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SRX21897921: GSM7807646: RPMA ONB tumor rep1; Mus musculus; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 364.5M spots, 50.3G bases, 15.6Gb downloads

External Id: GSM7807646_r1
Submitted by: theoliverlab, Pharmacology & Cancer Biology, Duke University
Study: Olfactory neuroblastoma mimics molecular subtypes and lineage trajectories of small cell lung cancer [Single cell RNA seq on RPM-GFP and RPMA ONB tumors]
show Abstracthide Abstract
The olfactory epithelium relies on active neuron regeneration from basal stem cells and is susceptible to olfactory neuroblastoma (ONB), a rare, aggressive tumor of unclear origins. Here, we establish a new, highly-penetrant, genetically-engineered mouse model of ONB with alterations in Rb1/Trp53/Myc that exhibit a NEUROD1+ immature neuronal state. ASCL1 loss leads to emergence of non-neuronal histopathologies, including a POU2F3+ microvillar-like state. We find ONB tumor heterogeneity to recapitulate developmental states of multipotent globose basal cells (GBCs), which our data demonstrate is a cell of origin for ONB. Similar to small cell lung cancer (SCLC), mouse and human ONB exhibit: mutually exclusive ASCL1, NEUROD1, and POU2F3- like states, an immune-cold tumor microenvironment, intratumoral subtype heterogeneity comprising neuronal and non-neuronal lineages, and subtype plasticity—as evidenced by barcode-based lineage tracing and single-cell transcriptomics. Collectively, our findings highlight conserved developmental trajectories between ONB and SCLC subtypes with significant implications for ONB classification and treatment. Overall design: We harvested olfactory neuroblastoma tumor cells from n=1 homozygous Rb1 fl/fl; Trp53 fl/fl; H11b-LSL-MycT58A-Ires-Luc (RPM)-Rosa26-LSL-Cas9-Ires-Gfp (RPM-GFP) mouse in which tumor cells are GFP+, and n=3 homozygous Rb1 fl/fl; Trp53 fl/fl; H11b-LSL-MycT58A-Ires-Luc; Ascl1 fl/fl (RPMA) to perform single cell RNA-sequencing (scRNA-seq). Tumors were micro-dissected from the olfactory cavity of each mouse, processed into single cell suspensions, and subject to 10X Genomics single-cell gene expression library construction (Dual-Index 3' GEX) and downstream Illumina-based sequencing.
Sample: RPMA ONB tumor rep1
SAMN37549891 • SRS18985144 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7807646
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC SINGLE CELL
Selection: cDNA
Layout: PAIRED
Construction protocol: Each tumor sample was subject to enzymatic/mechanical digestion into a single cell suspension. 10x Genomics gel beads and reverse transcription reagents were added to cell suspensions and loaded to a chromium single cell controller to form gel-bead-in emulsions (GEMs). From GEMs, cDNA was generated from barcoded mRNA and subsequent A tailing, end repair, adaptor ligation, and sample indexing was performed according to manufacturer. Libraries were assessed on Agilent D5000 ScreenTape on an Agilent Tech 2200 tapestation system and quantified by Kapa Biosystems Library Quantification Kit for Illumina Platforms. Libraries were sequenced on the Novaseq 6000 w 2x150 paired end seq targeting ~30k reads/cell. 10X Genomics Single-Cell 3' RNA Dual Index v3
Runs: 1 run, 364.5M spots, 50.3G bases, 15.6Gb
Run# of Spots# of BasesSizePublished
SRR26186081364,490,75350.3G15.6Gb2024-05-15

ID:
29793101

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