 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 30, 2023 |
| Title |
prenatal valproic acid treatment rep3 |
| Sample type |
SRA |
| |
|
| Source name |
female hippocampus
|
| Organism |
Mus musculus |
| Characteristics |
treatment: prenatal valproic acid treatment
Sex: female
strain: C57BL/6
tissue: hippocampus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
the hippocampus were cut into pieces and transferred it to a 1.5 mL microcentrifuge tube with 2 mg/mL isolation solution, containing pronase (Sigma, Cat# P6911-1G) and 50 μg/mL DNaseІ (Sigma, cat. no. D5025) in 1 mL Hibernate A (Invitrogen, cat. no. A1247501)/B27 (Invitrogen, cat. no. 17504) medium (HABG). The tissue and solution were mixed for 30 min at 37℃ in a horizontal shaker at 200 rpm. After incubation, the tissue was gently triturated by polished tips, and the single cells were released. The purified cells were obtained by density gradient centrifugation at 800 g for 15 min, resuspended in 1x PBS (calcium and magnesium-free) containing 1% BSA, and then centrifuged at 200 g for 2 min. Single cells were concentrated and resuspended in the desired medium.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
single cell
|
| Data processing |
bcl2fastq Conversion Software version 2.19 was used to convert bcl files to fastq files
The fastq files of each sample were aligned to the mm10 genome assembly using the 10X genomics software cellranger(version 3.1.0) with default parameters. The matrix of all samples were aggregated using 'cellranger aggr' command
The Seurat (version 3.2.2) was used to perform data normalization, batch effect removing, cell clustering and dimension reduction. Specifically, cells that contained fewer than 100 genes or more than 10% mitochondrial transcripts were removed. The count of each gene was normalized to the sequencing depth of the cell, multiplied by a scale factor 10000 and log-transformed. The top 2000 variable genes were selected and PCA was performed on these variable genes. The first 30 PCA components were used for the UMAP dimension reduction to obtain a two-dimensional representation of the cell state. For clustering, we used FindClusters function with resolution 0.9.
Genome_build: mm10
Supplementary_files_format_and_content: each sample contain three files which generated by 'cellranger count' command, it's a sparse matrix that contain the gene UMI count of each cell
Supplementary_files_format_and_content: Autism_gene_count_matrix.tsv.gz is a gzipped matrix table with filtered gene UMI counts for every gene and every cell
|
| |
|
| Submission date |
Jan 24, 2021 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Yijie Zhang |
| E-mail(s) |
yijiezhang@henu.edu.cn
|
| Organization name |
Henan University
|
| Street address |
Jinming Avenue
|
| City |
Kaifeng |
| ZIP/Postal code |
475001 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE165398 |
Single cell sequencing reveals sex bias in autism associated cells and genes |
|
| Relations |
| BioSample |
SAMN17524033 |
| SRA |
SRX9927648 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5032769_FM1_barcodes.tsv.gz |
28.7 Kb |
(ftp)(http) |
TSV |
| GSM5032769_FM1_features.tsv.gz |
245.2 Kb |
(ftp)(http) |
TSV |
| GSM5032769_FM1_matrix.mtx.gz |
40.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
