|
| Status |
Public on Sep 09, 2016 |
| Title |
SmartSeqA_F1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic cell line
|
| Organism |
Mus musculus |
| Characteristics |
library preparation: Smart-seq / C1
cell line: J1
|
| Growth protocol |
J1 mESC were cultured in ground pluripotency states by 2i/LIF culture as described previously.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
single-cell lysate
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Description |
Library preparation was performed with the Fluidigm C1 platform as per manufacturers' protocol.
|
| Data processing |
base-calls were performed with Illumina bcl2fastq
all cDNA reads were aligned with Star v2.4.0
SCRB-seq and Drop-seq protocol reads were tagged with its mate-pair UMI and cell barcode; unique reads were obtained; more information see README file
Smart-seq and Smart-seq2 reads were assigned to genes using Rsubread
only cells were considered with at least 1,000,000 reads; doublets discarded and failed libraries filtered by low nearest-neighbor correlation coefficients
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with unique gene-wise counts of cells considered for final analysis: ziegenhain_complete_data.txt
|
| |
|
| Submission date |
Jun 29, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
GPL18480 |
| Series (1) |
| GSE75790 |
Comparative analysis of single-cell RNA sequencing methods |
|
| Relations |
| BioSample |
SAMN05327239 |
| SRA |
SRX1886208 |
