|
| Status |
Public on Jul 26, 2018 |
| Title |
PBMC ATATAG mcSCRB-seq |
| Sample type |
SRA |
| |
|
| Source name |
peripheral mononuclear blood cells
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: mcSCRB-seq
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were FACS sorted into lysis buffer
Libraries were constructed using various developments of the SCRB-seq protocol, see sample description for more details
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Libraries were constructed using the mcSCRB-seq protocol (molecular crowding reverse transcription)
|
| Data processing |
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Human Genome (hg38) or Mouse genome (mm10) with STAR 2.5.3
Quantification was done with ENSEMBL gene models (GRCh38.84/GRCm38.75)
Genome_build: Human: hg38, Ensembl 84; Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table
|
| |
|
| Submission date |
May 02, 2018 |
| Last update date |
Jul 26, 2018 |
| Contact name |
Christoph Ziegenhain |
| E-mail(s) |
ziegenhain@bio.lmu.de
|
| Organization name |
Ludwig-Maximilians University Munich
|
| Department |
Department Biology II
|
| Lab |
Anthropology & Human genomics
|
| Street address |
Großhaderner Str. 2
|
| City |
Martinsried |
| State/province |
Bavaria |
| ZIP/Postal code |
82152 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18460 |
| Series (1) |
| GSE103568 |
Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq |
|
| Relations |
| BioSample |
SAMN09014829 |
| SRA |
SRX4023536 |
