The review discusses choices and challenges to be considered in each of the steps in planning omics experiments with a detailed discussion about strengths and weaknesses of various "healthy" tissue sources for omics and atlas studies.
Zhang D, Deng Y, Kukanja P, Agirre E, Bartosovic M, Dong M, Ma C, Ma S, Su G, Bao S, Liu Y, Xiao Y, Rosoklija GB, Dwork AJ, Mann JJ, Leong KW, Boldrini M, Wang L, Haeussler M, Raphael BJ, Kluger Y, Castelo-Branco G, Fan R.
Bueckle A, Qing C, Luley S, Kumar Y, Pandey N, Börner K.
This paper introduces ongoing research and development of the Human Reference Atlas (HRA) Organ Gallery, a virtual reality application offering an immersive view on the organs and tissue blocks of the HRA, and includes a description of use cases and current as well as planned features.
Swahn H, Li K, Duffy T, Olmer M, D'Lima DD, Mondala TS, Natarajan P, Head SR, Lotz MK.
We present a detailed single cell map of healthy human cartilage and meniscus describing markers, phenotypes, differentiation, regulation, and organization of cells, serving as reference for the analysis of joint diseases, such as osteoarthritis.
Jang H, Li Y, Fung AA, Bagheri P, Hoang K, Skowronska-Krawczyk D, Chen X, Wu JY, Bintu B, Shi L.
We present software tools for achieving super resolution (~60nm resolution) multiplex imaging of human organ tissues and cells, mapping spatial heterogeneity of metabolites and macromolecules relatively large scale tissue area to small cellular organelles.
Liao YC, Fulcher JM, Degnan DJ, Williams SM, Bramer LM, Veličković D, Zemaitis KJ, Veličković M, Sontag RL, Moore RJ, Paša-Tolić L, Zhu Y, Zhou M.
We highlight an integrated informatics workflow for regiospecific quantitation of hundreds of proteofroms from small dissected portions of tissue with nanodroplet processing in one pot for trace samples by top-down proteomics (nanoPOTS-TDP),
We outline the implementation of ultraviolet photodissociation (UVPD) for the confident characterization of proteoforms desorbed and ionized by MALDI for tandem mass spectrometry.
Tsai CF, Wang YT, Hsu CC, Kitata RB, Chu RK, Velickovic M, Zhao R, Williams SM, Chrisler WB, Jorgensen ML, Moore RJ, Zhu Y, Rodland KD, Smith RD, Wasserfall CH, Shi T, Liu T.
A streamlined nanoscale phosphoproteomics method for robust, sensitive, spatially resolved phosphoproteomics.
BigSpatial '22: Proceedings of the 10th ACM SIGSPATIAL International Workshop on Analytics for Big Geospatial Data 11/03/2022
Zemaitis KJ, Veličković D, Kew W, Fort KL, Reinhardt-Szyba M, Pamreddy A, Ding Y, Kaushik D, Sharma K, Makarov AA, Zhou M, Paša-Tolić L.
We demonstrate the first use of a custom ultrahigh mass range (UHMR) Orbitrap for the characterization of intact proteoforms up to 16.5 kDa directly from tissue with high mass resolving power and near cellular spatial resolution (20 μm) at high-throughput.
Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R.
We present spatially resolved chromatin accessibility profiling of tissue sections via next-generation sequencing by combining in situ ATAC-seq chemistry and microfluidic deterministic barcoding.
Su P, McGee JP, Durbin KR, Hollas MAR, Yang M, Neumann EK, Allen JL, Drown BS, Butun FA, Greer JB, Early BP, Fellers RT, Spraggins JM, Laskin J, Camarillo JM, Kafader JO, Kelleher NL.
Menon R, Bomback AS, Lake BB, Stutzke C, Grewenow SM, Menez S, D'Agati VD, Jain S.
We applied single cell and single nucleus RNAseq analysis and clinicopathological correlations using a biopsy from a single patient to delineate molecular features of acute kidney injury and insights into recovery.