Comment[GEAAccession]	E-GEAD-610
MAGE-TAB Version	1.1
Investigation Title	Spatio-temporal specific  gene expression analysis in embryonic growth plate chondrocytes
Experiment Description	The purpose of this study is to comprehensively analyze the developmental stages and spatially specific gene expression in the growth plate chondrocytes in femoral cartilage tissue during embryonic development. A series of analyses will identify spatiotemporally expressed membrane proteins in the tissue. Furthermore, the analysis will elucidate intracellular signals that are activated by their stimulation. We furthere aim to identify the way to artificially regulate physiological functions based on the molecular mechanisms elucidated.
Experimental Design	development or differentiation design	time series design
Experimental Factor Name	embryonic development	genotype
Experimental Factor Type	embryonic development	genotype
Person Last Name	Ichimura	Sequence
Person First Name	Atsuhiko	Kashiwa
Person Affiliation	Atsuhiko Ichimura Group. Kyoto University Graduate School of Biological Chemistry	
Person Roles	submitter	submitter
Public Release Date	2025-06-01
Protocol Name	P-GEAD-1797	P-GEAD-1798	P-GEAD-1799	P-GEAD-1800	P-GEAD-1801
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Isolate femoral and tibial bones from E16.5 or E17.5 mice, and immediately submerge bone tissues in 4% paraformaldehyde for 12-16 hours. Remove conective or muscle tissue aroud bone. Submerge tissues in 70% ethanol for 15 minutes, 90% ethanol for 15 minutes and then, 100% ethanol for 15, 15, 30 and 45 minutes. Submerge tissues in pathoclean (xylene substitute) for 20, 20 and 45 minutes. Place in 80 degrees Celsius paraffin for 30, 30 and 45 minutes. Embed tissues in paraffin. Incubate paraffin block on the ice bath for 20-30 minutes. Section tissue for 6?m and allow sections to float on milli-Q at 42 degrees Celsius for 20-30 minutes. Place the section to the allowable area on the slide. Incubate for 3 hours in an oven at 42 degrees Celsius. Place in a desiccator and keep overnight at room temperature.	Visium CytAssist Spatial Gene Expression Reagent Kits	The sequence library was constructed using the Visium CytAssist Spatial Gene Expression Reagent Kits(10x Genomics)	Sequencing was performed on the Illumina NovaSeq6000 in paired end mode; Read1:Spatial Barcode, UMI(28 bp), i7 Index:Sample Index(10 bp), i5 Index:Sample Index(10 bp), Read2:Insert(50 bp).	Sequenced reads were mapped to genome assembly by Mus musculus: GCF_000001635.20, using spaceranger v2.0.0(10x Genomics). Slide information; A_1_E17-5_E16-5:slide=V42Y23-293,area=A1, A_E16-5_17-5_5:slide=V42U13-60,area=A1, A_Tric_bKO_1:slide=V42U13-92,area=A1, A_Tric_bKO_5:slide=V42U13-58,area=A1, D_2_E17-5_E16-5:slide=V42Y23-293,area=D1, D_Fgfr3_Tg_3:slide=V42U13-92,area=D1, D_Npr2_fl_fl_Col2_Cre_plus_3:slide=V42U13-58,area=D1, D_Trick_bKO_2:slide=V42U13-60,area=D1
SDRF File	E-GEAD-610.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB15578
Comment[Last Update Date]	2025-06-01