GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Series GSE128350

Query DataSets for GSE128350

Status

Public on Jun 05, 2020

Title

Multi-species tomo-sequencing identifies new major hematopoietic stem cell regulators in the microenvironment of the embryonic aorta

Organisms

Danio rerio; Gallus gallus; Homo sapiens; Mus musculus

Experiment type

Expression profiling by high throughput sequencing

Summary

The behavior of (stem) cells is regulated by their local microenvironment through biochemical and biophysical interactions. To advance our understanding of the molecular characteristics and key components of the microenvironment, we applied a genome-wide RNA tomography sequencing approach in zebrafish, chicken, mouse and human embryos. The resulting anterior-posterior and/or dorsal-ventral transcriptional maps provide a powerful resource for identifying and comparing expression patterns in a given tissue or microenvironment along the embryonic axes of multiple species. We used these maps to explore the regulatory function of the aortic microenvironment, where the first hematopoietic stem cells are generated during embryonic development. By performing inter-species comparative analyses, we identified and functionally validated new conserved regulators of hematopoietic stem cell generation. Further analysis of spatial transcriptomics will elucidate the regulatory functions of the local microenvironment in vivo, paving the way for improved (stem) cell production in vitro and clinical cell therapy.

Overall design

Spatial transcriptomics by RNA-tomography (Tomo-seq) on whole or sub-dissected embryos (processed along the anterior-to-posterior axis) and on transversal thick slices (processed along the dorsal-to-ventral axis).

Contributor(s)

Yvernogeau L, Morin-Poulard I, Klaus A, Maas J, Schulte-Merker S, Berezikov E, Junker JP, Robin C

Citation(s)

Submission date

Mar 15, 2019

Last update date

Sep 07, 2020

Contact name

Catherine Robin

E-mail(s)

c.robin@hubrecht.eu

Organization name

Hubrecht Institute

Street address

Uppsalalaan 8

City

Utrecht

ZIP/Postal code

3584 CT

Country

Netherlands

Platforms (7)

More...

GPL16791	Illumina HiSeq 2500 (Homo sapiens)
GPL17021	Illumina HiSeq 2500 (Mus musculus)
GPL18573	Illumina NextSeq 500 (Homo sapiens)

Samples (27)

More...

GSM3672134	Extracted RNA 3-day old chicken embryo from posterior-to-anterior axis
GSM3672135	Extracted RNA 3-day old chicken sub-dissected aorta from posterior-to-anterior axis
GSM3672136	Extracted RNA 4-day old chicken anterior slice #1 from dorsal-to-ventral axis

GSM3672137	Extracted RNA 3-day old chicken posterior slice #1 from dorsal-to-ventral axis
GSM3672138	Extracted RNA 4-day old chicken posterior slice #1 from dorsal-to-ventral axis
GSM3672139	Extracted RNA 3-day old chicken anterior slice #1 from dorsal-to-ventral axis
GSM3672140	Extracted RNA 3-day old chicken IAHC cells
GSM3672141	Extracted RNA 10.5-day old mouse slice #3 from dorsal-to-ventral axis
GSM3672142	Extracted RNA 35-day old human slice #2 from dorsal-to-ventral axis (1st part)
GSM3672143	Extracted RNA 35-day old human slice #2 from dorsal-to-ventral axis (2nd part)
GSM3672144	Extracted RNA 35-day old human slice #1 from dorsal-to-ventral axis
GSM3672145	Extracted RNA 40 hpf whole zebrafish embryo #1 from anterior-to-posterior axis
GSM3672146	Extracted RNA 28 hpf whole zebrafish embryo #1 from anterior-to-posterior axis
GSM3672147	Extracted RNA 28 hpf whole zebrafish embryo #2 from anterior-to-posterior axis
GSM3672148	Extracted RNA 28 hpf zebrafish trunk #1 and #2 from dorsal-to-ventral axis
GSM3672149	Extracted RNA 40 hpf zebrafish trunk #1 and #2 from dorsal-to-ventral axis
GSM3672150	Extracted RNA 10.5-day old mouse slice #1 from dorsal-to-ventral axis
GSM3672151	Extracted RNA 10.5-day old mouse slice #2 from dorsal-to-ventral axis
GSM3672152	Extracted RNA 11.5-day old mouse slice #1 from dorsal-to-ventral axis
GSM3672153	Extracted RNA 11.5-day old mouse slice #2 from dorsal-to-ventral axis
GSM3672154	Extracted RNA 11.5-day old mouse slice #3 from dorsal-to-ventral axis
GSM3672155	Extracted RNA 3-day old chicken anterior slice #2 from dorsal-to-ventral axis
GSM3672156	Extracted RNA 3-day old chicken posterior slice #2 from dorsal-to-ventral axis
GSM3672157	Extracted RNA 40 hpf whole zebrafish embryo #2 from anterior-to-posterior axis
GSM3672158	Extracted RNA 28 hpf whole zebrafish embryo #3 from posterior-to-anterior axis
GSM3672159	Extracted RNA 3-day old chicken posterior slice #3 from dorsal-to-ventral axis
GSM3672160	Extracted RNA 3-day old chicken anterior slice #3 from dorsal-to-ventral axis

Relations

BioProject

SRA

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE128350_RAW.tar	15.1 Mb	(http)(custom)	TAR (of CSV)
GSE128350_readme_demultiplexing.pdf	31.8 Kb	(ftp)(http)	PDF
GSE128350_readme_sample_names_and_primers.xlsx	9.9 Kb	(ftp)(http)	XLSX
SRA Run Selector
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |