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Sample GSM7503661 Query DataSets for GSM7503661
Status Public on Jun 22, 2023
Title HFF PLEKHA1 transfected CGH bulk
Sample type genomic
 
Channel 1
Source name CGH PLEKHA1
Organism Homo sapiens
Characteristics cell line: HFF
Treatment protocol HFF cells were transfected with 16.9 μg Cas9 RNP and 5 μM of Alt-R® Cas9 Electroporation Enhancer by electroporation using the AMAXA™ 4D-499 Nucleofector™ device (Lonza®, Bale, Switzerland) with P3 Primary Cell Line and CZ-167
Growth protocol HFF cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM with glucose (4.5 g.L-473 1), L-Glutamine (1 g.L-1) and pyruvate supplemented with 20% fetal bovine serum, MEM non-essential 474 amino acids 100X (Gibco® by ThermoFisher scientific, Carlsabad, CA, USA), 100 U/mL penicillin, and 475 100μg/mL streptomycin (all from Eurobio, Courtaboeuf, France)
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from cultivated cells using the Wizard manual kit (Promega Corporation, Madison, USA).
Label Cy5
Label protocol DNA (minimum 125ng) was labeled (cyanine 3 or cyanine 5) using the Genomic DNA ULS Labeling Kit from Agilent Technologies (Agilent Technologies, Santa Clara, USA)
 
Channel 2
Source name A1-HFF WT Clone 6
Organism Homo sapiens
Characteristics cell line: HFF
Treatment protocol HFF cells were transfected with 16.9 μg Cas9 RNP and 5 μM of Alt-R® Cas9 Electroporation Enhancer by electroporation using the AMAXA™ 4D-499 Nucleofector™ device (Lonza®, Bale, Switzerland) with P3 Primary Cell Line and CZ-167
Growth protocol HFF cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM with glucose (4.5 g.L-473 1), L-Glutamine (1 g.L-1) and pyruvate supplemented with 20% fetal bovine serum, MEM non-essential 474 amino acids 100X (Gibco® by ThermoFisher scientific, Carlsabad, CA, USA), 100 U/mL penicillin, and 475 100μg/mL streptomycin (all from Eurobio, Courtaboeuf, France)
Extracted molecule genomic DNA
Extraction protocol DNA was extracted from cultivated cells using the Wizard manual kit (Promega Corporation, Madison, USA).
Label Cy3
Label protocol DNA (minimum 125ng) was labeled (cyanine 3 or cyanine 5) using the Genomic DNA ULS Labeling Kit from Agilent Technologies (Agilent Technologies, Santa Clara, USA)
 
 
Hybridization protocol Labeled DNAs were hybridized onto Agilent oligonucleotide microarrays (8x60K Agilent Genetisure) according to the manufacturer’s instructions (Agilent Technologies)
Scan protocol Scanning of the microarrays was performed using a G5761A scanner (Agilent Technologies).
Description Test 5
Agilent 60K CGH 021924
Data processing Data analysis was carried out with Agilent Technologies software, namely Feature Extraction for Cytogenomics Algorithm v5.0 for the fluorescence ratio calculation and Agilent CytoGenomics v5.2 for the localization of chromosomal imbalances.
Deletions and duplications in the heterozygous state were characterized by values of the log2 ratio of fluorescence intensities (cyanine5/cyanine3) below -0.5 and above +0.3, respectively, with the statistical algorithm ADM2 used at a threshold of five.
 
Submission date Jun 21, 2023
Last update date Jun 22, 2023
Contact name Julian Boutin
E-mail(s) julian.boutin@u-bordeaux.fr
Organization name INSERM U1312 BRIC
Lab BioGO team 8
Street address 146 rue Leo Saignat
City Bordeaux
State/province Nouvelle Aquitaine
ZIP/Postal code 33000
Country France
 
Platform ID GPL17052
Series (1)
GSE235487 Human HFF cells large rearrangements detection after CRISPR-Cas9 nuclease (Fig. 4C)

Supplementary file Size Download File type/resource
GSM7503661_F_PLE_SG20139159_258559012304_S001_CytoCGH_0500_8x_Nov17_2_2.txt.gz 6.4 Mb (ftp)(http) TXT
Processed data are available on Series record

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