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| Status |
Public on Sep 16, 2020 |
| Title |
0628cL |
| Sample type |
SRA |
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| Source name |
mouse embryo, day 12
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| Organism |
Mus musculus |
| Characteristics |
tissue: Embryo
developmental stage: Embryonic day 12
resolution: 50 micron
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| Extracted molecule |
total RNA |
| Extraction protocol |
The freshly dissected embryos were immersed into OCT and snapped frozen with liquid nitrogen. Before sectioning, the frozen tissue block was warmed to the temperature of cryotome cryostat (-20°C). Tissue block was then sectioned into thickness of <7 µm and placed in the center of a poly-L-lysine coated glass slide (CatLog no. 63478-AS, electron microscopy sciences). The slide was kept at -80 °C until use.
The sequencing library was built with a Nextera XT kit (Illumina) and sequenced using a HiSeq 4000 sequencer using a pair-end 100x100 mode.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
0628cL
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| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
The submitted raw data have been transformed from the original read data. Read 1 contains the barcode and UMI. Read 2 is the biological read. The submitted format is compatible with the software st-pipeline: https://github.com/SpatialTranscriptomicsResearch/st_pipeline
The image reformed.png illustrates the raw data transformation.
The processed read was trimmed, mapped against the mouse genome (GRCh38), demultiplexed and annotated (Gencode release M11) using the ST pipeline v1.7.2.
The file barcodes.merge.sort.txt includes the barcode for each position. Column 1 = barcode, Column 2 = X coordinate, Column 3 = Y coordinate.
Genome_build: GRCh38
Supplementary_files_format_and_content: *tsv: Tab-delimited text files include counts for each pixels for each Sample.
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| Submission date |
Nov 22, 2019 |
| Last update date |
Sep 16, 2020 |
| Contact name |
Mingyu Yang |
| E-mail(s) |
mingyu.yang@yale.edu
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| Phone |
2033618885
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| Organization name |
Yale
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| Department |
Biomedical Engineering
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| Lab |
Fan group
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| Street address |
55 Prospect St., Room 103
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| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06511 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (1) |
| GSE137986 |
High spatial resolution multi-omics atlas sequencing of mouse embryos |
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| Relations |
| BioSample |
SAMN13353851 |
| SRA |
SRX7202765 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4189612_0628cL-50um-e12.png.gz |
1.5 Mb |
(ftp)(http) |
PNG |
| GSM4189612_0628cL.tsv.gz |
5.3 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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