|
| Status |
Public on Jun 30, 2023 |
| Title |
HSPC_emptyLNPs_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Peripheral Blood
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Peripheral Blood
cell type: HSPC
donor: Pool
disease status: Healthy
treatment: Empty LNPs
replicate: Replicate2
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated at 12-24 hours after editing using RNeasy Micro Kit (QIAGEN), and DNase treatment was performed using RNase-free DNase Set (QIAGEN), according to the manufacturer’s instructions.
RNA was quantified with The Qubit 2.0 Fluorometer (Thermo Fisher) and its quality was assessed by a 2100 Agilent Bioanalyser (Agilent Technologies). Minimum quality was defined as RNA integrity number (RIN) of >8. 20-100 ng of total RNA were used for library preparation and subsequent ultra-low input or standard sequencing by Genewiz (Azenta Life Sciences).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Sample11
|
| Data processing |
Basecalling using blc2fastq and trimming using cutadapt.
Alignment using STAR and gene abundance estimation using featurecounts.
Differential gene expression computed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: *.tsv: Tab-separated count files.
|
| |
|
| Submission date |
Oct 20, 2022 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Stefano Beretta |
| E-mail(s) |
beretta.stefano1@hsr.it
|
| Organization name |
San Raffaele Telethon Institute for Gene Therapy
|
| Street address |
Via Olgettina, 60
|
| City |
Milan |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE216249 |
Lipid Nanoparticles Allow Efficient and Harmless Ex Vivo Gene Editing of Human Hematopoietic Cells [RNAseq_lnps] |
| GSE216250 |
Lipid Nanoparticles Allow Efficient and Harmless Ex Vivo Gene Editing of Human Hematopoietic Cells |
|
| Relations |
| BioSample |
SAMN31393775 |
| SRA |
SRX17978624 |
