Comprehensive database of Short Tandem Repeat DNA profiles for all of ATCC human cell lines. ATCC data collection as part of continuing efforts to characterize and authenticate cell lines in Cell Biology collection.

Short Tandem Repeat DNA Internet DataBase is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

Short tandem repeats (STRs) are short repeated sequences commonly found in the human genome and valuable in forensic science, used for human identity and relatedness markers. Next-generation sequencing (NGS) technologies, e.g., ForenSeq Signature Prep, can sequence STRs, inferring length-based alleles and single nucleotide polymorphisms (SNPs) and providing valuable insights into population and sub-population structures. Despite the potential benefits of NGS for STRs, no open-source software platform integrates the collection, management, and analysis of STR data from NGS into one place. Users must use multiple programs to process their STR data and then collect the results into a separate database or a file system folder. Moreover, analyzing repeat structures (STR repeat motifs) may require learning multiple software tools, making the process inefficient and cumbersome. To address this gap, we introduce the STRategy, a standalone web-based application supporting essential STR data management and analysis capabilities. The STRategy allows users to collect their data into its database, automatically calculates forensic parameters, and visualizes the analyzed data in various forms. Users can search the database using different options, such as by profile, loci, and genotypes, with and without a specific test kit. Moreover, users can also find the nucleotide variants of a locus among the samples. We designed the STRategy for internal use in a laboratory or an organization. Hence, our system includes role-based access control that allows users to search for or access specific data based on their responsibilities. The administrator role can customize the system, for example, configure maps according to the samples’ geographic data, and manage reference STR repeat motifs. A laboratory or an organization can download and install a copy of STRategy on their local system using Docker, as described in https://github.com/cucpbioinfo/STRategy. In summary, the STRategy is an end-to-end system that provides users with a database to collect the analyzed STR data from NGS, the dynamic analyses of forensic parameters, and the variants of STR patterns according to the newly added samples, which are then explorable via various search options and visualizations. The system is helpful for both forensic investigations and forensic genetics.

Dataset

This dataset was created by Dennis Mbugua

Contents

Background: Short tandem repeats (STRs) are highly variable elements that play a pivotal role in multiple genetic diseases and the regulation of gene expression. Long-read sequencing (LRS) offers a potential solution to genome-wide STR analysis. However, characterizing STRs in human genomes using LRS on a large population scale has not been reported.Methods: We conducted the large LRS-based STR analysis in 193 unrelated samples of the Chinese population and performed genome-wide profiling of STR variation in the human genome. The repeat dynamic index (RDI) was introduced to evaluate the variability of STR. We sourced the expression data from the Genotype-Tissue Expression to explore the tissue specificity of highly variable STRs related genes across tissues. Enrichment analyses were also conducted to identify potential functional roles of the high variable STRs.Results: This study reports the large-scale analysis of human STR variation by LRS and offers a reference STR database based on the LRS dataset. We found that the disease-associated STRs (dSTRs) and STRs associated with the expression of nearby genes (eSTRs) were highly variable in the general population. Moreover, tissue-specific expression analysis showed that those highly variable STRs related genes presented the highest expression level in brain tissues, and enrichment pathways analysis found those STRs are involved in synaptic function-related pathways.Conclusion: Our study profiled the genome-wide landscape of STR using LRS and highlighted the highly variable STRs in the human genome, which provide a valuable resource for studying the role of STRs in human disease and complex traits.

A database of information on short tandem repeat systems. It contains facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes.

This information and data are supplemental files associated with: Gettings, K.B., Borsuk, L.A., Steffen, C.R., Kiesler, K.M., and P.M.Vallone. Sequence-based U.S. population data for 27 autosomal STR loci, Forensic Science International Genetics (submitted for publication). The primary data consists of sequence-based allele frequencies for N=1036 anonymized U.S. population samples at 27 autosomal Short Tandem Repeat (auSTR) loci: D1S1656, TPOX, D2S441, D2S1338, D3S1358, D4S2408, FGA, D5S818, CSF1PO, D6S1043, D7S820, D8S1179, D9S1122, D10S1248, TH01, vWA, D12S391, D13S317, Penta E, D16S539, D17S1301, D18S51, D19S433, D20S482, D21S11, Penta D, and D22S1045. This information is expected to support the implementation of sequence-based STR analysis in forensic applications. /"NIST1036_auSTR_Seq_SuppTables.xls/" is an excel file containing the following worksheets: run metrics for the 42 sequencing runs performed to generate the allele frequency data (S1 - Run Metrics); coverage per locus per sample for all N=1036 at the 27auSTR, 7XSTR, and 24 YSTR loci reported by the manufacturer in this assay (S2 - Coverage); allele frequency data (S3 - Frequencies); GRCh38 reference coordinates for genomic regions reported in the 27 auSTRs (S4 - Ref Coordinates); summary of polymorphisms detected and reported in STR flanking regions (S5 - Flank Polymorph); number of alleles, expected and observed heterozygosity, and p-values associated with HWE testing by population for the 27 auSTR loci (S6 - Hexp_Hobs_pHW); p-values associated with testing for linkage disequilibrium (S7 - LD p-values); and pairwise Fst values by population for the 27 auSTR loci (Supp Table 8 - Pairwise Fst). Lastly, /"NIST1036_auSTR_Seq_SuppFile1.pdf/" contains information on optimization, sequencing, and quality control of the data.

These population data represent 23 Y-STR loci from 514 unrelated Kyrgyz males sampled from three geographically distinct regions: Northern East (N=134), Northern West (N=183), and Southern Kyrgyzstan (N=197): Table S1. The haplotype distributions of 23 Y-chromosomal STRs form Kyrgyz population (N=514). Table S2. The haplotype frequencies of 23 Y-chromosomal STRs in Kyrgyz population (N=514). Table S3. Allele frequencies and Forensic parameters values for 21 single-locus Y-STRs in Kyrgyz population (N=514). Table S4. Locus-specific haplotypes frequencies and Forensic parameters values for DYS385a/b in Kyrgyz population (N=514). Table S5. Abnormal alleles detected in Kyrgyz population. Table S5. Pairwise genetic distance (RST) between Kyrgyz populations and neighboring populations used for comparison from YHRD on 17 Y-STRs.

580 Global export shipment records of Silver str with prices, volume & current Buyer's suppliers relationships based on actual Global export trade database.

In genetics, lab activities can improve the learning process but are typically expensive and require teaching lab facilities. Sometimes, a hands-on in-class activity can help fulfill some of the same learning goals as a traditional lab. For this lesson, I created an activity on DNA fingerprinting where each student has their own unique data. Rather than having students obtain and analyze their own DNA, which would be time-consuming, require molecular biology equipment, and could share sensitive personal DNA information in a group setting, I created an activity with playing cards. The cards represent different possible alleles of short tandem repeats (STRs), non-coding DNA often used in actual “DNA fingerprinting.” For the activity, students work in groups to simulate DNA fingerprinting using standard playing cards to represent alleles for two different STRs. Students then determine if this small amount of genotype information is enough to uniquely identify individuals in their group as well as between two student groups, and these data can also be used to analyze the entire class. Students draw images of DNA gels to create a visual representation of their STR data and see how differing STR sizes result in DNA band patterns. This lesson is adaptable for both introductory and upper division courses, requires very few materials, and can be completed in a single class session in either a laboratory room or a standard classroom. Students report enjoying the activity and that it helps them make the connection between alleles, genotypes, and DNA gels.

Primary Image: Playing card genotypes and DNA gel drawing. An example of playing card “genotypes” for four individual students and the accompanying DNA fingerprint gel sketch. Drawing and photograph by AL Klocko.

229 Global import shipment records of Silver Str with prices, volume & current Buyer's suppliers relationships based on actual Global export trade database.

215 Global import shipment records of Silver,str with prices, volume & current Buyer's suppliers relationships based on actual Global export trade database.

The Y-chromosomal short tandem repeat (Y-STR) is an effective forensic tool in familial searches and patrilineal relationship evaluation. However, currently available Y-STR panels often lack sufficient discriminatory power to resolve genetic relationships between distant relatives or within patrilocal populations. This study aims to establish a novel Y-STR amplification system for forensic casework analysis and database construction, which contains 44 slowly and moderately mutating and one rapidly mutating Y-STR. The validation of the assay was conducted following the recommendations of SWGDAM developmental validation guidelines. Different types of casework samples were tested and reliable profiles were obtained. Furthermore, we genotyped and analyzed 141 unrelated Han Chinese male samples. The results showed that this Y45 kit could improve the performance of identifying male individuals, higher haplotype diversity, and discrimination capacity when compared to the previous widely used Yfiler Plus kit. In general, the validation study demonstrated that the newly developed Y45 kit possesses high sensitivity, inhibitor tolerance, male specificity in a mixture, species specificity, and precision and is capable of forensic casework analysis and database construction.

All Active Short-Term Licenses. This dataset includes Commercial, Non-Commercial, and Operator Licenses, as well as listings for lodging providers exempt from STR licensing (i.e., licensed Hotels, Motels, and Bed and Breakfasts who may list their properties on Short-Term Rental platforms).

Non-traditional data signals from social media and employment platforms for STR stock analysis

2806 Global export shipment records of Steel Str with prices, volume & current Buyer's suppliers relationships based on actual Global export trade database.

2913 Global import shipment records of Pc Str with prices, volume & current Buyer's suppliers relationships based on actual Global export trade database.

Microsatellite markers have played a major role in ecological, evolutionary and conservation research during the past 20 years. However, technical constrains related to the use of capillary electrophoresis and a recent technological revolution that has impacted other marker types have brought to question the continued use of microsatellites for certain applications. We present a study for improving microsatellite genotyping in ecology using high-throughput sequencing (HTS). This approach entails selection of short markers suitable for HTS, sequencing PCR-amplified microsatellites on an Illumina platform and bioinformatic treatment of the sequence data to obtain multilocus genotypes. It takes advantage of the fact that HTS gives direct access to microsatellite sequences, allowing unambiguous allele identification and enabling automation of the genotyping process through bioinformatics. In addition, the massive parallel sequencing abilities expand the information content of single experimental runs far beyond capillary electrophoresis. We illustrated the method by genotyping brown bear samples amplified with a multiplex PCR of 13 new microsatellite markers and a sex marker. HTS of microsatellites provided accurate individual identification and parentage assignment and resulted in a significant improvement of genotyping success (84%) of faecal degraded DNA and costs reduction compared to capillary electrophoresis. The HTS approach holds vast potential for improving success, accuracy, efficiency and standardization of microsatellite genotyping in ecological and conservation applications, especially those that rely on profiling of low-quantity/quality DNA and on the construction of genetic databases. We discuss and give perspectives for the implementation of the method in the light of the challenges encountered in wildlife studies.

This data repository is meant to provide the supplementary files, tables, and figures included in the peer-reviewed research article entitled: "Sequence-based allelic variations and frequencies for 22 autosomal STR Loci in the Lebanese population". The article can be found at the following link (https://doi.org/10.1016/j.fsigen.2023.102872) and describes the sequencing of the 22 autosomal Short Tandem Repeat (aSTR) loci, using the PowerSeq 46GY System Prototype, in 195 individuals of self-reported Lebanese admixed ancestry. The supplemental files contain the sequence strings for each allele at each autosomal STR locus, length- and sequence- based allelic frequencies, quality control metrics for the sequencing runs, flanking region polymorphisms, as well as population and forensic genetic statistics. Any future changes to the supplements will be listed in the "Change Log" tab within each spreadsheet.

Known for its rich history and culture, Qingdao is a typical symbol of Chinese maritime culture. Its unique genetic landscape has aroused interest among geneticists and forensic scientists. However, the genetic landscape of Qingdao has never been uncovered. This investigation intends to provide light on Qingdao’s paternal genetic diversity and its evolutionary connections to other Han subgroups. The genetic polymorphisms of 41 Y-chromosomal short tandem repeat (STR) loci in the Qingdao Han were investigated using SureID® PathFinder Plus Kit. Phylogenetic studies were performed using genotype data from 52 East Asian groups at 23 common Y-STR loci. A multidimensional scaling plot and cladogram were constructed. Linear Discriminant Analysis (LDA) was carried out for predicting categories among the Han people. The k-nearest neighbour (kNN) algorithm was utilised to designate Y-SNP haplogroups for each haplotype. The Qingdao Han were genetically far from the Tibeto-Burman populations and close with the Han people from northern China. LDA indicated a deep integration among the present-day Han people. By the kNN model, the predicted O2a2 and O2a1 were shown to be the predominant Y-SNP haplogroups. This study would be helpful for reconstructing the patrilineal history in China and establishing a more comprehensive Y-STR database.