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Sample GSM4113554 Query DataSets for GSM4113554
Status Public on Mar 08, 2020
Title control-3
Sample type SRA
Source name Fagopyrum tataricum Dingku 1
Organism Fagopyrum tataricum
Characteristics tissue: plants stems and leaves
group: control
Treatment protocol The seedlings were in a growth chamber (12/12h light/dark; light intensity 300 μmol m−2 s−1), the control group was at a constant temperature 16-21 ºC; the momery group with cold acclimation (4ºC 6h repeat 4 times ) then 0 ºC 6h; the shock group without cold acclimation 0 ºC 6h directly.
Growth protocol The three leaf age seedlings were cultivated in pots of nutritious soil
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen). Following purification, the mRNA is fragmented into small pieces 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 mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Description mRNA sequencing
Data processing Prior to assembly, we removed the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) in the raw data.Reference genome alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference.Tophat build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions. Transcript abundance estimation and differentially expressed testing The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragement counts to measure the relative abundances of the tianscripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The feference GTF annotation file used in Cufflinks was downloaded from the JGI database. Cufflink was used to de novo assemble the transcripiome at first; The second ,Cuffmerge was used to comerge all transcripts of sample A and B to generate unique transcripts. The downloaded JGI GTF file was passed to Cuffdiff along with the original alinment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the GTF file using aligments from the SAM file and concurrently test for different expression. Only the comparisons with “q_value”less than 0.05 and status marked as “OK” in the Cuffdiff output were regarded as showing differential expression.
Genome_build: Tartary Buckwheat (Pinku1) Genome 
Supplementary_files_format_and_content: FPKM,expression profiles
Submission date Oct 08, 2019
Last update date Mar 08, 2020
Contact name Yuan Song
Phone 86-0931-8912560
Organization name Lanzhou university
Street address the south of Tianshui road
City Lanzhou
ZIP/Postal code 730000
Country China
Platform ID GPL24740
Series (2)
GSE138546 Changes of Gene expression in Tartary Buckwheat (Fagopyrum tataricum) under Frozen stress [RNA-Seq]
GSE138547 Changes of Gene expression in Tartary Buckwheat (Fagopyrum tataricum) under Frozen stress
BioSample SAMN12991216
SRA SRX6961544

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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