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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 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 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
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
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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