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| Status |
Public on Sep 02, 2016 |
| Title |
R_communis_sRNA |
| Sample type |
SRA |
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| Source name |
Ricinus communis sRNA
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| Organism |
Ricinus communis |
| Characteristics |
accession: –
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
Small RNA-seq: Libraries were constructed using the TruSeq Small RNA Library Preparation Kit (Illumina Inc).
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
small RNA sequencing of R. communis
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| Data processing |
Small RNA-seq data: bed files of mapped sRNAs
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P. virgatum = v1.1; P. vulgaris = v1.0; R. communis = v0.1; S. bicolor = v2.1; S. lycopersicum = iTAG2.3; S. viridis = unpublished; T. cacao = V1.1; V. vinifera = GENOSCOPE.12X; Z. mays = AGPv3.21 (6a)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: Small RNA-seq data: bed files of mapped sRNAs
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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 |
GPL21641 |
| Series (1) |
| GSE79526 |
Widespread natural variation of DNA methylation within angiosperms |
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| Relations |
| BioSample |
SAMN04576106 |
| SRA |
SRX1656940 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2096991_R_communis_mCHH_regions_sRNA.tsv.gz |
2.3 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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