|
| Status |
Public on Sep 22, 2017 |
| Title |
2nd leaf, DAH28_Replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
2nd leaf, DAH28
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
cultivar: Asian rice cultivar, Dongjin
tissue: 2nd leaf
time: DAH28
replicate: 1
|
| Treatment protocol |
mRNA expression profiles of the flag leaf and 2nd leaf of Oryza Sativa during grain filling (Day After Heading, DAH, 4-44) were examined by Illumina Hi-seq 2500.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Rice leaf tissue was ground using a mortar and pestle, and total RNA was extracted from ~100 mg of tissue using RNeasy Plant Mini Kit (Qiagen). Total RNA integrity was confirmed using the Agilent Technologies 2100 BioAnalyzer (RNA integrity number >8.0). Poly(A) mRNA isolation from total RNA and fragmentation were performed using the Illumina Truseq Stranded mRNA LT Sample Prep Kit with poly-T oligo-attached magnetic beads, according to the manufacturer’s instructions.
Libraries were prepared for multiplex sequencing using Illumina Truseq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina CASAVA v1.8.2 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences using Cutadapt v1.2.1, and then mapped to Oryza sativa IRGSP-1.0.22 genome using TopHat v2.0.10 with parameters -r 100 --library-type fr-firststrand --mate-std-dev 100 --solexa-quals -p 24 --bowtie-n.
After removing duplicate reads, the number of reads mapped to gene features were counted using HTSeq v0.6.1.
The number of reads counted by HTseq were normalized into count per million (CPM) by TMM normalization method using edgeR package.
Genome_build: Oryza sativa IRGSP-1.0.22
Supplementary_files_format_and_content: tab-delimited text file including normalized read counts for each sample
|
| |
|
| Submission date |
Oct 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyobin Jeong |
| E-mail(s) |
h.jeong@imb-mainz.de
|
| Organization name |
IMB
|
| Street address |
Richard shirrmann Str 12.
|
| City |
Mainz |
| State/province |
Germany |
| ZIP/Postal code |
55112 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE89233 |
Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice |
|
| Relations |
| BioSample |
SAMN05947073 |
| SRA |
SRX2273224 |
