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Sample GSM8156215 Query DataSets for GSM8156215
Status Public on May 21, 2024
Title PBMCs_VEH_2
Sample type RNA
 
Source name PBMCs from Eμ-TCL1 adoptive transfer mice, treated for 4 weeks with vehicle control
Organism Mus musculus
Characteristics tissue: Peripheral blood mononuclear cells
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) dalia.elgamal@unmc.edu
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

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
4930578C19Rik 4.49
A2m 6.97
Acvr1c 4.49
Adam12 4.49
Adgre1 24.38
Adm 126.55
Adora2a 75.47
Akt1 89.4
Aldoa 936.94
Aldoc 15.09
Angpt1 5.81
Angpt2 4.49
Angptl4 6.97
Anln 6.97
Apc 16.25
Aph1b 9.29
Api5 365.72
Aplnr 4.49
Apoe 284.45
Apol6 4.49

Total number of rows: 784

Table truncated, full table size 8 Kbytes.




Supplementary file Size Download File type/resource
GSM8156215_PV2.RCC.gz 8.4 Kb (ftp)(http) RCC
Raw data provided as supplementary file
Processed data included within Sample table

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