|
| Status |
Public on Feb 21, 2023 |
| Title |
paps1-1 rep 2 random hexamers |
| Sample type |
SRA |
| |
|
| Source name |
pollen tubes
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: pollen tubes
ecotype: Col-0
genotype: paps1-1 mutant
priming: random hexamer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from semi-in vivo grown pollen tubes were isolated using the Arcturus® PicoPure® RNA Isolation Kit.
Sequencing libraries were generated using the Ovation RNA-Seq System 1-16 for Arabidopsis, which includes an rRNA depletion step and allows for adjusting the balance between random-hexamer and oligo(dT) primers in the initital reverse transcription. For each pollen-tube sample, we split the extracted RNA and generated one library using only random-hexamer primers and one library using only oligo(dT) primers. The libraries were sequenced on an Illumina NextSeq550 instrument using a high-output flow cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Mutant, random hexamer priming
|
| Data processing |
Reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using STAR (Dobin et al., 2013; doi:10.1093/bioinformatics/bts635) version 2.7.3a with the –quantMode GeneCounts option to get mapping counts at gene level.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Raw gene read counts for each sample.
|
| |
|
| Submission date |
Jul 05, 2022 |
| Last update date |
Feb 22, 2023 |
| Contact name |
Michael Lenhard |
| E-mail(s) |
michael.lenhard@uni-potsdam.de
|
| Phone |
+49-331-9775580
|
| Organization name |
Universität Potsdam
|
| Department |
Institut für Biochemie und Biologie
|
| Street address |
Karl-Liebknecht-Str. 24-25, Haus 26
|
| City |
Potsdam |
| ZIP/Postal code |
14476 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE207509 |
Transcriptomic analyses to estimated poly(A)-tail lengths in paps1-1 mutant pollen tubes |
|
| Relations |
| BioSample |
SAMN29507282 |
| SRA |
SRX16029212 |
