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| Status |
Public on Oct 15, 2024 |
| Title |
PBMCs + CD34+ Tapestri |
| Sample type |
SRA |
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| Source name |
Peripheral Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral Blood
cell type: PBMCs and CD34+ cells
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen PBMC’s were thawed following 10X Genomics “Sample Preparation Demostrated Protocol”. Immunomagnetic selection of CD34+ cell population was then performed by means of “CD34 Microbead kit, human” (Miltenyi Biotec) following the protocol provided by the manufacturer.
100000 cells (a mix of PBMCs and CD34+ cells) were resuspended in cell buffer and loaded in the Tapestri Platform as recommended in manufacturer protocol. Samples were processed using the Tapestri® Single-Cell DNA Sequencing V2 (Mission Bio, San Francisco, California, USA) and the libraries were sequenced on a NovaSeq 6000 using High Output Kit v2.5 chemistry (Illumina, San Diego, California, USA).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
FASTQ files for single-cell DNA libraries were processed through the Tapestri Pipeline V2, for adapter trimming, sequence alignment, barcode correction, cell finding, and variant calling.
Assembly: hg19
Supplementary files format and content: custom_Tapestri_panel.zip is a folder containing the .bed files of the custom DNA panel employed in the experiment. It can be uploaded into Tapestri pipeline in order to analyze the raw fastq sequencing data.
Supplementary files format and content: MPN_DNA.loom is a file generated from the Tapestri Pipeline that can be further analyzed through Tapestri Insights software to retrieve mutational data at the single-cell level.
Library strategy: scDNA-seq
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| Submission date |
Dec 20, 2023 |
| Last update date |
Oct 15, 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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| Street address |
Via Gottardi 100
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| City |
Modena |
| ZIP/Postal code |
41125 |
| Country |
Italy |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE251689 |
Single cell genomic analysis of PBMCs cells from a primary myelofibrosis patient |
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| Relations |
| BioSample |
SAMN38983928 |
| SRA |
SRX22985269 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7986055_MPN_DNA.loom.gz |
702.4 Mb |
(ftp)(http) |
LOOM |
| GSM7986055_custom_Tapestri_panel.tar.gz |
7.0 Kb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
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