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Series GSE134812 Query DataSets for GSE134812
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
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.
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.
Contributor(s) LaFave LM, Kartha VK, Ma S
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Submission date Jul 24, 2019
Last update date Jul 23, 2020
Contact name Lindsay M LaFave
Organization name MIT
Department Biology
Lab Dr. Tyler Jacks
Street address 77 Massachusetts Avenue; 76-453
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (8)
GSM3972129 T-M5, M-M5
GSM3972130 3T3 and GM12878 mix
GSM3972131 Normal-1, Normal-2, T-M1Pool, T-M1T1, T-M1T2, T-M1T3, T-M1T4, and M-M1N1
This SubSeries is part of SuperSeries:
GSE145194 Single-cell epigenomics identifies a premetastatic regulatory program in lung adenocarcinoma
BioProject PRJNA556490
SRA SRP216280

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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
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