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Status |
Public on Jun 02, 2021 |
Title |
CH1YM1 |
Sample type |
SRA |
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Source name |
leaf
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Organism |
Oryza sativa |
Characteristics |
variety type: CHT025 Stage: on the first day after flowering enviroment: middle rice
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeq sample preparation kit (Illumina, San Diego, USA). Paired-end RNA-seq
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Description |
CH1YMVSCH10YM_Gene_differential_expression.tsv
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Data processing |
A cDNA library constructed by technology from leaves of rice was sequenced run with Illumina 4000 sequence platform. Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon paired-end reads of bp length. This yielded gigabases (Gb) of sequence. we aligned reads to rice reference genome using HISAT package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.HISAT build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs and genes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package. Genome_build: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Osativa Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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Submission date |
Jun 01, 2021 |
Last update date |
Jun 02, 2021 |
Contact name |
Jianmin Bian |
E-mail(s) |
jmbian81@126.com
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Organization name |
江西农业大学
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Street address |
志敏大道1101
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City |
南昌 |
State/province |
江西 (Jiāngxī) |
ZIP/Postal code |
330045 |
Country |
China |
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Platform ID |
GPL23013 |
Series (1) |
GSE175967 |
Unique transcriptome and gene expression analysis of flag leaves of a super-hybrid rice WFYT025 |
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Relations |
BioSample |
SAMN19490622 |
SRA |
SRX11042909 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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