|
| Status |
Public on Mar 24, 2016 |
| Title |
PbfRNAi;o2 rep1 |
| Sample type |
SRA |
| |
|
| Source name |
endosperm 16 day after pollination (DAP)
|
| Organism |
Zea mays |
| Characteristics |
tissue: endosperm
genotype/variation: PbfRNAi;opaque2
|
| Treatment protocol |
Fresh materials
|
| Growth protocol |
The four maize genetic materials are cultivated in the field of the Institute of Plant Physiology & Ecology in Shanghai, China.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA are extracted from 16-DAP endosperm using TRIzol reagent (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen). The mRNA are captured by Epicenter Ribo-Zero™ Magnetic Kit (No. MRZPL116-6).
The libraries are prepared according Illumina Standard library preparation kit (Illumina USA) and sequenced to generate 125nt paired-end reads on Illumina HiSeqTM2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
FastQC is used for quality control checks on raw sequence data combining with NGS QC TOOLKIT v2.3.3
Clean reads are aligned to the B73 reference genome (download in ftp://ftp.ensemblgenomes.org/pub/plants/release-26/fasta/zea_mays/dna/Zea_mays.AGPv3.26.dna.genome.fa) and the B73 reference gene model (download in ftp://ftp.ensemblgenomes.org/pub/plants/release-26/fasta/zea_mays/cdna/Zea_mays.AGPv3.26.cdna.all.fa) using tophat/bowtie2
The gene expression value is normalized as fragments per kilobase of transcript per million mapped reads (FPKM) from "Trapnell C, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562-578."
|
| |
|
| Submission date |
Mar 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Joachim Messing |
| E-mail(s) |
messing@waksman.rutgers.edu
|
| Organization name |
Waksman Institute of Microbiology, Rutgers University
|
| Street address |
190 Frelinghuysen Rd
|
| City |
Piscataway |
| State/province |
NJ |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE79513 |
Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes for Wild Type and Mutants including opaque2, PbfRNAi and PbfRNAi;o2 in Maize (Zea mays) |
|
| Relations |
| BioSample |
SAMN04574812 |
| SRA |
SRX1655624 |
