|
| Status |
Public on May 15, 2019 |
| Title |
wt Col - rep1 [small RNA-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
|
| 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 |
Inflorescence small RNA was isolated with Trizol reagent (Invitrogen) and concentrated using the mirVana microRNA Isolation Kit (Ambion).
Size-enriched small RNAs were prepared using the TruSeq Small RNA Library Preparation Kit (Illumina).
Multiplexed libraries were sequenced on a HiSeq2500.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Total small RNA
|
| Data processing |
Small RNA sequencing reads were processed as in McCue et al., PMID: 25388951 to remove adapters, tRNAs, rRNAs and filtered for size 18-28 nt.
Shortstack (Johnson et al., PMID: 27175019) was used to map the reads to the Arabidopsis genome (TAIR10) with fractional seeded guide used for multi-mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: *_normalized_counts.tsv: Reads per million sequenced (RPM) is provided for each filtered small-RNA read.
|
| |
|
| Submission date |
Aug 17, 2018 |
| Last update date |
May 15, 2019 |
| Contact name |
R. Keith Slotkin |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17639 |
| Series (2) |
| GSE118705 |
Small RNA-seq 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 |
| Reanalysis of |
GSM1023591 |
| BioSample |
SAMN09848122 |
| SRA |
SRX4563545 |
