|
Status |
Public on Nov 26, 2024 |
Title |
GF Ileum 2 |
Sample type |
SRA |
|
|
Source name |
Ileum
|
Organism |
Mus musculus |
Characteristics |
tissue: Ileum cell line: NA cell type: intestinal tissue genotype: WT treatment: GF
|
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 |
SAMN37802633 |
SRA |
SRX22081848 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7840119_V11Y24-012_B_aligned_fiducials.jpg.gz |
1.3 Mb |
(ftp)(http) |
JPG |
GSM7840119_V11Y24-012_B_barcodes.tsv.gz |
16.5 Kb |
(ftp)(http) |
TSV |
GSM7840119_V11Y24-012_B_detected_tissue_image.jpg.gz |
1.4 Mb |
(ftp)(http) |
JPG |
GSM7840119_V11Y24-012_B_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
GSM7840119_V11Y24-012_B_matrix.mtx.gz |
37.6 Mb |
(ftp)(http) |
MTX |
GSM7840119_V11Y24-012_B_scalefactors_json.json.gz |
173 b |
(ftp)(http) |
JSON |
GSM7840119_V11Y24-012_B_tissue_hires_image.png.gz |
3.4 Mb |
(ftp)(http) |
PNG |
GSM7840119_V11Y24-012_B_tissue_lowres_image.png.gz |
376.5 Kb |
(ftp)(http) |
PNG |
GSM7840119_V11Y24-012_B_tissue_positions_list.csv.gz |
64.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |