|
| Status |
Public on Jul 06, 2012 |
| Title |
WT-Flower-RNAseq-2 |
| Sample type |
SRA |
| |
|
| Source name |
flower
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: flower
genotype/variation: wild type
|
| Growth protocol |
Homozygous seeds of Arabidopsis thaliana mutants in the background of Columbia ecotypes for ddm1-2 were kindly provided by Dr. Olivier Mathieu from Clermont Université in France. After five-day germination in half of MS medium, the seedlings of wild type (Col-0) and ddm1-2 either continued to grow under 16-hour light/8-hour dark cycles at 23 degree for collecting young leave tissues or were transferred into potting soil to grow under the same light-dark condition until flowering. Two-week old leave tissues and closed flower buds from both wild type and ddm1-2 were collected and immediately frozen in liquid nitrogen, respectively. All collected samples were ground into powder for the following DNased-seq and RNA-seq experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Protocols for nuclei isolation, DNaseI digestion and DNased-seq library preparation were performed exactly as described ( Zhang et al., 2012 in press, GSE26734). Two biological DNased-seq replicates from leave and flower tissues of both wild type and ddm1-2 were sequenced by using Illumina Genome Analyzer II. The experimental procedures for the total RNA extraction, cDNA synthesis and preparation of barcoded RNA-seq libraries were the same as the published protocol (Zhang et al., 2012 in press). Three biological RNA-seq replicates from both leave and flower tissues of the wild type Col-0 were prepared for Illumina sequencing. We generated 58 M RNA-seq reads of flower and 43M of leaf. We found that 90.3% ind leaf and 89.6% in flower can be mapped on TAIR10 reference genome using TopHat. Then we use Cufflink to measure the expression level (FPKM) of arabidopsis annotated genes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RNAseq of wild type flower replicate 2
|
| Data processing |
ath_buds_rep2.bam; genome build: TAIR release 10
The reads from DNase-seqs were aligned to Arabidopsis genome (TAIR release 10) with non-mismatch allowed using Bowtie. Only the reads mapped to a unique position of Arabidopsis genome were used for further analysis. We used F-seq to identify DH sites with 300bp bandwidth. To detect the FDR, we generated 10 random data sets, which contain the same reads number as then DNase-seqs data set. We set the threshold in F-seq to control the FDR less than 0.01. To count the distribution of DNase I reads on Arabidopsis genome, we calculated percentage of 20-bp unique reads in each 100kb non-overlap window from entire chromosome. Then we using this percentage to adjust the reads count on each 100-kb non-overlap window from five chromosomes of Arabidopsis. To measure the fold change of DH region on each chromosome, we count the normalized reads in 100kb window and calculated the log2 ratio of each 100kb window between ddm1 and wild type. Note that the raw data included the linker sequence (TCGTATGCCGTCTTCT)
|
| |
|
| Submission date |
Dec 09, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Yufeng Wu |
| E-mail(s) |
yfwu@njau.edu.cn
|
| Organization name |
UW-Madison
|
| Lab |
Jiming Jiang
|
| Street address |
1575 Linden Drive
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL9302 |
| Series (1) |
| GSE34318 |
Mapping regulatory elements using signatures of open chromatin in Arabidopsis thaliana |
|
| Relations |
| SRA |
SRX111016 |
| BioSample |
SAMN00765116 |
