 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 03, 2023 |
| Title |
Full-length RNA-seq of short RNAs from Cuscuta campestris |
| Organism |
Cuscuta campestris |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Cuscuta campestris is an obligate parasitic plant that attaches to the stems of host plants to obtain water and nutrients. C. campestris produces a specialized set of microRNAs specifically at the host-parasite interface. Many of these interface-induced microRNAs target mRNAs from the host. This experiment was designed to capture full-length primary transcripts that give rise to C. campestris interface-induced microRNAs. C. campestris shoot tips were stimulated to produce haustoria, then harvested to extract total RNA. RNA was then treated with various enzymes to modify 5' ends. Libraries were then made and sequenced. Importantly the library method only captures RNAs with a 5'-monophosphate. Therefore the specific enzymatic treatments can reveal the native 5' ends of the sequenced RNAs. Data were used to identify the primary transcripts for many of the known C. campestris primary microRNA transcripts. The data were also interrogated to tally specific snRNAs (U1, U2, U4, and U5) that are known to have a 2,2,7mGppp cap, and the tally pre-tRNAs, which are known to have a ppp 5' end. The analyzed results indicated that C. campestris interface-induced microRNA primary transcripts likely have a 5' ppp, not a cap, consistent with transcription by RNA polymerase III. The analysis also demonstrated that C. campestris interface-induced microRNA primary transcripts mostly terminate within stretches of polyT and lack polyA tails, also features consistent with Pol III transcription. Finally, the analysis indicated that the transcriptional start sites were located ~ 55 bp downstream of a common ten-base pair promoter element (the upstream sequence element). The 55bp spacing is also consistent with Pol III transcription.
|
| |
|
| Overall design |
Cuscuta campestris were cultivated on beets. Shoot tips 4-6cm in length were cut and stimulated to form haustoria by treatment with far-red light and physical pressure (stack of microscope slides pressing the tips against 3% agar) for 4 days. The regions with visible haustoria were dissected with a scalpel and collected for RNA extractions. 3 RNA samples were collected (numbered 1, 2, and 3).
|
| |
|
| Contributor(s) |
Axtell MJ |
| Citation(s) |
36896651 |
| |
| Submission date |
Dec 19, 2022 |
| Last update date |
Apr 07, 2023 |
| Contact name |
Michael J Axtell |
| E-mail(s) |
mja18@psu.edu
|
| Organization name |
Pennsylvania State University
|
| Department |
Biology
|
| Lab |
Axtell
|
| Street address |
280 Mueller Lab
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL32961 |
NextSeq 550 (Cuscuta campestris) |
|
| Samples (9)
|
| GSM6858877 |
In vitro haustoria, Dcp-treated RNA, replicate 1 |
| GSM6858878 |
In vitro haustoria, RppH-treated RNA, replicate 1 |
| GSM6858879 |
In vitro haustoria, untreated RNA, replicate 1 |
| GSM6858880 |
In vitro haustoria, Dcp-treated RNA, replicate 2 |
| GSM6858881 |
In vitro haustoria, RppH-treated RNA, replicate 2 |
| GSM6858882 |
In vitro haustoria, untreated RNA, replicate 2 |
| GSM6858883 |
In vitro haustoria, Dcp-treated RNA, replicate 3 |
| GSM6858884 |
In vitro haustoria, RppH-treated RNA, replicate 3 |
| GSM6858885 |
In vitro haustoria, untreated RNA, replicate 3 |
|
| Relations |
| BioProject |
PRJNA913936 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE221347_TPMs.tsv.gz |
178.3 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...