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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 26, 2013 |
| Title |
WT2007 mRNA-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: polyA mRNA
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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 |
Total RNA (10 ug) for each sample was used to purify poly-A mRNA; this mRNA was used for synthesis and amplification of cDNA. The RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit from Illumina (San Diego, CA).
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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 |
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 |
SRX235856 |
| BioSample |
SAMN01919750 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1081573_sample02_mRNA.txt.gz |
366.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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