|
| Status |
Public on May 27, 2024 |
| Title |
L. albus 15 min 10 mM sucrose replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
5-6 cm root sections with tip
|
| Organism |
Lupinus albus |
| Characteristics |
tissue: 5-6 cm root sections with tip
genotype: wildtype
treatment: 15 min 10 mM sucrose
|
| Treatment protocol |
For treatment, the plant roots of selected pots were exposed to sucrose by adding 8.5 ml of 1 M sucrose (prepared in Hoagland solution) directly to the hydroponic solution, for a final concentration of 10 mM sucrose. Harvesting was done after exposing the plants to sucrose for different periods: 0 minutes (control), 10 minutes, 15 minutes and 20 minutes. All time points were done in 3 biological replications (3 plants each). For harvesting, about 100 mg of the root tip sections with a length of about 5 cm were harvested in liquid nitrogen from each plant and stored immediately at -80 deg C
|
| Growth protocol |
White lupin (Lupinus albus cv. Amiga) seeds were sterilized by shaking for 3 minutes in 10% bleach, followed by several rinses with sterile water. Sterile seeds were then spread out on sterile petri dishes (10-20 seeds per dish) and covered about halfway with sterile water to germinate at room temperature in the dark for 3-4 days. Once the radicles reached a length of 2-3 cm, the seedlings were transferred to containers filled with 850 ml of Hoagland solution, which was changed about every 4 days. The temperature of the growth chamber was maintained at ~21°C with a light cycle of 16 hours and a dark cycle of 8 hours.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from white lupin samples was isolated following the protocol for “Purification of Total RNA from Plant Cells and Tissues, and Filamentous fungi” from RNasy Plant Mini kit (Qiagen). The Qubit 4 Fluorometer in conjunction with an RNA-High Sensitivity assay was used to quantify the samples. In addition, the RNA IQ assay was used to determine the RNA integrity number (RIN). This RIN is based on the ratio of large and/or structured RNA to small RNA in the sample. Only samples with RIN of 8 or higher were used for RNA sequencing.
Using the PCR-cDNA sequencing-barcoding (SQK-PCB111) kit of Oxford Nanopore Technologies, the extracted RNA was converted into cDNA and uniquely barcoded, following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
| |
|
| Description |
Oxford Nanopore
|
| Data processing |
Equal concentration of the four cDNA libraries for each biological replication were pooled and sequenced on three separate MinION FLO-MIN106 flow cells (Oxford Nanopore Technology, ONT), using a MinION MK1C running Minknow v20.06.5 and guppy v4.09. Basecalling was performed during the run using the fast-basecalling algorithm with a Q score cutoff >7.
Demultiplexed sequencing reads in fastq format were transferred from the Mk1C device to a PC with Epi2me installed. The data was analyzed using the Epi2me wf-transcriptomes workflow version 1.1. available at https://github.com/epi2me-labs/wf-transcriptomes. Resulting read data was analyzed for differential expression using DESeq2 (time course option).
Assembly: CNRS_Lalb_1.0/GCA_009771035.1 assembly
Supplementary files format and content: csv file containing CPM (counts per million) results for each sample (CPM_genes_Lupinus_albus_sucrose.csv)
Supplementary files format and content: csv file containing DESeq2 data for 10 min (t10), 15 min (t15) and 20 min (t20) of sucrose treatment (DESeq2_all_genes_t10-t15-t20_annotated.csv)
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| |
|
| Submission date |
May 22, 2024 |
| Last update date |
May 27, 2024 |
| Contact name |
Claudia Uhde-Stone |
| E-mail(s) |
[email protected]
|
| Organization name |
California State University, East Bay
|
| Department |
Biological Sciences
|
| Lab |
Stone lab
|
| Street address |
25800 Carlos Bee Blvd
|
| City |
Hayward |
| State/province |
CA |
| ZIP/Postal code |
94542 |
| Country |
USA |
| |
|
| Platform ID |
GPL34521 |
| Series (1) |
| GSE268152 |
Transcriptomics Provide Insights into Early Responses to Sucrose Signaling in Lupinus albus. |
|
| Relations |
| BioSample |
SAMN41494864 |
| SRA |
SRX24656140 |
