The TSHR targeted panel was designed based on the Illumina Sequencing Assay Designer, including entire coding regions and exon-intron boundaries of TSHR(chr14:81421965–81610778). Heel blood of patients was collected, and genomic DNA was extracted using the QIAGEN QIAamp DNA Blood Kit according to the manufacturer’s protocol. Oligonucleotide probes were synthesized and pooled into a custom amplicon tube containing all the probes to generate attempted amplicons. Sample-specific indices were then added to each library by PCR using common primers from the TruSeq Amplicon Index Kit. After a normalization procedure enables simple volumetric pooling of libraries, sequencing was performed on the Illumina MiSeq 2000 system.
Miseq 2000 system
Manufactured by Illumina
Sourced in United States, China
The MiSeq 2000 system is a benchtop DNA sequencing platform designed for targeted sequencing applications. It utilizes Illumina's proprietary sequencing-by-synthesis technology to perform high-throughput DNA sequencing. The system is capable of generating DNA sequence data from a variety of sample types, including genomic DNA, amplicons, and targeted enrichment libraries.
Automatically generated - may contain errors
Lab products found in correlation
Qiaamp dna blood kit, by Qiagen (1 mentions)
4200 tapestation system, by Agilent Technologies (1 mentions)
Paired end miseq sequencing, by Illumina (1 mentions)
Miseq reagent nano kit v2, by Illumina (1 mentions)
Phix dna, by Illumina (1 mentions)
Nextflex 16s v4 amplicon seq kit, by PSC Biotech (1 mentions)
4 protocols using miseq 2000 system
1
TSHR Targeted Panel Sequencing
2
Genome Sequencing of Aspergillus niger Strains
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Genome sequencing of A. niger H915-1, L2, and A1 was performed with an Illumina Miseq 2000 system using paired-end libraries. After clean data were obtained, reads of A. niger A1 were assembled by using the Celera Assembler with the optimal linear combination algorithm11 (link). The sequence data for A. niger A1 were deposited at DDBJ/EMBL/GenBank under the accession number LMYC00000000.
3
16S rRNA Gene Sequencing Protocol
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In this study, we amplified and sequenced the V4 region of the 16S rRNA gene. The extracted DNA was then utilized to construct a 16S rRNA gene library, employing the NEXTflex 16S V4 Amplicon-Seq kit from BioO Scientific (Austin, TX, USA). The quality of the prepared library was assessed using the 4200 Tape Station System from Agilent Technologies (Santa Clara, CA, USA). Meanwhile, we conducted paired-end sequencing using the MiSeq Reagent Kit v2 nano on a MiSeq 2000 system, following the instructions provided by Illumina (San Diego, CA, USA). To evaluate the overall quality of the Illumina MiSeq paired-end sequencing (PE, 2 × 250 nucleotides), we incorporated 12% PhiX DNA from Illumina (USA) into the sequencing runs.
4
Genome Sequencing and Variant Analysis
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The processes for sample preparation and genome sequencing were carried out according to a previously reported method [47 (link)]. Genomic DNA was purified using the Wizard Genomic DNA Purification Kit. The average insert size of the library was 500 bp, and the average read length was 150 bp. Sequencing was performed using an Illumina Miseq 2000 system (Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China). The raw sequence reads were sub-sampled and trimmed by removing low quality bases. The resulted reads were aligned onto the reference genome of MU-11 (unpublished data). The alignment result was visualized for assembly. SNP and Indel variants were analyzed, and relevant gene annotation was performed.
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