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| Status |
Public on Aug 20, 2024 |
| Title |
L056_8_TCDD |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
org ontology: NCBITAXON:10090
strain: C57BL/6
strain ontology: MGI:2159769
tissue: Liver
tissue ontology: UBERON:0002107
Sex: male
sex ontology: PATO:0000384
start age: 28
end age: 28
age unit: days
age unit_ontology: UO:0000033
duration: 8
duration unit: hours
duration unit_ontology: UO:0000032
house temperature: 23
temperature unit: degree Celcius
temperature unit_ontology: UO:0000027
housing humidity: 35
humidity unit: percent
humidity unit_ontology: UO:0000187
light cycle: 12:12
cage type: Innovive cage
bedding: ALHPA-dri (Shepherd Specialty Papers)
water: Aquavive water (Innovive)
feed: Harlan Teklad 22/5 Rodent Diet 8940
toxic substance: Harlan Teklad
toxic substance: 2,3,7,8-tetrachlorodibenzodioxine
toxic substance_ontology: CHEBI:28119
toxic substance_vendor: Accustandard
toxic substance_catalog__number: D-404N
vehicle substance: sesame oil
vehicle substance_ontology: NCIT:C66537
administration route: oral gavage
administration route_ontology: XCO:0000581
treatment: TCDD
dose: 30
dose unit: microgram per kilogram
dose unit_ontology: EFO:0002899
library kit: 10X Genomics Chromium Single Cell 3’ v3 kit
biological replicate: 1
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| Treatment protocol |
Mice were gavaged once with sesame oil vehicle or 30 ug/kg TCDD and livers collected at 2, 4, 8, 12, 24, or 72 hours following gavage.
Mice given a single bolus dose by oral gavage
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| Extracted molecule |
nuclear RNA |
| Extraction protocol |
Nuclei were isolated from frozen liver samples (~200mg) as previously described (dx.doi.org/10.17504/protocols.io.3fkgjkw). Briefly, livers were diced in EZ Lysis Buffer (Sigma-Aldrich), homogenized using a disposable dounce homogenizer, and incubated on ice for 5 minutes. The homogenate was filtered using a 70 μm cell strainer, transferred to microcentrifuge tube, and centrifuged at 500 x g and 4°C for 5 minutes. The supernatant was removed and fresh EZ lysis buffer was added for an additional 5 minutes on ice following by centrifugation at 500 x g and 4°C for 5 minutes. The nuclei pellet was washed twice in nuclei wash and resuspend buffer (1X PBS, 1% BSA, 0.2 U/μL RNAse inhibitor) with 5 minute incubations on ice. Following the washes, the nuclei pellet was resuspended in nuclei wash and resuspend buffer containing DAPI (10 μg/mL). The resuspended nuclei were filtered with 40 μm strainer and immediately underwent fluorescence activated cell sorting (FACS) using a BD FACSAria IIu (BD Biosciences, San Jose, CA) with 70 μm nozzle.
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) - CG000315 Rev A
snRNAseq (Single-Nuclei RNA-Sequencing)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
L056
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| Data processing |
CellRanger 4.0.0 was used to align reads to a custom reference genome which included introns and exons to consider pre-mRNA and mature mRNA present in the nuclei.
Raw counts were further analysed using Scanpy v1.9.3. Each sample was filtered for (i) genes expressed in at least 3 nuclei, (ii) nuclei which express at least 100 genes, and (iii) ≤1% mitochondrial genes
Scrublet v0.2.3 was used to remove putative doublets.
All libraries were integrated using using scVI v0.20.3, while accounting for dose and time as categorical covariates and using a latent variable of 40.
Assembly: mm10
Supplementary files format and content: Processed data files for individual sample are CellRanger filtered_feature_bc_matrix.H5 Hierarchical Data Format version 5 (HDF5) files.
Supplementary files format and content: The HDF5 Annotated Data (.h5ad) file represents the full scVI processed anndata object.
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| Submission date |
Jan 24, 2024 |
| Last update date |
Aug 20, 2024 |
| Contact name |
Timothy Zacharewski |
| E-mail(s) |
tzachare@msu.edu
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| Organization name |
Michigan State University
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| Department |
Biochemistry and Molecular Biology
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| Street address |
603 Wilson Rd., BCH Building RM#212
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| City |
East Lansing |
| State/province |
MI |
| ZIP/Postal code |
48823 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE254121 |
Time-Course Analysis of Hepatic Single-Nuclei RNA-Sequencing in Mice Treated with 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) |
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| Relations |
| BioSample |
SAMN39600348 |
| SRA |
SRX23385255 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8033598_L056_filtered_feature_bc_matrix.h5 |
15.9 Mb |
(ftp)(http) |
H5 |
SRA Run Selector |
| Raw data are available in SRA |
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