|
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.
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|
|
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
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|
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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 |