SRP001603 Evolutionary Genomics of Cotton - cDNA
Study Type:
Transcriptome Analysis
Submission:
SRA010363 by on 2010-01-06 11:58:40
Abstract:
This study includes the generation of a pan-transcriptome from domesticated and wild cotton accessions from both Gossypium hirsutum and G. barbadense.
Description:
RNA was extracted from whole seedlings, leaves, roots, floral organs, and fiber of each accession (Acala Maxxa and Tx2094, G. hirsutum; K101 and S6, G. barbadense). RNA pooled in equimolar amounts for each sample. cDNA was generated using a poly-T primer and amplified using the Clontech SMRT technology. Samples were normalized using the Evrogen Trimmer Kit (DSN). Some samples were sequenced after cutting off the poly-A tails using MmeI nuclease. For other samples, the 5' and interior portions of the transcripts were preferentially amplified using ligation mediated PCR-suppression. Samples were sequenced on both FLX and Titanium 454 techologies. Sequence of expressed genes were also generated by Illumina sequencing from 10 and 20 dpa fiber (days post-anthesis). From each stage, sequence was generated from A2 (G. arboreum), D5 (G. raimondii), Acala Maxxa (G. hirsutum), TX2094 (G. hirsutum), Pima-S6 (G. barbadense), and K101 (G. barbadense). Sequence was generated using Illumina's recommended protocols, including cDNA synthesis, cluster generation, and sequencing. These reads were used to validate and identify SNPs between the A and D genomes of diploid cotton and SNPs between the A- and D-genomes of tetraploid cotton.
BioProject:
12541 (primary)
Show Entrez docsums for all experiments
Download reads for entire study in sra format
Experiments
| Show RUNs for each experimentHide RUNs for each experiment | |||
| ⇑Accession | Spots | Bases | |
|---|---|---|---|
| Total: 21 | 160.0 M | 16.2 G | |
 |
SRX015389 | 607,711 | 157.1 M |
| SRR032799 | 607,711 | 157.1 M | |
|
SRX015428 | 830,252 | 446.0 M |
| SRR032877 | 830,252 | 446.0 M | |
|
SRX015429 | 860,395 | 453.2 M |
| SRR032878 | 860,395 | 453.2 M | |
|
SRX015430 | 713,451 | 349.7 M |
| SRR032879 | 713,451 | 349.7 M | |
|
SRX015431 | 169,930 | 45.6 M |
| SRR032880 | 169,930 | 45.6 M | |
|
SRX015432 | 710,918 | 185.3 M |
| SRR032882 | 710,918 | 185.3 M | |
|
SRX015433 | 743,168 | 440.6 M |
| SRR032881 | 743,168 | 440.6 M | |
|
SRX062245 | 12.0 M | 981.2 M |
| SRR203239 | 12.0 M | 981.2 M | |
|
SRX062246 | 10.5 M | 857.1 M |
| SRR203240 | 10.5 M | 857.1 M | |
|
SRX062247 | 11.2 M | 915.4 M |
| SRR203241 | 11.2 M | 915.4 M | |
|
SRX062248 | 13.6 M | 1.1 G |
| SRR203242 | 13.6 M | 1.1 G | |
|
SRX062249 | 9.8 M | 807.5 M |
| SRR203243 | 9.8 M | 807.5 M | |
|
SRX062250 | 13.0 M | 1.1 G |
| SRR203244 | 13.0 M | 1.1 G | |
|
SRX062251 | 10.4 M | 851.5 M |
| SRR203245 | 10.4 M | 851.5 M | |
|
SRX062252 | 17.2 M | 1.4 G |
| SRR203246 | 17.2 M | 1.4 G | |
|
SRX062253 | 11.9 M | 972.8 M |
| SRR203247 | 11.9 M | 972.8 M | |
|
SRX062254 | 12.3 M | 1.0 G |
| SRR203250 | 12.3 M | 1.0 G | |
|
SRX062255 | 15.7 M | 1.3 G |
| SRR203248 | 15.7 M | 1.3 G | |
|
SRX062256 | 14.4 M | 1.2 G |
| SRR203249 | 14.4 M | 1.2 G | |
|
SRX112513 | 1.9 M | 899.2 M |
| SRR391533 | 1.9 M | 899.2 M | |
|
SRX112514 | 1.7 M | 782.3 M |
| SRR391534 | 1.7 M | 782.3 M | |