 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 15, 2013 |
| Title |
TH-2000 |
| Sample type |
SRA |
| |
|
| Source name |
thiamethoxam-resistant
|
| Organism |
Bemisia tabaci |
| Characteristics |
strain: TH-2000
tissue: total insect
development stage: adult
|
| Growth protocol |
The B-biotype B. tabaci susceptible strain (TH-S) and resistant strain to thiamethoxam (TH-R) were maintained on cabbage under the same conditions. The TH-S strain was cultured without exposure to any chemical insecticides. While the TH-R strain exhibited >70-fold resistance to thiamethoxam compared to the TH-S.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from TH-S and TH-2000 whitefly samples with Trizol reagent. Briefly, mRNA was purified from each sample with Dynal oligo (dT) beads, respectively, Then fragmented the mRNA by using the RNA fragmentation kit, first and second strand cDNA was synthesized using random hexamer primers, The double-stranded cDNA fragments were further processed by an end repair using T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase (NEB) followed by a single <A> base addition using Klenow 3’ to 5’ exo-polymerase, and then ligated with Illumina ’ s adaptor.Finally, the library products were then subjected to sequencing analysis on the flow cell via Illumina HiSeq™ 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whitefly transcriptome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads per kilobase of exon model per million mapped reads (RPKM) were calculated using a protocol from Mortazavi et al.,2008 . In short, The RPKM measure of read density reflects the molar concentration of a transcript in the starting sample by normalizing for RNA length and for the total read number in the measurement. This facilitates transparent comparison of transcript levels both within and between samples.
Genome_build: whitefly transciptome (see transcript_IDs.fa file)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample. Transcript IDs and sequences can be found in the transcript_IDs.fa file on the Series record.
|
| |
|
| Submission date |
Nov 07, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Nina Yang |
| E-mail(s) |
nina809@163.com
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Street address |
12 Zhongguancun Nandajie, Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL16220 |
| Series (1) |
| GSE42102 |
Proteomic and transcriptomic responses to thiamethoxam in the Sweetpotato whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae) |
|
| Relations |
| SRA |
SRX203191 |
| BioSample |
SAMN01803675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1032557_TH-2000.Gene.rpkm.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
