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| Status |
Public on Sep 16, 2020 |
| Title |
E11-2L |
| Sample type |
SRA |
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| Source name |
mouse embryo, day 11
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| Organism |
Mus musculus |
| Characteristics |
tissue: embryo
developmental stage: Embryonic Day 11
resolution: 25 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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| Data processing |
Illumina Casava 1.8.2 software used for basecalling.
The processed read was trimmed, mapped against the mouse genome(GRCh38), demultiplexed and annotated(Gencode release M11) using the ST pipeline v1.7.2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts for each pixels for each Sample
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| Submission date |
Feb 27, 2020 |
| 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 |
SAMN14238175 |
| SRA |
SRX7815846 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4364243_E11-2L.png.gz |
701.1 Kb |
(ftp)(http) |
PNG |
| GSM4364243_E11-2L.tsv.gz |
5.7 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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