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| Status |
Public on Apr 02, 2019 |
| Title |
Gtr_12S2 |
| Sample type |
SRA |
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| Source name |
cotton plant
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| Organism |
Gossypium trilobum |
| Characteristics |
tissue: Stem
developmental stage: one true leaf stage
time point (hour): 12
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| Treatment protocol |
At one true leaf stage, the plants were inoculated with 8 ml suspension of V. dahliae at 1 × 107 conidia per mL. The samples were then taken at 0h, 12h and 48h for RNA sequencing.
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| Growth protocol |
To ensure maximum germination, a small slit was made on the seed coat, and then pre-germinated in the incubator using sterilized moist filter paper for 2-3 days until the radicle was approximately 1 cm long, the condition of the incubator was set at 28℃ and with > 90% ambient humidity. The seedlings were then transplanted into sterilized vermiculite filled in small conical pots, with dimensions of 5 cm bottom region, 7 cm top region and 8 cm in depth
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh tissues were harvested at 0h, 12h and 48h of post inoculation,flash frozen into liquid nitrogen.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.Approximately 10 ug of total RNArepresenting a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into smallpieces using divalent cations under elevated temperature. Then the cleaved RNA fragments werereverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNASeqsample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-endlibraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an IlluminaHiseq4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.
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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 |
A cDNA library constructed by technology from the pooled RNA from brain samples of pig 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. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed .After that, a total of G bp of cleaned ,paired-end reads were produced. The raw sequence data have been submitted to the NCBI Short Read Archive with accession number .
we aligned reads of sample A and sample B to the UCSC (http://genome.ucsc.edu/) homo sapiens 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 Ballgown 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 – Ballgown.
Genome_build: ftp://ftp.bioinfo.wsu.edu/species/Gossypium_raimondii/JGI_221_G.raimondii_Dgenome/assembly/G.raimondii_JGI_221_v2.0.assembly.fasta.gz
Supplementary_files_format_and_content: xls include RPKM values，time point and tissue.
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| Submission date |
Nov 30, 2018 |
| Last update date |
Apr 02, 2019 |
| Contact name |
Dong Odongo Qi |
| E-mail(s) |
dongqi9208@163.com
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| Phone |
17630550692
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| Organization name |
Chinese Academy of Agricultural Sciences
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| Department |
Cotton research Institute
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| Lab |
Cotton Germplasm Resources
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| Street address |
HUANGHE ROAD, No 38.
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| City |
Anyang |
| State/province |
Henan |
| ZIP/Postal code |
455000 |
| Country |
China |
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| Platform ID |
GPL25875 |
| Series (1) |
| GSE123175 |
RNA-Sequencing, Physiological and RNAi Analyses Provide Insights into the Response Mechanism of the ABC-Mediated Resistance to Verticillium Dahliae Infection In cotton |
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| Relations |
| BioSample |
SAMN10505255 |
| SRA |
SRX5084519 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3498008_Gtr_12S2.xlsx.gz |
3.2 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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