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| Status |
Public on May 01, 2017 |
| Title |
DGE_Bp4_B |
| Sample type |
SRA |
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| Source name |
fat body and ovary
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| Organism |
Locusta migratoria |
| Characteristics |
tissue: the mixture of the fat body and ovary
age: adult locust
treament: infected with M. luteus
post-treament time: 4h
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| Treatment protocol |
The second generation adult female insects were divided into four treatment groups. The female locusts on the first day of molting were collected and underwent the parasite treatments at 12:00 a.m. of the day. The treatment site for all of the various groups was sealed with petroleum jelly to prevent exogenous natural infection. The pronotum of the locusts in the first group was stabbed using an alcohol-sterilized needle to simulate the treatment in the other groups. The second group received a treatment that simulated parasitism. Their pronotum was injected with 100 µl of 50 mg/ml Sephadex G-50 (medium grade, Solarbio, Beijing, China) in 0.9% saline solution. We designated this experimental group as the “Co” in tables and figures. The third group was infected with the bacterial parasite, M. luteus (American Type Culture Collection, Manassas, VA, USA). The bacteria were cultured to the log phase, according to the manufacturer’s instructions, and the pronotum of each locust was injected with 10 μl of bacterial culture with an optical density of approximately 0.9 at 600 nm using a nanofil syringe. We designated this group as the “Bp” in tables and figures. The fourth group was parasitized with the larvae of the dipteran insect, B. lapidosa, a natural parasite of locusts. The tympanic membrane of the locusts was ruptured with an alcohol sterilized needle, and the fly larvae were placed in the wound. We designated the fourth group as the “Di” in tables and figures.
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| Growth protocol |
The locust models were established by rearing the insects in five surface net cages (25 ×25 × 25 cm) at densities of 200 to 300 insects per cage . The insects were reared using a 14:10 light/dark photo regime at 29°C ± 2°C, and were fed a diet of fresh greenhouse-grown wheat seedlings
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| Extracted molecule |
total RNA |
| Extraction protocol |
The fat body and ovary were collected from different females in each group at the following post-treatment time points: (1) the Sephadex group: 4 hours, 6 days; (2) the bacterial parasite group: 4 hours,6 days;(3) the dipteran parasite group: 4 hours,6 days.
The RNA was extracted using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s instructions. Three micrograms of total RNA was used as the input material for sequencing. All of the samples had RIN values greater than 8.The sequencing library was generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, USA), according to the manufacturer’s recommendations. Four index codes were added to the sequence. The mRNA was purified from the total RNA using poly(T)-oligo-conjugated magnetic beads. Fragmentation was performed by heating the RNA in fragmentation buffer (Illumina) containing divalent cations. First-strand complementary DNA (cDNA) was performed using random oligonucleotides and SuperScript II reverse transcriptase (Invitrogen). Second-strand cDNA synthesis and RNA degradation was performed using DNA Polymerase I and RNase H. The overhangs were converted to blunt ends through the exonuclease activity of the polymerase, and the double-stranded DNA fragments were purified. The 3' ends of the DNA fragments were adenylated, and Illumina PE adapter oligonucleotides were ligated to both termini of the adenylated fragments for hybridization. To select the adaptor-ligated cDNA fragments approximately 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Brea, CA, USA). The purified cDNA fragments were selectively enriched during 10 cycles of polymerase chain reaction (PCR) using the Illumina PCR Primer Cocktail. Products were purified again, and quantified by performing the High-sensitivity DNA Assay (Agilent Technologies, Santa Clara, CA, USA) using the Bioanalyzer 2100 system (Agilent). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina), according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
female
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| Data processing |
Raw data (raw reads) in FASTQ format were processed using in-house Perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter or poly(N) sequences and low-quality reads from the raw data.
the transcriptome was assembled using the Trinity program using an min_kmer_cov value of 2 and the default settings for the other parameters.
The annotation of the unigene sequences was conducted by comparing them to the sequences in the GenBank databases using the BLASTx computational tool.
The levels of gene expression were estimated based on the RNA-Seq by Expectation-Maximization (RSEM) for each sample.
Raw reads of the transcriptome have been deposited in the GenBank sequence read archive under accession code SRR1262364. The assembly data of the transcriptome have been deposited in the GenBank transcriptome shotgun assembly archive under accession code GBFE00000000.
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| Submission date |
May 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiaojun Liu |
| E-mail(s) |
xiaojunhappy123@126.com
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| Phone |
86-571-28865077
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| Organization name |
Hangzhou Normal University
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| Department |
College of Life and Environmental Sciences
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| Lab |
Hangzhou Key Laboratory of Animal Adaptation and Evolution
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| Street address |
No 16, Xuelin Street
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310036 |
| Country |
China |
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| Platform ID |
GPL18662 |
| Series (1) |
| GSE57437 |
Transcriptome Analysis of Immunity- and Reproduction-related Differential Gene Expression in Parasitized Locusta migratoria |
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| Relations |
| BioSample |
SAMN02769499 |
| SRA |
SRX540150 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1382491_Bp4B_DGE.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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