|
| Status |
Public on Apr 25, 2023 |
| Title |
ATH1052 |
| Sample type |
SRA |
| |
|
| Source name |
two-week-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
genotype/variation: xrn4
rep: rep2
|
| Growth protocol |
Seedlings grown on 1X MS, 1% (w/v) sucrose, 1% (w/v) agar for two-weeks in a climate-controlled growth chamber (21C; 16h day: 8h night); Fully expanded rosette leaves were collected from adult plants grown in soil under long day growth chamber conditions at 21/22C
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
PARE libraries were prepared as per Nagarajan et al., (2019); GMUCT libraries were prepared according to Wilmann et al., 2014 with modifications suggested in Carpentier et al., 2021; RNA-seq libraries: 50 ug polyA+ RNA (2x enriched) prepared as per NEBNext Ultra II Directional Library Preparation kit;
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
RNA-seq
gene_exp.diff
|
| Data processing |
PARE libraries (Illumina HiSeq 2500); GMUCT and RNA-seq libraries (Illumina NextSeq 550)
Reads were mapped to Arabidopsis TAIR10 genome using Tophat v2.0
PARE and GMUCT libraries were analyzed as per Hurtig et al., 2021 (PNAS) using the ComPARE pipeline
Bedgraph files contain ComPARE scores from PARE and GMUCT libraries comparing normalized abundances (expressed as counts per million, CPM) at every 5'P site between Col-0, xrn4 and mfl1xrn4
Genome_build: Arabidopsis TAIR10 (Ensemble v49)
Supplementary_files_format_and_content: RNA-seq: gene_exp.diff is a cuffdiff output file; PARE and GMUCT: Genomic coordinate file (with annotations) containing RNA Degradome scores where 5'P site CPM >= 1 in xrn4 in both replicates (bedgraph files)
|
| |
|
| Submission date |
Jan 07, 2022 |
| Last update date |
Apr 25, 2023 |
| Contact name |
Pamela J Green |
| E-mail(s) |
green@dbi.udel.edu
|
| Organization name |
Delaware Biotechnology Institute
|
| Department |
Plant and Soil Sciences
|
| Street address |
15 Innovation Way
|
| City |
Newark |
| State/province |
DE |
| ZIP/Postal code |
19711 |
| Country |
USA |
| |
|
| Platform ID |
GPL24270 |
| Series (1) |
| GSE193247 |
RNA degradome analysis reveals substrates of NYN-domain containing DNE1 endoribonuclease in Arabidopsis |
|
| Relations |
| BioSample |
SAMN24724711 |
| SRA |
SRX13658012 |
