|
| Status |
Public on Jun 23, 2024 |
| Title |
IMR4, replicate1, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Brain Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Brain Tumor
cell type: Leukocytes
diagnosis: Oligodendroglioma
genotype: IDH Mutant
primary/recurrent: Recurrent
treatment: Standard of care
|
| Extracted molecule |
total RNA |
| Extraction protocol |
scRNA-seq was performed using 10x Genomics Chromium Single Cell Controller. Sorted cells were washed with 1X PBS and suspended in PBS/0.04% BSA. Cells were double-checked for viability and cell number by using the countess II FL and microscope. All cells were diluted to a concentration of 500-1000 cells/μl in PBS/0.04% BSA before being used for single cell 10X 3’v3. Single cells were captured using the 10X genomic controller according to the bead types and chip used for the experiments. The 10X genomic Chromium Single cell 3’ GEM, library and Gel bead Kit ’v3 (Catalogue #1000075) and chromium chip B single cell kit (Part# 1000073) were used to capture cells on the controller; cell recovery targeted was in a range of 5000 - 10000 cells. Captured cells then undergo a GEM-RT, cDNA amplification, and all purification in accordance to the 10X protocol. Cleanup cDNA was checked via a tape station (Agilent 42000) HSD5000 (Catalogue# Part# 5067-5593) for cDNA traces. 25% of the cDNA was used to generate the library, and the Chromium i7 multiplex kit (Part# 120262) was used to identify each sample. Library cleanup was performed using AMPure beads and QC was done again with tape station D1000 tapes (Part # 5067-5583). Ten libraries of equal amount were pooled to give a final concentration of 10nM and submitted for sequencing with the NovaSeq6000 S2 sequencer, 28 cycles for read1, 8 cycles for i7 index, and 91 cycles for read 2 through the ATGC core at MD Anderson. Sequence data was then put through the 10X genomic cell ranger 3.0 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Jan 10, 2023 |
| Last update date |
Jun 23, 2024 |
| Contact name |
Jeffrey Andrew How |
| E-mail(s) |
jahow@mdanderson.org
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Department |
Gyn Onc & Reproductive Med
|
| Street address |
1515 Holcombe Blvd. Unit 1362
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030-4009 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE222520 |
Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas [scRNA-seq] |
| GSE222522 |
Immune landscape of Isocitrate Dehydrogenase (IDH) stratified human gliomas |
|
