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Sample GSM2286710 Query DataSets for GSM2286710
Status Public on Dec 31, 2016
Title MCF10A_sc_1
Sample type SRA
 
Source name MCF10A cell line
Organism Homo sapiens
Characteristics cell line: MCF10A
sample type: single cell
Growth protocol HEK293T cells were grown in DMEM/High Glucose medium (ThermoFisher Scientific) with 10% FBS (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies). Cells were passed every 2-3 days.
MCF10A cells were grown in DMEM/F12 medium with 5% Horse Serum, 20ng/ml EGF, 100ng/ml Cholera Toxin, 10ug/ml Insulin, 500ng/ml Hydrocortisone, and 1% Penicillin Streptomycin.
Extracted molecule total RNA
Extraction protocol cDNA libraries were prepared for sequencing using standard Illumina Truseq protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing The raw sequencing data was trimmed using skewer package.
The reads were mapped to the transcriptome using TOPHAT
A Python program using HT-seq package was written to analyze the barcode information
Genome_build: Hg19
Supplementary_files_format_and_content: dat files include the read count and barcode count for exon-based and intron-based analyses
 
Submission date Aug 21, 2016
Last update date May 15, 2019
Contact name Kuanwei Sheng
E-mail(s) sheng@bcm.edu
Organization name Baylor College of Medicine
Department Molecular and Human Genetics
Lab Zong Lab
Street address ONE BAYLOR PALAZA
City HOUSTON
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL18573
Series (1)
GSE78968 Effective Detection of Variation in Single Cell Transcriptome using MATQ-seq
Relations
BioSample SAMN05601488
SRA SRX2036969

Supplementary file Size Download File type/resource
GSM2286710_MCF10A_SC1.tscounts.mapq50.exon.dat.gz 685.5 Kb (ftp)(http) DAT
GSM2286710_MCF10A_SC1.tscounts.mapq50.gene.dat.gz 538.0 Kb (ftp)(http) DAT
GSM2286710_MCF10A_SC1.tscounts.mapq50.intron.dat.gz 576.5 Kb (ftp)(http) DAT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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