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| Status |
Public on Feb 19, 2023 |
| Title |
B104 ck rep1 |
| Sample type |
SRA |
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| Source name |
B104 ck leaf
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| Organism |
Zea mays |
| Characteristics |
line: B104
treatment: none
tissue: leaf
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| Treatment protocol |
26℃ for control, 4℃ for chilling treatment
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| Growth protocol |
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 |
11607_5751_115988_H7HC7BGXF_maize_4lines_C01_B104_ck_1_CAAGCA
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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: raw gene counts for every gene and every sample
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| Submission date |
Feb 20, 2021 |
| Last update date |
Feb 19, 2023 |
| Contact name |
yuan jiang |
| E-mail(s) |
jygg0508@gmail.com
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| Phone |
6072290253
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| Organization name |
cornell university
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| Street address |
306 Tower Rd
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| City |
Ithaca |
| ZIP/Postal code |
14850 |
| Country |
USA |
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| Platform ID |
GPL20156 |
| Series (1) |
| GSE167156 |
Transcriptome analysis of four maize lines to detect the different responses to chilling stress and reveal the survival mechanisms in maize |
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| Relations |
| BioSample |
SAMN18016462 |
| SRA |
SRX10142273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5098158_B104-ckrep1.txt.gz |
149.6 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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