|
| Status |
Public on Nov 02, 2018 |
| Title |
Species_mix_closed-environment_format |
| Sample type |
SRA |
| |
|
| Source name |
cell lines
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell type: NIH3T3 mouse fibroblast, K562 erythroleukemic cell line
passages: 5-8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
mRNA captured on barcoded beads were reverse transcribed and amplified using half a PCR reaction. Tagmentation and final library preparation was performed using Illumina Nextera XT Kit (FC-131-1024) according to manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Base calling, alignment, filtering and generation of gene expression matrices are all performed according to the protocols described in Macosko et al. Cell 2015
Genome_build: hg19, mm10
Supplementary_files_format_and_content: tab limited text files include transcript counts for each gene for individual cells
|
| |
|
| Submission date |
Jan 23, 2018 |
| Last update date |
Nov 03, 2018 |
| Contact name |
Burak Dura |
| E-mail(s) |
burak.dura@yale.edu
|
| Phone |
6173350782
|
| Organization name |
Yale University
|
| Department |
Biomedical Engineering
|
| Lab |
Rong Fan Lab
|
| Street address |
55 Prospect St
|
| City |
New Haven |
| State/province |
Connecticut |
| ZIP/Postal code |
06511 |
| Country |
USA |
| |
|
| Platform ID |
GPL22245 |
| Series (1) |
| GSE109535 |
scFTD-seq: freeze-thaw lysis based, portable approach toward highly distributed single-cell 3’ mRNA profiling |
|
| Relations |
| BioSample |
SAMN08388608 |
| SRA |
SRX3593665 |
