Addgene (tool)

RRID:SCR_002037

Non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Facilitates archiving and distributing DNA-based research reagents and associated data to scientists worldwide. Repository contains over 65,000 plasmids, including special collections on CRISPR, fluorescent proteins, and ready-to-use viral preparations. There is no cost for scientists to deposit plasmids, which saves time and money associated with shipping plasmids themselves. All plasmids are fully sequenced for validation and sequencing data is openly available. We handle the appropriate Material Transfer Agreements (MTA) with institutions, facilitating open exchange and offering intellectual property and liability protection for depositing scientists. Furthermore, we curate free educational resources for the scientific community including a blog, eBooks, video protocols, and detailed molecular biology resources.

Cell Signaling Technology (tool)

RRID:SCR_002071

Privately held company that develops and produces antibodies, ELISA kits, ChIP kits, proteomic kits, and other related reagents used to study cell signaling pathways that impact human health.

Bio-Rad Laboratories (tool)

RRID:SCR_008426

Commercial instrument and chemical vendor. Developer and manufacturer of specialized technological products for life science research and clinical diagnostics markets.

Thermo Fisher Scientific (tool)

RRID:SCR_008452

Commercial vendor and service provider of laboratory reagents and antibodies. Supplier of scientific instrumentation, reagents and consumables, and software services.

QIAGEN (tool)

RRID:SCR_008539

A commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.

Millipore (tool)

RRID:SCR_008983

An Antibody supplier

Santa Cruz Biotechnology (tool)

RRID:SCR_008987

An Antibody supplier

Gecko (tool)

RRID:SCR_009001

A complete, high-capacity centralized gene expression analysis system, developed in response to the needs of a distributed user community.

Jackson ImmunoResearch (tool)

RRID:SCR_010488

A commercial antibody vendor, specializing in secondary antibodies.

Abcam (tool)

RRID:SCR_012931

A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.

New England Biolabs (tool)

RRID:SCR_013517

An Antibody supplier

Agilent Technologies (tool)

RRID:SCR_013575

Company provides laboratories worldwide with analytical instruments and supplies, clinical and diagnostic testing services, consumables, applications and expertise in life sciences and applied chemical markets.

Biotin-SP-AffiniPure Fab Fragment Goat Anti-Mouse IgG (H+L) (antibody)

RRID:AB_2338586

This unknown targets Mouse IgG (H+L)

Anti-Actin antibody produced in rabbit (antibody)

RRID:AB_476693

This polyclonal targets Actin

c-Myc Antibody (9E10) (antibody)

RRID:AB_627268

This monoclonal targets c-Myc

DYRK1A Antibody (antibody)

RRID:AB_915851

This polyclonal targets DYRK1A

Tau (D1M9X) XP (antibody)

RRID:AB_2783844

This monoclonal targets MAPT

Phospho-Tau (Ser404) (D2Z4G) Rabbit mAb (IF preferred) (antibody)

RRID:AB_2798837

This monoclonal targets Tau iso8

Cytokeratin 1/2/3/4/5/6/7/8 antibody [Ks1-8] (antibody)

RRID:AB_11162687

This monoclonal targets Cytokeratin 1/2/3/4/5/6/7/8 antibody [Ks1-8]

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

RRID:AB_2620142

This monoclonal targets Ki-67

p130 (C-20) (antibody)

RRID:AB_632093

This polyclonal targets RBL2

Netrin 1 antibody [EPR5428] (antibody)

RRID:AB_11131145

This monoclonal targets Netrin 1 antibody [EPR5428]

α-Tubulin (11H10) Rabbit mAb (antibody)

RRID:AB_2619646

This monoclonal targets alpha-Tubulin

EpCAM (E6V8Y) XP® Rabbit mAb (Mouse Preferred) (antibody)

RRID:AB_2800214

This monoclonal targets EPCAM

Phospho-p38 MAPK (Thr180/Tyr182) (D3F9) XP(tm) Rabbit mAb (antibody)

RRID:AB_2139682

This monoclonal targets Mapk14

Phospho-p38 MAPK (Thr180/Tyr182) (3D7) Rabbit mAb (antibody)

RRID:AB_331762

This monoclonal targets Phospho-p38 MAPK (Thr180/Tyr182) (3D7) Rabbit mAb

p44/42 MAPK (Erk1/2) (137F5) Rabbit mAb (antibody)

RRID:AB_390779

This monoclonal targets p44/42 MAPK (Erk1/2)

Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) (D13.14.4E) XP® Rabbit mAb (antibody)

RRID:AB_2315112

This monoclonal targets Phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204)

Rabbit Anti-p53 Monoclonal Antibody, Unconjugated, Clone 7F5 (antibody)

RRID:AB_10695803

This monoclonal targets p53

Recombinant Anti-Ki67 antibody [SP6] (antibody)

RRID:AB_302459

This recombinant monoclonal targets Ki67

Toronto KnockOut version 3 library (TKOv3) (plasmid)

RRID:Addgene_90294

R Project for Statistical Computing (software resource)

RRID:SCR_001905

Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS.

The Cancer Genome Atlas (biomaterial supply resource)

RRID:SCR_003193

Project exploring the spectrum of genomic changes involved in more than 20 types of human cancer that provides a platform for researchers to search, download, and analyze data sets generated. As a pilot project it confirmed that an atlas of changes could be created for specific cancer types. It also showed that a national network of research and technology teams working on distinct but related projects could pool the results of their efforts, create an economy of scale and develop an infrastructure for making the data publicly accessible. Its success committed resources to collect and characterize more than 20 additional tumor types. Components of the TCGA Research Network: * Biospecimen Core Resource (BCR); Tissue samples are carefully cataloged, processed, checked for quality and stored, complete with important medical information about the patient. * Genome Characterization Centers (GCCs); Several technologies will be used to analyze genomic changes involved in cancer. The genomic changes that are identified will be further studied by the Genome Sequencing Centers. * Genome Sequencing Centers (GSCs); High-throughput Genome Sequencing Centers will identify the changes in DNA sequences that are associated with specific types of cancer. * Proteome Characterization Centers (PCCs); The centers, a component of NCI's Clinical Proteomic Tumor Analysis Consortium, will ascertain and analyze the total proteomic content of a subset of TCGA samples. * Data Coordinating Center (DCC); The information that is generated by TCGA will be centrally managed at the DCC and entered into the TCGA Data Portal and Cancer Genomics Hub as it becomes available. Centralization of data facilitates data transfer between the network and the research community, and makes data analysis more efficient. The DCC manages the TCGA Data Portal. * Cancer Genomics Hub (CGHub); Lower level sequence data will be deposited into a secure repository. This database stores cancer genome sequences and alignments. * Genome Data Analysis Centers (GDACs) - Immense amounts of data from array and second-generation sequencing technologies must be integrated across thousands of samples. These centers will provide novel informatics tools to the entire research community to facilitate broader use of TCGA data. TCGA is actively developing a network of collaborators who are able to provide samples that are collected retrospectively (tissues that had already been collected and stored) or prospectively (tissues that will be collected in the future).

ConsensusPathDB (data or information resource)

RRID:SCR_002231

An integrative interaction database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With human, yeast and mouse complex functional interactions, it currently constitutes the most comprehensive publicly available interaction repository for these species. Different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways is offered.

cBioPortal (data or information resource)

RRID:SCR_014555

A portal that provides visualization, analysis and download of large-scale cancer genomics data sets.

DESeq2 (software resource)

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.

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.

Reactome (data analysis service)

RRID:SCR_003485

Collection of pathways and pathway annotations. The core unit of the Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes and small molecules) participating in reactions form a network of biological interactions and are grouped into pathways (signaling, innate and acquired immune function, transcriptional regulation, translation, apoptosis and classical intermediary metabolism) . Provides website to navigate pathway knowledge and a suite of data analysis tools to support the pathway-based analysis of complex experimental and computational data sets.

SAMTOOLS (software resource)

RRID:SCR_002105

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

Aperio ImageScope (software resource)

RRID:SCR_020993

Software tool for pathology slide viewing. Used for access to color digital slide images to which you can adjust magnification, pan and zoom, compare different stains, annotate areas of interest, perform image analysis, and more. Allows to view slide images taken by Leica biosystems scanner.

Image Lab Software (software resource)

RRID:SCR_014210

Imaging software used to acquire and analyze images from specific Bio-Rad imaging systems. Users can analyze gel or blot features, capture optimized image data, and generate a report of the data. Image Lab software exclusively runs on the Gel Doc EZ imager, Gel Doc XR+ imaging system, ChemiDo MP, ChemiDoc XRS+ imaging systems, Criterion Stain Free imager, and the GS-900calibrated densitometer.

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.

Bowtie 2 (software resource)

RRID:SCR_016368

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

cutadapt (software resource)

RRID:SCR_011841

Software tool that removes adapter sequences from DNA sequencing reads.

FUtdTW (plasmid)

RRID:Addgene_22478

Ntn3-Fc-His (plasmid)

RRID:Addgene_72105

Ntn1-Fc-His (plasmid)

RRID:Addgene_72104

pSpCas9(BB)-2A-GFP (PX458) (plasmid)

RRID:Addgene_48138

lentiCRISPR v2 (plasmid)

RRID:Addgene_52961

lentiCas9-Blast (plasmid)

RRID:Addgene_52962

BaseSpace (service resource)

RRID:SCR_011881

Cloud platform to be directly integrated in to the industry?s leading sequencing platforms, with no cumbersome and time consuming data transfer steps.

HEK293T (cell line)

RRID:CVCL_0063

Cell line HEK293T is a Transformed cell line with a species of origin Homo sapiens (Human)

TOV-1946 (cell line)

RRID:CVCL_4062

Cell line TOV-1946 is a Cancer cell line with a species of origin Homo sapiens (Human)

OVCAR-8 (cell line)

RRID:CVCL_1629

Cell line OVCAR-8 is a Cancer cell line with a species of origin Homo sapiens (Human)