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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 26, 2013 |
| Title |
WT2007 smRNA-seq |
| Sample type |
SRA |
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| Source name |
3wk-old leaf tissue
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| Organism |
Oryza sativa |
| Characteristics |
tissue: leaf
genotype: Wild type
ecotype: Nipponbare
rna subtype: Small RNA
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| Treatment protocol |
RNA-seq libraries were constructed from total RNA isolated using TRIzol reagent (Invitrogen, Life Technologies, USA) from leaf tissues
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| Extracted molecule |
total RNA |
| Extraction protocol |
smRNA-seq libraries were constructed from total RNA isolated from the same tissues as described for the mRNA libraries, using the TruSeq Small RNA Sample Prep Kit from Illumina (San Diego, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
mRNA-seq reads were uniquely mapped to the genome using Bowtie (Langmead et al., 2009) allowing two mismatches. For smRNA-seq reads, adapter sequences were trimmed first, and then were uniquely mapped to the genome using Bowtie allowing no mismatches, and reads were categorized by their lengths for analyses
Genome_build: MSU 6.1
Supplementary_files_format_and_content: Column 1 is the read sequence. Column 2 is the number of reads with the given sequence.
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| Submission date |
Feb 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hume Stroud |
| Organization name |
UT Southwestern
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL13160 |
| Series (1) |
| GSE42410 |
Plants regenerated from tissue culture contain stable epigenome changes in rice |
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| Relations |
| SRA |
SRX235847 |
| BioSample |
SAMN01919741 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1081564_sample02_smRNA.txt.gz |
16.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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