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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Oct 20, 2023 |
| Title |
txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We develop a large-scale single-cell ATAC-seq method by combining Tn5-based pre-indexing with 10X Genomics barcoding, enabling the indexing of up to 200,000 nuclei across multiple samples in a single reaction. We profile 449,953 nuclei across diverse tissues, including the human cortex, mouse brain, human lung, mouse lung, mouse liver, and lung tissue from a club cell secretory protein knockout (CC16-/-) model. Our study of CC16-/- nuclei uncovers previously underappreciated technical artifacts derived from remnant 129 mouse strain genetic material, which cause profound cell-type-specific changes in regulatory elements near many genes, thereby confounding the interpretation of this commonly referenced mouse model.
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| Overall design |
txci-ATAC-seq using brain tissue samples using replicates of Human Cortex and Mouse whole brain tissue loaded at ~20k and ~70k cells. Human raw data will be made available through the NeMO Archive.
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| Contributor(s) |
Zhang H, Mulqueen R, Iannuzo N, Farrera D, Polverino F, Galligan J, Ledford J, Adey A, Cusanovich D |
| Citation(s) |
38519979 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R35 GM124704 |
Defining the epigenetic landscape at single cell resolution |
OREGON HEALTH & SCIENCE UNIVERSITY |
Andrew Adey |
| RF1 MH128842 |
High-content single-cell epigenetic technologies scalable to the human brain |
OREGON HEALTH & SCIENCE UNIVERSITY |
Andrew Adey |
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| Submission date |
Oct 20, 2023 |
| Last update date |
Apr 02, 2024 |
| Contact name |
Ryan Mulqueen Mulqueen |
| E-mail(s) |
RMulqueen@mdanderson.org
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| Phone |
6319883467
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| Organization name |
Oregon Health and Science
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| Department |
Molecular and Medical Genetics
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| Lab |
Andrew Adey
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| Street address |
3181 S.W. Sam Jackson Park Road
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| City |
Portland |
| State/province |
OR |
| ZIP/Postal code |
97239-3098 |
| Country |
USA |
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| Platforms (2) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA1030440 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE245957_RAW.tar |
55.3 Gb |
(http)(custom) |
TAR (of RDS, TBI, TSV, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
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