|
| Status |
Public on Apr 13, 2017 |
| Title |
K562 + MEF, 11 PCR1 cycles, 100 cells per ul, one-third 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 |
|
| Relations |
| BioSample |
SAMN05176167 |
| SRA |
SRX1799781 |
