 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 13, 2022 |
| Title |
WFTM1 |
| Sample type |
SRA |
| |
|
| Source name |
male, antennae, rep1
|
| Organism |
Frankliniella occidentalis |
| Characteristics |
tissue: antennae
Sex: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribe™ Reverse Transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5’ end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand,indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
Salmon [4] was used to perform expression level for Unigenes by calculating TPM
Assembly: Trinity.gene.fasta
Supplementary files format and content: xlsx files include TPM values for each Sample
|
| |
|
| Submission date |
Sep 10, 2022 |
| Last update date |
Sep 13, 2022 |
| Contact name |
Xiaowei Li |
| E-mail(s) |
lixiaowei@zaas.ac.cn
|
| Phone |
13588281346
|
| Organization name |
Zhejiang Academy of Agricultural Sciences
|
| Street address |
No. 298 Deshengzhong road
|
| City |
Hangzhou, Zhejiang, China |
| ZIP/Postal code |
310021 |
| Country |
China |
| |
|
| Platform ID |
GPL32653 |
| Series (1) |
| GSE213075 |
Comparison and functional analysis of odorant-binding proteins and chemosensory proteins in two closely related thrips species, Frankliniella occidentalis and Frankliniella intonsa (Thysanoptera: Thripidae) |
|
| Relations |
| BioSample |
SAMN30789048 |
| SRA |
SRX17520852 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
