Log In Sign up
The largest database of trusted experimental protocols

Genemaker software v2

Manufactured by SoftGenetics
Visit Supplier

GeneMaker software v2.4.0 is a bioinformatics tool designed for genetic analysis and sequence editing. The software provides a suite of features for tasks such as DNA/RNA sequence manipulation, primer design, and sequence alignment.

Automatically generated - may contain errors

Lab products found in correlation

Flexigene kit, by Qiagen (2 mentions) Genescan 600 liz size standard, by Thermo Fisher Scientific (2 mentions) Abi prism 3130xl genetic analyzer, by Thermo Fisher Scientific (2 mentions) P388 a2 salsa mlpa kit, by MRC-Holland (2 mentions)

2 protocols using genemaker software v2

1

RNASEH2B Gene Deletion Detection in CLL

Check if the same lab product or an alternative is used in the 5 most similar protocols
Genomic DNA was isolated from primary CLL cells using the Flexigene kit (Qiagen). To identify deletions in RNASEH2B gene the MLPA assay was performed on approximately 100 ng of genomic DNA (gDNA) per sample using the P388-A2 SALSA MLPA kit (MRC-Holland) according to the manufacturer’s protocol. 2 µl of amplified products were separated by capillary electrophoresis on an ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems) with a GeneScan 600 LIZ Size Standard (Thermo Fisher). Data were analyzed using GeneMaker software v2.4.0 (SoftGenetics). Data were normalized using gDNA from 4 control reference samples. Copy number changes represented as a MLPA ratio were detected by comparing normalized peak intensities between the reference and the CLL samples. The MPLA ratio thresholds (X) were set as follows: 0.75 ≥ X ≤ 1.25, diploid sample; 0.4 ≥ X < 0.75, monoallelic deletion; X < 0.4, biallelic deletion. Samples showing either a standard deviation (SD) of control probes above 0.15, or samples with large Q fragment peaks and with more than 4 control probes having MLPA ratios out of diploid range were excluded from the analysis.
Zimmermann M., Murina O., Reijns M.A., Agathanggelou A., Challis R., Tarnauskaitė Ž., Muir M., Fluteau A., Aregger M., McEwan A., Yuan W., Clarke M., Lambros M.B., Paneesha S., Moss P., Chandrashekhar M., Angers S., Moffat J., Brunton V.G., Hart T., de Bono J., Stankovic T., Jackson A.P, & Durocher D. (2018). CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Nature, 559(7713), 285-289.
+ Open protocol
+ Expand
2

RNASEH2B Gene Deletion Detection in CLL

Check if the same lab product or an alternative is used in the 5 most similar protocols
Genomic DNA was isolated from primary CLL cells using the Flexigene kit (Qiagen). To identify deletions in RNASEH2B gene the MLPA assay was performed on approximately 100 ng of genomic DNA (gDNA) per sample using the P388-A2 SALSA MLPA kit (MRC-Holland) according to the manufacturer’s protocol. 2 µl of amplified products were separated by capillary electrophoresis on an ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems) with a GeneScan 600 LIZ Size Standard (Thermo Fisher). Data were analyzed using GeneMaker software v2.4.0 (SoftGenetics). Data were normalized using gDNA from 4 control reference samples. Copy number changes represented as a MLPA ratio were detected by comparing normalized peak intensities between the reference and the CLL samples. The MPLA ratio thresholds (X) were set as follows: 0.75 ≥ X ≤ 1.25, diploid sample; 0.4 ≥ X < 0.75, monoallelic deletion; X < 0.4, biallelic deletion. Samples showing either a standard deviation (SD) of control probes above 0.15, or samples with large Q fragment peaks and with more than 4 control probes having MLPA ratios out of diploid range were excluded from the analysis.
Zimmermann M., Murina O., Reijns M.A., Agathanggelou A., Challis R., Tarnauskaitė Ž., Muir M., Fluteau A., Aregger M., McEwan A., Yuan W., Clarke M., Lambros M.B., Paneesha S., Moss P., Chandrashekhar M., Angers S., Moffat J., Brunton V.G., Hart T., de Bono J., Stankovic T., Jackson A.P, & Durocher D. (2018). CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions. Nature, 559(7713), 285-289.
+ 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?

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!