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Sample GSM2176660 Query DataSets for GSM2176660
Status Public on Apr 13, 2017
Title K562 + MEF, 11 PCR1 cycles, 300 cells per ul, two-thirds beads for RT
Sample type SRA
Source name K562 cells, mouse embryonic fibroblasts
Organisms Homo sapiens; Mus musculus
Characteristics cell type: human K562 cells and mouse embryonic fibroblasts
Growth protocol K562 were cultured in IMDM plus 10% FBS and pen/strep at 37C and 5% CO2.
Extracted molecule total RNA
Extraction protocol K562 and MEF cells were mixed and single cell RNA sequencing was performed using the Drop-Seq method. Briefly, single cells, polyA-containing barcoded beads (ChemGenes), and droplet generation oil (Bio-Rad) were each flowed into individual input ports on a microfluidic device (NanoShift). Cells in droplets were lysed and hybridized to beads. Beads were isolated and subjected to reverse transcription (Thermo Fisher) and exonuclease I (NEB) treatment, followed by PCR of full length transcripts (Kapa). Final libraries were created by Tn5-mediated tagmentation of cDNA, and amplified by PCR (Kapa) and purified by SPRI beads.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
Data processing Basecalls performed by Picard ExtractIlluminaBarcodes v1.117.
Drop-Seq data were mapped using Drop-Seq Tools to a combined human and mouse genome. Uniquely mapping reads with mapping quality ≥ 10 were subjected to PCR duplicate removal by examining the unique molecular identifiers (UMI) for each read. Reads were then partitioned to individual cells based on cell barcodes.
Read counts were tabulated with featureCounts v1.5.0.
Genome_build: hg19
Genome_build: mm9
Supplementary_files_format_and_content: read counts for all genes
Submission date May 24, 2016
Last update date May 15, 2019
Contact name Gary Chung Hon
Organization name UT Southwestern
Department OB/GYN
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
Platform ID GPL19415
Series (2)
GSE81848 Multiplexed engineering and analysis of endogenous enhancer activity in single cells: Human/mouse mixing Drop-Seq experiments for K562 and MEFs
GSE81884 Multiplexed engineering and analysis of endogenous enhancer activity in single cells
BioSample SAMN05176177
SRA SRX1799791

Supplementary file Size Download File type/resource
GSM2176660_K562_+_MEF_11_PCR1_cycles_300_cells_per_ul_two-thirds_beads_for_RT.counts.txt.gz 4.8 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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