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| Status |
Public on Aug 09, 2020 |
| Title |
Hypothalamus, E12 Nkx2.1 CreERT2/CreERT2 (1) |
| Sample type |
SRA |
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| Source name |
Hypothalamus
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1 & C57BL/6J
tissue: Hypothalamus
age: embryonic 12 days
genotype: mutant
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| Extracted molecule |
total RNA |
| Extraction protocol |
scRNA-Seq - following the manufacturer's (10x Genomics)
scRNA-Seq (Illumina NextSeq500)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
E12-Nkx2-1-Mutant-1
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| Data processing |
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat and Scanpy were used to perform downstream analysis following the standard pipeline using cells with more than 500 genes and 1000 UMI counts. Clusters were annotated based on previous literature, and differential gene expression test was performed in each cluster, between treatment groups.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx (scRNA-Seq count matrix), barcodes.tsv (scRNA-Seq barcodes list) , genes.tsv (scRNA-Seq genes list), log2cpm*.rds (log2cpm matrix of aggregated dataset), tSNE.rds (tSNE data of aggregated dataset), umap.rds (UMAP data of aggregated dataset)
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| Submission date |
Jun 07, 2019 |
| Last update date |
Aug 09, 2020 |
| Contact name |
Dong Won Thomas Kim |
| E-mail(s) |
kimtho87@gmail.com
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| Organization name |
Johns Hopkins University
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| Department |
Neuroscience
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| Lab |
Blackshaw lab
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| Street address |
733 N.Broadway, MRB building (Rm 332)
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| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE132355 |
Single cell RNA-Seq identifies mechanisms controlling hypothalamic patterning and differentiation |
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| Relations |
| BioSample |
SAMN11975079 |
| SRA |
SRX5984848 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3860749_E12-Foxd1-Nkx2-1-Mutant-1-tSNE.rds.gz |
190.9 Kb |
(ftp)(http) |
RDS |
| GSM3860749_E12-Nkx2-1-Mutant-1_barcodes.tsv.gz |
2.2 Mb |
(ftp)(http) |
TSV |
| GSM3860749_E12-Nkx2-1-Mutant-1_genes.tsv.gz |
212.8 Kb |
(ftp)(http) |
TSV |
| GSM3860749_E12-Nkx2-1-Mutant-1_matrix.mtx.gz |
77.1 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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