|
| Status |
Public on Jul 10, 2024 |
| Title |
HF, coronal, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
genotype: wild-type
treatment: high folate
|
| Treatment protocol |
Adult female mice (8 weeks old) were randomly assigned to either a control folic acid (FA) diet (2mg/kg) or an excessive FA diet (20mg/kg) for two weeks before mating with males. These diets were maintained throughout pregnancy and lactation.
|
| Growth protocol |
Adult female C57BL/6J mice (8 weeks) were purchased from Jaxson laboratory and maintained in a 12-hour light/dark cycle under standard pathogen-free conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pups were harvested on postnatal day 21 (P21) and fresh mouse brain tissues were fixed in 10% neutral buffered formalin (NBF) at room temperature (RT) overnight for preparing formalin-fixed paraffin-embedded (FFPE) tissue blocks.
Visium Spatial Gene Expression (VGSE) libraries were prepared using the Visium Spatial Gene Expression Slide Kit (10x genomics, cat# PN-1000185) following the manufacturer’s User Guide (CG000407).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
FFPE spatial transcriptome sequencing
|
| Data processing |
*library strategy: Spatial transcriptomics
Fastq files were mapped to mm10 genome to quantify gene expression using Space ranger default setting
The data were further analyze using R package Seurat
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 lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.ipg.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 ison.ison.gz:scalefactors in ison 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
|
| |
|
| Submission date |
Jun 11, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Timothy Jarome |
| Organization name |
Virginia Tech
|
| Street address |
Mail Stop: 0306,ANIMAL SCIENCES MC0306,LITTON REEVES STE 3490
|
| City |
Blacksburg |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE269543 |
Multi-omics Analysis Revealing the Impact of Excessive Maternal Folate Supplementation on Offspring Brain Development [spatial transcriptome] |
|
| Relations |
| BioSample |
SAMN41785247 |
| SRA |
SRX24870670 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8321865_HF_rep1_aligned_fiducials.jpg.gz |
1.5 Mb |
(ftp)(http) |
JPG |
| GSM8321865_HF_rep1_barcodes.tsv.gz |
18.0 Kb |
(ftp)(http) |
TSV |
| GSM8321865_HF_rep1_detected_tissue_image.jpg.gz |
793.0 Kb |
(ftp)(http) |
JPG |
| GSM8321865_HF_rep1_features.tsv.gz |
164.2 Kb |
(ftp)(http) |
TSV |
| GSM8321865_HF_rep1_matrix.mtx.gz |
47.4 Mb |
(ftp)(http) |
MTX |
| GSM8321865_HF_rep1_scalefactors_json.json.gz |
173 b |
(ftp)(http) |
JSON |
| GSM8321865_HF_rep1_spatial_enrichment.csv.gz |
760.9 Kb |
(ftp)(http) |
CSV |
| GSM8321865_HF_rep1_tissue_hires_image.png.gz |
3.8 Mb |
(ftp)(http) |
PNG |
| GSM8321865_HF_rep1_tissue_lowres_image.png.gz |
385.7 Kb |
(ftp)(http) |
PNG |
| GSM8321865_HF_rep1_tissue_positions.csv.gz |
66.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
