ArrayExpress (tool)

RRID:SCR_002964

International functional genomics data collection generated from microarray or next-generation sequencing (NGS) platforms. Repository of functional genomics data supporting publications. Provides genes expression data for reuse to the research community where they can be queried and downloaded. Integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Contains a subset of curated and re-annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments. Data collected to MIAME and MINSEQE standards. Data are submitted by users or are imported directly from the NCBI Gene Expression Omnibus.

FinchTV (tool)

RRID:SCR_005584

Chromatogram viewer that can display an entire trace in a scalable multi-pane view, allows raw data views, BLAST searching and the ability to reverse complement sequences and traces.

Bioconductor (tool)

RRID:SCR_006442

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Sigma-Aldrich (tool)

RRID:SCR_008988

American chemical, life science and biotechnology company owned by Merck KGaA. Merger of Sigma Chemical Company and Aldrich Chemical Company. Provides organic and inorganic chemicals, building blocks, reagents, advanced materials and stable isotopes for chemical synthesis, medicinal chemistry and materials science, antibiotics, buffers, carbohydrates, enzymes, forensic tools, hematology and histology, nucleotides, proteins, peptides, amino acids and their derivatives.

BD Biosciences (tool)

RRID:SCR_013311

An Antibody supplier

New England Biolabs (tool)

RRID:SCR_013517

An Antibody supplier

FastQC (tool)

RRID:SCR_014583

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

DESeq2 (tool)

RRID:SCR_015687

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

CRISPOR (tool)

RRID:SCR_015935

Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.

clusterProfiler (tool)

RRID:SCR_016884

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

C57BL/6J (tool)

RRID:IMSR_JAX:000664

Mus musculus with name C57BL/6J from IMSR.

CD4 Monoclonal Antibody (GK1.5) (antibody)

RRID:AB_2536856

This monoclonal targets CD4

Rabbit monoclonal D4W2Z anti-CD8 (antibody)

RRID:AB_2756376

This recombinant monoclonal targets CD8

Ki-67 (D3B5) Rabbit mAb (Mouse Preferred; IHC Formulated) (antibody)

RRID:AB_2620142

This monoclonal targets Ki-67

Monoclonal Anti-β-Actin antibody produced in mouse (antibody)

RRID:AB_476697

This monoclonal targets β-Actin

Purified anti-mouse Galectin-9 (antibody)

RRID:AB_10568691

This monoclonal targets Galectin-9

Mouse Anti-Galectin-3 Monoclonal antibody, Unconjugated, Clone b2c10 (antibody)

RRID:AB_627657

This monoclonal targets LGALS3

Mouse Galectin-1 Affinity Purified Polyclonal Ab (antibody)

RRID:AB_354693

This polyclonal targets Mouse Galectin-1 Affinity Purified Ab

APC anti-mouse Galectin-9 (antibody)

RRID:AB_2750154

This monoclonal targets Galectin-9

GraphPad Prism (software resource)

RRID:SCR_002798

Statistical analysis software that combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. Designed for biological research applications in pharmacology, physiology, and other biological fields for data analysis, hypothesis testing, and modeling.

Molecular Signatures Database (data or information resource)

RRID:SCR_016863

Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.

pheatmap (software resource)

RRID:SCR_016418

Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.

RUVSeq (software resource)

RRID:SCR_006263

Software package that implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples.

HTSeq (software resource)

RRID:SCR_005514

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

GENCODE (data or information resource)

RRID:SCR_014966

Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.

STAR (software resource)

RRID:SCR_004463

Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.

Thermo Scientific Nanodrop 2000 microvolume spectrophotometer (instrument resource)

RRID:SCR_018042

NanoDrop 2000 is full-spectrum, UV-Vis spectrophotometer that quantifies and assesses purity of DNA, RNA, Protein and more. The NanoDrop 2000 and its series companion 2000c have patented sample retention technology that measure sample volumes as small as 0.5 uL.

lentiCRISPR v2 (plasmid)

RRID:Addgene_52961

MB49 (cell line)

RRID:CVCL_7076

Cell line MB49 is a Cancer cell line with a species of origin Mus musculus