|
| Status |
Public on Aug 03, 2012 |
| Title |
mRNASeq_ibm1_3 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: two-leaf stage
strain: ibm1-3 mutant
rna subtype: polyA RNA isolated
|
| Growth protocol |
The seeds are sterilized with 2.25% bleach, washed with sterilized water, kept for three days at 4C, and then dispersed on Murashige and Skoog (MS) medium (Sigma-Aldrich) containing 1% sucrose and 0.3% phytagel (Sigma-Aldrich). Before be harvested,seedlings were growth 10 days under 160 umolm-2s-1 cool white fluorescent light and LD (16 h of light, 22C/8 h of dark, 18C) condition in a growth chamber (Percival CU36L5).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from 10 days seedlings grown on MS plates using RNAiso plus (Takara) according to the manufacturer's instructions, and was treated with RNase-free DNase (Promega) to remove any possible contaminating genomic DNA.mRNA was extracted from total RNA using Dynabeads Oligo(dT) (Invitrogen Dynal) following the manufacturer's directions. First-and second strand cDNA was generated using SuperscriptII reverse transcriptase (Invitrogen) and random hexamers primers. Double-stranded cDNA was fragmented by nebulization and used for mRNA library construction following the standard Illumina protocol. Small RNAs were gel isolated from total RNA, and were used to create libraries for Illumina sequencing essentially as described previously (Mi et al., 2008).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
polyA RNA isolated
|
| Data processing |
mRNA seq reads were mapped to the reference genome of Arabidopsis thaliana (TAIR10). Bowtie was used to map the sequence reads with no more than three mismatches. The 3' adapter sequences for smRNA seq were removed by a custom Perl script. The trimmed smRNA reads were mapped to the Arabidopsis genome using Bowtie with perfect matches.
|
| |
|
| Submission date |
Sep 21, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Di Fan |
| E-mail(s) |
scwwxc@163.com
|
| Organization name |
National Institute of Biological Sciences
|
| Street address |
7# Science Park Road Zhongguancun Life Science Park
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
10085 |
| Country |
China |
| |
|
| Platform ID |
GPL9062 |
| Series (1) |
| GSE32284 |
IBM1, a JmjC domain histone demethylase, is involved in the regulation of RNA-directed DNA methylation through epigenetic control of RDR2 and DCL3 expression in Arabidopsis. |
|
| Relations |
| SRA |
SRX099068 |
| BioSample |
SAMN00727825 |
