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| Status |
Public on Sep 02, 2016 |
| Title |
B_rapa_RNA |
| Sample type |
SRA |
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| Source name |
B. rapa RNA
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| Organism |
Brassica rapa |
| Characteristics |
accession: FPsc
tissue: leaf
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue was flash frozen in liquid nitrogen for all experiments including ChIP-seq, RNA-seq and MethylC-seq. DNA was isolated using a Qiagen Plant DNeasy kit (Qiagen, Valencia, CA) following the manufacturer’s recommendations. RNA was isolated using TRIzol (Thermo Scientific, Waltham, MA) following the manufacturer’s instructions
RNA-seq: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
RNA sequencing of B. rapa
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| Data processing |
For RNA-seq data: Raw FASTQ reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32 (Bolger et al. 2014). Reads were aligned using Tophat v2.0.13 (Trapnell et al. 2010) supplied with a reference GFF file and the following arguments: -I 50000 --b2-very-sensitive --b2-D 50. Transcripts were then quantified using Cufflinks v2.2.1 (Trapnell et al. 2012) supplied with a reference GFF file.
genome build: A. lyrata = v1.0; A. thaliana = TAIR10; A. trichopoda = v1.0; B. distachyon = v2.1; B. oleracea = TO1000 v1.0; B. rapa = FPsc v1.3; B. vulgaris = v1.1; C. clementina = v1.0; C. rubella = v1.0; C. sativa = canSat3; C. sativus = v1.0; E. grandis = v1.1; E. salsugineum = v1.0, F. vesca = v1.1; G. max = w82.a2.v1; G. raimondii = v2.1; L. japonicus = v2.5; M. domestica = v1.0; M. esculenta = v4.1; M. guttatus = v2.0; M. truncatula = Mt4.0v1; O. sativa = v7.0; P. hallii = v0.5; P. persica = v1.0; P trichocarpa = v3.0; P. virgatum = v1.1; P. vulgaris = v1.0; R. communis = v0.1; S. bicolor = v2.1; S. lycopersicum = iTAG2.3; S. viridis = unpublished; T. cacao = V1.1; V. vinifera = GENOSCOPE.12X; Z. mays = AGPv3.21 (6a)
processed data files format and content: RNA-seq data column 1 = gene_ID = gene identifier; column 2 = FPKM = gene expression in fragments per kilobase per million (FPKM)
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| Submission date |
Mar 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL21644 |
| Series (1) |
| GSE79526 |
Widespread natural variation of DNA methylation within angiosperms |
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| Relations |
| BioSample |
SAMN04576069 |
| SRA |
SRX1656945 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2096996_B_rapa_RNAseq_fpkm.tsv.gz |
231.9 Kb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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