GenomeScan protocols

View GenomeScan computational protocol

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GenomeScan specifications

Information


Unique identifier OMICS_07792
Name GenomeScan
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Chris Burge <>

Publications for GenomeScan

GenomeScan in pipelines

 (6)
2018
PMCID: 5764939
PMID: 29326215
DOI: 10.1128/genomeA.01430-17

[…] (ctab)-based extraction buffer (). concentration and quality of the samples were determined using the life technology qubit and 0.6% agarose gel, respectively. genome sequencing was performed at genomescan. the nebnext ultra dna library preparation kit from illumina (catalog number neb e7370s/l) was used according to the manual for library preparation. quality and yield after sample […]

2017
PMCID: 5683368
PMID: 29158777
DOI: 10.1186/s13068-017-0956-0

[…] clustering and dna sequencing were performed using the illumina cbot and hiseq 2500 systems with a dna concentration of 8.0 pm, using 250-bp paired-end reads. procedures were carried out by genomescan b.v., leiden. image analysis, base calling and quality check were performed with the illumina data analysis pipelines rta v1.18.64 and bcl2fastq v1.8.4. for adapter trimming, presumed […]

2013
PMCID: 3758364
PMID: 23872635
DOI: 10.1038/ng.2705

[…] and mice., we updated and corrected the human gene set to reflect our shims sequence assembly across ampliconic regions. we searched novel genomic sequence generated in this study for genes using genomescan and blast analyses of human est databases. in the case of ampliconic regions that were either expanded or contracted in our revised assembly, we recounted the numbers of genes […]

2012
PMCID: 3342946
PMID: 22258146
DOI: 10.4161/rna.9.1.18121

[…] or rat beadchips, respectively, using the illumina whole genome gene expression direct hybridization protocol. the beadchips were scanned using illumina iscan and the raw data were generated by genomescan software (illumina). the raw data were then log2 transformed and quantile normalized without background subtraction. anova statistical tests were performed in order to calculate samples’ p […]

2007
PMCID: 1963337
PMID: 17640376
DOI: 10.1186/1471-2148-7-120

[…] [] as well as the zebrafish est, genomic, and whole genome shotgun (wgs) databases [], using tblastn. all independent sequences possessing e values > 0.1 were extracted for further analysis. genomescan [] was used to predict coding exons from sequences derived solely from wgs or genomic scaffolds, some of which were manually adjusted on the basis of known intron-exon boundaries […]


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GenomeScan in publications

 (58)
PMCID: 5923239
PMID: 29703914
DOI: 10.1038/s41598-018-25152-x

[…] in a spectrophotometer (biochrom libra s22). the rna quality was analyzed with an agilent 2100 bioanalyzer using a rna6000 labchip kit (agilent technology). microarray hybridization was performed at genomescan (leiden, the netherlands). microarray data was analyzed using affymetrix expression console software v1.4.1.46 with the normalized values in linear scale. the probe intensities […]

PMCID: 5887033
PMID: 29622620
DOI: 10.1128/genomeA.01414-17

[…] the concentration and quality of the dna were determined using a qubit fluorometer (life technologies) and 0.6% agarose gel, respectively. genome and transcriptome sequencing were performed at genomescan., the dna was fragmented using a focused-ultrasonicator (covaris). the nebnext ultra dna library prep kit and nebnext ultra directional rna library prep kit for illumina (catalog numbers […]

PMCID: 5852574
PMID: 29419728
DOI: 10.3390/genes9020078

[…] cpg sites was analyzed using the infinium 450k humanmethylation beadchip (illumina, san diego, ca, usa) following the manufacturer’s instructions at either the leiden university medical center or genomescan b.v., leiden, the netherlands. beadchip images were scanned using the iscan system. twin pairs were analyzed on the same array. the three datasets were analyzed on different occasions., […]

PMCID: 5905499
PMID: 29253216
DOI: 10.1093/gigascience/gix125

[…] erythranthe guttata, solanum lycopersicum, solanum tuberosum, populus trichocarpa, and vitis vinifera. gene structures were predicted by homology-based predictors, fgenesh++, fgenesh_est [, ], and genomescan []. gene predictions were improved by program to assemble spliced alignment (pasa, rrid:scr_014656) [], including adding untranslated regions (utrs), correcting splicing, and adding […]

PMCID: 5701360
PMID: 29169319
DOI: 10.1186/s12864-017-4164-x

[…] the rna was analyzed with an agilent 2100 bioanalyzer using a rna6000 labchip kit (agilent technology). microarray hybridization using the affymetrix genechips a. niger genome array was performed at genomescan (leiden, the netherlands)., microarray data was analyzed using the bioconductor tool package version 2.8 (http://www.bioconductor.org/) together with house-made perl (version .5.0) […]


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GenomeScan institution(s)
Department of Mathematics Stanford University, Stanford CA, USA

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