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Series GSE97390 Query DataSets for GSE97390
Status Public on Oct 17, 2017
Title Mouse embryonic stem cells can differentiate via multiple paths to the same state [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary In embryonic development, cells must differentiate through stereotypical sequences of intermediate states to generate mature states of a particular fate. By contrast, direct programming can generate similar fates through alternative routes, by directly expressing terminal transcription factors. Yet the cell state transitions defining these new routes are unclear. We applied single-cell RNA sequencing to compare two mouse motor neuron differentiation protocols: a standard protocol approximating the embryonic lineage, and a direct programming method. Both undergo similar early neural commitment. Then, rather than transitioning through spinal intermediates like the standard protocol, the direct programming path diverges into a novel transitional state. This state has specific and abnormal gene expression. It opens a 'loop' or 'worm hole' in gene expression that converges separately onto the final motor neuron state of the standard path. Despite their different developmental histories, motor neurons from both protocols structurally, functionally, and transcriptionally resemble motor neurons from embryos.
Overall design 2 protocols were profiled at 3 timepoints each (samples 1-5), and compared to primary embryonic motor neurons (sample 6). Each sample contains 667-1,057 single-cell transcriptomes (total = 5,405).
Contributor(s) Briggs JA, Li VC, Lee S, Woolf CJ, Klein AM, Kirschner MW
Citation(s) 28990928
Submission date Apr 04, 2017
Last update date May 15, 2019
Contact name James Alexander Briggs
Organization name Harvard Medical School
Department Department of Systems Biology
Lab Kirschner / Klein labs
Street address 200 Longwood Avenue, Harvard Medical School
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
Platforms (3)
GPL16417 Illumina MiSeq (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (6)
GSM2563704 day0_ES
GSM2563705 day5_direct_programming
GSM2563706 day11_direct_programming
This SubSeries is part of SuperSeries:
GSE97391 Mouse embryonic stem cells can differentiate via multiple paths to the same state
BioProject PRJNA381617
SRA SRP103028

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Supplementary file Size Download File type/resource
GSE97390_E13.5_primary_motor_neuron.filtered_normalized_counts.csv.gz 3.6 Mb (ftp)(http) CSV
GSE97390_E13.5_primary_motor_neuron.raw_umifm_counts.csv.gz 1.9 Mb (ftp)(http) CSV
GSE97390_SPRING_combined_trajectories.filtered_normalized_counts.csv.gz 32.5 Mb (ftp)(http) CSV
GSE97390_direct_programming.filtered_normalized_counts.csv.gz 26.1 Mb (ftp)(http) CSV
GSE97390_direct_programming.raw_umifm_counts.csv.gz 8.8 Mb (ftp)(http) CSV
GSE97390_standard_protocol.filtered_normalized_counts.csv.gz 28.2 Mb (ftp)(http) CSV
GSE97390_standard_protocol.raw_umifm_counts.csv.gz 8.9 Mb (ftp)(http) CSV
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