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| Status |
Public on Jul 31, 2020 |
| Title |
EPN_1101 |
| Sample type |
SRA |
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| Source name |
Ependymoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Ependymoma
subtype: PFA2
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Surgical material was collected at our institution at the time of surgery with consent (COMIRB 95-500) and processed identically. Samples were rapidly dissociated into single cells using a mechanical process as described previously, viably cryopreserved and banked at <80C for later use. Samples were thawed in 2 batches and flow sorted (Astrios EQ) to obtain viable single cells based on propidium iodide (PI) exclusion. Cells were processed using the 10x chromium platform to generate single cell RNA-Seq libraries, which were sequenced on the Illumina HiSeq or NovaSeq.
10x Genomics 3' end library kit (v2)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
UMI count matrices were generated using the 10X Genomics Cell Ranger (3.0.1) pipeline with default parameters.
The Seurat package in R was then used to aggregate the matrices, which were further filtered to exclude cells not passing the following QC measures: at least 200 genes detected (UMI > 0), fewer than 30% of UMIs derived from mitochondia, and fewer than 70,000 UMIs (to exclude putative doublets). . Genes were also excluded if they were not expressed in at least 5 cells (UMI count > 0).
Next, we applied Harmony alignment to correct for inter-sample variation due to experimental or sequencing batch effects.
After alignment, the harmony reduction used for UMAP projection and graph based clustering.
Genome_build: GRCh38
Supplementary_files_format_and_content: Count matrix with UMI counts per gene per cell. Cell_metadata.tsv contains information about each cell in the count matrix.
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| Submission date |
Oct 21, 2019 |
| Last update date |
Jul 31, 2020 |
| Contact name |
Andrew M Donson |
| E-mail(s) |
andrew.donson@cuanschutz.edu
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| Phone |
303 724 4012
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| Organization name |
CU Anschutz Medical Campus
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| Department |
Pediatrics
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| Lab |
RC1 North, P18-4401M
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| Street address |
12800 E 19th Ave
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| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80010 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE125969 |
Ependymoma subpopulation lineages underlie clinical classification and outcome (scRNAseq data set) |
| GSE126025 |
Ependymoma subpopulation lineages underlie clinical classification and outcome |
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| Relations |
| BioSample |
SAMN13067496 |
| SRA |
SRX7027766 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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