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| Status |
Public on Aug 15, 2012 |
| Title |
14 DPA En |
| Sample type |
SRA |
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| Source name |
Seed
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| Organism |
Triticum aestivum |
| Characteristics |
tissue: Starchy endosperm
developmental stage: 14 DPA
cultivar: Banks
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared using a Trizol (Invitrogen, Carlsbad, CA) protocol and purified using an RNeasy Plant Kit (Qiagen, Hilden, Germany).
Tissues were microdissected on ice and snap frozen. Total RNA was isolated and cDNA prepared using MessageAmpII (Invitrogen) using a modified first strand primer including a BpuE1 site which was used to remove the polyA tail. Libraries were prepared according to Illumina's instructions. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~300 +/- 45 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Data processing |
Sequenicng performed on Illumina Genome Analyzer IIx
Approximately 25—55 million reads were obtained per tissue. Sequences were initially trimmed using default quality parameters of the CLC Genomics Workbench Version 4.0. (CLC bio, Aarhus, Denmark).
Remaining contaminating sequences were removed using an editing package (010 Editor, http:// www.sweetscape.com/010editor/) and the reads returned to CLC for a further round of trimming based on quality scores
Trimmed sequences were sent through the RNA-Seq analysis program of the CLC platform, mapping against the unannotated reference sequences derived from the DFCI Wheat Gene Index, Release 12.0 (The Computational Biology and Functional Genomics Laboratory, Dana Farber Cancer Institute and Harvard School of Public Health) using default parameters. The minimum length fraction was 0.9 and the minimum similarity fraction was 0.8. RPKM was selected as the normalized expression value.
Genome_build: DFCI Wheat Gene Index, Release 12.0
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| Submission date |
May 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Susan Alana Gillies |
| E-mail(s) |
susan.gillies@scu.edu.au
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| Phone |
61266203466
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| Organization name |
Southern Cross University
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| Department |
Plant Science
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| Street address |
Miliatary Rd
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| City |
Lismore |
| State/province |
NSW |
| ZIP/Postal code |
2480 |
| Country |
Australia |
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| Platform ID |
GPL15632 |
| Series (1) |
| GSE38344 |
Gene expression in the developing aleurone and starchy endosperm of wheat |
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| Relations |
| SRA |
SRX150765 |
| BioSample |
SAMN01001221 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM940351_14E_RNA-Seq.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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