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| Status |
Public on Apr 17, 2019 |
| Title |
Diesel_exhaust_sample_7 |
| Sample type |
SRA |
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| Source name |
Neonatal cardiomyocytes
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| Organism |
Mus musculus |
| Characteristics |
tissue: Neonatal cardiomyocytes
treatment: Diesel exhaust
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| Biomaterial provider |
University of Washington (Seattle, WA, USA)
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was purified from frozen p0 isolated NCMs using Trizol (Thermo Fisher Scientific, Waltham, MA, USA), following the manufacturer’s protocol. Ribosomal RNA was depleted by poly-A enrichment, and sample libraries were created using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA)
Each library was barcoded using the Illumina adapters, and amplified with 13 cycles of PCR. Library concentrations were quantified using the Quant-it dsDNA Assay (Life Technologies, Carlsbad, CA). Libraries were normalized and pooled based on Agilent 2100 Bioanalyzer results (Agilent Technologies, Santa Clara, CA), and the pools were sequenced on an Illumina HiSeq 2500.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
DE11-7
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| Data processing |
To process sequences, Illumina RTA-generated BCL files were converted to FASTQ files and sequence read and base quality were checked using the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) and FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Sequences were aligned to mm10 with reference transcriptome Ensembl v67 using Tophat (26). Lane level bam data files were merged using the Picard MergeSamFiles tool and suspected PCR duplicates were marked, not removed, in the alignment files using the Picard MarkDuplicates tool (http://broadinstitute.github.io/picard/). Local realignment was performed around indels, and base quality score recalibration was run using GATK tools. Variant detection was performed with the GATK Unified Genotyper version 2.6.5, and aligned data were used for isoform assembly and quantitation with Cufflinks. Fragment counts were generated using the featureCounts function in the Bioconductor Rsubread package.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data consist of tab-delimited counts per gene for each sample. The first column contains the NCBI Gene ID, and the remaining columns are counts for each gene per sample.
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| Submission date |
Feb 16, 2018 |
| Last update date |
Apr 17, 2019 |
| Contact name |
James William MacDonald |
| E-mail(s) |
[email protected]
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| Organization name |
University of Washington
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| Department |
Environmental and Occupational Health Sciences
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| Street address |
4225 Roosevelt Way NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98105-6099 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE110748 |
In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation. [RNA-Seq] |
| GSE110793 |
In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation. |
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| Relations |
| BioSample |
SAMN08558992 |
| SRA |
SRX3716586 |
| 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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