SCPortalen


Validation of noise models for single-cell transcriptomics.


Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity among single cells. Here we identify two major sources of technical variability: sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to correct for this, which we validate using single-molecule FISH. We demonstrate that gene expression variability in mouse embryonic stem cells depends on the culture condition.

GSE54695 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
SRR1161549 SAMN02628454 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S
SRR1161550 SAMN02628466 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S
SRR1161551 SAMN02628451 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S
SRR1161552 SAMN02628457 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S
SRR1161553 SAMN02628463 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] M.G1
SRR1161554 SAMN02628453 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] M.G1
SRR1161555 SAMN02628459 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] G2
SRR1161556 SAMN02628462 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] G2
SRR1161557 SAMN02628456 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S
SRR1161558 SAMN02628458 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S
SRR1161559 SAMN02628465 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] G2.M
SRR1161560 SAMN02628461 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] G2.M
SRR1161561 SAMN02628468 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] M.G1
SRR1161562 SAMN02628469 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] G2
SRR1161563 SAMN02628460 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S
SRR1161564 SAMN02628467 Mus musculus Embryo Embryo mESC Illumina HiSeq 2500 CEL-Seq RNA-Seq Paired-End EFO:0004990[mESC] S

FASTQC Report



FASTQC File ID Cell Accession Number FASTQC Report Link No. Sequence Tags
SRR1161549_1 SRR1161549 Preview 41751147
SRR1161549_2 SRR1161549 Preview 41751147
SRR1161550_1 SRR1161550 Preview 42211075
SRR1161550_2 SRR1161550 Preview 42211075
SRR1161551_1 SRR1161551 Preview 23764721
SRR1161551_2 SRR1161551 Preview 23764721
SRR1161552_1 SRR1161552 Preview 24027498
SRR1161552_2 SRR1161552 Preview 24027498
SRR1161553_1 SRR1161553 Preview 31287097
SRR1161553_2 SRR1161553 Preview 31287097
SRR1161554_1 SRR1161554 Preview 31273378
SRR1161554_2 SRR1161554 Preview 31273378
SRR1161555_1 SRR1161555 Preview 20117132
SRR1161555_2 SRR1161555 Preview 20117132
SRR1161556_1 SRR1161556 Preview 20307476
SRR1161556_2 SRR1161556 Preview 20307476
SRR1161557_1 SRR1161557 Preview 34439319
SRR1161557_2 SRR1161557 Preview 34439319
SRR1161558_1 SRR1161558 Preview 34143410
SRR1161558_2 SRR1161558 Preview 34143410
SRR1161559_1 SRR1161559 Preview 31821460
SRR1161559_2 SRR1161559 Preview 31821460
SRR1161560_1 SRR1161560 Preview 32160773
SRR1161560_2 SRR1161560 Preview 32160773
SRR1161561_1 SRR1161561 Preview 33219585
SRR1161561_2 SRR1161561 Preview 33219585
SRR1161562_1 SRR1161562 Preview 33616668
SRR1161562_2 SRR1161562 Preview 33616668
SRR1161563_1 SRR1161563 Preview 30956532
SRR1161563_2 SRR1161563 Preview 30956532
SRR1161564_1 SRR1161564 Preview 31252645
SRR1161564_2 SRR1161564 Preview 31252645

Organism : Mus musculus

Download :

File Size : 35M

Mouse Cell Data

Image Currently Unavailable
tSNE image.
Image Currently Unavailable
PCA image.
Image Currently Unavailable
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
Mus musculus