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| Status |
Public on Sep 14, 2021 |
| Title |
LCWE [Spatial transcriptomics] |
| Sample type |
SRA |
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| Source name |
whole slide
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
condition: LCWE
tissue: heart
10xgenomics_protocol: Visium, Spatial 3' V1, 10x Genomics
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| Treatment protocol |
none
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| Growth protocol |
none
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
WT mice were injected with either PBS or LCWE and one week later, heart tissues collected, embedded in OCT and sectioned on a cryostat at a thickness of 10µm. Tissue was enzymatically permeabelized accroding to the Visium protocol.
RNA libraries were prepared for sequencing using the Visium Spatial 3' V1, 10x Genomics protocol. Sequencing was done with NovaSeq 6000 using a custom paired-end sequencing protocol, consisting of: read 1, 28 cycles; index 1, 10 cycles; index 2, 10 cycles; read 2, 120 cycles.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20.
Space Ranger software v1.0.0 (10X Genomics) was used for reads alignment, tissue detection, fiducial detection, and barcode/UMI counting with default parameters to obtain possorted_genome_bam.bam and processed data files
Genome_build: mm10
Supplementary_files_format_and_content: count_matrix.csv, barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_feature_bc_matrix.h5, tissue_hires_image.png
Supplementary_files_format_and_content: count matrix for all cells from all samples in matrix.mtx. Cell ID in barcodes.tsv. Genes in genes.tsv. Metadata in metadata.tsv
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| Submission date |
Jun 23, 2021 |
| Last update date |
Sep 16, 2021 |
| Contact name |
David Zemmour |
| E-mail(s) |
davidpz@fas.harvard.edu, david.puyraimond@gmail.com
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| Organization name |
Harvard Medical Schol
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| Street address |
77 avenue Louis Pasteur
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| City |
Boston |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE178799 |
Spatial transcriptomics (Visium, Spatial 3' V1, 10x Genomics) analysis of heart tissues in a murine model of Kawasaki disease vasculitis |
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| Relations |
| BioSample |
SAMN19843138 |
| SRA |
SRX11217056 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5397926_LCWE_barcodes.tsv.gz |
6.9 Kb |
(ftp)(http) |
TSV |
| GSM5397926_LCWE_count_matrix.csv.gz |
2.8 Mb |
(ftp)(http) |
CSV |
| GSM5397926_LCWE_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM5397926_LCWE_filtered_feature_bc_matrix.h5 |
6.1 Mb |
(ftp)(http) |
H5 |
| GSM5397926_LCWE_matrix.mtx.gz |
15.5 Mb |
(ftp)(http) |
MTX |
| GSM5397926_LCWE_tissue_hires_image.png.gz |
3.4 Mb |
(ftp)(http) |
PNG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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