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Sample GSM5319536 Query DataSets for GSM5319536
Status Public on Jul 05, 2022
Title GBM SF10441_snRNA
Sample type SRA
 
Source name Brain
Organism Homo sapiens
Characteristics progression: Recurrent
diagnosis: GBM
age: 56
gender: Male
pair#: #9
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Single Nuceli RNA-Seq
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.
Genome_build: 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.
 
Submission date May 17, 2021
Last update date Jul 05, 2022
Contact name Aaron Diaz
E-mail(s) aaron.diaz@ucsf.edu
Organization name University of California, San Francisco
Department Neurological Surgery
Lab Diaz Lab
Street address 1450 3rd St
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
 
Platform ID GPL24676
Series (1)
GSE174554 A single cell atlas of human glioma under therapy
Relations
BioSample SAMN19233368

Supplementary file Size Download File type/resource
GSM5319536_SF10441_barcodes.tsv.gz 5.7 Kb (ftp)(http) TSV
GSM5319536_SF10441_features.tsv.gz 126.6 Kb (ftp)(http) TSV
GSM5319536_SF10441_matrix.mtx.gz 4.1 Mb (ftp)(http) MTX
Raw data not provided for this record
Processed data provided as supplementary file
Raw data are available in SRA

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