SCPortalen


Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells.


Intra-tumoral genetic and functional heterogeneity correlates with cancer clinical prognoses. However, the mechanisms by which intra-tumoral heterogeneity impacts therapeutic outcome remain poorly understood. RNA sequencing (RNA-seq) of single tumor cells can provide comprehensive information about gene expression and single-nucleotide variations in individual tumor cells, which may allow for the translation of heterogeneous tumor cell functional responses into customized anti-cancer treatments. We isolated 34 patient-derived xenograft (PDX) tumor cells from a lung adenocarcinoma patient tumor xenograft. Individual tumor cells were subjected to single cell RNA-seq for gene expression profiling and expressed mutation profiling. Fifty tumor-specific single-nucleotide variations, including KRAS(G12D), were observed to be heterogeneous in individual PDX cells. Semi-supervised clustering, based on KRAS(G12D) mutant expression and a risk score representing expression of 69 lung adenocarcinoma-prognostic genes, classified PDX cells into four groups. PDX cells that survived in vitro anti-cancer drug treatment displayed transcriptome signatures consistent with the group characterized by KRAS(G12D) and low risk score. Single-cell RNA-seq on viable PDX cells identified a candidate tumor cell subgroup associated with anti-cancer drug resistance. Thus, single-cell RNA-seq is a powerful approach for identifying unique tumor cell-specific gene expression profiles which could facilitate the development of optimized clinical anti-cancer strategies.

GSE69405 Samples



Cell Metadata and BAM Files

Bulk Download

BAM Files Run Accession Number Sample Accession Number Organism Organ/Tissue Dev. Stage Cell Type Sequencer Protocol Assay Type Library Layout Ontology Term Cell Cycle Phase

FASTQC Report



FASTQC File ID Cell Accession Number FASTQC Report Link No. Sequence Tags
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SRR2049339_2 SRR2049339 Preview 9972985
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SRR2049340_2 SRR2049340 Preview 5636377
SRR2049341_1 SRR2049341 Preview 4339329
SRR2049341_2 SRR2049341 Preview 4339329
SRR2049342_1 SRR2049342 Preview 4390376
SRR2049342_2 SRR2049342 Preview 4390376
SRR2049343_1 SRR2049343 Preview 4239956
SRR2049343_2 SRR2049343 Preview 4239956
SRR2049344_1 SRR2049344 Preview 5611676
SRR2049344_2 SRR2049344 Preview 5611676
SRR2049345_1 SRR2049345 Preview 5625619
SRR2049345_2 SRR2049345 Preview 5625619
SRR2049346_1 SRR2049346 Preview 5246857
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SRR2049347_1 SRR2049347 Preview 4935310
SRR2049347_2 SRR2049347 Preview 4935310
SRR2049348_1 SRR2049348 Preview 4596488
SRR2049348_2 SRR2049348 Preview 4596488
SRR2049349_1 SRR2049349 Preview 5597736
SRR2049349_2 SRR2049349 Preview 5597736
SRR2049350_1 SRR2049350 Preview 6103281
SRR2049350_2 SRR2049350 Preview 6103281
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SRR2049399_1 SRR2049399 Preview 9401040
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SRR2049403_1 SRR2049403 Preview 7102389
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SRR2049405_2 SRR2049405 Preview 6855780
SRR2049406_1 SRR2049406 Preview 10904028
SRR2049406_2 SRR2049406 Preview 10904028
SRR2049407_1 SRR2049407 Preview 10899923
SRR2049407_2 SRR2049407 Preview 10899923
SRR2049408_1 SRR2049408 Preview 10509883
SRR2049408_2 SRR2049408 Preview 10509883
SRR2049409_1 SRR2049409 Preview 9784483
SRR2049409_2 SRR2049409 Preview 9784483
SRR2049410_1 SRR2049410 Preview 11339856
SRR2049410_2 SRR2049410 Preview 11339856
SRR2049411_1 SRR2049411 Preview 8006890
SRR2049411_2 SRR2049411 Preview 8006890
SRR2049412_1 SRR2049412 Preview 12555090
SRR2049412_2 SRR2049412 Preview 12555090
SRR2049413_1 SRR2049413 Preview 13343689
SRR2049413_2 SRR2049413 Preview 13343689
SRR2049414_1 SRR2049414 Preview 14056026
SRR2049414_2 SRR2049414 Preview 14056026
SRR2049415_1 SRR2049415 Preview 10315257
SRR2049415_2 SRR2049415 Preview 10315257
SRR2049416_1 SRR2049416 Preview 5627185
SRR2049416_2 SRR2049416 Preview 5627185
SRR2049417_1 SRR2049417 Preview 11566793
SRR2049417_2 SRR2049417 Preview 11566793
SRR2049418_1 SRR2049418 Preview 8081789
SRR2049418_2 SRR2049418 Preview 8081789
SRR2049419_1 SRR2049419 Preview 10596136
SRR2049419_2 SRR2049419 Preview 10596136
SRR2049420_1 SRR2049420 Preview 13553994
SRR2049420_2 SRR2049420 Preview 13553994
SRR2049421_1 SRR2049421 Preview 12050490
SRR2049421_2 SRR2049421 Preview 12050490
SRR2049422_1 SRR2049422 Preview 9608918
SRR2049422_2 SRR2049422 Preview 9608918
SRR2049423_1 SRR2049423 Preview 11379479
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SRR2049425_1 SRR2049425 Preview 6156549
SRR2049425_2 SRR2049425 Preview 6156549
SRR2049426_1 SRR2049426 Preview 7143771
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SRR2049428_1 SRR2049428 Preview 12621562
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SRR2049430_2 SRR2049430 Preview 12377698
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SRR2049431_2 SRR2049431 Preview 5810060
SRR2049432_1 SRR2049432 Preview 10829927
SRR2049432_2 SRR2049432 Preview 10829927
SRR2049433_1 SRR2049433 Preview 9370424
SRR2049433_2 SRR2049433 Preview 9370424
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SRR2049434_2 SRR2049434 Preview 7506399
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SRR2049435_2 SRR2049435 Preview 7068222
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SRR2049436_2 SRR2049436 Preview 10037069
SRR2049437_1 SRR2049437 Preview 6402531
SRR2049437_2 SRR2049437 Preview 6402531
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SRR2049439_1 SRR2049439 Preview 6536585
SRR2049439_2 SRR2049439 Preview 6536585
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SRR2049540_2 SRR2049540 Preview 55376546
SRR2049541_1 SRR2049541 Preview 64045590
SRR2049541_2 SRR2049541 Preview 64045590
SRR2049542_1 SRR2049542 Preview 59045363
SRR2049542_2 SRR2049542 Preview 59045363
SRR2049543_1 SRR2049543 Preview 85700132
SRR2049543_2 SRR2049543 Preview 85700132
SRR2049544_1 SRR2049544 Preview 71022171
SRR2049544_2 SRR2049544 Preview 71022171
SRR2049545_1 SRR2049545 Preview 69743960
SRR2049545_2 SRR2049545 Preview 69743960
SRR2049546_1 SRR2049546 Preview 66642938
SRR2049546_2 SRR2049546 Preview 66642938


Organism : Homo sapiens

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File Size : 528M

Human Cell Data

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tSNE image.
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PCA image.
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Gene Body Coverage image.

Data Resources


Organism Run Metadata Link Data Repository Link Pubmed Record Link Author Provided Files DAVID Annotation Chart Link DAVID Annotation Table Link Gene Body Coverage Matrix Link PCA Matrix Link Krona Plot Img Link Unmapped Reads Link Expression Correlation
Homo sapiens