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Series GSE111831 Query DataSets for GSE111831
Status Public on Apr 09, 2018
Title The transcriptomic profile of stem-cell derived neurons in 3D culture conditions and stem-cell derived astrocytic cells
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Understanding neurological diseases requires tractable genetic systems. Three-dimensional (3D) neural tissue systems are an attractive choice, but it is not well understood how the transcriptome profile of these tissues is affected by encapsulating materials. Here we characterize the effect of different culturing conditions on the transcriptomic profile of induced neuronal cells and develop a method for rapid generation of 3D co-cultures of neuronal and astrocytic cells from hESCs. We perform transcriptome analysis of cells resulting from astrocytic cell differentiation. Using single-cell sequencing, we find that our system recapitulates transcriptional patterns of cell types in the human brain.
Overall design Refer to individual samples.
Contributor(s) Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich M, Pan JQ, Levin JZ, Zhang F
Citation(s) 30271673
Halil Tekin, Sean Simmons, Beryl Cummings, Linyi Gao, Xian Adiconis, Cynthia C. Hession, Ayan Ghoshal, Danielle Dionne, Sourav R. Choudhury, Volkan Yesilyurt, Neville E. Sanjana, Xi Shi, Congyi Lu, Matthias Heidenreich, Jen Q. Pan, Joshua Z. Levin and Feng Zhang. Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons. Nature Biomedical Engineering 2018;2:540-554. doi: 10.1038/s41551-018-0219-9
Submission date Mar 14, 2018
Last update date May 13, 2019
Contact name Halil Tekin
Organization name Broad Institute of MIT and Harvard
Street address 75 Ames St.
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL19415 Illumina NextSeq 500 (Homo sapiens; Mus musculus)
Samples (159)
GSM3040336 day3_iN_rep1
GSM3040337 day3_iN_rep2
GSM3040338 2D_1wk_iN_rep1
BioProject PRJNA438297
SRA SRP135684

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Supplementary file Size Download File type/resource
GSE111831_count_matrix.txt.gz 3.4 Mb (ftp)(http) TXT
GSE111831_singleCell_count1.txt.gz 1.8 Mb (ftp)(http) TXT
GSE111831_singleCell_count2.txt.gz 10.3 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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