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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 11, 2023 |
| Title |
Single-cell co-profiling of gene expression and chromatin accessibility in the mice striatum with varied genetic backgrounds |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
To investigate the influence of genetic background and sex on addiction, we conducted a study on the striatum of mice, a crucial brain structure linked to various substance abuse disorders, at the single-cell level. We utilized single-cell multi-omics technology to analyze the gene expression and chromatin accessibility of individual cells in the mice striatum.
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| Overall design |
Mouse striatum were from 8 inbred strains: A/J, C57BL/6J, 129S1/SvImJ, NOD/ShiLtJ, NZO/H1LtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ. A total of 32 striatum samples were divided in 4 batches, with each batch consisting of 4 male and 4 female samples, and each strain represented in each batch.
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| Contributor(s) |
Zuo W, Spruce C, Poirion O, White B, Baker C |
| Citation(s) |
39223609 |
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| Submission date |
Mar 29, 2023 |
| Last update date |
Oct 01, 2024 |
| Contact name |
Christopher Lee Baker |
| E-mail(s) |
christopher.baker@jax.org
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| Phone |
2072886365
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| Organization name |
The Jackson Laboratory
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| Department |
Research
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| Street address |
600 Main Street
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| City |
Bar Harbor |
| State/province |
ME |
| ZIP/Postal code |
04609 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (8)
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| GSM7123489 |
Striatum, batch 1, single-cell multi-omics [scRNA-seq] |
| GSM7123490 |
Striatum, batch 1, single-cell multi-omics [scATAC-seq] |
| GSM7123491 |
Striatum, batch 2, single-cell multi-omics [scRNA-seq] |
| GSM7123492 |
Striatum, batch 2, single-cell multi-omics [scATAC-seq] |
| GSM7123493 |
Striatum, batch 3, single-cell multi-omics [scRNA-seq] |
| GSM7123494 |
Striatum, batch 3, single-cell multi-omics [scATAC-seq] |
| GSM7123495 |
Striatum, batch 4, single-cell multi-omics [scRNA-seq] |
| GSM7123496 |
Striatum, batch 4, single-cell multi-omics [scATAC-seq] |
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| Relations |
| BioProject |
PRJNA950125 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE228530_RAW.tar |
220.4 Mb |
(http)(custom) |
TAR (of CSV) |
| GSE228530_metadata.csv.gz |
908.7 Kb |
(ftp)(http) |
CSV |
| GSE228530_processed_data_file_descriptions.txt.gz |
571 b |
(ftp)(http) |
TXT |
| GSE228530_tmp.repl1_atac.all.v2.all_peaks.npz |
1.1 Gb |
(ftp)(http) |
NPZ |
| GSE228530_tmp.repl1_atac.all.v2.xgi.txt.gz |
331.4 Kb |
(ftp)(http) |
TXT |
| GSE228530_tmp.repl1_atac.all.v2_peaks.all.ygi.txt.gz |
2.3 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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