SOLiD BioScope Software protocols

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SOLiD BioScope Software specifications

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Unique identifier OMICS_19505
Name SOLiD BioScope Software
Alternative name BioScope Software
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use License purchase required
Biological technology Life Technologies
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained No

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SOLiD BioScope Software in pipelines

 (15)
2017
PMCID: 5319761
PMID: 28222152
DOI: 10.1371/journal.pone.0171988

[…] barcode trimming, we assessed the quality of the sequencing data using fastqc software. the data were mapped to the reference comprising 980 repeat sequences presented in the mus musculus genome. bioscope software version 1.3 was used for mapping. read counts per repeat family were normalized by library size and then log-transformed. to estimate tumour-associated gene coverage, the data […]

2017
PMCID: 5441048
PMID: 28532469
DOI: 10.1186/s40246-017-0107-5

[…] [], and fastqc software (babraham bioinformatics), and shorter reads (<25) as well as all duplicate reads were deleted. the reads were aligned with the reference genome (grch37 hg19) with bioscope™ (applied biosystems, foster city, ca, usa) using the default settings. results from bioscope™ were filtered by depth >30 reads [] and quality of the assigned genotype ≥100. this analysis […]

2016
PMCID: 4982761
PMID: 27331609
DOI: 10.7554/eLife.16030.035

[…] to the instructions provided with the solid fragment library barcoding kit (life technologies, carlsbad, ca). the libraries were sequenced with solid 4. the resulting reads were mapped using bioscope software (life technologies) with the default configuration, combined biological replicates, and analyzed using homer (), ceas () and r software programs. the mapping results are shown in […]

2016
PMCID: 4982761
PMID: 27331609
DOI: 10.7554/eLife.16030.035

[…] and low categories included 90, 717, and 5516 genes, respectively., the expression of read-through rna (fpkm > 0.5) was measured within 5 kb in ecms and in nkx2-5-deficient embryonic hearts using bioscope (life technologies). genes with an average change in read-through rna expression of more than a 1.4-fold compared with control sirna-treated ecms or wild-type littermate hearts were analyzed […]

2016
PMCID: 5025636
PMID: 27634286
DOI: 10.1186/s12920-016-0221-6

[…] substrate (thermo scientific)., immunoprecipitated dna was subjected to sequencing library preparation and sequenced on applied biosystems solid (v3). reads were aligned to hg18 (ncbi36) using bioscope 1.2.1, finding all alignments between the first 25 bp of the read (seed) and the reference sequence with up to two mismatches. each match is extended to the full length of the read, scoring […]


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SOLiD BioScope Software in publications

 (354)
PMCID: 5863964
PMID: 29565978
DOI: 10.1371/journal.pone.0193763

[…] on freshly cleaved mica for 4 minutes. these samples were subsequently gently washed twice with 100 μl milli-q water and dried using a gentle stream of nitrogen gas. afm images were acquired on a bioscope catalyst (bruker) in tapping mode in air using a silicon probe (nsc36, tip b; mikromasch). all images were captured with 512x512 pixels at a scan rate of 0.5 or 2.0 hz. the images were plane […]

PMCID: 5849720
PMID: 29535366
DOI: 10.1038/s41598-018-22741-8

[…] tendons., afm imaging and tensile testing of the single collagen fibrils extracted from cde and sdf tendons (n = 21 cde fibrils, n = 17 sdf fibrils) was performed using an atomic force microscope (bioscope catalyst, bruker, usa) mounted on an inverted optical microscope (ix71, olympus, usa) outfitted with a 100x, 1.3 na objective (olympus, usa) and a grasshopper ccd camera (point grey, […]

PMCID: 5837425
PMID: 29511739
DOI: 10.1126/sciadv.aar4906

[…] nd:yag) with an emission wavelength of 532 nm to illuminate the sample via a beam splitter (ratio, 50:50) and a high numerical aperture (na) objective (plan apo tirf 100×, na 1.45, nikon). the afm (bioscope, bruker) is mounted on a customized stage on top of the sample holder stage. a 720-nm low-pass (lp) filter is used to filter the fluorescence light and to suppress the light of the broad afm […]

PMCID: 5897718
PMID: 29361531
DOI: 10.1242/jcs.208223

[…] gels were mounted on glass slides and hydrated, then nano-indented with a spherically tipped cantilever (nominal radius 5 µm, spring constant 1 nm−1, windsor scientific ltd, slough, uk) fitted to a bioscope catalyst afm (bruker, coventry, uk) mounted on an eclipse t1 inverted optical microscope (nikon, kingston, uk). gels were indented 25 times over a 50 µm×50 µm area, with contact points […]

PMCID: 5881631
PMID: 29472250
DOI: 10.15252/embj.201798049

[…] laser power, ≤ 50 mw) with a water immersion objective (25×, na = 1.05; olympus). image processing was performed in imagej (national institutes of health)., afm images were recorded in pbs with a bioscope resolve microscope (bruker) equipped with a 100 × 100 × 15 μm (x, y, z) piezoelectric scanner. afm cantilevers (pfqnm‐lc from bruker) had nominal spring constants of ≈0.08 n/m, had resonance […]


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