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.
Collection 14-4KG6: Single-Nucleus versus Single-Cell RNA Sequencing of Adult Mouse Kidney
Protocol N-H9AY: Digestion protocol for kidney single cell suspension
scRNA-Seq Study 14-4KBA: Single-Nucleus versus Single-Cell RNA Sequencing of Adult Mouse Kidney
Protocol N-H9DA: Psychrophilic (Cold) protease dissociation of mouse kidney
Protocol N-H9AT: Adult Mouse Kidney Dissociation
Sequencing Experiment 14-4KBE: Characterizing UUO kidney using snRNA-seq
Principal Investigator W-Q5HT: Steve Potter, CCHMC
Parental Cell-Line Q-2D6W: BJFF6
Protocol W-R934: Dissociating adult human kidney tissue (on ice)
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:
RBK has released 25 protocols in subjects ranging from experimental organisms, immunological techniques, to gene expression analysis.
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.
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:
RBK has uploaded 29 immunohistochemistry datasets for mouse and human.
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 for data by genes of interest. To search by multiple genes, enter a list of genes separated by the pipe
| character. For example:
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!
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. ↩