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Sample GSM1629193 Query DataSets for GSM1629193
Status Public on May 20, 2015
Title ERCC at high sequencing depth (84 beads)
Sample type SRA
 
Source name ERCC spike-in molecules
Organism synthetic construct
Characteristics cell type: ERCCs at a concentration of 100,000 molecules per droplet were used in Drop-Seq.
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 84 beads) 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 ERCC spike-ins: external RNA controls developed by the External RNA Controls Consortium (ERCC)
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.
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: ERCC and hg19 (dual reference)
Supplementary_files_format_and_content: compressed, flat text file with tab delimiters
 
Submission date Mar 09, 2015
Last update date May 20, 2015
Contact name Evan Macosko
E-mail emacosko@genetics.med.harvard.edu
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 GPL19424
Series (2)
GSE63473 Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets
GSE66694 Drop-Seq analysis of ERCC spike in capture
Relations
BioSample SAMN03395043
SRA SRX914968

Supplementary file Size Download File type/resource
GSM1629193_ERCC.bam 10.5 Gb (ftp)(http) BAM
GSM1629193_ERCC.digital_expression.txt.gz 6.3 Kb (ftp)(http) TXT
GSM1629193_hg19_ERCC.dict.txt.gz 5.1 Kb (ftp)(http) TXT
GSM1629193_hg19_ERCC.fasta.gz 847.6 Mb (ftp)(http) FASTA
GSM1629193_hg19_ERCC.gtf.gz 27.4 Mb (ftp)(http) GTF
GSM1629193_hg19_ERCC.refFlat.txt.gz 6.3 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data provided as supplementary file

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