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| Status |
Public on Jul 26, 2019 |
| Title |
WT rep1 |
| Sample type |
SRA |
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| Source name |
WT_Cabbage leaf
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| Organism |
Brassica oleracea var. capitata |
| Characteristics |
genotype/variation: wild type
development stage: harvesting stage
tissue: leaf
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from collected leaves of nwgl and WT plants at harvesting stage using RNAprep Pure Plant kit (Polysaccarides & Polyphenolics-rich) (Tiangen, Beijing, China) according to the manufacturer’s instructions.
Six cDNA libraries (three biological replicates per genotype) were constructed using NEBNextUltraTM Directional RNA library Prep kit (NEB, Ipswich, MA, USA) for Illumina (Illumina, San Diego, CA, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS(Illumia) according to the manufacturer’s instructions.
Raw data were filtered using inhouse perl scripts available with Biomarker Technologies Co. Ltd. (Biomarker, Beijing, China).
Clean reads were aligned to the cabbage genome (www.ocri-genomics.org/bolbase/index.html) using HISAT 2.
The mapped reads were assembled using the StringTie (V1.3.1) with gffcompare program annotation.
Genes and lncRNAs expression level was estimated by calculating FPKM values using StringTie (v1.3.1).
Genome_build: cabbage genome (www.ocri-genomics.org/bolbase/index.html) verison 1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
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| Submission date |
Apr 27, 2019 |
| Last update date |
Jul 26, 2019 |
| Contact name |
Xiaowei Zhu |
| E-mail(s) |
xiaoweizhusaas@163.com
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| Organization name |
Shanghai Academy of Agricultural Sciences
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| Street address |
Jinqi Road No.1000
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| City |
Shanghai |
| ZIP/Postal code |
201403 |
| Country |
China |
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| Platform ID |
GPL16893 |
| Series (1) |
| GSE130405 |
Genome-wide analysis of coding and long non-coding RNAs involved in cabbage cuticular wax biosynthesis |
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| Relations |
| BioSample |
SAMN11520692 |
| SRA |
SRX5760145 |
| 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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