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| Status |
Public on Oct 01, 2019 |
| Title |
MPs200vm.3 |
| Sample type |
SRA |
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| Source name |
Intestinal contents
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| Organism |
Danio rerio |
| Characteristics |
age: 16-weeks-old
exposed pollutants: 200vm PS-MPs
tissue: intestine
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| Treatment protocol |
Exposure solutions were prepared by adding 100nm, 5μm or 200μm PS-MPs to culture water with a final concentration of 500μg/L. The exposure solution were was replaced every 2 days. Exposure solution in all tanks were was continuously aerated to maintain the dispersion of particles (no filtering systems were used in the tanks). After 21-d exposure, zebrafish were collected and intestine were rapidly extracted on ice.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The contents of the separated intestine are extruded. Total DNA in the intestinal contents was isolated with DNeasy Blood & Tissue Kit (QIAGEN,Germany). DNA concentration was measured using a NanoDrop spectrophotometer (NanoDrop One,Thermo, USA). After DNA quality analysis by electrophoresis, the extracted DNA was amplified using primers(Forward primer:5’-CCTAYGGGRBGCASCAG-3’; Reverse primer: 5’-GGACTACNNGGGTATCTAAT-3’) to target the V3-V4 regions of the bacterial 16S rRNA gene.
The obtained PCR products were purified by GeneJET Gel Extraction Kit (Thermofisher, USA) and applied to construct the sequencing library. The library was sequenced on an Ion S5TM XL platform.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Ion Torrent S5 XL |
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| Data processing |
Single-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence.
Quality filtering on the raw reads were performed under specific filtering conditions to obtain the high-quality clean reads according to the Cutadapt (V1.9.1, http://cutadapt.readthedocs.io/en/stable/) quality controlled process.
The reads were compared with the reference database (Silva database, https://www.arb-silva.de/) using UCHIME algorithm (UCHIME Algorithm, http://www.drive5.com/usearch/manual/uchime_algo.html) to detect chimera sequences, and then the chimera sequences were removed. Then the Clean Reads finally obtained.
Sequences analysis were performed by Uparse software (Uparse v7.0.1001，http://drive5.com/uparse/). Sequences with ≥97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation.
Genome_build: none
Supplementary_files_format_and_content: tables of relative abundance after homogenization
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| Submission date |
Aug 21, 2019 |
| Last update date |
Oct 02, 2019 |
| Contact name |
Gu Weiqing |
| E-mail(s) |
gwq960722@sina.com
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| Phone |
13962113111
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| Organization name |
Nanjing University
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| Street address |
Xianlin
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| City |
Nanjing |
| ZIP/Postal code |
210023 |
| Country |
China |
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| Platform ID |
GPL27125 |
| Series (2) |
| GSE136108 |
16S rDNA Amplicon Sequencing Analysis of Polystyrene Microplastic Exposed Zebrafish Intestine |
| GSE136109 |
Single Cell RNA Sequencing and Intestinal Microbial Analysis of Polystyrene Microplastic Exposed Zebrafish Intestine |
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| Relations |
| BioSample |
SAMN12614853 |
| SRA |
SRX6747970 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4041277_MPs200vm.3_otu_table.relative.xlsx |
83.3 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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