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| Status |
Public on Mar 19, 2020 |
| Title |
HX17_CB1 |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Brassica napus |
| Characteristics |
variety: HX17
tissue: leaves
treatment: 4 degree Celsius
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| Treatment protocol |
Cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were collected and flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Rapeseed variety HX17
HX17 treated with 4℃ replicate 1.
processed data file: gene.description_fin.txt
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| Data processing |
Raw data (raw reads) of fastq format were first processed through in-house perl scripts. In this step, clean data/reads were obtained by removing reads containing adapter or reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content for the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website (http://www.genoscope.cns.fr/brassicanapus/data/) directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end reads were aligned to the reference genome using Hisat2 v2.0.4. Hisat2 was selected as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file, thus providing better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads mapped to each gene. FPKM of each gene was calculated based on the length of the gene and read counts mapped to the gene. FPKM considers the combined effects of sequencing depth and gene length for the read counts, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: Brassica napus “Aarmor-bzh”; Genoscope Brassica_napus_v4.1.chromosomes.fa, Brassica_napus.annotation_v5.gff3, Brassica_napus.annotation_v5.cds.fa, Brassica_napus.annotation_v5.pep.fa files.
Supplementary_files_format_and_content: gene.description_fin.txt: Tab-delimited text file includes read counts and FPKM values for all samples.
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| Submission date |
Apr 02, 2019 |
| Last update date |
Mar 20, 2020 |
| Contact name |
Xin He |
| E-mail(s) |
[email protected]
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| Organization name |
Hunan Agricultural University
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| Street address |
No. 1 Nongda Road, Furong district, Changsha, China
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| City |
Changsha |
| State/province |
Hunan |
| ZIP/Postal code |
410128 |
| Country |
China |
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| Platform ID |
GPL26378 |
| Series (1) |
| GSE129220 |
RNA-seq of two early-maturing rapeseed varieties treated with different cold stress |
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| Relations |
| BioSample |
SAMN11318023 |
| SRA |
SRX5624941 |
| 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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