|
| Status |
Public on May 15, 2019 |
| Title |
wt Col - rep1 [mRNA-seq] |
| Sample type |
SRA |
| |
|
| Source name |
inflorescence (stage 1-12) immature flower buds
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype/background: Columbia
genotype/variation: wt
tissue: inflorescence (stage 1-12) immature flower buds
fraction: total
|
| Growth protocol |
Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissue is inflorescence (stage 1-12) immature flower buds.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total, Nuclear, and Cytoplasmic cell extracts were obtained as in the Cellular Fractionation protocol from Park et al., PMID: 15738428, with the following modification: Miracloth was substituted for using a 100 µm cell strainer. RNA was extracted using the Trizol LS protocol (Invitrogen) and enriched for poly(A)+ mRNAs using the NEBNext Poly(A) mRNA Magnetic Isolation Module.
Libraries were prepared using the NEBNext Ultra II Directional RNA library prep kit and dual-indexed.
Multiplexed libraries were sequenced on a HiSeq4000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
PolyA RNA
|
| Data processing |
Raw RNA-seq paired-end reads were processed to remove adapter sequences from both 3' and 5' ends using BBDuk2 program from BBTools package (https://jgi.doe.gov/data-and-tools/bbtools/) with the following parameters: “k=23 mink=11 hdist=1 tbo”. Adapter-trimmed reads were further processed to remove bases below the Phred quality score Q30 at both 3' and 5' ends by using BBDuk2.
The resulting quality-trimmed reads were aligned to reference TAIR10 Arabidopsis thaliana genome using STAR version 2.5.1b (Dobin et al., PMID: 23104886) with the parameters “--outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100”. To improve accuracy of STAR alignment, Arabidopsis gene and TE annotations from Araport11 (https://www.araport.org/) were also provided along with the reference genome sequence.
Read alignments against Arabidopsis genes and TEs were counted using featureCounts (Liao et al., PMID: 24227677) from the Subread package version 1.6.1 with the parameters “ -p -B -C -g gene_id -M --fraction -s 2”. The resulting read counts were used for all subsequent analyses.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_geneCounts.tsv: Raw counts of reads for each gene or TE as calculated using featureCounts (described in data processing above), is provided.
|
| |
|
| Submission date |
Aug 17, 2018 |
| Last update date |
May 15, 2019 |
| Contact name |
R. Keith Slotkin |
| E-mail(s) |
kslotkin@danforthcenter.org
|
| Organization name |
Donald Danforth Plant Science Center
|
| Street address |
975 North Warson Road
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL21785 |
| Series (2) |
| GSE118708 |
Transcriptome of the Arabidopsis mRNA export mutant aly1 and associated controls |
| GSE118709 |
Methylome, transcriptome, RIP-seq and small RNA-seq of the Arabidopsis mRNA export mutant aly1 and associated controls |
|
| Relations |
| BioSample |
SAMN09848246 |
| SRA |
SRX4563743 |
