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Sample GSM4409677 Query DataSets for GSM4409677
Status Public on Mar 13, 2020
Title mouse_AdultPleura_1 (For supplementing the Mouse Cell Atlas data)
Sample type SRA
 
Source name mouse_AdultPleura_1
Organism Mus musculus
Characteristics developmental stage: Adult
Sex: Female
tissue: Pleura
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 HiSeq X Ten
 
Description Microwell-seq analysis
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 reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp); UMI:In read1, the bases 49-54 (6bp)
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.The cellbarcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
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 Mar 13, 2020
Last update date Mar 14, 2020
Contact name Guoji Guo
Organization name Center for Stem Cell and Regenerative Medicine
Department Zhejiang University School of Medicine
Street address Yuhangtang street 866
City Hanzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL21273
Series (1)
GSE134355 Construction of A Human Cell Landscape by Single-cell mRNA-seq
Relations
BioSample SAMN14372181
SRA SRX7906593

Supplementary file Size Download File type/resource
GSM4409677_mouse_AdultPleura_1_dge.txt.gz 4.5 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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