|
| Status |
Public on Aug 11, 2016 |
| Title |
WT_mock_2 |
| Sample type |
SRA |
| |
|
| Source name |
WT_mock
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
age: 10-day-old
exposed to: none (mock control)
tissue: whole seedlings
|
| Treatment protocol |
10-day-old Arabidopsis wildtype (Col) seedlings were mock treated, or exposed to 50μM ABA, PA, or DPA for 3 h in biological duplicates
|
| Growth protocol |
Arabidopsis thaliana seeds were germinated on MS medium under continuous light at 22 °C untill 10 days old.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction using RNeasy Plant Mini Kit (Qiagen)
Multiplex RNA library construction and Illumina sequencing were carried out at the Beijing Genome Institute (BGI). The total RNA samples are first treated with DNase I. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.
Approximately 20 million reads of 50 bp single-ended sequences were generated per sample using Illumina HiSeq2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mock treated biological replicate 2
|
| Data processing |
Raw reads were mapped onto the Arabidopsis gene model (TAIR10_GFF3_genes.gff downloaded from ftp://ftp.arabidopsis.org/Maps/gbrowse_data/TAIR10/) using TOPHAT (version 1.4.1)
Number of reads mapped to each gene were then counted using htseq-count, a component of the HTSeq framework (version 0.5.3p3)
Differential Expression was evaluated using DESeq (version 1.8.3)
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel spread sheets concontaining cross-treatment comparisons based on normalized read counts
|
| |
|
| Submission date |
Feb 09, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jing-Ke Weng |
| E-mail(s) |
wengj@wi.mit.edu
|
| Phone |
617-324-4921
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142-1479 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE65739 |
Coevolution of hormone metabolism and signaling networks expands plant adaptive plasticity |
|
| Relations |
| BioSample |
SAMN03333294 |
| SRA |
SRX868995 |
