biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsHEENA AGGARWALtranscription profiling by arrayMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16828Microarray profiling of leukocytes from drug treated tumor bearing mice. After dosing with the drug, blood was collected at 9th day and RBCs were lysed. Leukocytes were sent for array hybridization and scanning. 2 Control samples (without drug tumor bearing), 3 Responders (drug treated reduced tumor), 3 Non- Responders (drug treated, tumor size not reduced) Array analysis: Software used- Genespring GX14.5 Normalization method: Percentile shift Data processing and analysis. Agilent one-color microarray data were processed to obtain background-corrected gProcessedSignal values and analyzed in GeneSpring GX using 75th percentile shift normalization. Signal intensities were log2-transformed and normalized across arrays, after which fold-change values were calculated relative to a control reference derived from both control samples. Individual fold values for each sample represent normalized log2 deviations from the control baseline; therefore, control samples were centered around zero and showed symmetric positive and negative fold values by design. For comparison, one representative control sample was used and displayed, while both controls were included in normalization and fold-change calculations. For B cell proloferation genes - B cell activation Gene Ontology Term (GO:0042113) and MGI data base were used Exclusion criteria: Probes flagged as “Compromised” were excluded from downstream analysis. In case of multiple annotations: representative reads were taken In case of double annotations: higher value was consideredbiostudies-arrayexpressHybridization - RNA samples were amplified and labeled using the Agilent one-color Low Input Quick Amp Labeling Kit following the manufacturer’s protocol. Briefly, total RNA was reverse transcribed to cDNA, followed by in vitro transcription to generate Cyanine-3 (Cy3)-labeled complementary RNA (cRNA). Labeled cRNA was purified and quantified prior to hybridization.Labeling - RNA samples were amplified and labeled using the Agilent one-color Low Input Quick Amp Labeling Kit following the manufacturer’s protocol. Briefly, total RNA was reverse transcribed to cDNA, followed by in vitro transcription to generate Cyanine-3 (Cy3)-labeled complementary RNA (cRNA). Labeled cRNA was purified and quantified prior to hybridization.Scaning - Agilent one-color microarray data were processed to obtain background-corrected gProcessedSignal values and analyzed in GeneSpring GX using 75th percentile shift normalization. Signal intensities were log2-transformed and normalized across arrays, after which fold-change values were calculated relative to a control reference derived from both control samples. Individual fold values for each sample represent normalized log2 deviations from the control baseline. Array analysis was done using GeneSpring GX 14.5 and percentile shift method was used for normalization. Genes database used for mouse immune gene signature analysis: Mouse Genome Informatics (MGI) (http://www.informatics.jax.org/vocab/gene_ontology/GO:0042113 and B cell ontology Tool used for two dimensional hierarchical clustering of genes in heat maps Morpheus (developed by Broad Institute, MIT), link: https://software.broadinstitute.org/morpheus).Sample Collection - BALB/c mice (6-8 weeks, female) were inoculated with 0.7 x 106 4T1 cells. AT-1965 (88 mg/kg) treatment was started at 70-110 mm3 tumor size. Each injection was given on day 1, 2, 6 and 7. At day 9, post drug treatment, blood samples were collected. RBC kysis was done using RBC lysis buffer. Leukocytes were sent for array hybridization and scanning.2 Control samples (without drug tumor bearing), 3 Responders (drug treated reduced tumor), 3 Non- Responders (drug treated, tumor size not reduced)Nucleic Acid Extraction - Nucleic acid was extracted using TRIZOL, concentration and integrity was measured Samples were hybridized to microarray chips following manufacturer protocols.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsHEENA AGGARWALData Transformation - Raw signal intensities obtained from Agilent Feature Extraction software were background corrected and log2 transformed. Data were normalized using the 75th percentile shift normalization method in GeneSpring software to reduce technical variation across arrays. Probes were flagged as “Detected” or “Compromised” based on signal intensity relative to background. Probes flagged as compromised were excluded from downstream analysis. For genes with multiple probe annotations, representative probes were selected, and in cases of duplicate annotations, the probe with higher expression value was retained. Fold change values were calculated from normalized data for comparative analysis between control, responder, and non-responder groups.falseImmune response analysisMicroarray profiling of leukocytes from drug treated tumor bearing mice. After dosing with the drug, blood was collected at 9th day and RBCs were lysed. Leukocytes were sent for array hybridization and scanning. 2 Control samples (without drug tumor bearing), 3 Responders (drug treated reduced tumor), 3 Non- Responders (drug treated, tumor size not reduced) Array analysis: Software used- Genespring GX14.5 Normalization method: Percentile shift Data processing and analysis. Agilent one-color microarray data were processed to obtain background-corrected gProcessedSignal values and analyzed in GeneSpring GX using 75th percentile shift normalization. Signal intensities were log2-transformed and normalized across arrays, after which fold-change values were calculated relative to a control reference derived from both control samples. Individual fold values for each sample represent normalized log2 deviations from the control baseline; therefore, control samples were centered around zero and showed symmetric positive and negative fold values by design. For comparison, one representative control sample was used and displayed, while both controls were included in normalization and fold-change calculations. For B cell proloferation genes - B cell activation Gene Ontology Term (GO:0042113) and MGI data base were used Exclusion criteria: Probes flagged as “Compromised” were excluded from downstream analysis. In case of multiple annotations: representative reads were taken In case of double annotations: higher value was considered2026-04-10T00:00:00Z2026-04-10T01:02:14.193Z2026-03-30T13:39:38.339ZE-MTAB-16828EFO_0002768EFO_0002944EFO_0003814EFO_0003813EFO_0005518EFO_0003816EFO_0003815