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Series GSE204691 Query DataSets for GSE204691
Status Public on Jul 04, 2023
Title Droplet-based bisulfite sequencing for high-throughput profiling of single-cell DNA methylomes
Organisms Homo sapiens; Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Summary We present a high-throughput and droplet-based bisulfite sequencing library preparation platform. Our protocol allows production of BS library of 2,000-10,000 single cells within 2 days. In addition to validation using mixed cell lines, we also used the technology to profile various cell types in mouse and human brain samples.
Overall design We used our developed Drop-BS platform to profile single-cell methylomes on one human-mouse mixed sample, four cell line samples, one mouse brain PFC sample, and two human brain PFC samples. In the “Human_mouse_species_mixing”, we mixed equal amounts of GM12878 nuclei and mouse brain nuclei as the input nuclei to prepare a sequencing library using Drop-BS. We used GM12878 cell line, HEK293 cell line, MCF7 cell line separately to prepare three cell line Drop-BS samples. The Drop-BS library of “Three_cell_lines_mixing” was prepared using a mixture of the three with equal portions. We extracted nuclei from mouse, the first human brain PFC tissue, and the second human brain PFC tissue to prepare the “Mouse_brain” library, “Human_brain” library, and “Human_brain2” library respectively.

>>> Submitter states that raw data for the Human_brain sample will be submitted to dbGaP due to patient privacy concerns.<<<
Contributor(s) Zhang Q, Lu C
Citation(s) 37537185
Submission date May 24, 2022
Last update date Sep 24, 2023
Contact name Chang Lu
Phone 5402318681
Organization name Virginia Tech
Department Chemical Engineering
Lab Chang Lu
Street address 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech
City Blacksburg
State/province VA
ZIP/Postal code 24061
Country USA
Platforms (3)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
GPL26363 HiSeq X Ten (Homo sapiens; Mus musculus)
Samples (8)
GSM6185938 Human_mouse_species_mixing
GSM6185939 GM12878
GSM6185940 HEK293
BioProject PRJNA841973

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
GSE204691_RAW.tar 7.4 Gb (http)(custom) TAR (of TAR)
Raw data are available in SRA
Processed data provided as supplementary file

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