|
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
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|
|
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.
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|
|
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 |