Nimblegen signalmap software

Manufactured by Roche

NimbleGen SignalMap software is a data analysis tool designed for processing and visualizing data from Roche NimbleGen microarray experiments. The software provides functionalities for importing, normalizing, and analyzing microarray data, as well as generating interactive visualizations of the results.

Automatically generated - may contain errors

Lab products found in correlation

Nimblegen human cgh 12 135 k whole genome tiling v3.1 array, by Agilent Technologies (1 mentions) Cgh explorer v2, by Roche (1 mentions) Accuprep genomic dna extraction kit, by Bioneer (1 mentions) Nimblescan v2, by Roche (1 mentions) Nimblescan software, by Roche (1 mentions)

4 protocols using nimblegen signalmap software

Genome-wide Copy Number Variation Analysis

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

Human fibroblast GM00637 cells were stably transfected with control or ID3 shRNA, and genomic DNA was isolated using AccuPrep® Genomic DNA Extraction kit (Bioneer) according to the manufacturer’s instructions. Array CGH analysis was performed using the NimbleGen Human CGH 12 × 135 K whole-genome tiling v3.1 Array (Agilent Technologies). Human genomic DNA (1 μg) from ID3-depleted cells and reference DNA samples from control cells were independently labeled with fluorescent dyes (Cy3/Cy5), co-hybridized at 65 °C for 24 h, and then subjected to the array. The hybridized array was scanned using NimbleGen’s MS200 scanner (NimbleGen systems Inc.) with 2 μm resolution. Log2-ratio values of the probe signal intensities were calculated and plotted vs. genomic position using Roche NimbleGen’s NimbleScan v2.5 software. Data are displayed and analyzed in Roche NimbleGen SignalMap software and CGH-explorer v2.55.

Lee J.H., Park S.J., Hariharasudhan G., Kim M.J., Jung S.M., Jeong S.Y., Chang I.Y., Kim C., Kim E., Yu J., Bae S, & You H.J. (2017). ID3 regulates the MDC1-mediated DNA damage response in order to maintain genome stability. Nature Communications, 8, 903.

+ Open protocol

+ Expand

Colorectal Adenocarcinoma Genome Profiling

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

DNA from 24 fresh tissue specimens of colorectal adenocarcinomas was analyzed versus reference DNA. Test and reference gDNAs were independently labeled with fluorescent dyes, co-hybridized to a NimbleGen Human CGH 135K Whole-Genome Tiling array (Roche NimbleGen Inc, Madison, WI, USA), and scanned using a 2 µm scanner. Log2-ratio values of the probe signal intensities (Cy3/Cy5) were calculated and plotted versus genomic position using Roche NimbleGen NimbleScan software. Data are displayed in Roche NimbleGen SignalMap software.

Koh H.M., Jang B.G., Hyun C.L., Kim Y.S., Hyun J.W., Chang W.Y, & Maeng Y.H. (2016). Aurora Kinase A Is a Prognostic Marker in Colorectal Adenocarcinoma. Journal of Pathology and Translational Medicine, 51(1), 32-39.

+ Open protocol

+ Expand

Copy Number Variation Analysis by CGH

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

CGH was performed on test DNA (affected male, IV17) and reference DNA (unaffected male, IV10) for the determination of copy number variants (Macrogen Inc., Seoul, Korea). DNAs were independently labelled with fluorescent dyes, co-hybridized to a NimbleGen Human CGH 385K chromosome X Tiling array, and scanned using a 2-μm scanner. Log2-ratio values of the probe signal intensities (Cy3/Cy5) were calculated and plotted versus genomic position using Roche NimbleGen NimbleScan software. Data are displayed in Roche NimbleGen SignalMap software. CGH did not show any imbalances in the critical region.

Lindert U., Cabral W.A., Ausavarat S., Tongkobpetch S., Ludin K., Barnes A.M., Yeetong P., Weis M., Krabichler B., Srichomthong C., Makareeva E.N., Janecke A.R., Leikin S., Röthlisberger B., Rohrbach M., Kennerknecht I., Eyre D.R., Suphapeetiporn K., Giunta C., Marini J.C, & Shotelersuk V. (2016). MBTPS2 mutations cause defective regulated intramembrane proteolysis in X-linked osteogenesis imperfecta. Nature Communications, 7, 11920.

+ Open protocol

+ Expand

Genome-Wide Array CGH Profiling

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

Array-based comparative genomic hybridization (array CGH) was carried out using the Roche NimbleGen Genome-Wide array CGH 3*720K containing over 720,000 copy-number probes. Genomic DNA samples were genotyped at the CapitalBio Corporation (Beijing, China) with the CGH array in accordance with the manufacturer’s protocols. Genotype calling, genotyping quality control, and copy number variation (CNV) identification were performed with the Roche NimbleGen SignalMap software. The data accessed at Gene Expression Omnibus (GEO, No: GSE55181).

Dai L., Liu D., Song M., Xu X., Xiong G., Yang K., Zhang K., Meng H., Guo H, & Bai Y. (2014). Mutations in the Homeodomain of HOXD13 Cause Syndactyly Type 1-c in Two Chinese Families. PLoS ONE, 9(5), e96192.

+ 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!