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Sample GSM1656317 Query DataSets for GSM1656317
Status Public on Apr 14, 2015
Title brat1nrpe1_mRNA_rep1
Sample type SRA
 
Source name Seedlings
Organism Arabidopsis thaliana
Characteristics ecotype: Columbia
genotype/variation: brat1nrpe1
Growth protocol Arabidopsis seeds were surface-sterilized and placed on MS (Murashige and Skoog) agar medium. Then the MS plates were incubated at 23ºC with 16-h-light and 8-h-dark for 10 days.
Extracted molecule total RNA
Extraction protocol Seeding materials was ground into powder in liquid nitrogen; Total RNA was extracted from 0.2 g of 10-day-old Arabidopsis seedlings with Trizol reagent (Invitrogen) ; then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Arabidopsis thaliana (tair10) whole genome using tophat v2.0.12 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.1) with the provision of a GTF annotation file (tair10).
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
 
Submission date Apr 13, 2015
Last update date May 15, 2019
Contact name huanwei huang
E-mail(s) hhw2436@gmail.com
Organization name NIBS
Street address 7 Science Park Rd., ZGC life science park
City Beijing
ZIP/Postal code 102206
Country China
 
Platform ID GPL17639
Series (2)
GSE67797 A novel BRAT1–BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis [RNA-Seq]
GSE67799 A novel BRAT1-BRP1 complex recognizes histone acetylation and mediates active DNA demethylation and transcriptional activation in Arabidopsis
Relations
BioSample SAMN03481140
SRA SRX992493

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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