKM(reads per kilobase per million) value for each gene was calculated by “intersect” command from the BEDTools suite.
Genome_build: tair10
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include the log2(fold_change) of normalized read counts and P value for wild type and each mutant to figure out the differentially expressed genes and transposons(TEs)
Supplementary_files_format_and_content: ChIP-seq: tab-delimited text files include RPKM value of each gene for wild type, sant1234-null and hda6, and .csv files include the log2 (fold_change) of normalized read counts falling in each peak and FDR value for wild type, sant1234-null and hda6 to figure out the differentially enriched peaks
|
| |
|
| Submission date |
Feb 22, 2021 |
| Last update date |
May 10, 2021 |
| Contact name |
Xishi Zhou |
| E-mail(s) |
zhouxishi@caas.cn
|
| Organization name |
Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences
|
| Lab |
Cuijun Zhang
|
| Street address |
No 7, Pengfei Road
|
| City |
Shenzhen |
| ZIP/Postal code |
518120 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE167288 |
A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis |
|
| Relations |
| BioSample |
SAMN18029323 |
| SRA |
SRX10152109 |
