153 research outputs found
Illuminating tissue organization by imaging the spatial transcriptome
No full textOur bodies consist of a large collection of cells that each have their own function in the organ that they reside in. The cells are grouped by functionality in cell types that arise during development as the result of the gene regulatory network encoded in the genome. With the development of novel single cell technologies, we are starting to understand just how diverse our cells are. In the brain for instance there are at least 3,000 distinguishable types. However, we have little understanding of how all these cell types are spatially organized in the tissue, because conventional labeling and microscopy techniques are incapable of resolving such high complexity in a single experiment.In this thesis I present the development of two methods that can resolve the cellular complexity and spatial organization of mouse and (developmental) human brain samples. These methods are built upon the concept of cyclic RNA labeling with single molecule Fluorescent in situ Hybridization (smFISH) to detect hundreds of gene targets in tissue samples. The resulting RNA localizations can then be used to study spatial gene expression and to identify the cell type of each cell in the sample. The cellular identity and position can then be used to study spatial relationships between cells to understand the tissue architecture.To place the development of these two methods into context, I will first review the field of spatially resolved transcriptomics. I will discuss the methods that are based on microscopy and spatially tagged RNA sequencing, where I will compare their strengths and weaknesses.Then I will present the two projects: Paper I presents the development of a cyclic smFISH protocol called osmFISH that leverages the high detection efficiency of smFISH to measure the gene expression of 33 cell type marker genes in the mouse somatosensory cortex at single cell resolution. We developed the labeling technology, instrumentation and analysis software to enable the study of cellular organization at multiple length scales.Even though osmFISH and related microscopy-based methods generate high quality data they are limited by the spatial throughput so that only small tissue areas can be processed. In paper II I present another method called EEL FISH that uses electrophoresis to transfer the RNA from a 3D tissue section onto a flat surface. The collapsing of one dimension substantially reduces the time needed to image, while retaining the information, so that the complex spatial gene expression profiles of entire mouse brain sections, sub-structures of the human brain and human developmental tissues can be studied.Lastly, I will discuss these results and look at the future of the field of spatially resolved transcriptomics.List of scientific papersI. Spatial organization of the somatosensory cortex revealed by osmFISH. Simone Codeluppi*, Lars E. Borm*, Amit Zeisel, Gioele La Manno, Josina A. van Lunteren, Camilla Svensson & Sten Linnarsson. Nature Methods. 2018 November;15(11):932-935. *Equal contribution. https://doi.org/10.1038/s41592-018-0175-z II. Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH. Lars E. Borm, Alejandro Mossi Albiach, Camiel C.A. Mannens, Jokubas Janusauskas, Ceren Özgün, David Fernández-García, Rebecca Hodge, Francisca Castillo, Charlotte R.H. Hedin, Eduardo J. Villablanca, Per Uhlén, Ed S. Lein, Simone Codeluppi & Sten Linnarsson. Nature Biotechnology. 2022 September. https://doi.org/10.1038/s41587-022-01455-3 </p
A note on games corresponding to sequencing situations with due dates
No full textconvex cooperative games;one-machine sequencing situations;due dates;ready times
Refinement of solutions to the linear complimentarity problem
No full textNash equilibrium;game theaory;matrices
Inter-Nord
No full textOn 5 February 2024, Professor Jean Malaurie passed away at his home in Dieppe at the age of 101. Having refused to join the compulsory work service (STO – Service du travail obligatoire) of the Nazi occupant in 1943, he went into hiding, joining the Résistance movement, an act of recalcitrance which characterized him profoundly and which was to entitle him to military honours during his funeral. The ceremony took place at the Saint-Louis-des-Invalides Cathedral in Paris on 14 February 2024, followed by the military honours and eulogy pronounced by the French Minister of Higher Education and Research, Professor Sylvie Retailleau.
It is with emotion that the editorial board of Inter-Nord wishes him farewell, paying a last tribute to the President of honour of our journal which he had founded with historian Fernand Braudel at the CNRS in the 1960s. We are publishing in French and English the homily of Father Geoffroy de la Tousche, the final remarks by Jean Malaurie’s son Guillaume and the minister’s speech, as well as a homage published in Le Canard enchaîné and a letter of condolences by Mrs Audrey Azoulay, Director-General of UNESCO.
Inter-Nord 23 continues in the interdisciplinary and intersectorial vein which has been its imprint introduced by Jean Malaurie right from the start, trying to propose bilingual versions of texts as far as possible. The current issue contains a special section with three scientific research articles on Iceland, two of which were first presented at the annual Humanities conference of the University of Iceland in 2023. These texts are accompanied by graphic works of the Icelandic artist Thóra Sigurðardóttir. Many thanks to Thóra for letting us publish some of her intriguing artwork discussed in a stunning piece by the Icelandic poetess Sigurbjörg Thrastardóttir.
In the creative writing section, we are also publishing two pieces by the Quebecois author Monique Durand about the Faroe Islands and interviews with Alaskan author Nancy Lord and the journalist Olivera Tornau. Other contributions include a viewpoint signed by four UArctic Chairs, an original French research project and some reviews of Malaurie’s and other works
Inter-Nord
No full textInter-Nord 24 is largely dedicated to Alaska. On the front and back covers feature three Yup’ik masks brought back to Pennsylvania by Moravian missionaries in the early 20th century. They are now held in the collections of the Moravian Historical Society in Nazareth, PA, USA, to which we are grateful for granting permission to publish these images. The front cover also includes a photograph from a series taken by Bruce Jackson during his field trip with Jean Malaurie to Nome and its region in 1997. Many thanks to Bruce for letting us reprint several of his images.
The issue’s contributions dedicated to Alaska include three peer-reviewed scientific articles, two student research papers from the University of Vienna based on field work, introduced by Peter Schweitzer and Olga Povoroznyuk, and two interviews: one with Iñupiaq contemporary artist Aisa Warden conducted by Daniel Chartier and the other with Mrs Lyn Trodahl Chynoweth, daughter of a Moravian missionary who grew up at Nunapitsinghak, site of the Moravian Children’s Home on the Kwethluk, a tributary to the Kuskokwim river, conducted by Benjamin Ferguson, as well as polar readings offered by Muriel Brot.
Inter-Nord 24 also pays homage to British poet and anthropologist Tom Lowenstein who passed away in March 2025 in his 84th year. Tom was notably the author of the acclaimed volume Ancient Land: Sacred Whale (1993, republished 1999). We are grateful to his literary executors to have authorised us to republish two longer excerpts, accompanied by translations into French for which we would like to sincerely thank Professor Hélène Aji of the École normale supérieure in Paris. Hélène had translated these poems on the occasion of the international conference “Problèmes arctiques : environnement, sociétés et patrimoine/ Arctic problems: environment, societies and heritage” organised by Jean Malaurie and myself at the National Museum of Natural History in Paris in March 2007 during the Fourth International Polar Year. Tom was one of the invited speakers, contributing a paper about his then forthcoming history of Point Hope, Alaska, Ultimate Americans (University of Alaska Press, 2008) published in Inter-Nord 21 (2011, pp. 149-152). Tom has published a fascinating volume about his field work, The Structure of Days Out (2021) which has not received the attention it deserves so far. Farewell to the poet!
Inter-Nord 24 also features three other peer-reviewed scientific articles in the section entitled “Varia”, illustrating the fact that we are open to scientific papers on any topic in relation to the Arctic. It also contains a viewpoint. Many thanks to all contributors
S.L.I.M., a small linear interdependent model of eight EU-member states, the USA and Japan
No full textInternational Economics;EU
Herd behavior, the "Penguin effect", and the suppression of informational diffusion: An analysis of informational externalities and payoff interdependency
No full textTechnology;Information;Econometric Models;Group Behaviour
Optimal design of experiments with simulation models of nearly saturated queues
No full textexperimental design;simulation models;queueing network;regression analysis
EEL Mouse 440 genes single cell data
No full textCell by gene matrix of the EEL mouse 440 gene experiment.
Single cell data generated by EEL FISH on a saggital mouse brain section. The dataset is available in 3 file formats:
.loom Loom file see: http://loompy.org/
.h5ad AnnData file see: https://anndata.readthedocs.io/en/latest/index.html
.tab Tab-delimited file.
Metadata
Age - Age of animal.
Codebook - Name of EEL codebook.
ColorDict - Cell cluster color dictionary.
Cycles - Number of barcoding cycles.
Expansion - Pixels the nuceli were expanded (pixelsize = 0.27um).
Expansion_um - Expansion of nuclei in micrometer.
Experiment - Experiment ID.
ExperimentDate - Date of experiment.
FOVoverlapPercentage - Overlap between field of view.
GenerationDate - Loom file generation date.
LOOM_SPEC_VERSION - Loompy version.
MaxHammingDist - maximum allowed Hamming distance.
Operator - Experiment operator.
Orientation - Cutting orientation.
Probes - Probe sequences file.
Protocol - Protocol used.
Quality - Manual evaluation of quality.
RNAfile - RNA file used
Removal - Method of removal of overlapping RNA in overlapping fields of view.
Sample - Sample ID
Segmentation - Segmentation algorithm.
Species - Species of sample.
Stitching - Field of view stitching method.
StitchingChannel - Between cycle alignment channel.
Strain - Strain of animal.
System - Microscope system used.
Tissue - Tissue in experiment.
TotalMolecules - Total number of molecules assigned to cells.
Column metadata
X - X coordinate in pixels of 0.27um (multiply by 0.27 to get micrometer).
X_um - X coordinate in micrometer.
Y - Y coordinate in pixels of 0.27um (multiply by 0.27 to get micrometer).
Y_um - Y coordinate in micrometer.
tSNE_X - tSNE component 1.
tSNE_Y - tSNE component 2.
Clusters - Cluster label of each cell.
TotalMolecules - Total molecules per cell.
Cluster colors are saved as individual RGB values:
R - Red.
G - Green.
B - Blue.
(In the AnnData file, the tSNE and RGB values are availabe as a single array under "obsm" with keys "tSNE" and "RGB" respectively. )
Row metadata
Gene - Gene name.
GeneTotal - Total number of detected molecules per gene.</p
EEL mouse sagittal atlas 168 genes spatial RNA data
No full textRaw RNA locations of the mouse atlas produced by EEL FISH for 168 genes.
RNA files are in the .parquet format which can be opened with FISHscale (https://github.com/linnarsson-lab/FISHscale) or any other parquet file reader (https://arrow.apache.org/docs/index.html)
RNA .parquet files
Seven sagittal sections of the mouse brain with 168 detected genes, sampled at the medial-lateral positions of -140 µm, 600 µm, 1200 µm, 1810 µm, 2420 µm, 3000 µm and 3600 µm measured from the midline.
Position and gene label for all RNA molecules.
"c_px_microscope_stitched" contains X coordinates.
"r_px_microscope_stitched" contians Y coordinates.
The unit are pixels with a size of 0.18 micrometer. Multiply by 0.18 to get um scale.
"Valid" Boolean column where a 1 means that the molecule is detected inside the tissue section. A zero means the molecule is detected outside.
Tissue polygons .csv files
CSV files demarking the sample borders for the 7 mouse atlas sections. -140 µm, 600 µm, 1200 µm, 1810 µm, 2420 µm, 3000 µm, 3600 µm.
These polygons were used to generate the "Valid" column. If you want to make your own selection please have a look at the code in: https://github.com/linnarsson-lab/FISHscale/blob/master/FISHscale/utils/inside_polygon.py
Gene colors .pkl file
Pickled Python dictionary with gene colors used in the paper for the mouse atlas.</p
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