 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 23, 2020 |
| Title |
GLY2 |
| Sample type |
SRA |
| |
|
| Source name |
plants leaves
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: leaf
cultivar: glyphosate-tolerant CA21
agent: glyphosate
|
| Treatment protocol |
Glyphosate (100% glyphosate powder, Zhejiang Xin ’an Chemical Group Co., Ltd.) with an effective spray dose of 2 mg·ml-1 to treat the rice seedlings at the third-leaf stage.
|
| Growth protocol |
The glyphosate-tolerant rice CA21 was developed by Institute of Crop and Nuclear Technology Utilization. They were planted in 60 × 30 cm bowls.Three replications were maintained for each group.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA).
Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (LC Bio, China) following the vendor's recommended protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts were considered as lncRNAs
StringTie was used to perform expression level for mRNAs and lncRNAs by calculating FPKM . The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown .
genome build: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Osativa Version JGI 323 v7.0
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Dec 19, 2019 |
| Last update date |
Mar 24, 2020 |
| Contact name |
li lei |
| E-mail(s) |
lilei@lc-bio.com
|
| Organization name |
LC_Sciences
|
| Street address |
xiashas street num 6
|
| City |
Hangzhou |
| ZIP/Postal code |
310021 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (1) |
| GSE142323 |
Identification and integrated analysis of glyphosate stress-responsive microRNAs, lncRNAs, and mRNAs in rice using genome-wide high-throughput sequencing |
|
| Relations |
| BioSample |
SAMN13632978 |
| SRA |
SRX7415620 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
