|
| Status |
Public on Jul 09, 2024 |
| Title |
IL15 CBNK GBM Day 3 coculture 124610 RNA |
| Sample type |
SRA |
| |
|
| Source name |
IL-15 NK cells + GSC20 3 days coculture
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: CBNK
treatment: IL-15 NK cells + GSC20 3 days coculture
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For sc-RNA seq, single cell capture, barcoding and library preparation were performed following the 10X Genomics Single Cell Chromium 3’ protocols (CG000183, V3.1). Ten libraries were pooled to give a final concentration of 10 nM. Pooled samples underwent further qPCR to determine the final concentration before submission for sequencing with the NovaSeq6000 sequencer using the S2 100 cycles flow cell and sequenced for 28 cycles for read1, 8 cycles for i7 index, and 91 cycles for read 2 through the ATGC (Advanced Technology Genomics Core) core at MD Anderson.
By applying RNA and ATAC sequencing, we want to investigate the epigenetic factors that contributing for IL-21-induced memory formation in NK cells
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
scRNAseq
rna_IL21_15.RDS
|
| Data processing |
Cellranger mkfastq v3.01 to generate FASTQ
Cellranger count v3.01 to generate count matrix
Assembly: GRCh38
Supplementary files format and content: [Cellranger files] comprising a MatrixMarket file (matrix.mtx) and two tab separated metadata files (barcodes.tsv, features.tsv)
|
| |
|
| Submission date |
Mar 10, 2023 |
| Last update date |
Jul 09, 2024 |
| Contact name |
Katayoun Rezvani |
| E-mail(s) |
krezvani@mdanderson.org
|
| Organization name |
The University of Texas MD Anderson Cancer Center
|
| Street address |
1515 Holcombe Blvd
|
| City |
HOUSTON |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE227098 |
IL-21 induces antitumor response in NK cells via CEBPD |
|
| Relations |
| BioSample |
SAMN33715564 |
| SRA |
SRX19635471 |
