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| Status |
Public on Nov 22, 2021 |
| Title |
Vehicle_replicate_4 |
| Sample type |
SRA |
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| Source name |
Immune Infiltrate
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| Organism |
Mus musculus |
| Characteristics |
cell type: CD45+ Immune Cells
background strain: C57BL/6
treatment: Vehicle
tissue: mIDH1 (R132C) orthotopic ICC
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| Treatment protocol |
Mice were administered AG120 treatment for six days, starting on the 7th day following challenge.
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| Growth protocol |
Mice were inoculated, orthotopically, with mIDH1 ICC tumor cells.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were harvested on day 13 post-inoculation, disassociated using the Miltenyi Mouse Tumor Dissociation Kit and gentleMACS Octo-Dissociator (Miltenyi) as per manufacturer's instructions. Tumor-infiltrating lymphocytes were enriched using Lymphocyte-M (Fisher Scientific) density gradient followed by CD45+ positive selection (Miltenyi). Cells were counted and loaded on to 10x device (10X Genomics).
Libraries were generated following standard 10X protocol (Manual CG000086 Revision K to L) for 10X single-cell 5' RNA-seq v1.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v3.0.1).
Data normalization, filtering, dimensional reduction, and gene set scoring was done using Scanpy package (v1.7).
Differential expression was performed using a logistic regression model.
GSEA Pre-ranked was used to find enriched hallmark gene sets (v4.1.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: matrix.mtx file is count matrix in sparse matrix format; barcodes.tsv is list of barcodes for each sample; genes.tsv is list of genes detected in samples.
Supplementary_files_format_and_content: h5 files
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| Submission date |
Apr 29, 2021 |
| Last update date |
Nov 23, 2021 |
| Contact name |
Kira Eileen Olander |
| E-mail(s) |
kolander@broadinstitute.org
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| Phone |
6096106769
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| Organization name |
Broad Institute
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| Department |
Cancer Program
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| Lab |
Manguso Lab
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| Street address |
75 Ames St
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02140 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE173612 |
10X single-cell RNASeq profiling of immune infiltrate from mutant IDH1 ICC tumors treated with AG120 (mIDH1 inhibitor) or vehicle |
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| Relations |
| BioSample |
SAMN18927091 |
| SRA |
SRX10716650 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5272597_IDH1_orthotopic_vehicle_4_counts.h5 |
15.2 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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