|
| Status |
Public on Apr 19, 2024 |
| Title |
murine_glioma_control_gex |
| Sample type |
SRA |
| |
|
| Source name |
glioma tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL6
tissue: brain (glioma tissue)
treatment: control
|
| Treatment protocol |
Mice were treated with 10 mg/kg all-trans retinoic acid or control every other day.
|
| Growth protocol |
Neurospheres were maintained in DMEM-F12 with 20 ng/mL bEGF, bFGF and 1 ug/mL Normocin.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumors were dissected with normal surrounding brain tissue, chopped into 1-2 mm pieces and incubated in Accutase for 10 minutes at 37degreesC. The suspension was then passed through 25 mL, 10 ml and 5 mL pipettes beforre finally being passed through 18G needle 3 times and filtered through a 100 micron strainer. Immune cells were sorted from dissected tissue by CD45 expression.
Libraries were contructed accoding to the manufactuerer's protocol for the 5-prime v1 kit from 10X Genomics.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
gene expression data
|
| Data processing |
bcl2fastq (version 2.20.0) to demultiplex reads
cellranger (version 3.1.0) to align reads and generated gene barcode matrices
Genome_build: GRCm38
Supplementary_files_format_and_content: gene_barcode_matrix, cellranger gene barcode expression matrix consisting of features (genes), cell barcodes, and UMI counts. filtered_contig_annotations, cellranger output of vdj
|
| |
|
| Submission date |
Apr 20, 2021 |
| Last update date |
Apr 19, 2024 |
| Contact name |
Nduka Amankulor |
| E-mail(s) |
amankulornm@upmc.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Neurological Surgery
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE172387 |
Loss of retinoic acid signaling drives immune escape in IDH mutant gliomas |
|
| Relations |
| BioSample |
SAMN18806728 |
| SRA |
SRX10641142 |
