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Series GSE119428 Query DataSets for GSE119428
Status Public on Sep 04, 2018
Title Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. We applied the method in both a cell-centric and gene-centric mode to isolate mRNA fragments from scRNA-seq libraries.
Overall design targeted resequencing and original untargeted datasets of various scRNA-Seq libraries from the 10x genomics and wafergen platform
Contributor(s) Riemondy KA, Hesselberth JR
Citation(s) 30496484
Submission date Sep 04, 2018
Last update date Mar 21, 2019
Contact name Kent Augustus Riemondy
Organization name University of Colorado School of Medicine
Department Biochemistry and Molecular Genetics
Street address 12801 E 17th Ave
City Aurora
State/province Colorado
ZIP/Postal code 80045
Country USA
Platforms (5)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (13)
GSM3374607 pcr_wafergen_expt_original
GSM3374608 pcr_wafergen_expt_standard
GSM3374609 pcr_wafergen_expt_biotinylated
BioProject PRJNA489248
SRA SRP159524

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
GSE119428_RAW.tar 36.0 Mb (http)(custom) TAR (of JSON, TSV)
GSE119428_lna_cell_jurkattcr_bcs.txt.gz 85 b (ftp)(http) TXT
GSE119428_lna_cell_mousehuman_bcs.txt.gz 11.0 Kb (ftp)(http) TXT
GSE119428_lna_cell_pbmc_bcs.txt.gz 20.5 Kb (ftp)(http) TXT
GSE119428_lna_gene_jurkat_bcs.txt.gz 24.4 Kb (ftp)(http) TXT
GSE119428_pcr_wafergen_expt_bcs.txt.gz 3.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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