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| Status |
Public on Apr 29, 2024 |
| Title |
Sample_2_scATACseq |
| Sample type |
SRA |
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| Source name |
sAML
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone Marrow
cell type: Hematopoietic Stem and Progenitor Cells (HSPCs)
disease state: secondary Acute Myeloid Leukemia
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| Extracted molecule |
genomic DNA |
| 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
10x Genomics
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| 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
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| Submission date |
Dec 30, 2022 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Rossella Manfredini |
| E-mail(s) |
rossella.manfredini@unimore.it
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| Organization name |
University of Modena and Reggio Emilia
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| Department |
Department of Biomedical, Metabolic and Neural Sciences
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| Street address |
Via Gottardi 100
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| City |
Modena |
| ZIP/Postal code |
41125 |
| Country |
Italy |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE221946 |
Single-Cell ATAC+RNAseq from CD34+ cells of a Primary Myelofibrosis patient evolved to secondary Acute Myeloid Leukemia |
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| Relations |
| BioSample |
SAMN32512882 |
| SRA |
SRX18895486 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6910350_S2_ATAC_counts.csv.gz |
73.6 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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