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Sample GSM3835727 Query DataSets for GSM3835727
Status Public on Jun 01, 2019
Title Mixture1.CAPTEANXX.CELseq2
Sample type SRA
 
Source name Mixture of human HEK293 and murine NIH3T3 cell lines
Organisms Homo sapiens; Mus musculus
Characteristics Sex: Pooled male and female
library construction: CEL-Seq2
Extracted molecule total RNA
Extraction protocol Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv
Data processing For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements
 
Submission date May 31, 2019
Last update date Jun 05, 2019
Contact name Aviv Regev
Organization name Broad Institute
Department Klarman Cell Observatory
Lab Aviv Regev
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL22245
Series (1)
GSE132044 Systematic comparative analysis of single cell RNA-sequencing methods
Relations
BioSample SAMN11912992
SRA SRX5940209

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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