|
| Status |
Public on Jul 22, 2017 |
| Title |
WT-3 |
| Sample type |
SRA |
| |
|
| Source name |
10 DAF endosperm
|
| Organism |
Zea mays |
| Characteristics |
sample type: 10 DAF endosperm
|
| Treatment protocol |
Developing endosperm that were harvested from both fl3 and WT at 10 DAF
|
| Growth protocol |
maize were grown during summer under natural environmental conditions in Songjiang experimental field
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs was extracted from 10-DAP old endosperms of WT and fl3 using TRIzol reagent (Invitrogen) and were then purified with the RNeasy Mini Kit (Qiagen).
RNA-seq libraries were prepared according to the Illumina Standard library preparation kit. Illumina HiSeqTM 2500 was used as a platform for RNA-seq at Shanghai OE Biotech Co, Ltd.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQC combined with the NGS QC TOOLKIT v2.3.3 were used for quality control checks on raw sequencing data.
Clean reads were aligned to the B73 reference genome (RefGen_v3) and the reference gene model dataset (FGS 5b) using TopHat/Bowtie2 (ccb.jhu.edu/software/tophat/).
The gene expression value was normalized as fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: the B73 reference genome (RefGen_v3) and the reference gene model dataset (FGS 5b)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sampleļ¼ the clean reads aligned to reference genome were saved as BAM files
|
| |
|
| Submission date |
Feb 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jie-chen Wang |
| E-mail(s) |
jcwang@sibs.ac.cn
|
| Organization name |
SIPPE, CAS
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE95039 |
Next Generation Sequencing Analysis of Wild Type and fl3 Transcriptomes in 10DAP(day after pollination) endosperm |
|
| Relations |
| BioSample |
SAMN06345906 |
| SRA |
SRX2574386 |
