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Series GSE239290 Query DataSets for GSE239290
Status Public on Feb 27, 2024
Title Optimizing the experimental and computational methods for Infinium DNA methylation BeadChip on low input and single cells
Organism Mus musculus
Experiment type Methylation profiling by genome tiling array
Summary In this study, the Infinium BeadChip DNA methylome profiling technology was optimized for suboptimal input DNA conditions, including ultra-low input down to single cells. We acquired knowledge on the boundaries and limits of the Infinium DNA methylation BeadChips with suboptimal input DNA. These findings offer comprehensive solutions to expand the application of this technology to cases with limited DNA.
 
Overall design We tested multiple worflows using cell line (NIH3T3, B16-F0 and PGCs) DNA and evaluate performance at low input ranges
 
Contributor(s) Lee S, Zhou W
Citation(s) 38407446
NIH grant(s)
Grant ID Grant title Affiliation Name
R35 GM146978 Decoding Single-cell DNA Methylomes for Epigenetic Cell Identity CHILDREN'S HOSPITAL OF PHILADELPHIA Wanding Zhou
Submission date Jul 26, 2023
Last update date Feb 28, 2024
Contact name Wanding Zhou
E-mail(s) ZHOUW3@chop.edu
Organization name Children's Hospital of Philadelphia
Department Pathology & Lab Medicine
Lab Zhou Lab
Street address 3501 Civic Center Blvd, Philadelphia, PA 19104, Colket Translational Research Building, 9300, Colket Translational Research Building
City Phialdelphia
State/province Pennsylvania
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL30650 Infinium Mouse Methylation BeadChip
Samples (146)
GSM7662741 NIH3T3_EZkit_50ng_WorkflowC_03
GSM7662742 NIH3T3_EZkit_1ng_WorkflowC_03
GSM7662743 NIH3T3_EZkit_0.5ng_WorkflowC_03
Relations
BioProject PRJNA998765

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE239290_20230725_GEO_processed_matrix_GPL30650.csv.gz 606.9 Mb (ftp)(http) CSV
GSE239290_20230725_GEO_signal_intensity_matrix_GPL30650.csv.gz 964.9 Mb (ftp)(http) CSV
GSE239290_20240207_GEO_processed_matrix_GPL30650.csv.gz 17.3 Mb (ftp)(http) CSV
GSE239290_20240207_GEO_signal_intensity_matrix_GPL30650.csv.gz 17.7 Mb (ftp)(http) CSV
GSE239290_RAW.tar 731.5 Mb (http)(custom) TAR (of IDAT)
Processed data are available on Series record
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