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Series GSE67310 Query DataSets for GSE67310
Status Public on Jun 08, 2016
Title Dissecting the direct reprogramming path of fibroblasts into neurons by single cell RNA-sequencing
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Direct lineage reprogramming represents a remarkable conversion of cellular and transcriptome states. However, the intermediates through which individual cells progress are largely undefined. Here we used single cell RNA-seq at multiple time points to dissect direct reprogramming from mouse embryonic fibroblasts (MEFs) to induced neuronal (iN) cells. By deconstructing heterogeneity at each time point and ordering cells by transcriptome similarity rather than time we reconstructed a continuous reprogramming path. We find that overexpression of a single factor (Ascl1) results in a well-defined initialization causing cells to exit the cell cycle and re-focus gene expression through distinct neural transcription factors. However, overexpression of Ascl1 alone leads to abundant alternative fates that are suppressed by the combination of additional factors (Myt1l, Pou3f2). We find transgene silencing and emergence of alternative fates are the major efficiency limits of direct reprogramming. These data provide a high-resolution approach for understanding transcriptome states during lineage differentiation.
Overall design 405 single-cell transcriptomes from 5 time points (0 days, 2 days, 5 days, 20 days and 22 days upon Ascl1 induction) during reprogramming of MEFs into iN cells were analyzed in total; All single cells contain 92 external RNA spike-ins; The following single cell transcriptomes were sequenced: 73 single MEF cells (day 0, iN2), 81 single cells at day 2 (iN1), 55 single cells at day 5 (iN3), 33 single cells at day 20 (iN6) and 73 single cells at day 22 (iN7,iN8) upon Ascl1 induction from virally transfected MEFs. Additionally, we generated the transcriptome of 47 single cells that were induced with Ascl1 for 2 days from a clonal MEF line with a uniform Ascl1 transgene copy number (iN5). Finally, we sequenced the transcriptome of 43 single cells at day 22 (iN4) upon induction of Ascl1, Brn2 and Myt1l. All single cell samples were processed on the microfluidic Fluidigm C1 platform.
Contributor(s) Treutlein B, Quake SR
Citation(s) 27281220
Submission date Mar 26, 2015
Last update date May 15, 2019
Contact name Barbara Treutlein
Organization name Stanford University
Department Bioengineering
Lab Quake
Street address 318 Campus Drive
City Stanford CA
State/province CA
ZIP/Postal code 94305-5432
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (405)
GSM1644192 0d-MEFs_iN2_1
GSM1644193 0d-MEFs_iN2_2
GSM1644194 0d-MEFs_iN2_3
BioProject PRJNA279486
SRA SRP056585

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Supplementary file Size Download File type/resource
GSE67310_iN_data_log2FPKM_annotated.txt.gz 17.2 Mb (ftp)(http) TXT
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