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Sample GSM2388465 Query DataSets for GSM2388465
Status Public on Jan 25, 2017
Title pwr rep3
Sample type SRA
Source name Young seedlings
Organism Arabidopsis thaliana
Characteristics tissue: Seedling
developmental stage: 10-day-old
genotype/variation: pwr-2
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
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.
BioSample SAMN06009999
SRA SRX2342112

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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