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Series GSE117529 Query DataSets for GSE117529
Status Public on Jun 14, 2021
Title RNA/WES/ATAC/scRNA sequencing of murine melanoma primary and LN metastases
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary The purpose of this study is to identify transcriptional, mutational, andepigenetic differences between LN metastases from primary tumors. Using in vivo serial passaging of the minimally metastatic syngeneic murine melanoma cell line B16-F0, we have generated nearly 300 unique cell lines spanning nine generations of in vivo passaging, derived from LNs, and exhibiting varying degrees of metastatic potential to LNs. Here, we perform mRNAseq on 30 of the lines representing a range of anatomical locations (distinct LNs), generations, and phylogenetic lineages. The subsequent differential expression analysis reveals a marked upregulation of immune-related genes. Additionally, we perform WES to identify differences in particular mutations, total mutational burden, and predicted neoantigen burden. Additionally, we perform ATAC-seq to assess changes in chromatin accessibility hat correlate with LN metastasis. We also perform scRNA-seq on dissociated LNs from mice with and without LN metastases.
Overall design mRNA profiles were generated from 30 cell lines derived from the various LN lines and parental. The parental was sequenced in triplicate where each replicate was harvested at distinct passage numbers to account for variability in the profile due to culture. Samples were sequenced on an Illumina HiSeq 2500 to a depth of 50M reads. Following quality filtering, transcript abundance was quantified using Salmon and differential gene expression analysis was performed using DESeq2. LN lines from later generations were compared to the parental or early generation lines.

For WES, 10 cell lines were analyzed. These data are accessible directly from SRA at Accession PRJNA820881.
For ATAC-seq, 3 samples each from parental, LN3, and LN7 generations were analyzed.
For scRNAseq, a LN from tumor naive, parental (non-metastatic) tumor, and LN6 (LN-metastatic) tumor mice each were analyzed.
Contributor(s) Reticker-Flynn NE, Engleman EG
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NIH grant(s)
Grant ID Grant title Affiliation Name
F32 CA189408 Development of a glycopeptide vaccine for cancer metastasis STANFORD UNIVERSITY Nathan Edward Reticker-Flynn
R01 CA251174 Targeting Lymph Node Dependent Immune Tolerance in Cancer STANFORD UNIVERSITY EDGAR G. ENGLEMAN
U54 CA209971 Spatial-Genomic Integrative Multi-Species Analysis of Lymph Node Metastasis STANFORD UNIVERSITY SYLVIA KATINA PLEVRITIS
Submission date Jul 23, 2018
Last update date Apr 22, 2022
Contact name Nathan Edward Reticker-Flynn
Organization name Stanford University
Department Pathology
Lab Engleman Lab
Street address 3373 Hillview Ave
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (58)
GSM3302492 B16-F0 #1
GSM3302493 B16-F0 #2
GSM3302494 B16-F0 #3
BioProject PRJNA482417
SRA SRP154917

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE117529_RAW.tar 4.9 Gb (http)(custom) TAR (of BW, MTX, TSV)
GSE117529_Reticker-Flynn_GEOExport_TPM.txt.gz 4.1 Mb (ftp)(http) TXT
GSE117529_RetickerFlynn_GEO_IFN_TPM.txt.gz 1.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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