|
| Status |
Public on May 21, 2024 |
| Title |
Spleen_VEH_3 |
| Sample type |
RNA |
| |
|
| Source name |
Spleen from Eμ-TCL1 adoptive transfer mice, treated for 4 weeks with vehicle control
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Spleen
treatment: Vehicle
|
| Treatment protocol |
Mice were treated via oral gavage with 20 mg/kg OPN-51107 dissolved in [10% N-methyl-2-pyrrolidone plus diluent (40% PEG400, 5% TPGS, 5% Poloxamer 407, and 50% water)] or vehicle equivalent, daily for 3 weeks.
|
| Growth protocol |
Wild-type C57BL/6J mice (8 weeks old) were engrafted with 1e7 spleen-derived lymphocytes from a moribund Eμ-TCL1 mouse. Once mice displayed evident disease in the peripheral blood (2 weeks post-engraftment), they were randomize to receive treatment with OPN-51107 or vehicle control. Mice were sacrificied for tissue sequencing after 3 weeks of treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Murine splenocytes or peripheral blood mononuclear cells (PBMCs) were homogenized into a single cell suspension, then 1e7 cells were pelleted and snap frozen for each sample. Total RNA was isolated using RNeasy Mini Kit (Qiagen; Hilden, Germany) following manufacturer instructions. RNA was cleaned up via DNAse and ethanol treatment. RNA quantity and quality was assesed using a Qubit fluorometer (Thermo Fisher Scientific) and fragment analysis was performed with Bioanalyzer (Agilent) prior sequencing.
|
| Label |
NanoString
|
| Label protocol |
Performed according to NanoString protocol for the PanCancer IO 360™ Panel at the UNMC Genomics Core Facility
|
| |
|
| Hybridization protocol |
Performed according to NanoString protocol for the PanCancer IO 360™ Panel at the UNMC Genomics Core Facility
|
| Scan protocol |
Performed according to NanoString protocol on an nCounter Pro Analysis System at the UNMC Genomics Core Facility
|
| Data processing |
Data was acquired by the University of Nebraska Medical Center (UNMC) Genomics Core using an nCounter Pro Analysis System. Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC steps. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. The nCounter® Advanced Analysis protocol was followed to divide counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Abundance of various cell populations is calculated using the Nanostring Cell Type Profiling Module. Fold changes and p-values are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Several database sources were referenced for enrichment analysis, including Integrated Pathway Anlaysis (IPA), MSigDB, and EnrichR.
|
| |
|
| Submission date |
Mar 20, 2024 |
| Last update date |
May 21, 2024 |
| Contact name |
Dalia El-Gamal |
| E-mail(s) |
[email protected]
|
| Phone |
4025595241
|
| Organization name |
University of Nebraska Medical Center
|
| Department |
Eppley Institute
|
| Street address |
986805 NE Med Center BCC 4.12.396
|
| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68198-6805 |
| Country |
USA |
| |
|
| Platform ID |
GPL34315 |
| Series (1) |
| GSE262027 |
BET inhibition reforms the immune microenvironment and alleviates T-cell dysfunction in chronic lymphocytic leukemia |
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