|
| Status |
Public on Mar 01, 2019 |
| Title |
HS/AAV6 GFP- |
| Sample type |
SRA |
| |
|
| Source name |
FACS-sorted primitive and progenitors HSPC in ratio 1 to 1
|
| Organism |
Homo sapiens |
| Characteristics |
time point: 24h upon nuclease delivery
cell type: Cord blood derived CD34+ cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Droplet-based digital 3′ end scRNA-Seq was performed on a Chromium Single-Cell Controller (10X Genomics) using the Chromium Single Cell 3′ Reagent Kit v2 according to the manufacturer’s instructions. Single cells were partitioned in Gel Beads in Emulsion (GEMs) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (12-14 cycles, according to the available cDNA quantity).
scRNA-Seq libraries were prepared according to the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| 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
Computation of pseudotime trajectories using the R package Monocle
Genome_build: GRCh38
|
| |
|
| Submission date |
Sep 06, 2018 |
| Last update date |
Mar 01, 2019 |
| 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 |
GPL18573 |
| Series (2) |
| GSE119594 |
Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [scRNA-seq] |
| GSE119597 |
Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response |
|
| Relations |
| BioSample |
SAMN09984863 |
| SRA |
SRX4649192 |
