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Key Resources Tables

Pranav Kumar Mishra 2023-10-16

Adapted from the Cell Press STAR Methods to help produce Structured, Transparent, Accessible Reporting in research.

This page is a living document and a work-in-progress. With the goal of improving research reproducibility, several major journals now require a detailed listing of the key resources required to conduct the experiments described.

Schedule permitting, I will update the “csv databases”, which can be found on GitHub. Using Quarto and Python, the csv files are rendered into HTML and GitHub-flavored Markdown. The markdown file is additionally rendered in my Wordpress post.

Antibodies

REAGENT or RESOURCE SOURCE IDENTIFIER Size (kDA) Source Target RRID
ADAMTS4 Ab RnD Cat# MAB4307; RRID:AB_2222318 58 Mouse Human AB_2222318
Aggrecan Ab RnD Cat# AF1220; RRID:AB_2219833 120 Goat Human AB_2219833
Collagen II Ab Abcam Cat# ab34712; RRID:AB_731688 141 Rabbit Human AB_731688
IL-1β Ab Santa Cruz Cat# SC-32294; RRID:AB_627790 17 Mouse Human AB_627790
IL-36RA Ab RnD Cat# AF1275; RRID:AB_2124757 17 Goat Human AB_2124757
IL-36α Ab RnD Cat# AF1078; RRID:AB_2124771 16 Goat Human AB_2124771
Lubricin (PRG4) Ab Rush U – – Rabbit Human –
MMP13 Ab RnD Cat# AF511; RRID:AB_355401 55 Goat Human AB_355401
SOX-9 Ab Abcam Cat# ab185966; RRID:AB_2728660 70 Rabbit Human AB_2728660

Note: RRIDs are sourced from the Antibody Registry, via SciCrunch

Acknowledgement: We would like to acknowledge Dr. Thomas Schmid at Rush University for preparing and sharing the Lubricin (PRG4) antibody with our group.

Biological Samples

REAGENT or RESOURCE SOURCE IDENTIFIER

Chemicals; peptides; and recombinant proteins

REAGENT or RESOURCE SOURCE IDENTIFIER Experiment
Alcohol 100% Sigma-Aldrich 65347-M Histology
EM-400 Embedding Medium Paraffin Leica 3801320 Histology
Paraplast X-tra Leica 39603002 Histology
Reagent Alcohol 95% Histoprep Fisher HC13001GL Histology
Tissue Path™ Disposable Embedding Rings Fisher 22038198 Histology
Xylenes (Histological) Fisher Chemical X3P-1GAL Histology
10x Tris/Glycine/SDS Buffer Bio-Rad 1610732 Western Blot
2-Mercaptoethanol Bio-Rad 1610710 Western Blot
4x Laemmli Sample Buffer Bio-Rad 1610747 Western Blot
BCA Protein Assay Kit Pierce 23225 Western Blot
Glycine Sigma G-7126 Western Blot
Methanol (100%) Ficher A412-4 Western Blot
Pierce Protease and Phosphatase Inhibitor Mini Tablets EDTA-Free Thermo A32961 Western Blot
Pierce RIPA Buffer Thermo Scientific 89901 Western Blot
Precision Plus Protein Dual Color Standards Bio-Rad 1610374 Western Blot
Restore Western Blot Stripping Buffer Thermo 21059 Western Blot
SDS Fisher BP166-500 Western Blot
Spectra Multicolor High Range Protein Ladder Thermo Scientific 26625 Western Blot
TRIzol Reagent Ambion 15596018 Western Blot
Tris Base Fisher BP154-1 Western Blot
Tween-20 Santa Cruz SC-29913 Western Blot
PowerUp SYBR Green Master Mix Applied Biosystems A25742 qPCR
RNaseZap Sigma R2020-250ML qPCR
SuperScript IV VILO Master Mix Invitrogen 11766050 qPCR
TRIzol™ Reagent Invitrogen 15-596-018 qPCR
Sodium Chloride Fisher S630-10 –

Deposited Data

REAGENT or RESOURCE SOURCE IDENTIFIER
A molecular single-cell lung atlas of lethal COVID-19 GEO GSE171524 – Learning
Cells of the adult human heart Human Cell Atlas DOI: 10.1038/s41586-020-2797-4 – Learning

Experimental models: Cell Lines

REAGENT or RESOURCE SOURCE IDENTIFIER Project Purpose

Experimental models: Organisms and Strains

REAGENT or RESOURCE SOURCE IDENTIFIER

Oligonucleotides

REAGENT or RESOURCE SOURCE IDENTIFIER

Recominant DNA

REAGENT or RESOURCE SOURCE IDENTIFIER

Software Algorithms

REAGENT or RESOURCE SOURCE IDENTIFIER

Other

REAGENT or RESOURCE SOURCE IDENTIFIER Experiment Category
BD Vacutainer Serum BD 367815 Blood test –
BD Vacutainer Sodium Herparin BD 367878 Blood test –
HbA1c Controls Afinion 1115178 Blood test –
HbA1c Test Kit Afinion 1115015 Blood test –
Nova Max Glucose Test Strips Nova 43523 Blood test –
Nova Max Plus Nova 43436 Blood test Hardware
Gentamicin (50 mg/mL) Glibco 15750060 Cell culture Drug
MicroAmp EnduraPlate Optical 384-well clear reaction plate with barcode Applied Biosystems 4483285 qPCR –
MicroAmp Fast 96-well Reaction Plate (0.1mL) Applied Biosystems 4346907 qPCR –
#10 Surgical Blade Bard-Parker 371110 – –
Dr. Pranav Mishra

Dr. Pranav Mishra

Dr. Pranav Mishra is a physician-scientist in-training. He is currently a post-doctoral research fellow in the Departments of Surgery and Orthopedic Surgery at Rush University. As a hobby, he enjoys learning about programming, self-hosting, and open-source software through personal projects. This sparked his interest in data science / bioinformatics, developing reproducible and auditable environments for his research projects. You can find his contact information listed on his website and connect with him on most socials @drpranavmishra.