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Sample GSM4189613 Query DataSets for GSM4189613
Status Public on Sep 16, 2020
Title 0702cL
Sample type SRA
 
Source name mouse embryo, day 10
Organism Mus musculus
Characteristics tissue: Embryo
developmental stage: Embryonic day 10
resolution: 50 micron
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description 0702cL
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.
 
Submission date Nov 22, 2019
Last update date Sep 16, 2020
Contact name Mingyu Yang
E-mail(s) mingyu.yang@yale.edu
Phone 2033618885
Organization name Yale
Department Biomedical Engineering
Lab Fan group
Street address 55 Prospect St., Room 103
City New Haven
State/province CT
ZIP/Postal code 06511
Country USA
 
Platform ID GPL21103
Series (1)
GSE137986 High spatial resolution multi-omics atlas sequencing of mouse embryos
Relations
BioSample SAMN13353850
SRA SRX7202766

Supplementary file Size Download File type/resource
GSM4189613_0702cL-50um-e10.png.gz 477.7 Kb (ftp)(http) PNG
GSM4189613_0702cL.tsv.gz 5.3 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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