|
| Status |
Public on Apr 21, 2022 |
| Title |
Mouse heart encasing a 4-mm section of human skin (sample HM-3 in the manuscript) |
| Sample type |
SRA |
| |
|
| Source name |
Mouse heart and human skin
|
| Organisms |
Homo sapiens; Mus musculus |
| Characteristics |
mouse strain: C57BL/6J
tissue: Mouse heart and human skin
age: 10 week old mouse and 52 year old human
genotype: wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Moue tissues and human skin were harvested on the same day and manually prepared into chimera tissue blocks on ice, then flash frozen in OCT histology media. Spatial transcriptomics was performed using standard 10x protocol for the Visium Spatial Gene Expression kit (Cat no. PN-1000-187) with permeabilization time of 12 min.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Chimera of mouse heart encasing a 4-mm section of human skin (sample MS-3 in the manuscript)
|
| Data processing |
bcl2fastq v2.20.0.422 was used for basecalling and demultiplexing.
Tissues were manually aligned using Loupe Browser v4.2.0.
Raw fastq files were aligned and quantified using Space Ranger v1.2.2 under default settings. The Visium slide ID is V10F06-009. The capture areas for 1_S1, 2_S2, 3_S3 are A1, B1, C1.
Genome_build: GRCh38+mm10
Supplementary_files_format_and_content: tar.gz: A tarball for each sample containing all outputs from Space Ranger pipeline, except for BAM file.
|
| |
|
| Submission date |
Jun 15, 2021 |
| Last update date |
Apr 21, 2022 |
| Contact name |
Zijian Ni |
| E-mail(s) |
zni25@wisc.edu
|
| Organization name |
University of Wisconsin-Madison
|
| Street address |
425 Henry Mall
|
| City |
Madison |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platform ID |
GPL25526 |
| Series (1) |
| GSE178221 |
SpotClean adjusts for spot swapping in spatial transcriptomics data |
|
| Relations |
| BioSample |
SAMN19711198 |
| SRA |
SRX11148821 |
