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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 23, 2020 |
| Title |
Single-cell epigenomics identifies a premetastatic regulatory program in lung adenocarcinoma [sciATAC-seq] |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Here we use an improved single-cell chromatin profiling approach to determine epigenomic alterations across tumor progression in a mouse model of lung adenocarcinoma (LUAD). Specifically, we induced tumors by providing Adeno-SPC-Cre virus to mice intratracheally to induce tumors due to conditional expression the Kras G12D mutation and loss of p53 (termed the KPT model). Mice also expressed a tdTomato reporter allele allowing for the sorting of tumor cells in late-stages of tumor progression. Using a combinatorial indexing approach (sciATAC-seq), we identify an epigenomic continuum representing a loss of cellular identity and progression towards a metastatic state.
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| Overall design |
sciATAC-Sequencing profiles of normal lung and lung adenocarcinoma murine samples. We profiled 44 individual samples including 2 normal murine lungs, 1 CD45 depleted murine lungs, and 44 tdTom sorted KPT lung primary lung and metastatic samples. Species mixing experiments were also completed with GM12878 and 3T3 cell lines.
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| Contributor(s) |
LaFave LM, Kartha VK, Ma S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 24, 2019 |
| Last update date |
Jul 23, 2020 |
| Contact name |
Lindsay M LaFave |
| E-mail(s) |
lmlafave@mit.edu
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| Organization name |
MIT
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| Department |
Biology
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| Lab |
Dr. Tyler Jacks
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| Street address |
77 Massachusetts Avenue; 76-453
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
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| Samples (8)
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| GSM3972132 |
T-M4 |
| GSM3972133 |
T-M2, T-M2Pool, T-M2T1, T-M2T2, T-M2T3, T-M3, T-M3Pool, T-M3T1, T-M3T2, T-M3T3 |
| GSM3972134 |
Normal-CD45neg |
| GSM4677544 |
T-M6T2, T-M7Pool, T-M7T1, T-M7T2, T-M7T3, T-M7T4, M-M13N1, M-M12N1, M-M12N2, M-M13N1, M-M12N1, M-M12N2 |
| GSM4677545 |
M-M11N2, M-M8N1, M-M10N1, M-M11N1, M-M12, M-M10N3, M-M11N3, M-M9N1, M-M9N2, M-M9N3, M-M10N2, M-M10N4, M-M10N5 |
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| This SubSeries is part of SuperSeries: |
| GSE145194 |
Single-cell epigenomics identifies a premetastatic regulatory program in lung adenocarcinoma |
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| Relations |
| BioProject |
PRJNA556490 |
| SRA |
SRP216280 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE134812_scATACseq_3t3_p1_counts.txt.gz |
14.4 Mb |
(ftp)(http) |
TXT |
| GSE134812_scATACseq_3t3_p1_peaks.bed.gz |
874.2 Kb |
(ftp)(http) |
BED |
| GSE134812_scATACseq_GM12878_counts.txt.gz |
7.8 Mb |
(ftp)(http) |
TXT |
| GSE134812_scATACseq_GM12878_peaks.bed.gz |
3.8 Mb |
(ftp)(http) |
BED |
| GSE134812_scATACseq_colData.txt.gz |
198.4 Kb |
(ftp)(http) |
TXT |
| GSE134812_scATACseq_mouse_lung_counts.txt.gz |
447.5 Mb |
(ftp)(http) |
TXT |
| GSE134812_scATACseq_mouse_lung_peaks.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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