|
| Status |
Public on May 20, 2015 |
| Title |
SpeciesMix_ThousandSTAMPs_50cellspermicroliter |
| Sample type |
SRA |
| |
|
| Source name |
HEK and 3T3 mix
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: HEK and 3T3 mix at final droplet concentration of 50 cells per microliter.
|
| 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 1000 cells for sample 1, or 100 cells for sample 2) 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 |
This experiment was sequenced at a mean depth of 69,004 reads per cell. We estimated 1000 STAMPs by counting the beads; the actual number we uncovered in analysis is 1020
|
| 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, and barcodes collapsed by ED=1 using custom software available at the Drop-Seq portal.
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: mm10 and hg19 (dual reference)
|
| |
|
| Submission date |
Nov 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Evan Macosko |
| E-mail(s) |
emacosko@genetics.med.harvard.edu
|
| 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 |
GPL19415 |
| Series (2) |
| GSE63269 |
Drop-Seq analysis of mixtures of human (HEK) and mouse (3T3) cells (1000/100 STAMPs) at 50 cells per microliter |
| GSE63473 |
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets |
|
| Relations |
| BioSample |
SAMN03178019 |
| SRA |
SRX835915 |
