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Sample GSM4135781 Query DataSets for GSM4135781
Status Public on Oct 06, 2020
Title P10
Sample type SRA
 
Source name BMMC
Organism Homo sapiens
Characteristics cell type: BMMC
tumor stage: de novo AML
gender: M
age: 29
disease state: acute myeloid leukemia
Extracted molecule total RNA
Extraction protocol Cells were isolated from bone marrow aspirates by Ficoll Hypaque Solution.
Library preparations were performed according to the Microwell-seq protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
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.
ScRNA-seq reads were aligned to the Homo_sapiens GRCh38 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: Homo_sapiens GRCh38 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 Oct 22, 2019
Last update date Mar 13, 2024
Contact name Junqing Wu
E-mail(s) wujunqing@zju.edu.cn
Organization name Zhejiang University
Street address Yuhangtang Road 866
City Hangzhou
ZIP/Postal code 310058
Country China
 
Platform ID GPL20795
Series (1)
GSE130756 A single-cell survey of cellular hierarchy in acute myeloid leukemia
Relations
BioSample SAMN13088626
SRA SRX7036737

Supplementary file Size Download File type/resource
GSM4135781_P10_dge.txt.gz 4.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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