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| Status |
Public on Oct 01, 2020 |
| Title |
MH63_3 |
| Sample type |
SRA |
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| Source name |
rice plant leaves
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| Organism |
Oryza sativa |
| Characteristics |
line: MH63
method: conventional cross-breeding
tissue: leaves
age: five weeks
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| Treatment protocol |
During the rice plants tillering stage, leaf samples were collected for the analyses. From each plant, a leaf section (approximately 2 cm) was sampled from the middle part of 2nd leaf blade from top. Samples from five plants were pooled together as one biological replicate, and three replicates were collected for each rice line.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and treated with RNase-free DNase I (NEB, USA) to remove any genomic DNA.
A total amount of 3 µg of total RNA per sample was used for the preparation of RNA-seq library. Sequencing libraries were prepared using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
For transcriptome data, raw Illumina data of fastq format were first processed using in-house perl scripts. After removing reads containing adaptors, reads containing poly-N and low-quality reads from raw data, we obtained the clean data. The Q20, Q30, GC (guanine-cytosine)-content and sequence duplication level of the clean data were calculated. The clean reads were aligned to the reference genome IRGSP-1.0 (https://rapdb.dna.affrc.go.jp)using HISAT2 tools (version 2.09)
Feature Counts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. Gene expression levels were estimated using fragments per kilobase of transcript per million mapped reads (FPKM) based on the length of the gene and reads count mapped to this gene. Differentially expressed genes analysis was performed using the DESeq2 R package.
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab_delimited text files include FPKM values for each sample.
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| Submission date |
Jun 17, 2020 |
| Last update date |
Oct 02, 2020 |
| Contact name |
Qingsong Liu |
| E-mail(s) |
liuqingsong@xynu.edu.cn
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| Phone |
86-18537688228
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| Organization name |
Xinyang Normal University
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| Street address |
No. 237, Nanhu road
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| City |
Xinyang |
| State/province |
Henan |
| ZIP/Postal code |
464000 |
| Country |
China |
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| Platform ID |
GPL23013 |
| Series (1) |
| GSE152572 |
Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding |
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| Relations |
| BioSample |
SAMN15297894 |
| SRA |
SRX8565945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4623406_MH63_3.txt.gz |
566.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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