|
| Status |
Public on Sep 04, 2019 |
| Title |
COL_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: post germinal day 4
growth condition: grown in the dark for 4 days, at 22°C .
genotype: Wild type
|
| Growth protocol |
After surface-sterilizing, the seeds were stratified at 4 °C for 3 d in darkness.The seeds were irradiated with continuous white light for 12h,and then placed in the dark and at 22°C for 4 days before havresting.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4-day-old dark-grown seedlings were ground into powder in liquid nitrogen, and total RNA was extracted by using the RNeasy Plant Mini Kit(QIAGEN).
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 |
Casava1.8.2 software was used for basecalling.
Trimmomatic and/or fastx_clipper were used to remove adapters. Poor quality bases (less than Phred-20) were removed (clipped) from both the 5' and 3' ends of the Unaligned reads. After adapter removal and quality clipping any reads below a minimum (30 bases) length were discarded. Reads were then mapped to TAIR10 assembly of the Arabidopsis genome using Tophat v2.1.0 with default parameters.
Digital gene expression (counts) was determined for each sample using HTSeq-count v0.6.1 (Anders et al., 2015) with the following parameters: -s reverse -r pos -m intersection-nonempty -t exon -i gene_id.
Differential expression analysis was performed using the edgeR package as follows: edgeR analysis began with a count table comprising 33,602 genes. Genes expressed at low levels were then filtered out by removing any genes for which there was not at least 1 count per million in at least four of the samples. This resulted in a list of 18,842 expressed genes. Counts were then normalized using TMM normalization. Next, the “ANOVA-like” procedure in EdgeR was used to identify genes that were differentially expressed between any of the genotypes (FDR < 0.05). This resulted in a list of 14,688 differentially expressed genes. To determine which of these genes were differentially expressed in each of the mutants compared to wild type, the exact test for the negative binomial distribution (Robinson and Smyth, 2008) was used followed by a Bonferroni correction to maintain a gene-wise error rate of 0.05
Genome_build: Tair10
Supplementary_files_format_and_content: tab-delimited text files include counts values or normalized count values for each sample.
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Sep 04, 2019 |
| Contact name |
xiaodan yu |
| E-mail(s) |
ppaofish@126.com
|
| Phone |
13476069559
|
| Organization name |
Huazhong Agricultural University
|
| Department |
College of Life Science and Technology
|
| Street address |
No.1,Shizishan Street · Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei Province |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE128498 |
Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to repress photomorphogenesis. |
|
| Relations |
| BioSample |
SAMN11162477 |
| SRA |
SRX5539420 |
