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| Status |
Public on Nov 28, 2017 |
| Title |
GCF-0 RNA-seq |
| Sample type |
SRA |
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| Source name |
Green cotton fiber 0 day
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| Organism |
Gossypium hirsutum |
| Characteristics |
day post-anthesis: fiber development 0 day
tissue: cotton fiber
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted according to a guanidine thiocyanate method
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. These products are then purified and enriched with PCR to create the final cDNA library. The cDNA library of each sample was constructed according to the instructions given in “Preparing Samples for Sequencing of mRNA Test Kits” (Illumina). Products were checked to verify the cDNA library quality and fragment length using an Agilent 2100 DNA 1000 Kit. Sequencing of the resulting cDNA library was carried out on an Illumina HiSeq 2000 paired-end 100-bp (PE 100) system.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
GCF-0 RNA-seq
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| Data processing |
Illumina Casava1.7 software used for basecalling.
FastQC v0.10.1 used for quality control （default parameter）
Sequenced reads were trimmed by Trimmomatic v0.32 (parameter: PE -threads 16 -phred33 HEADCROP:9 MINLEN:19)
Reads were mapped to JGI 221 G.raimondii D genome using TopHat v2.0.13(bowtie2 v2.2.4) (default parameter)
Alignment results converted from bam file to sam file and sorted by samtools(0.1.19)
Counting reads in genes using HTSeq( 0.6.0)(parameter: -t CDS -s no)
Calculating the adjusted p-value of genes(padj) of different samples by R package DESeq(1.18.0)
Genome_build: Gossypium raimondii (D5) genome JGI assembly v2.0 (annot v2.1)
Supplementary_files_format_and_content: Excel file contains DESeq output where all cotton color genotypes have been combined for a comparison between day 0 and day 12.
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| Submission date |
Dec 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hailiang Liu |
| E-mail(s) |
HaiLiang_1111@tongji.edu.cn
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| Organization name |
Tongji university
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| Street address |
NO 1239, siping road
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| City |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| Platform ID |
GPL16485 |
| Series (1) |
| GSE76400 |
Control of Fiber Color in Naturally Colored Cotton by Flavonoid Biosynthesis |
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| Relations |
| BioSample |
SAMN04376500 |
| SRA |
SRX1506879 |
| 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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