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Sample GSM7840102 Query DataSets for GSM7840102
Status Public on Nov 26, 2024
Title SPF Duodenum 1
Sample type SRA
 
Source name Duodenum
Organism Mus musculus
Characteristics tissue: Duodenum
cell line: NA
cell type: intestinal tissue
genotype: WT
treatment: SPF
Extracted molecule polyA RNA
Extraction protocol Fresh frozen intestinal tissue from WT SPF, GF, and FMT mice and DSS treated WT mice was swiss rolled and OCT embedded, and 10um frozen sections were cut with cryostat.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit following the manufacturer's instruction.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Fresh frozen spatial transcriptome sequencing
Data processing Raw sequencing BCL files were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to generate gene expression counts using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
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
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics
 
Submission date Oct 13, 2023
Last update date Nov 26, 2024
Contact name Ramnik Xavier
E-mail(s) xaviergeo@broadinstitute.org
Organization name Broad Institute of MIT and Harvard
Lab Xavier Lab
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL24247
Series (2)
GSE245274 Spatially restricted immune and microbiota-driven adaptation of the gut [Spatial Transcriptomics]
GSE245316 Spatially restricted immune and microbiota-driven adaptation of the gut
Relations
BioSample SAMN37802650
SRA SRX22081831

Supplementary file Size Download File type/resource
GSM7840102_V11Y11-297_D_aligned_fiducials.jpg.gz 1.2 Mb (ftp)(http) JPG
GSM7840102_V11Y11-297_D_barcodes.tsv.gz 17.2 Kb (ftp)(http) TSV
GSM7840102_V11Y11-297_D_detected_tissue_image.jpg.gz 1.4 Mb (ftp)(http) JPG
GSM7840102_V11Y11-297_D_features.tsv.gz 284.1 Kb (ftp)(http) TSV
GSM7840102_V11Y11-297_D_matrix.mtx.gz 44.1 Mb (ftp)(http) MTX
GSM7840102_V11Y11-297_D_scalefactors_json.json.gz 172 b (ftp)(http) JSON
GSM7840102_V11Y11-297_D_tissue_hires_image.png.gz 3.5 Mb (ftp)(http) PNG
GSM7840102_V11Y11-297_D_tissue_lowres_image.png.gz 365.2 Kb (ftp)(http) PNG
GSM7840102_V11Y11-297_D_tissue_positions_list.csv.gz 57.9 Kb (ftp)(http) CSV
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Raw data are available in SRA

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