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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 05, 2022 |
| Title |
Mouse_IR_Treated |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
progression: Primary
diagnosis: Brain tumor
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| Extracted molecule |
total RNA |
| Extraction protocol |
Nuclei were extracted from frozen tissues following the “Frakenstein” protocol developed by Luciano Martelotto, Ph.D., Melbourne, Centre for Cancer Research, Victorian Comprehensive Cancer Centre, and available from 10X Genomics
For snRNA-seq(frozen tissues), ~15,000 nuclei were loaded per capture. Single-nucleus capture, reverse transcription, cell lysis, and library preparation were performed per manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq using a paired-end 100bp protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
RNA-Seq
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| Data processing |
We utilized CellRanger (version 3.0.2) for data pre-processing and gene expression quantification, following the guidelines from the CellRanger website (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#premrna).
The CellRanger ATAC software (version 1.1.0) was used for read alignment, deduplication, and identifying transposase cut sites.
The presence/absence of somatic CNVs was assessed with CONICSmat. ELSA was used for cell type classification.
Assembly: hg38
Supplementary files format and content: SnRNA-seq: feature read count matrix (.txt) files. Includes cell barcodes, genes and count. SnATAC-seq: peak, matrix, barcode file.
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| Submission date |
May 26, 2022 |
| Last update date |
Jul 13, 2022 |
| Contact name |
Aaron Diaz |
| E-mail(s) |
aaron.diaz@ucsf.edu
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| Organization name |
University of California, San Francisco
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| Department |
Neurological Surgery
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| Lab |
Diaz Lab
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| Street address |
1450 3rd St
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE174554 |
A single cell atlas of human glioma under therapy |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM6199403_Mouse_IR_Treated_feature_count.txt.gz |
155.0 Kb |
(ftp)(http) |
TXT |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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