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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 24, 2024 |
| Title |
HCA RNAseq |
| Sample type |
SRA |
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| Source name |
HCA
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Astrocytes
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| Extracted molecule |
total RNA |
| Extraction protocol |
For whole cell samples (PGPC14WT, HCA), 1µg was provided The Centre for Applied Genomics, Hospital for Sick Children, Toronto. For ADEV samples, all isolates were provided for bioanalyzer and sequencing.
Sequencing libraries were made using the Small RNA library preparation kit NEBNext (NEB) Small RNA library prep set according to the manufacturer’s instructions. Sequencing was performed using Illumina NovaSeq SP flowcell for single end 50bp length reads, aiming for 40M reads per transcript. Library preparation and sequencing were done at TCAG.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing data was processed into count data using the open source web-based platform galaxy.org MiRDeep2 tool as previously, mapping reads to hg38 human genome annotation and mature and precursor miRNA sequences from miRbase database. To generate a counts table for differential gene expression, miRNA counts for same mature miRNA from different precursor origin were averaged. Differential expression analysis was performed using DESeq2 package in R. Quality of samples was analyzed using principal component analysis (PCA) in DESeq2 package and pheatmap function was used to display variance between samples and replicates.
Assembly: hg38
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| Submission date |
Apr 05, 2023 |
| Last update date |
Apr 24, 2024 |
| Contact name |
Lina Antounians |
| E-mail(s) |
lina.antounians@sickkids.ca
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| Organization name |
The Hospital for Sick Children
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| Street address |
686 Bay St
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| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M4P 1R4 |
| Country |
Canada |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE229016 |
iPSC-derived healthy human astrocytes selectively load miRNAs targeting neuronal genes into extracellular vesicles |
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| Relations |
| BioSample |
SAMN34085125 |
| SRA |
SRX19888215 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7147869_HCA1_TOTALRNA.tab.gz |
23.2 Kb |
(ftp)(http) |
TAB |
| GSM7147869_HCA3_TOTALRNA.tab.gz |
22.6 Kb |
(ftp)(http) |
TAB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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