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Series GSE104054 Query DataSets for GSE104054
Status Public on Dec 22, 2017
Title Spatial reconstruction of immune niches by combining photoactivatable reporter and single-cell RNA-seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Cellular function is strongly dependent on surrounding cells and environmental factors. Current technologies are limited in characterizing the spatial location and unique gene-programs of cells in less structured and dynamic niches. Here we developed a method (NICHE-seq) that combines photoactivatable fluorescent reporters, two-photon microscopy and single-cell RNA-seq to infer the cellular and molecular composition of niches. We applied NICHE-seq to examine the high-order assembly of immune cell networks. NICHE-seq is highly reproducible in spatial tissue reconstruction, enabling identification of rare niche-specific immune subpopulations and unique gene-programs, including natural killer cells within infected B cell follicles and distinct myeloid states in the marginal zone. This study establishes NICHE-seq as a broadly applicable method for elucidating high-order spatial organization of cell types and their molecular pathways.
Overall design Transcriptional profiling of single cells from the specific immune niches in the lymph node and spleen, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500
Contributor(s) Amit I, Shulman Z, Iannacone M, Medaglia C, Giladi A, Stoler Barak L, De Giovanni M
Citation(s) 29217582
Submission date Sep 20, 2017
Last update date May 15, 2019
Contact name Ido Amit
Phone 972-8-9343338
Organization name Weizmann Institute of Science
Department Immunology
Street address 234 Herzl st.
City Rehovot
ZIP/Postal code 760001
Country Israel
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (149)
GSM2788364 AB1655
GSM2788365 AB1656
GSM2788366 AB1657
BioProject PRJNA408125
SRA SRP118316

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Supplementary file Size Download File type/resource
GSE104054_RAW.tar 88.0 Mb (http)(custom) TAR (of TXT)
GSE104054_metadata.txt.gz 729.7 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file

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