Four SBT samples were examined for sequence variants by comparing whole exome or transcriptome sequencing data to the human reference genome. To obtain whole exome sequences, whole exome libraries with ~ 280 base inserts and paired-end index adapters were prepared from 1 μg genomic DNA, according to Illumina’s TruSeq DNA Sample Preparation v2 method. Five hundred nanograms of each of four libraries were pooled together for enrichment. Exome capture was performed according to Illumina’s TruSeq Exome Enrichment Kit protocol. Each captured exome pool was sequenced in two lanes on a HiSeq 2000 using version 3 chemistry. At least 40 million paired-end 100 base reads were obtained for each sample. Data was processed using the Illumina data analysis pipeline RTA v1.13.48 and CASAVA v1.8.2.
Truseq dna sample preparation v2
Manufactured by Illumina
The TruSeq DNA Sample Preparation v2 is a laboratory equipment product from Illumina. It is designed to prepare DNA samples for sequencing on Illumina's sequencing platforms. The core function of this product is to generate library templates from DNA samples in a standardized and automated manner.
Automatically generated - may contain errors
Lab products found in correlation
Hiseq 2000, by Illumina (4 mentions)
Truseq pe cluster kit v3, by Illumina (2 mentions)
Truseq sbs v3 chemistry, by Illumina (2 mentions)
Truseq dna sample prep kit v2 set a, by Illumina (2 mentions)
Casava 1, by Illumina (2 mentions)
Casava v1, by Illumina (1 mentions)
Truseq exome enrichment kit, by Illumina (1 mentions)
Genome analyzer pipeline software, by Illumina (1 mentions)
Miseq 2000, by Illumina (1 mentions)
Adaptor oligo mix, by Illumina (1 mentions)
6 protocols using truseq dna sample preparation v2
1
Whole Exome Sequencing for Variant Detection
2
Whole Exome Sequencing of Family
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Genomic DNA was extracted from EDTA‐treated blood, as described by Bellus et al. (1995 (link)). WES was performed in the patient plus his parents and two unaffected siblings using the TruSeq DNA Sample Preparation v2 method (Illumina, San Diego), followed with Illumina's TruSeq Exome Enrichment Kit protocol and sequenced using the Illumina HiSeq2000 with version 3 chemistry to a depth of at least 40 million paired‐end 100 base reads for each sample. Image analysis and base calling were performed with default parameters using Illumina Genome Analyzer Pipeline software (RTA version 1.17.20 and CASAVA 1.8.2).
3
Gut Microbiome Profiling via 16S rDNA
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
At the end of lactation, fecal samples were collected from the colon after the sacrifice of dams and stored in a -80 °C freezer. Total DNA was extracted with a QIAmp PowerFecal® DNA Kit, and for each sample, a region of approximately 426 bp encompassing the V3 and V4 hypervariable regions of the 16S rDNA gene was targeted for sequencing. To amplify and sequence the V3-V4 hypervariable region of the 16S rDNA gene, the primers used were 16S-V3F [CCTACGGGNGGCWGCAG] and 16S-V4R [GGACTACHVGGGTWTCTAAT].
To prevent problems due to Illumina low-diversity libraries, each index sequence differed from the others by at least two nucleotides, and each nucleotide position in the sets of indices contained approximately 25% of each base (Table 2). For the preparation of the libraries, "Illumina TruseqDNA Sample Preparation v2" was used, labeling each sample with a bar code. Sequencing was performed using the equipment Illumina Miseq2000. More than 100 000 reads per sample were generated, commonly recognized as sufficient for metagenomic research. The sequencing was performed using the Illumina MiSeq equipment purchased from the Biomnigene company (https://www.biomnigene.fr/en/).
To prevent problems due to Illumina low-diversity libraries, each index sequence differed from the others by at least two nucleotides, and each nucleotide position in the sets of indices contained approximately 25% of each base (Table 2). For the preparation of the libraries, "Illumina TruseqDNA Sample Preparation v2" was used, labeling each sample with a bar code. Sequencing was performed using the equipment Illumina Miseq2000. More than 100 000 reads per sample were generated, commonly recognized as sufficient for metagenomic research. The sequencing was performed using the Illumina MiSeq equipment purchased from the Biomnigene company (https://www.biomnigene.fr/en/).
4
Illumina Sequencing Library Preparation
5
Whole Genome Sequencing and Copy Number Analysis
6
Whole Genome Sequencing and Copy Number Analysis
Check if the same lab product or an alternative is used in the 5 most similar protocols
+ Expand
Sequencing libraries were prepared according to the TruSeq DNA v2 sample preparation EUC #15026489 revA using reagents from the TruSeq DNA v2 sample prep kit set A and set B (Illumina). A 14 pM solution of 5-6 DNA libraries pooled in equimolar amounts was subjected to cluster generation on the cBot instrument (Illumina Inc.) using the TruSeq PE cluster kit v3. Paired-end sequencing was performed for 100 cycles using a HiSeq2000 instrument (Illumina Inc.) using TruSeq SBS chemistry v3, according to the manufacturer’s protocols. Base calling was done on the instrument by RTA 1.13.48 and the resulting bcl files were filtered, demultiplexed, allowing for one mismatch base, and converted to fastq format with tools provided by CASAVA-1.8 (Illumina Inc.). Copy number profiles were computed from NGS-data using the Control-FREEC software40 (link). The sequence read depth was used to calculate an equivalent to the Log R Ratio using a sliding window approach. We applied a fixed window size of 5 kb and the other settings were default. The NGS dataset was composed of 100 whole genomes with 5x average coverage and additional exomes, with an average coverage of 17x.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!