General Information
- Experiment ID
- OEX021031
- Experiment Name
- Spatial transcriptome
- Experiment Type
- Transcriptomic
- Description
- Mouse organogenesis spatial atlas composing collective transverse-sections at embryonic day 13.5 (E13.5) generated by 10x Genomics Visium platform, sequenced by Ilumina Novaseq 6000.
- Protocol
- Organogenesis stage (embryonic day 13.5, E13.5) embryos were collected of C57BL/6 mice, and embryos images were taken for recording and conformation of developmental staging. Collected embryos were embedded in Tissue freezing medium and stored at -80°C until sectioning. The whole embryo tissue was serially cryo-sectioned along craniocaudal axis at 10μm, and about 1000 sections were harvested. Considering the morphology and uniform sampling, 10 sections were selected for spatial transcriptomic analysis by 10x Genomics Visium platform. The resulting cDNA were synthesized, amplificated and then purified using AMpure beads and size-selected approximately 300-500bp. The cDNA library was assessed by Qubit 4.0 Fluorometer and Qsep100 Bio-Fragment Analyzer (Bioptic). The cDNA libraries were sequenced on Illumina Novaseq 6000 system with paired-end 150 bp reads, aiming for 100k raw reads per spot.
Experiment information
- Attributes
-
library_strategy RNA-Seq library_selection cDNA library_layout Paired platform Illumina NovaSeq 6000 - Project
-
1
Project ID Project name Create Date OEP003721 Three-dimensional molecular architecture of mouse organogenesis 2022-10-30 - Samples
-
14
Sample ID Sample Name Organism Tissue Create Date OES251608 E135_sec10 Mus musculus whole embryo 2022-11-01 OES251599 E135_sec1 Mus musculus whole embryo 2022-11-01 OES251600 E135_sec2 Mus musculus whole embryo 2022-11-01 OES251601 E135_sec3 Mus musculus whole embryo 2022-11-01 OES251602 E135_sec4 Mus musculus whole embryo 2022-11-01 OES251603 E135_sec5 Mus musculus whole embryo 2022-11-01 OES251604 E135_sec6 Mus musculus whole embryo 2022-11-01 OES251605 E135_sec7 Mus musculus whole embryo 2022-11-01 OES251606 E135_sec8 Mus musculus whole embryo 2022-11-01 OES251607 E135_sec9 Mus musculus whole embryo 2022-11-01 OES312430 E135_F6.5 Mus musculus whole embryo 2023-06-09 OES312431 E135_F7.5 Mus musculus whole embryo 2023-06-09 OES312432 E135_F8.5 Mus musculus whole embryo 2023-06-09 OES312433 E135_F9.5 Mus musculus whole embryo 2023-06-09 - Runs
-
14
Run ID Run Name Sample Data Num Create Date OER295197 E135_sec10 E135_sec10 3 2022-11-01 OER295198 E135_sec1 E135_sec1 3 2022-11-01 OER295199 E135_sec2 E135_sec2 3 2022-11-01 OER295200 E135_sec3 E135_sec3 3 2022-11-01 OER295201 E135_sec4 E135_sec4 3 2022-11-01 OER295202 E135_sec5 E135_sec5 3 2022-11-01 OER295203 E135_sec6 E135_sec6 3 2022-11-01 OER295204 E135_sec7 E135_sec7 3 2022-11-01 OER295205 E135_sec8 E135_sec8 3 2022-11-01 OER295206 E135_sec9 E135_sec9 3 2022-11-01 OER398664 E135_F6.5 E135_F6.5 3 2023-06-09 OER398665 E135_F7.5 E135_F7.5 3 2023-06-09 OER398666 E135_F8.5 E135_F8.5 3 2023-06-09 OER398667 E135_F9.5 E135_F9.5 3 2023-06-09 - Analysis
-
1
Analysis ID Analysis Title Analysis Type Data Num Create Date OEZ013173 Processing Other 0 2022-11-01
Author Information
- Create Date
- 2022-11-01
- Last Modified
- 2023-06-09
- Submission
- Guangdun Peng