|
| Status |
Public on Apr 22, 2017 |
| Title |
SSF1163_A11_ACY1215_1_KP2313_P3 |
| Sample type |
SRA |
| |
|
| Source name |
Lung tumor Macrophage ACY1215
|
| Organism |
Mus musculus |
| Characteristics |
molecular_barcodes: TGCAGCTA_CTAGTCGA
plate_id: plate2
position: A11
tissue: Lung tumor
strain: Mixed background
gemm model: KrasTrp53
cell_type: Macrophage
treatment: ACY1215
|
| Treatment protocol |
Ricolinostat, 50 mg/kg, IP, QD
|
| Growth protocol |
Genetically engineered mouse model (GEMM) of conditional activating mutation that harboring endogenous Kras (KrasLSL-G12D/+) were crossed with p53 conditional knockout Trp53fl/fl. CRE recombinase was induced through intranasal inhalation of 5x106 p.f.u. adeno-Cre (University of Iowa adenoviral core).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Viable CD45+CD3+ T cells or CD45+CD11c+CD11blo macrophages were sorted from tumor cell suspensions into 2ul of Qiagen TCL buffer in 96-well plates
SmartSeq2 protocol with modifications (Trombetta et al., 2014)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were mapped to the mouse genome (mm10) by Tophat
Estimated transcript counts were retrieved via the Cufflinks suite version 2.2.1.
Only single cell samples with at least 100.000 paired-end reads and a minimum of 20% aligning to the transcriptome were retained for further analysis.
Processed counts only show samples that passed the minimum reads and alignment criteria.
Genome_build: mm10
Supplementary_files_format_and_content: processed_counts.txt: txt file with processed counts after cufflinks
|
| |
|
| Submission date |
Apr 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ruben Dries |
| E-mail(s) |
rubendries@gmail.com
|
| Organization name |
DFCI
|
| Department |
Computational Biology
|
| Lab |
Longwood Center
|
| Street address |
360 Longwood Ave
|
| City |
Boston |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE98048 |
Single-cell profiling of tumor infiltrating T cells and macrophages [RNA-Seq] |
| GSE98049 |
Synergistic Immunostimulatory Effects and Therapeutic Benefit of Combined Histone Deacetylase and Bromodomain Inhibition in Non-small Cell Lung Cancer. |
|
| Relations |
| BioSample |
SAMN06808278 |
| SRA |
SRX2751256 |
