|
| Status |
Public on Oct 01, 2021 |
| Title |
mIDH1_scRNASeq_1 [Run_2961 B1] |
| Sample type |
SRA |
| |
|
| Source name |
Brain Tumor
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
celltype: mIDH1 Tumor cells symptomatic stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
10X Genomics Cellranger v3.1 was used to process the raw sequencing data
First, CellRanger mkfastq demultiplexed libraries that are based on sample indices, converted the barcodes and read data to fastq files. Then, using STAR, CellRanger count aligned the reads to mm10 reference genome, filtered and counted unique molecular indentifiers (UMIs). Finally, CellRanger took multiple run outputs of CellRanger count and normalized them to same sequencing depth and recalculated the matrices and analyses of the gene-barcodes on the combined data.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
fastq files were created using Illumina NovaSeq 6000 and Cellranger v3.1
Cellranger v3.1 was also used to create the matrices of features (UMI counts linked to a gene and barcode)
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is filtered and presented as a matrix for input into data analysis programs
|
| |
|
| Submission date |
Jun 11, 2020 |
| Last update date |
Oct 01, 2021 |
| Contact name |
Maria Castro |
| E-mail(s) |
mariacas@med.umich.edu
|
| Organization name |
University of Michigan
|
| Department |
Neurosurgery
|
| Lab |
Castro-Lowenstein
|
| Street address |
1150 West Medical Center Drive
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE152276 |
G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT [Run2961] |
| GSE152277 |
G-CSF SECRETED BY EPIGENETICALLY REPROGRAMMED MUTANT IDH1 GLIOMA STEM CELLS, REVERSES THE MYELOID CELLS'-MEDIATED IMMUNOSUPPRESSIVE TUMOR MICROENVIRONMENT |
|
| Relations |
| BioSample |
SAMN15214361 |
| SRA |
SRX8530580 |
