|
| Status |
Public on Nov 10, 2016 |
| Title |
abc_10DAG_2 |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype: atbmi1abc triple mutant
age: 10DAG
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was performed using Qiagen-RNAesy mini-kit, following the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Quality control was performed using the software packges FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Read mapping to the reference genome was performed using Tophat (https://ccb.jhu.edu/software/tophat/index.shtml)
Transcript assembly was performed using Cufflinks and Cuffmerge (http://cole-trapnell-lab.github.io/cufflinks/)
Gene expression level measured in FPKM (fragments per kilobase of exon and million of mapped reads) was perfomed using Cufflinks and Cuffdiff
Subsequent data analysis and visualization was performed using the R bioconductor package cummeRbund (http://bioconductor.org/packages/release/bioc/html/cummeRbund.html)
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
|
| |
|
| Submission date |
Jun 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Myriam Calonje |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute for Plant Biochemistry and Photosynthesis (CSIC - University of Sevilla)
|
| Street address |
Americo Vespucio 49
|
| City |
Sevilla |
| ZIP/Postal code |
41092 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE83568 |
The Arabidopsis Polycomb Repressive Complex 1 (PRC1) components AtBMI1A, B and C impact gene networks throughout all stages of plant development |
|
| Relations |
| BioSample |
SAMN05277609 |
| SRA |
SRX1868573 |
