clc dna workbench software version 5.7.1  (CLC Bio)

Journal: Molecular Cytogenetics

Article Title: CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

doi: 10.1186/1755-8166-5-10

Figure Lengend Snippet: Examples of array CGH . A. Images produced using DNA extracted from bone marrow (BM) refrigerated for 1 day (diagnosis specimen of SVH05 ), 27 days (AML specimen from ) and 36 days. B. Images produced from fixed cytogenetic preparations (CHR) stored at -80°C for one year and 8 years. All of these 20q deletions were validated with the 20q12 Vysis probe, LSI D20S108 (20q12) SpectrumOrange. A 2 Mb moving average line is shown for each experiment. Each image represents duplicate experiments except for the 27 day old bone marrow, which represents one experiment. The catalog 60K array used for the BM 27 day result which has a median probe spacing of 41 kb and the other results are from a Agilent 44K custom array with probes 200 bp (20q11.21- > 20q11.22), 5 kb (20q11.22- > 20q12) and 9 kb (20p and 20q13- > 20qter) apart.

Article Snippet: The DNA Workbench software for Agilent array CGH has inbuilt Quality Control (QC) metrics.

Techniques: Produced

Journal: Molecular Cytogenetics

Article Title: CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

doi: 10.1186/1755-8166-5-10

Figure Lengend Snippet: A comparison of array CGH and SNP array results for chromosome 20 from 26 day old bone marrow . Bone marrow was refrigerated for 26 days before DNA extraction. Deletion, gain or amplification of different regions of 20q, and low level gain of 20p have been extensively validated by single locus FISH, G-banding, M-BAND and M-FISH (Case SVH01, ). Duplicate experiments were performed, and two 0.2 Mb moving average lines are shown for the array CGH specimen to show the peaks of localized amplification. The probes in the custom Agilent array are spaced between 200 bp and 9 kb apart (see Figure ) and the Illumina CytoSNP 12 array probes have a median spacing of 6.1 kb.

Article Snippet: The DNA Workbench software for Agilent array CGH has inbuilt Quality Control (QC) metrics.

Techniques: DNA Extraction, Amplification

Journal: Molecular Cytogenetics

Article Title: CGH and SNP array using DNA extracted from fixed cytogenetic preparations and long-term refrigerated bone marrow specimens

doi: 10.1186/1755-8166-5-10

Figure Lengend Snippet: A comparison of SNP array results for chromosome 2 using DNA from fresh and fixed cells . A. A comparison of SNP array results from fresh (left) and fixed (right) U937 cell line. Gain of a section of the long arm (brackets a, b) is denoted by a single vertical green bar for the fixed specimen (Found Reg = Found Region) (b) whereas in the fresh specimen (a) this is divided into two separate sections. This is representative of the minor boundary differences determined by the Karyostudio software, between the two experiments. B. The M-BAND pattern for chromosome 2. The idiograms below the banded chromosomes show the section of chromosome 2 present in each chromosome. The green bar represents the homolog from one parent and the blue bars represent the homolog from the other parent (inferred from B allele frequencies, see Methods). The Illumina CytoSNP 12 array probes have a median spacing of 6.1 kb.

Article Snippet: The DNA Workbench software for Agilent array CGH has inbuilt Quality Control (QC) metrics.

Techniques: Software