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Sample GSM2906480 Query DataSets for GSM2906480
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
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
BioSample SAMN08274350
SRA SRX3520274

Supplementary file Size Download File type/resource
GSM2906480_Mix-Human293T-Mouse3T3-mapped-bam.tar.gz 1.4 Gb (ftp)(http) TAR
GSM2906480_Mix-Human293T-Mouse3T3_dge.txt.gz 2.2 Mb (ftp)(http) TXT
GSM2906480_human-293T_dge.txt.gz 1.3 Mb (ftp)(http) TXT
GSM2906480_human-293T_summary.txt.gz 9.6 Kb (ftp)(http) TXT
GSM2906480_mouse-3T3_dge.txt.gz 1.7 Mb (ftp)(http) TXT
GSM2906480_mouse-3T3_summary.txt.gz 10.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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