Investigating the Mechanism of Neurotoxic Effects of PFAS in Differentiated Neuronal Cells through Transcriptomics and Lipidomics Analysis
RNA-seq (gene expression) · human · 21 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 21 samples: 17 distinct titles, 2 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Investigating the Mechanism of Neurotoxic Effects of PFAS in Differentiated Neuronal Cells through Transcriptomics and Lipidomics AnalysisACS chemical neuroscience · 2024
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE254408_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1070327 and SRA study SRP486648. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 21 sample titles: 17 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8041686 Control_1_S27, SH-SY5Y cells, Control
- GSM8041687 Control_2_S28, SH-SY5Y cells, Control
- GSM8041688 Control_3_S29, SH-SY5Y cells, Control
- GSM8041689 PFDA_1_S36, SH-SY5Y cells, PFDA
- GSM8041690 PFDA_2_S37, SH-SY5Y cells, PFDA
- GSM8041691 PFDA_3_S38, SH-SY5Y cells, PFDA
- GSM8041692 PFDS_1_S39, SH-SY5Y cells, PFDS
- GSM8041693 PFDS_2_S40, SH-SY5Y cells, PFDS
- GSM8041694 PFDS_3_S41, SH-SY5Y cells, PFDS
- GSM8041695 PFOA_1_S33, SH-SY5Y cells, PFOA
- GSM8041696 PFOA_2_S34, SH-SY5Y cells, PFOA
- GSM8041697 PFOA_3_S35, SH-SY5Y cells, PFOA
- GSM8041698 PFOS_1_S30, SH-SY5Y cells, PFOS
- GSM8041699 PFOS_2_S31, SH-SY5Y cells, PFOS
- GSM8041700 PFOS_3_S32, SH-SY5Y cells, PFOS
- GSM8041701 8_2_FTOH_1_S45, SH-SY5Y cells, 8:2 FTOH
- GSM8041702 8_2_FTOH_2_S46, SH-SY5Y cells, 8:2 FTOH
- GSM8041703 8_2_FTOH_3_S47, SH-SY5Y cells, 8:2 FTOH
- GSM8041704 8_2_FTS_1_S42, SH-SY5Y cells, 8:2 FTS
- GSM8041705 8_2_FTS_2_S43, SH-SY5Y cells, 8:2 FTS
- GSM8041706 8_2_FTS_3_S44, SH-SY5Y cells, 8:2 FTS
- GSE313992 Comparative Immunotoxicity and Transcriptomic Profiling of Seven PFAS in THP-1 Macrophages 252 samples shares pfas
- GSE311566 Mechanistic insights into PFAS-induced effects on B lymphocyte activation and antibody secretion [PBMCs] 41 samples shares pfas
- GSE311234 Mechanistic insights into PFAS-induced effects on B lymphocyte activation and antibody secretion 36 samples shares pfas
- GSE279836 Environmentally relevant concentrations of individual per- and polyfluoroalkyl substances (PFAS) and a PFAS mixture impact proliferation and gene transcription in a human myometrial cell line. 18 samples shares pfas
- GSE338576 Dissecting the molecular pathways through which long-chain PFAS disrupts dendritic cell maturation 15 samples shares pfas
- GSE246371 An environmentally relevant mixture of Perfluoroalkyl Substances (PFAS) impacts proliferation, steroid hormone synthesis, and gene transcription in primary human granulosa cells 12 samples shares pfas
- GSE284228 Per- and polyfluoroalkyl substances (PFAS) suppress macrophage alternative activation to disrupt hepatic lipid metabolism [RNA-seq I] 12 samples shares pfas
- GSE297059 Per- and polyfluoroalkyl substances (PFAS) suppress macrophage alternative activation to disrupt hepatic lipid metabolism 12 samples shares pfas
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.