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| Status |
Public on Jun 01, 2020 |
| Title |
T09 [1 dpi] |
| Sample type |
SRA |
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| Source name |
1 day post inoculation
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| Organism |
Physcomitrium patens |
| Characteristics |
genotype: wild type
treatment: Botrytis cinerea stress
time point: 1 day post inoculation
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| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA of Mock plants, 0.5, 1, 2, and 3 dpi were extracted using TAKARA Trizol Reagent according to the protocol of manufacture.
The total RNA was treated with RNase-free DNase I to eliminate DNA contamination.The enrichment of mRNA was performed with Oligo (dT)-attached magnetic beads,and fragmentation was performed using divalent cations under high temperature in NEBNext First Strand Synthesis Reaction Buffer (5×) to randomly interrupt mRNA. The first-strand cDNA chain was synthesized by random hexamers and M-MuLV Reverse Transcriptase (RNase H) with the mRNA template. Subsequently, the second-strand cDNA chain was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. The the double stranded cDNA was purified using AMPure XP beads. Following end-pair and single nucleotide A (adenine) addition for the purified cDNA, adapters were used to distinguish the different samples by selection with AMPure XP beads for PCR amplification, following which the cDNA library was obtained.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
Physcomitrella_B793-T09
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| Data processing |
Clean data were obtained from raw reads by filtering low-quality tags (those that contained ambiguous bases), and low-quality reads (reads containing more than 50% bases with Q-value≤10.
Using TopHat2 based on Bowtie2, we aligned all distinct clean data to the reference genome database of P. patens (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002425.1_V1.1). Data that mapped multigene were removed. The number of clean tags for each gene was calculated and then normalized. Saturation analysis was performed to check whether the data was satisfied for further analysis.
To compare the expression levels of transcripts in the different samples, FPKM fragments per kilobase of ranscript per million mapped reads) was used to normalize the gene expression according to the formula: FPKM = (106 × C × 103)/NL. C represents the number of reads uniquely aligned to a certain unigene, N indicates the total number of reads uniquely aligned to all unigenes, and L is the base number of this unigene.
Genome_build: GCA_000002425.1_V1.1
Supplementary_files_format_and_content: the text files include FPKM values for each Sample
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| Submission date |
Mar 08, 2020 |
| Last update date |
Jun 02, 2020 |
| Contact name |
Huiqing Yan |
| E-mail(s) |
yanhuiqing@gznu.edu.cn
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| Organization name |
Guizhou Normal University
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| Department |
School of Life Science
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| Street address |
Guizhou Normal University
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| City |
Guiyang |
| State/province |
Guizhou |
| ZIP/Postal code |
550025 |
| Country |
China |
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| Platform ID |
GPL28239 |
| Series (1) |
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| Relations |
| BioSample |
SAMN14331062 |
| SRA |
SRX7873153 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4396438_T09.geneExpression.xlsx |
813.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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