|
| Status |
Public on Jul 14, 2023 |
| Title |
4S26R_B73_bottom-crown_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
bottom-crown tissues
|
| Organism |
Zea mays |
| Characteristics |
tissue: bottom-crown tissues
treatment: shoot-only chilling (4℃ shoot + 26℃ root) for 24 hours
Stage: three-leaf stage
ecotype: B73
|
| Treatment protocol |
Normal condition (26℃ shoot + 26℃ root), whole-plant chilling (4℃ shoot + 4℃ root) for 24 hours, shoot-only chilling (4℃ shoot + 26℃ root) for 24 hours, root-only chilling (26℃ shoot + 0℃ root) for 24 hours
|
| Growth protocol |
Before treatment on three-leaf stage, the maize in growth chamber with temperature 26℃, photoperiod 14h/10h (day/night), light irradiance 250μmol·m-2·s-1 and humidity 50-70%
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested by using the Trizol Reagent (Invitrogen, Carlsbad, CA) and further purified by RNA Clean and Concentrator-5 (Zymo Research, Tustin, CA, USA; catalog number R1014).
3′ RNA libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) and were sequenced on Illumina NextSeq500 platform at the Cornell Genomic Facility.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
11211_5751_108465_H7WVVBGXC_cx_maize_A05_2_4_S_26_R_BC_AGATAG
|
| Data processing |
3′ RNA libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria) and were sequenced on Illumina NextSeq500 platform at the Cornell Genomic Facility.
Raw reads were cleaned up with bbduk (sourceforge.net/projects/bbmap/) to trim the adapter, poly-A and poly-G according to the instruction of 3′ RNA libraries preparation kit. The purified reads were mapped to Zea mays B73 reference genome V4 (http://plants.ensembl.org/index.html) with STAR
The Differentially Expressed Genes (DEGs) were identified in R program (https://www.r-project.org/) with EdgeR package
Genome_build: B73 reference genome V4 (http://plants.ensembl.org/index.html)
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for every gene and every sample; Tab-delimited text files include CPM values for each Sample.
|
| |
|
| Submission date |
Feb 28, 2021 |
| Last update date |
Jul 14, 2023 |
| Contact name |
Chunmei Xue |
| E-mail(s) |
ChunmeiXue@hotmail.com
|
| Organization name |
Jilin University
|
| Street address |
No. 5333 Xi’an Road, Lvyuan District
|
| City |
Changchun |
| State/province |
Jilin Province |
| ZIP/Postal code |
130062 |
| Country |
China |
| |
|
| Platform ID |
GPL20156 |
| Series (1) |
| GSE167881 |
Tissue-level transcriptome response to local and distal chilling reveals potential chilling survival mechanisms in maize |
|
| Relations |
| BioSample |
SAMN18089772 |
| SRA |
SRX10188891 |
