|
| Status |
Public on Apr 13, 2024 |
| Title |
Donor 2 (DN2) |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted primitive HSPC cells
|
| Organism |
Homo sapiens |
| Characteristics |
time point: 24h upon ZFN nuclease delivery
cell type: Cord blood derived CD34+ cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Droplet-based digital 5’scRNA-seq was performed on A Chromium Single-Cell Controller (10x Genomics, Pleasanton, CA) using the Chromium Single Cell 5’ Reagent Kit v2 coupled to feature barcoding technology for cell surface protein according to the manufacturer’s instructions.
scRNA-Seq libraries were prepared according to the manufacturer’s instructions
2x150nt of length through NovaSeq_6000_S1_300_cycles
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Preliminary analysis using the 10X Genomics pipeline relying on cellranger (base calling, alignment, feature count) using default parameters
Filtering, Normalization, Scaling using the R package Seurat
Identification of clusters using the Louvin algorithm privded by the R package Seurat
Identification of differentially expressed genes using the MAST algorithm provided by the R package Saurat
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X Genomics - Cellranger matrix
|
| |
|
| Submission date |
Feb 10, 2021 |
| Last update date |
Apr 13, 2024 |
| Contact name |
Ivan Merelli |
| E-mail(s) |
ivan.merelli@itb.cnr.it
|
| Phone |
+390226422600
|
| Organization name |
Consiglio Nazionale delle Ricerche
|
| Department |
Istituto di Tecnologie Biomediche
|
| Lab |
Bioinformatics
|
| Street address |
via F.lli Cervi 93
|
| City |
Segrate |
| State/province |
Milano |
| ZIP/Postal code |
20090 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE166507 |
CRISPR-based gene disruption coupled to targeted integration of novel, high-avidity, natural T cell receptors to WT1 for acute leukemia |
|
| Relations |
| BioSample |
SAMN17849342 |
| SRA |
SRX10064498 |
