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| Status |
Public on Nov 17, 2020 |
| Title |
Visium_10X |
| Sample type |
SRA |
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| Source name |
Saggital section
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
brain region: Saggital section
developmental stage: P8
strain: C57BL/6NTac
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| Extracted molecule |
total RNA |
| Extraction protocol |
As per recommendations of each individual platform
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
spatial sequencing
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| Data processing |
Illumina basecaller
PacBio IsoSeq basecaller
Oxford Nanopore Guppy basecaller
10X sequencing output processed with 10X cellranger v3
Cellranger output analyzed with Seurat v3
PacBio long read mapping done with STARlong
ONT long read mapping done with minimap2
Long read output processed with custom pipelines - Github
website with downloadable plots of the processed data: www.isoformAtlas.com
github repository with code: https://github.com/noush-joglekar/scisorseqr/
Genome_build: mm10
Supplementary_files_format_and_content: cellranger output for single-cell expression data
Supplementary_files_format_and_content: PacBio gff files: files were generated by mapping and aligning reads to the reference genome, and each line refers to an exon for a specific read. We selected reads that were uniquely mapped, spliced, and had consensus splice-sites. The files include 'hg19' but were from mm10 alignment.
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| Submission date |
Sep 23, 2020 |
| Last update date |
Nov 17, 2020 |
| Contact name |
Anoushka Joglekar |
| E-mail(s) |
anj2026@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Department |
Dept. of Neurogenetics
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| Lab |
Tilgner Lab
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| Street address |
413 E 69th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE158450 |
Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development |
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| Relations |
| BioSample |
SAMN16247268 |
| SRA |
SRX9178676 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4800808_Visium_10X_barcodes.tsv.gz |
17.0 Kb |
(ftp)(http) |
TSV |
| GSM4800808_Visium_10X_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM4800808_Visium_10X_hires_image.png.gz |
5.8 Mb |
(ftp)(http) |
PNG |
| GSM4800808_Visium_10X_matrix.mtx.gz |
62.6 Mb |
(ftp)(http) |
MTX |
| GSM4800808_Visium_10X_scalefactors_json.json.gz |
176 b |
(ftp)(http) |
JSON |
| GSM4800808_Visium_10X_tissue_positions_list.csv.gz |
62.4 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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