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Sample GSM6910349 Query DataSets for GSM6910349
Status Public on Apr 29, 2024
Title Sample_2_scRNAseq
Sample type SRA
 
Source name sAML
Organism Homo sapiens
Characteristics tissue: Bone Marrow
cell type: Hematopoietic Stem and Progenitor Cells (HSPCs)
disease state: secondary Acute Myeloid Leukemia
Extracted molecule nuclear RNA
Extraction protocol CD34+ cells were purified from frozen BMMNCs. Then, nuclei were isolated following “Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing'' protocol by 10X Genomics. Briefly, cells were resuspended in a lysis buffer containing 0.01% Digitonin for 3 mins, washed twice, resuspended and diluted in Nuclei Buffer in order to load 6000 nuclei for each sample onto 10X cartridge; 1 U/𝜇L RNase inhibitor (Sigma-Aldrich, St.Louis, MO, USA) was added to all nuclei preparation buffers.
Libraries were prepared according to “Nuclei Isolation for Single Cell Multiome ATAC + Gene Expression Sequencing'' protocol by 10X Genomics and sequenced on an Illumina NextSeq 550 (service by Biodiversa s.r.l, Rovereto, Italy). All samples were subjected to 2x75bp paired-end sequencing.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model NextSeq 550
 
Description 10x Genomics
Data processing Raw base call (BCL) files generated by NextSeq 550 sequencer were demultiplexed using Cell Ranger software to obtain FASTQ files
Alignment to the human reference genome (hg38), filtering and UMI counting are performed. The final output consists of two types of feature-barcode matrices, one in which features are represented by genes (RNA-seq data) and the other in which features are genomic regions (ATAC-seq data).
Assembly: hg38
Supplementary files format and content: Matrix files
 
Submission date Dec 30, 2022
Last update date Apr 29, 2024
Contact name Rossella Manfredini
E-mail(s) rossella.manfredini@unimore.it
Organization name University of Modena and Reggio Emilia
Department Department of Biomedical, Metabolic and Neural Sciences
Street address Via Gottardi 100
City Modena
ZIP/Postal code 41125
Country Italy
 
Platform ID GPL21697
Series (1)
GSE221946 Single-Cell ATAC+RNAseq from CD34+ cells of a Primary Myelofibrosis patient evolved to secondary Acute Myeloid Leukemia
Relations
BioSample SAMN32512883
SRA SRX18895485

Supplementary file Size Download File type/resource
GSM6910349_S2_RNA_counts.csv.gz 12.5 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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