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Sample GSM1544799 Query DataSets for GSM1544799
Status Public on May 20, 2015
Title SpeciesMix_HundredSTAMPs_50cellpermicroliter
Sample type SRA
Source name HEK and 3T3 mix
Organisms Homo sapiens; Mus musculus
Characteristics cell type: HEK and 3T3 mix at 50 cells per microliter final concentration in droplets.
Extracted molecule total RNA
Extraction protocol Single cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads
Microbeads were counted, and amplified (estimated 1000 cells for sample 1, or 100 cells for sample 2) by PCR, and the 3' end of the cDNA prepared for sequencing using a modified Nextera XT protocol.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Description The "100 STAMPs" experiment was sequenced at a mean depth of 769,000 reads per cell. We estimated 100 STAMPs by counting the beads; the actual number we uncovered in analysis is 83
Data processing Base calls performed with bcl2fastq2.15
Read 2 was aligned with Star v2.4.0
Each aligned read was tagged with its mate-pair UMI and cell barcode, and barcodes collapsed by ED=1 using custom software available at the Drop-Seq portal.
Each aligned exonic read was tagged with a gene name
A digital expression matrix was built by counting the number of unique UMIs per gene within each cell; columns are cells, and rows are genes. Gene expression from each organism is listed in a separate file.
Genome_build: mm10 and hg19 (dual reference)
Submission date Nov 13, 2014
Last update date May 15, 2019
Contact name Evan Macosko
Organization name Harvard Medical School
Department Genetics
Lab McCarroll Lab
Street address 77 Avenue Louis Pasteur, NRB 260
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
Platform ID GPL19415
Series (2)
GSE63269 Drop-Seq analysis of mixtures of human (HEK) and mouse (3T3) cells (1000/100 STAMPs) at 50 cells per microliter
GSE63473 Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
BioSample SAMN03178020
SRA SRX835916

Supplementary file Size Download File type/resource
GSM1544799_SpeciesMix_HundredSTAMPs.bam 7.2 Gb (ftp)(http) BAM
GSM1544799_SpeciesMix_HundredSTAMPs_HUMAN.digital_expression.txt.gz 771.7 Kb (ftp)(http) TXT
GSM1544799_SpeciesMix_HundredSTAMPs_MOUSE.digital_expression.txt.gz 494.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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