|
| Status |
Public on Dec 01, 2023 |
| Title |
B73_White_2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Zea mays |
| Characteristics |
tissue: leaf
developmental stage: 7 DAY OLD
genotype: Wild-type
treatment: white light
|
| Treatment protocol |
treat with or without UVB treatment 1 hour
|
| Growth protocol |
7 days of B73 and zmuvr8-1 seedlings grown in low white light
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Assembly: B73_RefGen_v4_gramene_63
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 04, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Zhao Zhiwei |
| E-mail(s) |
zwzhao@cemps.ac.cn
|
| Phone |
+8618817395284
|
| Organization name |
CAS Center for Excellence in Molecular Plant Sciences / Institute of Plant Physiology and Ecology
|
| Street address |
300 Feng Lin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL25410 |
| Series (1) |
| GSE240077 |
Next Generation Sequencing Facilitates Quantitative Analysis of B73 and zmuvr8-1 mutant in low white with or without UVB treat Transcriptomes |
|
| Relations |
| BioSample |
SAMN36839242 |
| SRA |
SRX21250290 |
