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Series GSE119097 Query DataSets for GSE119097
Status Public on Aug 28, 2018
Title SIS-seq, a molecular ‘time machine’, connects single cell fate with gene programs
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Conventional single cell RNA-seq methods are destructive, such that a given cell cannot also then be tested for fate and function, without a time machine. Here, we develop a clonal method SIS-seq, whereby single cells are allowed to divide, and progeny cells are assayed separately in SISter conditions; some for fate, others by RNA-seq. By cross-correlating fate and gene expression within a clone, and doing this for many clones, we can identify the earliest gene expression signatures of dendritic cell subset development. SIS-seq could be used to study other populations harboring clonal heterogeneity, including stem, reprogrammed and cancer cells to reveal the transcriptional origins of fate decisions.
Overall design Single ubiquitin C-GFP+ Sca1+ ckit+ HSPCs were isolated from BM and cultured amongst a pool of BM filler cells from C57BL/6 mice, and supplemented with Flt3 ligand. After 2.5 days, wells were visually inspected for GFP+ clones, and those with 10 or more cells were mixed by pipetting, followed by equal volume separation into three parts; two replicate wells for further culture to test for fate at day 8, and the remaining fraction for single cell, or small cell number RNA-seq, using CEL-Seq2 to provide a transcriptional 'snapshot' of the clone prior to fate acquisition.
Contributor(s) Tian L, Schreuder J, Amann-Zalcenstein D, Tran J, Su S, Ritchie ME, Naik SH
Submission date Aug 27, 2018
Last update date Jul 01, 2020
Contact name Luyi Tian
Phone 8577779729
Organization name Broad institute
Lab Fei Chen Lab
Street address 415 main st Cambridge
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (158)
GSM3357787 ILSGR0260r_S1_BC1
GSM3357788 ILSGR0260r_S1_BC2
GSM3357789 ILSGR0260r_S1_BC3
This SubSeries is part of SuperSeries:
GSE153676 Clonal multi-omics in DC development
BioProject PRJNA488094
SRA SRP158934

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE119097_gene_counts.csv.gz 1.5 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data are available on Series record

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