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| Status |
Public on Feb 26, 2024 |
| Title |
HepaPlate01_D20 |
| Sample type |
SRA |
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| Source name |
Blank
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Blank
cell type: Human induced pluripotent stem cell (iPSC)-derived cardiomyocytes
treatment: AFFF-5 (Solberg 6%)
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| Extracted molecule |
total RNA |
| Extraction protocol |
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing. The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
Quality control steps with the following criteria were performed: 1) genes with fewer than 5 mean counts across the entire sample spacewere removed, 2) samples with mean expression across all genes lower than 25 were removed, 3) outliers in vehicle control samples were identified and removed using mean correlation at <0.85 as the criteria to ensure the stability of further transcriptomic dose-response and differential expression analyses, 4) in addition, principal component analysis (PCA) was conducted on vehicle control samples using raw counts to identify any remaining outliers.
Assembly: Whole transcriptome assay
Supplementary files format and content: iHep_normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: iHep_hash.csv file with meta data of the QC samples
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| Submission date |
Sep 26, 2023 |
| Last update date |
Feb 26, 2024 |
| Contact name |
Ivan Rusyn |
| Organization name |
Texas A&M University
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| Department |
Department of Veterinary Integrative Biosciences
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| Street address |
4458 TAMU
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| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843-4458 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE244107 |
A New Approach Methods Strategy for Risk-based Prioritization of PFAS [hepatocytes] |
| GSE244110 |
Risk-based prioritization of PFAS using phenotypic and transcriptomic data from human induced pluripotent stem cell-derived hepatocytes and cardiomyocytes |
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| Relations |
| BioSample |
SAMN37548835 |
| SRA |
SRX21897487 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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