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Status |
Public on Jul 14, 2023 |
Title |
26S26R_B73_root_rep1 |
Sample type |
SRA |
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Source name |
root tissues
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Organism |
Zea mays |
Characteristics |
tissue: root tissues treatment: normal condition (26℃ shoot + 26℃ root) Stage: three-leaf stage ecotype: B73
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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
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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%
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
11211_5751_108434_H7WVVBGXC_cx_maize_B01_1_26_S_26_R_root_GATCAC
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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.
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Submission date |
Feb 28, 2021 |
Last update date |
Jul 14, 2023 |
Contact name |
Chunmei Xue |
E-mail(s) |
ChunmeiXue@hotmail.com
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Organization name |
Jilin University
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Street address |
No. 5333 Xi’an Road, Lvyuan District
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City |
Changchun |
State/province |
Jilin Province |
ZIP/Postal code |
130062 |
Country |
China |
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Platform ID |
GPL20156 |
Series (1) |
GSE167881 |
Tissue-level transcriptome response to local and distal chilling reveals potential chilling survival mechanisms in maize |
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Relations |
BioSample |
SAMN18089768 |
SRA |
SRX10188860 |
Supplementary file |
Size |
Download |
File type/resource |
GSM5114480_26S26R_B73_root_rep1.txt.gz |
156.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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