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Sample GSM8450394 Query DataSets for GSM8450394
Status Public on Jan 21, 2025
Title mouse eyelid, 8 weeks wildtype [Spatial transcriptomics]
Sample type SRA
 
Source name eyelid
Organism Mus musculus
Characteristics tissue: eyelid
strain: C57BL/6J
age: 8 weeks
genotype: wild type
Sex: male
Extracted molecule polyA RNA
Extraction protocol Eyelids from an 8-week-old male C57BL/6J mouse was dissected, OCT embedded, sectioned at 10 μM, and mounted onto the assay slide containing four capture areas (6.5mm x 6.5mm) with spatially barcoded poly T capture probes.
After permeabilization, the captured mRNAs underwent reverse transcription, followed by cleaving from the slide. cDNA amplification, fragmentation, end-repair, poly A-tailing, adapter ligation, and sample indexing were performed in accordance with the manufacturer’s protocol.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Fresh frozen spatial transcriptome sequencing
Data processing *library strategy: Spatial Transcriptomics
The sequencing data were aligned and quantified using Space Ranger Software Suite (v2.1.0, 10x Genomics) against the reference genome (mm10).
Assembly: GRCm38/mm10
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates sepcifying spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
 
Submission date Aug 10, 2024
Last update date Jan 21, 2025
Contact name Sarah E Millar
E-mail(s) sarah.millar@mssm.edu
Organization name Icahn School of Medicine at Mount Sinai
Department Developmental, Cell and Regenerative Biology
Street address Icahn Building, Floor 13 Room 020C, 1425 Madison Ave
City New York
State/province NY
ZIP/Postal code 10029
Country USA
 
Platform ID GPL24247
Series (1)
GSE274497 Spatial transcriptomics of murine eyelid
Relations
BioSample SAMN43110628
SRA SRX25662755

Supplementary file Size Download File type/resource
GSM8450394_aligned_fiducials.jpg.gz 787.7 Kb (ftp)(http) JPG
GSM8450394_barcodes.tsv.gz 2.3 Kb (ftp)(http) TSV
GSM8450394_detected_tissue_image.jpg.gz 1.2 Mb (ftp)(http) JPG
GSM8450394_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM8450394_matrix.mtx.gz 4.7 Mb (ftp)(http) MTX
GSM8450394_scalefactors_json.json.gz 165 b (ftp)(http) JSON
GSM8450394_tissue_hires_image.png.gz 3.3 Mb (ftp)(http) PNG
GSM8450394_tissue_lowres_image.png.gz 238.8 Kb (ftp)(http) PNG
GSM8450394_tissue_positions_list.csv.gz 59.6 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA

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