ChIP-seq (tool)

RRID:SCR_001237

Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface.

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.

Mendeley Data (tool)

RRID:SCR_002750

A free reference manager and academic social network to organize your research, collaborate with others online, and discover the latest research. Automatically generate bibliographies, Collaborate easily with other researchers online, Easily import papers from other research software, Find relevant papers based on what you're reading, Access your papers from anywhere online, Read papers on the go with the iPhone app. The software, Mendeley Desktop, offers: * Automatic extraction of document details * Efficient management of your papers * Sharing and synchronization of your library (or parts of it) * Additional features: A plug-in for citing your articles in Microsoft Word, OCR (image-to-text conversion, so you can full-text search all your scanned PDFs), etc The website, Mendeley Web, complements Mendeley Desktop by offering these features: * An online back up of your library * Statistics of all things interesting * A research network that allows you to keep track of your colleagues' publications, conference participations, awards etc * A recommendation engine for papers that might interest you

Millipore (tool)

RRID:SCR_008983

An Antibody supplier

Proteintech Group (tool)

RRID:SCR_008986

Proteintech Europe Ltd is an ISO 9001:2008 certified company

Santa Cruz Biotechnology (tool)

RRID:SCR_008987

An Antibody supplier

edgeR (tool)

RRID:SCR_012802

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

New England Biolabs (tool)

RRID:SCR_013517

An Antibody supplier

Bethyl (tool)

RRID:SCR_013554

An Antibody supplier

BWA-MEM2 (tool)

RRID:SCR_022192

Software tool for sequence mapping.The next version of BWA-MEM. Used for aligning sequencing reads against large reference genome.

Goat anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 488 (antibody)

RRID:AB_2576217

This polyclonal secondary targets IgG (H+L)

Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 594 (antibody)

RRID:AB_2534073

This polyclonal secondary targets IgG (H+L)

IRDye 800CW Goat anti-Rabbit IgG (antibody)

RRID:AB_621843

This polyclonal secondary targets IgG

IRDye 680LT Goat anti-Mouse IgG (antibody)

RRID:AB_10706161

This unknown targets IgG

Mouse (G3A1) mAb IgG1 Isotype Control (antibody)

RRID:AB_10829607

This monoclonal targets Mouse (G3A1) mAb IgG1 Isotype Control

COL7A1 (4D2) (antibody)

RRID:AB_2229746

This monoclonal targets Human COL7A1

Anti-SUMO-2/3/4 Antibody (C-3) (antibody)

RRID:AB_2905545

This monoclonal targets SUMO-2/3/4

SUMO-1 (D-11) (antibody)

RRID:AB_628300

This monoclonal targets SUMO-1 (D-11)

Lamin A/C (E-1) (antibody)

RRID:AB_10991536

This monoclonal targets Lamin A/C (E-1)

HA Tag antibody (antibody)

RRID:AB_2881490

This monoclonal targets HA Tag

HA-Tag (C29F4) Rabbit mAb (antibody)

RRID:AB_1549585

This monoclonal targets HA-Tag

Rabbit anti-BRD7 Antibody, Affinity Purified (antibody)

RRID:AB_1850214

This polyclonal targets BRD7

BAF250a (PSG3) (antibody)

RRID:AB_673396

This monoclonal targets ARID1A

Brg-1 (G-7) (antibody)

RRID:AB_626762

This monoclonal targets SMARCA4

ARID2 (D8D8U) Rabbit mAb (antibody)

RRID:AB_2799992

This monoclonal targets ARID2

PIAS 1 (F-1) (antibody)

RRID:AB_10707973

This monoclonal targets PIAS 1 (F-1)

Rabbit Anti-PIAS1 XP??? Monoclonal Antibody, Unconjugated, Clone D33A7 (antibody)

RRID:AB_1904090

This monoclonal targets PIAS1

Rabbit anti-PBRM1 Recombinant Monoclonal Antibody [BL-39-2C3] (antibody)

RRID:AB_2891820

This recombinant monoclonal targets PBRM1

LI-COR Image Studio Software (software resource)

RRID:SCR_015795

Image analysis software that acquires, analyzes, and archives research data without altering raw findings. It integrates data and changes how pixels are mapped to the screen for clearer display, rather than altering the pixels of the image data itself.

ChIPseeker (software resource)

RRID:SCR_021322

Software package to retrieve nearest genes around peak, annotate genomic region of peak, implements statstical methods for estimate significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare own dataset with those deposited in database.Several visualization functions are implemented to summarize coverage of peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.

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.

Deeptools (software resource)

RRID:SCR_016366

Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.

BEDTools (software resource)

RRID:SCR_006646

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

BWA (software resource)

RRID:SCR_010910

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

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.

Trim Galore (data processing software)

RRID:SCR_011847

Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data.

RStudio (software resource)

RRID:SCR_000432

Open source and enterprise ready professional software for R statistical computing environment. Integrated development environment for R. Includes console, syntax highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. Available in open source and commercial editions and runs on desktop Windows, Mac, and Linux or in browser connected to RStudio Server or RStudio Server Pro (Debian/Ubuntu, RedHat/CentOS, and SUSE Linux).

pCDH-puro-cMyc (plasmid)

RRID:Addgene_46970

TetO-FUW-PBRM1-pgk-puro (plasmid)

RRID:Addgene_85746

3xHA-TurboID-NLS_pCDNA3 (plasmid)

RRID:Addgene_107171

Scaffold (portal)

RRID:SCR_014321

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Visualize and validate complex MS/MS proteomics experiments

DiffBind (software resource)

RRID:SCR_012918

Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

UCSC Genome Browser (data or information resource)

RRID:SCR_005780

Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.

HOMER (software resource)

RRID:SCR_010881

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

MACS (software resource)

RRID:SCR_013291

Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity.

Salmon (software resource)

RRID:SCR_017036

Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.

FastQC (software resource)

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.

Nextflow (software resource)

RRID:SCR_024135

Software workflow manager that enables development of portable and reproducible workflows.Supports deploying workflows on variety of execution platforms including local, HPC schedulers, AWS Batch, Google Cloud Life Sciences, and Kubernetes. Provides support to manage workflow dependencies through built-in support for Conda, Spack, Docker, Podman, Singularity, Modules, and more.

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.

pLKO.1 puro (plasmid)

RRID:Addgene_8453