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| Status |
Public on Jun 18, 2021 |
| Title |
PBMCs, OIL 2 |
| Sample type |
SRA |
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| Source name |
PBMC
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| Organism |
Rattus norvegicus |
| Characteristics |
age: gestational day 13.5
treatment: control
cell type: PBMC
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| Extracted molecule |
total RNA |
| Extraction protocol |
Single cells were captured into droplets using 10x chromium device followed by preparation of single-cell cDNA libraries with the 10x protocol.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3' gene counting. The reads were aligned to the rn6 reference genome. BAM files produced by the 10x Genomics/Cell Ranger pipeline
Genome_build: rn6
Supplementary_files_format_and_content: Genes.tsv, Barcodes.tsv, Matrix.mtx
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| Submission date |
Jun 17, 2021 |
| Last update date |
Jun 18, 2021 |
| Contact name |
Khursheed Iqbal |
| E-mail(s) |
kiqbal@kumc.edu
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| Phone |
913 588 5690
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| Organization name |
University of Kansas Medical Center
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| Department |
Pathology
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| Street address |
3901 Rainbow Blvd
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| City |
Kansas City |
| State/province |
Kansas |
| ZIP/Postal code |
66160 |
| Country |
USA |
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| Platform ID |
GPL25947 |
| Series (1) |
| GSE178407 |
Environmental Stressors Impact Placentation Through Actions On Trophoblast, Immune, and Endothelial Cell Dynamics |
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| Relations |
| BioSample |
SAMN19763700 |
| SRA |
SRX11173013 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5390427_O2_barcodes.tsv.gz |
55.1 Kb |
(ftp)(http) |
TSV |
| GSM5390427_O2_features.tsv.gz |
222.7 Kb |
(ftp)(http) |
TSV |
| GSM5390427_O2_matrix.mtx.gz |
47.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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