Whole genome 1 m oligonucleotide array

Manufactured by Agilent Technologies

Sourced in United States

The Whole Genome 1 M Oligonucleotide Array is a high-density microarray designed for whole-genome analysis. The array contains approximately 1 million unique oligonucleotide probes that provide comprehensive coverage of the human genome.

Automatically generated - may contain errors

Lab products found in correlation

Cgh analytics v3, by Agilent Technologies (2 mentions) Cytogenomics v2, by Agilent Technologies (2 mentions) Feature extraction v9, by Agilent Technologies (2 mentions)

Close spelling variants of this product

Oligonucleotides

5 protocols using whole genome 1 m oligonucleotide array

Genome-wide Array CGH Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

All experiments were done with genomic DNA extracted from blood samples. Array CGH for family 1, 3, and 4 was carried out using a whole genome 1 M oligonucleotide array (Agilent, Santa Clara, CA). 1 M arrays were analyzed by Feature Extraction v9.5.3.1 and CGH Analytics v3.4.40 software or Cytogenomics v2.5.8.11, respectively (Agilent, Santa Clara, CA). Family 2 was tested on Roche NimbleGen platform with use of 1.4 M oligo arrays according to standard protocols provided by the manufacturer. Analysis settings: aberration algorithm: ADM-2; threshold: 6.0; window size: 0.2 Mb; filter: 5probes, log2ratio = 0.29. The genomic profile was visualized by the SignalMap software (SignalMap v1.9.0.03, NimbleGen Systems Inc.). Data were submitted to the DECIPHER database (http://decipher.sanger.ac.uk); accession numbers: BER284939, BER284938, BER284937, and BER285016.

Tayebi N., Jamsheer A., Flöttmann R., Sowinska-Seidler A., Doelken S.C., Oehl-Jaschkowitz B., Hülsemann W., Habenicht R., Klopocki E., Mundlos S, & Spielmann M. (2014). Deletions of exons with regulatory activity at the DYNC1I1 locus are associated with split-hand/split-foot malformation: array CGH screening of 134 unrelated families. Orphanet Journal of Rare Diseases, 9, 108.

+ Open protocol

+ Expand

Whole-Genome CMA Analysis Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols

CMA for individual V-3 was carried out using a whole-genome 1 M oligonucleotide array (Agilent; Santa Clara, CA). Data were analyzed as previously reported [22 (link)].

Boschann F., Moreno D.A., Mensah M.A., Sczakiel H.L., Skipalova K., Holtgrewe M., Mundlos S, & Fischer-Zirnsak B. (2022). Xq27.1 palindrome mediated interchromosomal insertion likely causes familial congenital bilateral laryngeal abductor paralysis (Plott syndrome). Journal of Human Genetics, 67(7), 405-410.

+ Open protocol

+ Expand

Comparative Genomic Hybridization via Array

Check if the same lab product or an alternative is used in the 5 most similar protocols

Microarray-based comparative genomic hybridization (array CGH) for family 2 was carried out using a whole-genome 1-M oligonucleotide array (Agilent); 1 M arrays were analyzed by feature extraction v9.5.3.1 and CGH analytics v3.4.40 software or cytogenomics v2.5.8.11, respectively (Agilent). Analysis settings were as follows: aberration algorithm, ADM-2; threshold, 6.0; window size, 0.2 Mb; filter, 5probes; log2ratio = 0.29. The genomic profile was visualized by the SignalMap software (SignalMap v1.9.0.03, NimbleGen Systems).

Spielmann M., Kakar N., Tayebi N., Leettola C., Nürnberg G., Sowada N., Lupiáñez D.G., Harabula I., Flöttmann R., Horn D., Chan W.L., Wittler L., Yilmaz R., Altmüller J., Thiele H., van Bokhoven H., Schwartz C.E., Nürnberg P., Bowie J.U., Ahmad J., Kubisch C., Mundlos S, & Borck G. (2016). Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice. Genome Research, 26(2), 183-191.

+ Open protocol

+ Expand

Genetic Analysis of Affected Individual

Check if the same lab product or an alternative is used in the 5 most similar protocols

Peripheral blood samples were obtained from the affected individual and his parents. Written informed consent for molecular genetic testing and for publication of photographs from the index patient was obtained from his legal representatives. Sequencing of all exons and the flanking intron regions of GORAB (NM_012463) was performed as described previously. 3 The Array-CGH (array-based comparative genomic hybridization) experiment for the index patient II-1 was carried out using a whole-genome 1M oligonucleotide array (Agilent, Santa Clara, CA, USA). The data were analyzed using CytoGenomics v.2.7.8.0 (Agilent) software. Analysis settings: ADM-2; Threshold: 6.0; Window Size: 0.2 Mb; Filter: 5 probes, log2ratio = 0.29. Analysis of the exact breakpoint was carried out using endpoint PCRs followed by sequencing. All primer sequences are available on request.

Al-Bughaili M., Neuhann T.M., Flöttmann R., Mundlos S., Spielmann M., Kornak U, & Fischer-Zirnsak B. (2017). A de novo 1q23.3-q24.2 deletion combined with a GORAB missense mutation causes a distinctive phenotype with cutis laxa. Journal of human genetics, 62(2).

+ Open protocol

+ Expand

Genome-wide Copy Number Variation Analysis

Check if the same lab product or an alternative is used in the 5 most similar protocols

Array CGH was carried out using a whole-genome 1 M oligonucleotide array (Agilent; Santa Clara, CA). 1 M arrays were analyzed by Feature Extraction version 9.5.3.1 and CGH Analytics version 3.4.40 or Cytogenomics version 2.5.8.11 software, respectively (Agilent). The analysis settings used were as follows: aberration algorithm: ADM-2; threshold: 6.0; window size: 0.2 Mb; filter: 5probes, log2 ratio = 0.29. Data were submitted to the Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources (DECIPHER; http://decipher.sanger.ac.uk); accession numbers are listed in Supplementary Tables S3-5.

Flöttmann R., Kragesteen B.K., Geuer S., Socha M., Allou L., Sowińska-Seidler A., Bosquillon de Jarcy L., Wagner J., Jamsheer A., Oehl-Jaschkowitz B., Wittler L., de Silva D., Kurth I., Maya I., Santos-Simarro F., Hülsemann W., Klopocki E., Mountford R., Fryer A., Borck G., Horn D., Lapunzina P., Wilson M., Mascrez B., Duboule D., Mundlos S, & Spielmann M. (2018). Noncoding copy-number variations are associated with congenital limb malformation. Genetics in medicine : official journal of the American College of Medical Genetics, 20(6).

+ Open protocol

+ Expand

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?

Revolutionizing how scientists
search and build protocols!