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Sample GSM4605301 Query DataSets for GSM4605301
Status Public on Sep 23, 2020
Title HRE1α OX_14DAG_rep2
Sample type SRA
Source name HRE1α OX, whole seedlings, 14 DAG, SD
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
age: 14 days after germination
genotype: HRE1alpha
tissue: whole seedlings
Treatment protocol No treatment
Growth protocol Arabidopsis plants were of the Columbia (Col-0) ecotype background. Arabidopsis seeds were surface-sterilized and water-imbibed in the dark for 2 d at 4℃. The seeds were sown on 0.7% (w/v) agar plates containing on-half-strength Murashige and Skoog (MS) media supplemented with B5 vitamins and 1.5% (w/v) sucrose. They were grown at 22℃ under SD conditions (8-h-light/16-h-dark cycle).
Extracted molecule total RNA
Extraction protocol RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description Gene expression in 14-day-old seedlings of HRE1α grown under SD conditions (8-h-light and 16-h-dark cycle). Whole seedlings were sampled and total RNA was analyzed.
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to TAIR10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
Submission date Jun 10, 2020
Last update date Sep 23, 2020
Contact name Yong-Hwan Moon
Phone +82515102592
Organization name Pusan National University
Department Molecular Biology
Lab Plant Molecular Genetics Lab
Street address Busandaehak-ro 63Beon-gil 2, Geumjeong-gu
City Busan
ZIP/Postal code 46241
Country South Korea
Platform ID GPL19580
Series (1)
GSE152166 Differentially expressed genes between WT and HRE1α OX, WT and HRE1β OX, and WT and AtRH17 OX
BioSample SAMN15196967
SRA SRX8517118

Supplementary file Size Download File type/resource
GSM4605301_HRE1aOX-2.txt.gz 161.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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