|
| Status |
Public on Jan 25, 2017 |
| Title |
hdac rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Young seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Seedling
developmental stage: 10-day-old
genotype/variation: hda9-1
ecotype: Col
|
| Growth protocol |
Seeds were surface-sterilized and sown on MS-agar plates. After two days of cold treatment, the plated seeds were transferred to 23°C under long-day (16 h light, 8 h dark) condition.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from 10-day old seedlings using the Trizol reagent (Invitrogen)
mRNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit). mRNA was purified and fragmented from total RNA (1 µg) using poly-T oligo-attached magnetic beads and two rounds of purification. Cleaved RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase, random primers and dUTP in place of dTTP. (The incorporation of dUTP quenches the second strand during amplification because the polymerase does not incorporate past this nucleotide.) A single adenine base was added to these cDNA fragments, followed by adapter ligation. The products were purified and amplified with PCR to create the final strand-specific cDNA library. The quality of the amplified libraries was verified by capillary electrophoresis (Bioanalyzer, Agilent). After qPCR using SYBR Green PCR Master Mix (Applied Biosystems), the index-tagged libraries were combined in equimolar amounts within a single pool.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Basecalls and quality control and pre-aligned (eland) were performed using Illumina Genome analyzer pipeline
The raw reads were aligned to the Arabidopsis genome (TAIR10) using hisat2. The reads mapped to more than one positions were removed.
The raw counts of gene were generated by perl script.
Genome_build: TAIR10
Supplementary_files_format_and_content: excel files of raw counts
|
| |
|
| Submission date |
Nov 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Lei Gao |
| E-mail(s) |
leigao@szu.edu.cn
|
| Organization name |
shenzhen university
|
| Department |
College of Life Sciences
|
| Street address |
Nanhai Ave 3688
|
| City |
shenzhen |
| State/province |
guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE89769 |
POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. [RNA-Seq] |
| GSE89770 |
POWERDERESS and HDA9 interact and promote histone H3 deacetylation at specific lysine residues in Arabidopsis. |
|
| Relations |
| BioSample |
SAMN06010002 |
| SRA |
SRX2342107 |
