|
| Status |
Public on Oct 01, 2019 |
| Title |
YE8001 |
| Sample type |
SRA |
| |
|
| Source name |
5-DAP kernel
|
| Organism |
Zea mays |
| Characteristics |
inbred lines: YE8001
tissue: kernel
developmental stage: 5 day after pollination
|
| Growth protocol |
A maize association mapping population consists of 318 inbred lines, including tropical, subtropical and temperate germplams was planted in one-row plots and incompletely randomized block design with three replicates in Hainan province of China in 2014. Eight ears in each block were self-pollinated, and 10-20 seeds from three to four ears in each block were collected at 5 DAP.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The collected seeds in three replications were mixed for total RNA preparation. Total RNA was extracted using RNAprep pure Kit For Plant (TIANGEN, Beijing, China) according to its protocol. Total mRNAs were accumulated using oligo(dT).
Library construction was following the standard protocol (Illumina, Inc.), and pair-end sequencing with 125 bp was carried out for each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were cleaned after removing low quality sequences and adapter. Then cleaned reads were mapped to maize B73 AGPv3 reference genome using tophat2 software with the following key parameters: “-i 5 -I 60000 --library-type fr-unstranded -r 250 --mate-std-dev 60 --no-novel-juncs --microexon-search”. The insertion size (-r) and standard deviation (--mate-std-dev) of paired reads were estimated using “CollectInsertSizeMetrics.jar” plugin in picard tools (http://picard.sourceforge.net). Only reads that are uniquely mapped to the genome were retained for further analysis
Reads count of annotated genes (AGPv3.27) were calculated using R packages “GenomicFeatures” and “GenomicAlignments”. DESeq2 package were used to normalize the reads count among samples and to calculate the FPKM value of genes.
Genome_build: maize B73 (AGPv3 )
Supplementary_files_format_and_content: tab-delimited text files include reads counts or FPKM values for each Sample
|
| |
|
| Submission date |
Feb 07, 2018 |
| Last update date |
Oct 01, 2019 |
| Contact name |
Junling Pang |
| E-mail(s) |
pjl_happy@126.com
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Street address |
No.12 Zhongguancun South St.,Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE110315 |
eQTL analysis of 5 DAP maize kernel |
|
| Relations |
| BioSample |
SAMN07759705 |
| SRA |
SRX3286809 |
