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| Status |
Public on Jan 25, 2019 |
| Title |
PBS_1 |
| Sample type |
SRA |
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| Source name |
Alveolar macrophages
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: wistar
Sex: male
cell type: Alveolar macrophages
days of exposure: 0
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| Treatment protocol |
Animals were anesthetized with 2.5% isofluorane, and then administered PBS or NM (0.125 mg/kg, mechlorethamine hydrochloride, Sigma-Aldrich, St. Louis, MO) intratracheally as previously described (Sunil et al., 2011). All instillations were performed by David Reimer, D.V.M., Comparative Medicine Resources, Rutgers University. NM was prepared immediately before administration in a designated room under a chemical hood following Rutgers University Environmental Health and Safety guidelines.
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| Growth protocol |
Male Wistar rats (225–250 g) were purchased from Harlan Laboratories (Indianapolis, IN) and maintained in an AALAC approved animal care facility. Animals were housed in filter top microisolation cages and provided food and water ad libitum. Animals received humane care in compliance with the guidelines outlined in the Guide for the Care and Use of Laboratory Animals, published by the National Institutes of Health.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted from lung macrophages using an RNeasy Mini kit (Qiagen, Valencia, CA) and RNA quality analyzed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA was converted into double stranded cDNA and amplified using Illumina TruSeq RNA Sample Preparation Kit following the manufacturer’s directions. Reads were sequenced as 2x75bp paired end.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
fpkm_isoform_matrix.csv
NM1d_vs_PBS_sig_isoforms.xlsx
NM28d_vs_PBS_sig_isoforms.xlsx
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| Data processing |
Raw sequence reads were aligned to rn4 rat reference genome using tophat.
Grouped bam files were compared using cuffdiff.
Output from cuffdiff was analyzed in cummeRbund.
Raw data file was uploaded from cuffdiff to Ingenuity Pathway Analysis.
Supplementary_files_format_and_content: csv file with fpkm, Excel file with differential expression.
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| Submission date |
Jan 24, 2019 |
| Last update date |
Jan 26, 2019 |
| Contact name |
Ley Cody Smith |
| E-mail(s) |
[email protected]
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| Phone |
4074510956
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| Organization name |
University of Florida
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| Street address |
2187 Mowry Rd
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| City |
Gainesville |
| State/province |
FL |
| ZIP/Postal code |
32611 |
| Country |
USA |
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| Platform ID |
GPL25029 |
| Series (1) |
| GSE125619 |
Regulation of Macrophage Foam Cell Formation during Nitrogen Mustard (NM)-Induced Pulmonary Fibrosis by Lung Lipids |
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| Relations |
| BioSample |
SAMN10815702 |
| SRA |
SRX5288868 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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