|
| Status |
Public on Nov 12, 2009 |
| Title |
Ovules (3 days prior to anthesis - 3 DPA) |
| Sample type |
SRA |
| |
|
| Source name |
-3 DPA ovules
|
| Organism |
Gossypium hirsutum |
| Characteristics |
strain: TM-1
tissue: -3 DPA ovules
|
| Treatment protocol |
Ovules at 3 days prior to anthesis (- 3DPA) on the day of anthesis (0 DPA) and 3 days post-anthesis (+3 DPA) and seedling leaves were harvested for total RNA extraction.
|
| Growth protocol |
G. hirsutum L. cv. Texas Marker-1 (TM-1) cotton plants were grown in a greenhouse at The University of Texas at Austin or in field in College Station Texas.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified and verified using the CTAB extraction method. Small RNAs (17-30-nt) were purified cloned barcoded using oligo adaptors and sequenced from 75 micrograms of cotton total RNA for each sample type using a protocol provided by Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
none
|
| Data processing |
The following adaptor sequence was cleaved from the 3' end of the small RNA if it was detected: TCGTATGCCGTCTTCTGCTTG. The 5' nucleotide of the small RNA was used as an indexing base that denoted the tissue that the read was derived from: A --> Leaf tissue, G --> -3 DPA ovule tissue, C --> 0 DPA ovule tissue, T --> +3 DPA ovule tissue. This nucleotide was cleaved to generate library-specific counts for each unique small RNA sequence, discarding small RNAs below 17 base pairs in length. Contaminant RNAs were annotated and removed based on homology to: 1) the A. thaliana and B. napus mitochondrial genomes, 2) the G. hirsutum chloroplast genome, 3) plant snRNAs and snoRNAs deposited in NCBI, 4) A. thaliana tRNA sequences, and 5) annotated A. thaliana and G. hirsutum rRNA sequences.
|
| |
|
| Submission date |
May 28, 2009 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Vikram Agarwal |
| E-mail(s) |
[email protected]
|
| Organization name |
Calico Life Sciences
|
| Street address |
1130 Veterans Blvd
|
| City |
South San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL9362 |
| Series (1) |
| GSE16332 |
Sequence and expression analysis of microRNAs during ovule and fiber development in cotton |
|
| Relations |
| BioSample |
SAMN02197728 |
