|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jun 01, 2019 |
Title |
Mixture1.CAPTEANXX.SciSeq10_B5 |
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: sci-RNA-seq
|
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 06, 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 |
SAMN11913024 |
SRA |
SRX5941411 |
Supplementary data files not provided |
SRA Run Selector |
Processed data are available on Series record |
Raw data are available in SRA |
|
|
|
|
|