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Sample GSM3429007 Query DataSets for GSM3429007
Status Public on Feb 12, 2019
Title 20170905-A04-NA18870
Sample type SRA
 
Source name LCL-derived iPSC
Organism Homo sapiens
Characteristics cell type: LCL-derived iPSC
experiment: 20170905
well: A04
individual: NA18870
Growth protocol We cultured Yoruba iPSCs (Banovich et al., 2018) in feeder-free conditions for at least ten passages in E8 medium (Life Technologies) (Chen et al., 2011).
Extracted molecule polyA RNA
Extraction protocol We collected cells using the C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm).
We performed single cell capture and library preparation as previously described using 6 bp Unique Molecular Identifiers (Tung et al., 2017). We pooled the 96 samples on each C1 chip and sequenced them on an Illumina HiSeq 2500 using the TruSeq SBS Kit v3-HS (FC-401-3002).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description eset-raw.rds
fucci-counts.txt.gz
fucci-annotation.txt
fucci-annotation-description.txt
eset-final.rds
Data processing We used `umi_tools extract` (UMI-tools 0.5.3) to extract the 6 base pair unique molecular identifier (UMI) from the 5’ end of each read.
We used `subjunc` (Subread 1.5.3) to map reads to the human genome (Ensembl GRCh37.75; chromosomes 1-22, X, Y, MT), ERCC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa), and the mCherry and EGFP open reading frames from the FUCCI plasmid.
We used `featureCounts` (Subread 1.5.3) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 75) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
We used `umi_tools dedup` (UMI-tools 0.5.3) to deduplicate reads with the same UMI and start position to molecules.
We used `verifyBamID` (1.1.3) to identify the individual of origin for each sample based on the overlap of the RNA-seq reads with the known genotypes.
Genome_build: GRCh37
Supplementary_files_format_and_content: The file eset-raw.rds is a serialized R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS(“eset-raw.rds”)`. It contains the gene counts, sample metadata, and feature metadata for 20,421 genes (H. sapiens, ERCC, EGFP, mCherry) and 1,536 single cells. The file fucci-counts.txt.gz is a gzipped tab-delimited plain text file that contains the counts for 20,421 genes for 1,536 single cells. The file fucci-annotation.txt is a tab-delimited plain text file that contains 43 metadata columns for the 1,536 single cells. The file fucci-annotation-description.txt is a tab-delimited plain text file that contains descriptions of the 43 metadata columns in fucci-annotation.txt. The file eset-final.rds is a serialized R object of the Bioconductor class ExpressionSet that contains the final data used to produce the results. It can be imported into R with `readRDS(“eset-final.rds”)`. It contains the gene counts, sample metadata, and feature metadata for the 11,093 genes (H. sapiens, ERCC, EGFP, mCherry) and 888 single cells that remained after applying filters for lowly expressed genes and low quality single cells.
 
Submission date Oct 15, 2018
Last update date Feb 12, 2019
Contact name John D Blischak
Organization name University of Chicago
Department Human Genetics
Lab Gilad
Street address 920 E. 58th Street, CLSC 317
City Chicago
State/province IL
ZIP/Postal code 60615
Country USA
 
Platform ID GPL16791
Series (1)
GSE121265 Quantifying continuous cell-cycle phase using single-cell gene expression data
Relations
BioSample SAMN10243666
SRA SRX4888648

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

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