|
| Status |
Public on Jul 10, 2024 |
| Title |
HF, Hippocampus, ATAC, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Hippocampus
treatment: HF
genotype: wild-type
|
| 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 |
genomic DNA |
| Extraction protocol |
Pups were harvested on postnatal day 21 (P21) and fresh hippocampus tissues were dissected and used to prepare debris-free single nuclei suspension.
Single nuclei RNA-seq (snRNA-seq) and single nuclei ATAC-seq (snATAC-seq) libraries were simultaneously constructed using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit (10x Genomics, cat# 1000285) according to the manufacturer’s User Guide (CG000338).
single nuclei multiome (snRNA-seq and snATAC-seq)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic single cell |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
HF_rep1_snATAC
single nuclei multiome sequencing (snRNA-seq and snATAC-seq)
|
| Data processing |
cellranger-arc-2.0.1 count function to quantify reads into single set barcodes.tsv.gz, feature.tsv.gz and matrix.mtx.gz
Using R Seurat::Read10X() and split the result into two set of files for GEX and Peak, respectively
Assembly: mm10
Supplementary files format and content: CellRanger output files: Gene Expression barcodes.tsv.gz, Gene Expression features.tsv.gz,Gene Expression matrix.mtx.gz
Supplementary files format and content: CellRanger output files: Peak barcodes.tsv.gz, Peak features.tsv.gz, Peak matrix.mtx.gz
|
| |
|
| Submission date |
Jun 11, 2024 |
| Last update date |
Jul 10, 2024 |
| Contact name |
Hehuang Xie |
| Organization name |
Virginia Tech
|
| Street address |
Mail Stop: 0477,Biomedical Science(MC0477),Steger Hall Virginia Tech
|
| City |
Blacksburg |
| ZIP/Postal code |
24061 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE269544 |
Multi-omics Analysis Revealing the Impact of Excessive Maternal Folate Supplementation on Offspring Brain Development [single nuclei multiome] |
|
| Relations |
| BioSample |
SAMN41785198 |
| SRA |
SRX24870666 |
