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Series GSE215901 Query DataSets for GSE215901
Status Public on Apr 14, 2024
Title SPATAC-seq: split-pool ligation-based single cell ATAC-seq method
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary To establish an ultra-high-throughput single cell chromatin accessibility profiling method that is cost-effective and widely accessible, we built on sci-ATAC-seq (Cusanovich, D. A. et al. Science. 2015; Amini, S. et al. Nature Genetics. 2014) and SPLIT-seq (Rosenberg, A. B. et al. Science. 2018) to design SPATAC-seq, which in situ label chromatin fragment in the same single cell through combinatorial barcoding. Briefly, in SPATAC-seq, (1) fixed nuclei are transposed in 48 different wells by 48 unique Tn5 transposase, which containing barcoded adaptors and 5'-phosphorylation; (2) the nuclei from all wells are collected and redistributed into second and third 48-well plate in turn, where the next two rounds of indexing are achieved through into either end of the custom transposome, which result in the generation of more than 110,000 (48^3) unique barcode combinations. (3) the nuclei are pooled, split into sublibraries and lysed, and the DNA was amplified by polymerase chain reaction (PCR), which introduce illumina sequencing barcodes and complete libraries construction. (4) After sequencing, fastq files were demultiplexed according to the same four-barcode combinations. For profiling more cells in one sublibrary, we can increase the number of barcode combinations by increase the number of indexing of each round to 96, which can produce about 1 million combinations. To assess the fidelity of SPATAC-seq, we performed a species-mixing experiment with cultured human (K562) and mouse (Hepa) cells. Here, we tagged mixed permeabilized nuclei with only 8 barcoded transposome. In round 4, we generated eight sublibraries with different cell-recovery targets, which can be used to evaluating the stability of this method and the correlation between real doublet rates and theoretical value.
Overall design We firstly assembled 48 indexed Tn5 transposome complexes, and then performed a species-mixing experiment with cultured human (K562) and mouse (Hepa) cells to prove the feasibility of SPATAC-seq. Here, we tagged mixed permeabilized nuclei with only 8 barcoded transposome, and generated eight sublibraries with different cell-recovery targets.
Web link
Contributor(s) Sun K, Lan X
Citation(s) 38977847
Submission date Oct 17, 2022
Last update date Jul 14, 2024
Contact name Keyong Sun
Organization name tsinghua university
Department School of Medicine
Street address Hai Dian street
City beijing
ZIP/Postal code 100084
Country China
Platforms (2)
GPL25526 Illumina NovaSeq 6000 (Homo sapiens; Mus musculus)
GPL26363 HiSeq X Ten (Homo sapiens; Mus musculus)
Samples (8)
GSM6645255 Sublibraries-1 of species-mixing experiment using SPATAC
GSM6645256 Sublibraries-2 of species-mixing experiment using SPATAC
GSM6645257 Sublibraries-3 of species-mixing experiment using SPATAC
BioProject PRJNA891243

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Supplementary file Size Download File type/resource
GSE215901_RAW.tar 892.3 Mb (http)(custom) TAR (of CSV, TSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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