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| Status |
Public on May 08, 2020 |
| Title |
Control1 |
| Sample type |
SRA |
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| Source name |
feces
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| Organism |
mouse gut metagenome |
| Characteristics |
strain/background: C57BL/6
age: Postnatal day 35
treatment: PBS
tissue: Feces
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genome DNA from samples was extracted using CTAB/SDS method. DNA concentration and purity were monitored on 1% agarose gels. According to the concentration, DNA was diluted to 1 ng/µL using sterile water.
Sequencing libraries were generated using Ion Plus Fragment Library Kit 48 rxns (Thermo Scientific) following manufacturer's recommendations.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Ion Torrent PGM |
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| Description |
processed data file: otu_table.txt
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| Data processing |
Library strategy: 16S rRNA sequencing
Sequencing libraries were generated using Ion Plus Fragment Library Kit 48 rxns (Thermo Scientific) following manufacturer's recommendations. The library quality was assessed on the Qubit@ 2.0 Fluorometer (Thermo Scientific). At last, the library was sequenced on an Ion S5TM XL platform and 400 bp/600 bp single-end reads were generated.
1. Single-end reads quality control:
1.1 Data split: Single-end reads was assigned to samples based on their unique barcode and truncated by cutting off the barcode and primer sequence. 1.2 Data Filtration: Quality filtering on the raw reads were performed under specific filtering conditions to obtain the high-quality clean reads according to the Cutadapt (Martin M. , 2011) [1] (V1.9.1, http://cutadapt.readthedocs.io/en/stable/) quality controlled process. 1.3 Chimera removal: The reads were compared with the reference database (Silva database, https://www.arb-silva.de/) [2] using UCHIME algorithm (UCHIME Algorithm, http://www.drive5.com/usearch/manual/uchime_algo.html) [3] to detect chimera sequences, and then the chimera sequences were removed [4]. Then the Clean Reads finally obtained.
2. OTU cluster and Species annotation:
2.1 OTU Production: Sequences analysis were performed by Uparse software (Uparse v7.0.1001, http://drive5.com/uparse/) [5]. Sequences with ≥97% similarity were assigned to the same OTUs. Representative sequence for each OTU was screened for further annotation. 2.2 Species annotation: For each representative sequence, the Silva Database (https://www.arb-silva.de/) [2] was used based on Mothur algorithm to annotate taxonomic information. 2.3 Phylogenetic Relationship Construction: In order to study phylogenetic relationship of different OTUs, and the difference of the dominant species in different samples (groups), multiple sequence alignment were conducted using the MUSCLE software (Version 3.8.31, http://www.drive5.com/muscle/) [6]. 2.4 Data Normalization: OTUs abundance information were normalized using a standard of sequence number corresponding to the sample with the least sequences. Subsequent analysis of alpha diversity and beta diversity were all performed basing on this output normalized data.
Genome_build: Silva database, https://www.arb-silva.de/
Supplementary_files_format_and_content: otu_table.txt: Tab-delimited text file; relative proportions.
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| Submission date |
Oct 25, 2019 |
| Last update date |
May 08, 2020 |
| Contact name |
Jinhuan Song |
| E-mail(s) |
sjh1207359577@gmail.com
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| Phone |
15603075151
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| Organization name |
Jinan University
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| Street address |
Jinan University, No.601, West Huangpu Avenue
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| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510632 |
| Country |
China |
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| Platform ID |
GPL27659 |
| Series (2) |
| GSE139422 |
Dysbacteriosis-induced LPS elevation disturbs the development of muscle progenitor cells by interfering with retinoic acid signaling [16S rRNA sequencing] |
| GSE139526 |
Dysbacteriosis-induced LPS elevation disturbs the development of muscle progenitor cells by interfering with retinoic acid signaling |
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| Relations |
| BioSample |
SAMN13117845 |
| SRA |
SRX7059701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4141505_Control1.fna.gz |
1.7 Mb |
(ftp)(http) |
FNA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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