|
| Status |
Public on Feb 14, 2018 |
| Title |
Mix3T3-293T |
| Sample type |
SRA |
| |
|
| Source name |
Mix3T3-293T
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
cell line: 3T3 and 293T
tissue: Mix3T3-293T
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue dissociation and single-cell lysate
Library preparations were performed with the Microwell-seq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
mouse3T3 is from Stuart Orkin Lab ,human293T is from Stuart Orkin Lab
|
| Data processing |
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed.
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a) with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.
|
| |
|
| Submission date |
Dec 28, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
guoji guo |
| E-mail(s) |
ggjlab@163.com
|
| Organization name |
Zhejiang University School of Medicine
|
| Department |
Center for Stem Cell and Regenerative Medicine
|
| Lab |
guoji guo lab
|
| Street address |
yuhangtang road 388
|
| City |
hangzhou |
| State/province |
zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL22245 |
| Series (1) |
| GSE108097 |
Mapping Mouse Cell Atlas by Microwell-seq |
|
| Relations |
| BioSample |
SAMN08274350 |
| SRA |
SRX3520274 |
