|
| Status |
Public on May 20, 2015 |
| Title |
ERCC at high sequencing depth (84 beads) |
| Sample type |
SRA |
| |
|
| Source name |
ERCC spike-in molecules
|
| Organism |
synthetic construct |
| Characteristics |
cell type: ERCCs at a concentration of 100,000 molecules per droplet were used in Drop-Seq.
|
| 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 84 beads) 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 |
ERCC spike-ins: external RNA controls developed by the External RNA Controls Consortium (ERCC)
|
| 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.
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: ERCC and hg19 (dual reference)
Supplementary_files_format_and_content: compressed, flat text file with tab delimiters
|
| |
|
| Submission date |
Mar 09, 2015 |
| 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 |
GPL19424 |
| Series (2) |
| GSE63473 |
Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets |
| GSE66694 |
Drop-Seq analysis of ERCC spike in capture |
|
| Relations |
| BioSample |
SAMN03395043 |
| SRA |
SRX914968 |
