News

RBK's data offerings to date

Mar 25, 2019

Following on the heels of last week’s announcement of our new single cell RNA-Sequencing visualizations, the RBK Hub will now be sending out regular updates when we publish new data offerings or features on rebuildingakidney.org.

To kick off, this news item will go over the kinds of data you can now find on our repository in our fourth year of funding. The Consortium has certainly been busy!

The following is a list of Top Ten most popular resources on our website for the past year1.

  1. Collection 14-4KG6: Single-Nucleus versus Single-Cell RNA Sequencing of Adult Mouse Kidney

  2. Protocol N-H9AY: Digestion protocol for kidney single cell suspension

  3. scRNA-Seq Study 14-4KBA: Single-Nucleus versus Single-Cell RNA Sequencing of Adult Mouse Kidney

  4. Protocol N-H9DA: Psychrophilic (Cold) protease dissociation of mouse kidney

  5. Protocol N-H9AT: Adult Mouse Kidney Dissociation

  6. Sequencing Experiment 14-4KBE: Characterizing UUO kidney using snRNA-seq

  7. Principal Investigator W-Q5HT: Steve Potter, CCHMC

  8. Parental Cell-Line Q-2D6W: BJFF6

  9. Protocol W-R934: Dissociating adult human kidney tissue (on ice)

  10. scRNA-Seq Experiment 14-4KBC: Comparison of scRNA-seq and snRNA-seq

And here’s an overview of the major types of data you can find:

Lab Protocols

RBK has released 25 protocols in subjects ranging from experimental organisms, immunological techniques, to gene expression analysis.

Antibody Validation

Our repository includes 192 records of antibody tests labeling known cell populations in the kidney, validated against mouse and human tissues under different fixation conditions.

Transgenic Lines

RBK offers characterization of the reporter and modified iPS cell lines used in the consortium. We now have 5 parental cell lines and 10 reporter cell lines.

Gene Expression Data

We offer 21 Sequencing studies that profile discrete cell populations in the developing kidney and are made available for download. The current breakdown of sequencing studies is:

Immunohistochemistry Data

RBK has uploaded 29 immunohistochemistry datasets for mouse and human.

Collections

Data Collections organize data outside of their own study/dataset into a citable “one-stop shop” of complete data related to a publication or collaboration. We currently host 12 collections for recent RBK publications.

Search by Genes

Search for data by genes of interest. To search by multiple genes, enter a list of genes separated by the pipe | character. For example: colx|six2|win

The RBK/GUDMAP repository includes data relevant to almost 23,000 genes. On each gene page you’ll find data available via microarray heatmaps, imaging data for specimens and expression scoring among others. Gene pages also provide convenient links to external reference sources such as NCBI, Ensembl, HGNC, MIM, and Vega.


Be on the lookout for our postings about the newest data on the RBK site soon!

  1. The ranking of most popular resources is based on the number of user pseudo IDs (if allowed) or IP addresses (if user pseudo IDs were denied) from the system logs.