title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_032_E10_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_100_G07_CH03]

status: Public on Oct 23 2024

type: SRA

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

country: USA

institute: US EPA

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH03_PFOA_FHM.txt

library_source: transcriptomic

data_processing:
Sequence reads were demultiplexed based on sample-specific bar codes and a FASTQ file was generated for each sample using Illumina’s bcl2fastq conversion software.
Resulting TempO-Seq data were analyzed by Biosypder using TempO-SeqR software implemented in R. FASTQ files are aligned to the known transcript composition of the reduced transcriptome and a count table (columns = samples, genes = rows) was generated.
The single count table for the entire project was parsed into chemical-specific sample sets (with plate matched controls), a pseudo-count of 1 was added, then data were log-base 2 transformed for use in the data analysis.
Assembly: Pimephales promelas genome assembly GCA_016745375.1
Supplementary files format and content: processed data file_all samples:  Count table for all samples, prior to chemical-specific parsing, pseudo count (+1), and log2 normalization
Supplementary files format and content: processed data file_chem specific: Chemical-specific count table with pseudo count (+1) added, followed by log2 normalization; control samples correspond to two different chemicals, thus two columns of chemical-specific processed data files are provided. These are the original files before curation to remove samples corresponding to mortalities.
Supplementary files format and content: processed data file_curated:  Chemical-specific count tables, with columns removed or re-grouped (into treatment groups), based on mortality data and analytical exposure verification results (data curation).

molecule: total RNA

organism: Pimephales promelas

source_name: whole body

growth_protocol: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use.  Vertebrate animal husbandry and use was performed according to an approved animal care and use plan reviewed by a local animal care and use committee in accordance with the Animals in Research Act and Guide for the Care and Use of Laboratory Animals (National Research Council, 2011)

extract_protocol:
For homogenization, 75 µl of Biospyder homogenization buffer and a 2.3 mm stainless steel bead added. The fish were then homogenized in 96 well plate format using a bead mixer mill (Omni-Bead Ruptor; 30 Hz for 2 min). Homogenates corresponding to the same well position on each of two replicate plates (both from the same treatment) were pooled together (except in the case of mortality on one or both plates). This resulted in five replicate pools (independent biological replicates) per treatment, each representing the mean of two individuals. For controls there were eight replicate pools, each representing the mean of two individuals, however, the controls were shared for both PFAS tested on the same plate.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification was performed with a DeNovix UV-Vis spectrophotometer (DeNovix Inc.). Ligated transcripts were subjected to PCR amplification which also introduces adaptors for sequencing and a sample-specific barcode. Resulting sample specific TempO-Seq libraries were subsequently pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2x50 bp, single-end reads, NovaSeq X 10B reagent kits.

treatment_protocol: Larval fathead minnows (Pimephales promelas; 5-6 days post-fertilization) were exposed to each of the 20 PFAS, in concentration response, for 24 h in 96-well plate format. For each assay, 30 mM and 9.5 mM stock solutions in DMSO were used to prepare a dilution series spanning from 30 mM to 0.0095 mM (1/2 log spacing between concentrations) in DMSO. Solutions in DMSO were then diluted 300-fold in sand filtered, UV-treated Lake Superior water (LSW) to generate a series of aqueous nominal concentrations ranging from 100 µM to 0.03 µM (1/2 log-spacing between concentrations), each, including control treatments, containing 0.33% DMSO. Larval fathead minnows (five days post fertilization) were transferred to wells of three 96-well (1 ml wells; NEST), one animal per well. The volume (variable from organism loading) in each well of the three plates was reduced to a uniform volume of 50 µl using a Biomek i5 liquid handler (Beckman), and then 550 µl of dosing solution was added to each well, bringing the total volume to 600 µl. On each of the three replicate plates five individual fish were exposed to each concentration of two PFAS test chemicals, eight individuals were exposed to control water, and the remaining eight wells were treated with reference chemicals (150 µg CuSO4/L). In total, 15 fish (distributed across 3 plates) were exposed to each PFAS treatment and 24 fish (distributed across 3 plates) were exposed to control water. Following the addition of the exposure solutions, plates were incubated at 25C for 24 h. At the end of each exposure period, each well was inspected under a dissecting microscope. Mortalities were enumerated wells containing dead animals noted. Any non-lethal phenotypic abnormalities such as edema, spinal malformations, or unusual behaviors were noted. A Biomek i5 liquid handler was used to transfer 100 µl of exposure water from one of the plates (Plate A) to be used for exposure verification (below) to a new 96 well plate. All wells from plates B and C were de-watered and frozen at -80 until homogenized. For homogenization, 75 µl of Biospyder homogenization buffer and a 2.3 mm stainless steel bead added. The fish were then homogenized in 96 well plate format using a bead mixer mill (Omni-Bead Ruptor; 30 Hz for 2 min). Homogenates corresponding to the same well position on each of two replicate plates (both from the same treatment) were pooled together (except in the case of mortality on one or both plates). This resulted in five replicate pools (independent biological replicates) per treatment, each representing the mean of two individuals. For controls there were eight replicate pools, each representing the mean of two individuals, however, the controls were shared for both PFAS tested on the same plate. PFAS concentrations in the exposure medium (collected from plate A) were measured at the end of each 24 h exposure.

tag: tissue

value: whole body

tag: cell line

tag: cell type

tag: genotype

value: US EPA GLTED wild type

tag: treatment

value: PFOA (DTXSID8031865)

tag: conc.

tag: conc. units

value: microg/L

tag: exposure duration

tag: age

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_032_C11_CH03]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_3_2_H08_CH02]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH02_62FTS_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_3_2_G05_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_3_2_D12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_3_2_D06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_3_2_B08_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_32_H10_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_32_F03_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_32_E08_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_32_D03_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_32_B12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_1_H07_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_1_F08_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_1_E12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_1_E06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_10_H09_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_1_B02_CH02]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_1_E03_CH03]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_10_C12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_10_B09_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_10_E09_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_10_D09_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_100_G07_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_100_A12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_100_D04_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_100_F11_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_32_H06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_32_G08_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_100_H11_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_32_E02_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_1_H05_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_1_G02_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_1_B10_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_32_B07_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_1_E03_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_1_G12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_32_F12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_032_H04_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_032_G10_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_032_H12_CH02]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_3_2_D01_AF05]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF11_FC8DoD_FHM.txt

value: FC8DoD (DTXSID70381090)


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_032_C11_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 6:2 FTS (DTXSID6067331) [CH02_0_032_E10_CH02]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_3_2_D11_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_1_E11_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_3_2_C06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_1_E07_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_32_G04_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_3_2_C09_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_32_D07_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_32_G03_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_3_2_A05_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_1_B11_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_10_A04_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_32_B01_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_100_F02_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_100_A02_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_1_E01_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_1_A06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_32_G06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_32_C07_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_10_F06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_32_A03_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_100_A01_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_32_F01_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_10_B05_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_10_C08_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_10_C01_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_100_D02_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_1_F05_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_1_A08_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_032_H01_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_3_2_D11_AF07]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF10_PF4OPeA_FHM.txt

value: PF4OPeA (DTXSID70191136)


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_1_G01_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_3_2_D01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_32_D10_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_1_C03_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_32_A07_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_1_B06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_032_D05_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_32_G04_AF07]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_100_F09_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_032_A09_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_32_B01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_32_A03_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_32_D07_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_3_2_C06_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_1_B11_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_3_2_C09_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_10_C08_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_32_G03_AF07]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_032_B03_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8DoD (DTXSID70381090) [AF11_0_032_F04_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_1_A06_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_3_2_A05_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_10_B05_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_1_E11_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_1_E07_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_10_F06_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_10_A04_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_100_F09_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_100_D02_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_100_F02_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_10_C01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_100_A02_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_32_G06_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_32_D10_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_100_A01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_32_C07_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_32_F01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_1_G01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_32_A07_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_1_E01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_1_F05_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_032_D05_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_1_A08_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_032_A09_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_1_B06_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_032_B03_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_032_H01_AF07]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_3_2_D01_CH04]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF09_FHxSA_FHM.txt
Normalized+1_AF09_FHxSA_FHM_toxic_removed.txt

value: FHxSA (DTXSID50469320)


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_3_2_D11_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_3_2_C09_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_3_2_A05_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_32_A03_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_1_E01_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_032_F04_AF07]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_32_G04_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_32_G03_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_32_B01_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_1_E11_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_1_A06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_10_C08_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_10_C01_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_100_F09_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_1_B11_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PF4OPeA (DTXSID70191136) [AF10_0_1_C03_AF07]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_3_2_C06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_100_D02_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_10_B05_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_10_A04_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_32_F01_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_32_A07_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_10_F06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_1_G01_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_1_C03_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_100_F02_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_32_D07_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_1_B06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_100_A01_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_032_D05_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_032_H01_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_032_A09_CH04]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_3_2_D01_CH02]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF08_42FTS_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_32_G06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_32_C07_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_32_D10_CH04]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_3_2_A05_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_32_G04_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_3_2_C06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_32_G03_CH02]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_1_A08_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_032_F04_CH04]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_032_B03_CH04]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_32_D07_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_1_E01_CH02]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_0_1_F05_CH04]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_3_2_D11_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_3_2_C09_CH02]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_100_A02_CH04]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_1_A06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_10_C08_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_100_D02_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_1_E11_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_32_A03_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_32_B01_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_100_A01_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_32_F01_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_10_F06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_1_E07_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_10_C01_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_1_F05_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_10_A04_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_1_C03_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_1_B06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_100_F09_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_100_F02_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_032_D05_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_100_A02_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_32_A07_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_32_G06_CH02]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_3_2_D06_AF07]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF07_PFTP_FHM.txt

value: PFTP (DTXSID70379295)


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_32_D10_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_1_G01_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_1_B11_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_1_A08_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_032_F04_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_10_B05_CH02]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_32_F03_AF07]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_032_B03_CH02]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_32_H10_AF07]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_032_A09_CH02]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_032_H01_CH02]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_32_E08_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_3_2_G05_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_1_H07_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_3_2_D12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_32_D03_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_1_F08_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_10_H09_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_10_E09_AF07]


title: TempO-Seq larval whole body after 24 h exposure to 4:2 FTS (DTXSID30891564) [AF08_0_32_C07_CH02]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_10_C12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_1_E12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_3_2_B08_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_1_B02_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_3_2_H08_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_10_D09_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_10_B09_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_100_H11_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_100_D04_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_100_F11_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_32_H06_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_1_H05_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_32_G08_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_100_A12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_32_B12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_32_F12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_32_B07_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_1_E06_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_32_E02_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_1_G02_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_1_B10_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_1_G12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_032_H12_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_032_E10_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_032_C11_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_032_H04_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_1_E03_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_0_032_G10_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTP (DTXSID70379295) [AF07_100_G07_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_3_2_D11_CH05]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF06_PFHpA_FHM.txt

value: PFHpA (DTXSID1037303)


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_3_2_D01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_3_2_C06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_3_2_A05_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_32_D07_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_32_G03_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_32_B01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_32_A03_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_1_E11_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_1_E07_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_1_E01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_1_B11_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_10_F06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_1_A06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_10_C08_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_10_C01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_10_B05_CH05]


title: TempO-Seq larval whole body after 24 h exposure to FHxSA (DTXSID50469320) [AF09_1_E07_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_100_D02_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_10_A04_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_100_A01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_100_F02_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_100_A02_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_3_2_C09_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_32_F01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_32_C07_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_32_G04_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_32_A07_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_1_F05_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_1_B06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_1_C03_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_32_D10_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_032_H01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_032_D05_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_1_A08_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_032_B03_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_032_A09_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_032_F04_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_3_2_H08_AF05]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF05_PFHxS_FHM.txt

value: PFHxS (DTXSID3037709)


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_3_2_B08_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_3_2_D12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_32_G06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_100_F09_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_3_2_D06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHpA (DTXSID1037303) [AF06_0_1_G01_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_32_B12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_32_D03_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_32_H10_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_32_E08_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_1_E12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_1_H07_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_1_E06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_1_B02_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_3_2_G05_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_100_H11_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_100_G07_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_100_D04_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_10_B09_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_10_E09_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_10_H09_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_32_F03_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_32_F12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_100_F11_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_10_C12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_1_H05_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_32_G08_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_32_H06_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_10_D09_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_32_E02_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_1_F08_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_32_B07_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_1_G12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_1_E03_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_1_B10_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_032_C11_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_1_G02_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_032_H04_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_032_E10_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_032_H12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_100_A12_AF05]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_3_2_D01_AF03]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF04_FC8diol_FHM.txt
Normalized+1_AF04_FC8diol_FHM_onesamp_removed.txt

value: FC8diol (DTXSID30396867)


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_3_2_A05_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_3_2_C06_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_32_G03_AF03]


title: NHK2 3D (F0753-E3a)

city: Aulnay-sous-Boi

first: Claire

last: Marionnet

address: 1 avenue Eugène Schueller

country: France

institute: L'Oréal

library_source: other

data_processing:
Raw reads were trimmed using Trimmomatic to remove low quality sequences and adaptors
Trimmed reads were aligned on the miRBase database release 21 using blastn
Custom R script were used to compile and collapse counts belonging to the same miRNA
The edgeR package was used for the differential expression analysis.
Assembly: miRBase release 21
Supplementary files format and content: Comma-delimited file include raw counts for each sample

molecule: other

organism: Homo sapiens

source_name: skin

extract_protocol:
NHK  were lysed in TRI reagent (Merck, Darmstadt, Germany). Total RNA was then extracted according to the supplier’s instructions.
TruSeq Small RNA Librar

value: skin

value: normal human primary skin keratinocyte

value: reconstructed epidermis on dermal equivalent (3D culture) as described (Bernerd and Asselineau, 1997). Total RNA was extracted from epidermis on D8 of emersion phase (when epidemis achieved full differentiation process).


title: NHK3 3D (F07-53-E5a)


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_3_2_C09_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_32_G04_AF03]


title: NCI-H660, shFOXA2, Rep2

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

data_processing:
Base calling and de-multiplexing were performed using bcl-convert (v3.9.5) with default parameters as per Illumina recommendation.
The final base plus any bases with PHRED quality score <10 and potential adapter sequences (AGATCGGAAGAGCACACGTCTGAAC for Read 1 and AGATCGGAAGAGCGTCGTGTAGGGA for Read 2) were trimmed from the 3’ end of paired RNA-seq reads using CutAdapt (version 4.5).
Reads shorter than 21 bases after trimming were discarded. Trimmed reads were aligned to the hg38 human reference genome (GENCODE GRCh38 v39 primary assembly) using Spliced Transcripts Alignment to a Reference (STAR; version 2.7.11a) with the -peOverlapNbasesMin option set to 6.
Duplicate fragments were marked (though still retained) using Samtools markdup (Samtools version 2.16.0) with the optical distance (-d) option set to value 2500, as recommended for patterned flow cells, and the --no-multi-dup option applied.
The numbers of aligned fragments per gene were counted using featureCounts (Subread version 2.0.6) with the following options: -F GTF -t exon -g gene_id -p -C -d 21. The -p option specifies that fragments (which generally correspond to read pairs) should be counted rather than individual reads. The -C option specifies that read pairs whose ends map to different chromosomes or to different strands of the same chromosome should not be counted. The “-d 21” indicates that only fragments at least 21 bases long should be counted.
FastQC (version 0.12.1)59 and QualiMap (version 2.2.2-dev)60 were used for quality control (QC), and various QC metrics for all samples were aggregated into a single report using MultiQC (version 1.17).
Assembly: hg38
Supplementary files format and content: tab-delimited *.txt file containing raw count matrix

molecule: polyA RNA

source_name: Prostate

growth_protocol: NCI-H660 (ATCC cat. #CRL-5813) cell line was cultured in HITES medium following ATCC recommendation in humidified atmospheric air with 5% CO2 at 37°C. Then FOXA2 was knocked out using shRNA.

extract_protocol:
Cells were washed with 1x PBS, pelleted and re-suspended in TRIzol for total RNA extraction.
Sample quality control wasperformed using the Agilent 2100 Bioanalyzer or the Agilent 4200 Tapestation. Qualifying samples were then prepped following the standard protocol for the Illumina Stranded mRNA prep (Illumina). Sequencing was performed on the Illumina NextSeq2000 with Paired End 59bp × 59bp reads.

value: Prostate

value: Neuroendocrine prostate cancer


title: NCI-H660, shFOXA2, Rep1


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_32_D07_AF03]

value: whole body


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_32_B01_AF03]

value: US EPA GLTED wild type


title: NHK1 3D (F0753-E1a)


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_32_A03_AF03]


title: NHK3 2D (F0750-46a)

value: grown in monolayer (2D culture). NHK were cultured as described (Rheinwald and Green, 1975). Total RNA was extracted when NHK reached 80% confluency (proliferating keratinocytes).


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_1_E07_AF03]

value: microg/L


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_1_E11_AF03]

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFHxS (DTXSID3037709) [AF05_0_032_G10_AF05]


title: bulk_BCR_sequences_postive_control_technical_rep1_biological_rep1

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

data_processing:
Sequencing raw data were analyzed using the iRmap program. Briefly, sequence reads were de-multiplexed according to Illumina dual indices and barcode sequences. Merged reads were mapped to germline V, D, J, and C reference sequences using an IMGT reference library. CDR3 regions were defined by mapping results and extracted and translated into amino acids. The dataset was condensed by combining UMIs and CDR3 regions to remove incorrect CDR3s introduced by sequencing and amplification. Reads with the same combination of CDR3 and UMI were condensed into one UMI count.
Assembly: mm10
Supplementary files format and content: comma seperated value file

organism: Mus musculus

source_name: B cells

extract_protocol:
High-throughput sequencing of the adaptome in the study samples was conducted using the iR-RepSeq+ service provided by iRepertoire, Inc. (Huntsville, AL, US). Next-generation sequencing libraries were generated for each of the 12 samples in replicate, encompassing the BCR heavy chain, with coverage and distinction of IgM, IgD, IgE, IgA, IgG1, IgG2 (IgG2A/IgG2B/IgG2C), and IgG3 subtypes. This technology facilitates amplification of the BCR heavy chain while addressing known sources of errors in AIRR-seq analyses. The sequencing protocol involves the initial utilization of primer pairs for each V-D-J combination, enabling extension with tags for subsequent global amplification of the heavy chains. This amplification process is conducted in a single assay, incorporating unique molecular identifiers (UMIs) during the reverse transcription step to distinguish between individual RNA molecules and minimize the impact of PCR duplicates and sequencing errors. Reverse transcription was performed using Qiagen OneStep RT-PCR mix, followed by selection of first- strand cDNA and removal of remnant primers using SPRIselect bead selection (Beckman Coulter). Subsequently, a second round of binding and extension was carried out with a V-gene primer mix, and SPRIselect beads were employed to purify the first and second-strand synthesis products.
Library amplification was achieved using primers specific to communal sites engineered onto the 5′ end of the C- and V-primers employed in the initial synthesis steps. The final constructed library includes Illumina dual index sequencing adapters, a 10-nucleotide UMI, and an 8-nucleotide internal barcode associated with the C gene primer.
Amplified libraries were multiplexed and pooled for sequencing on the Illumina NextSeq 1000 platform with one P1 600-cycle kit (300 paired-end reads) at iRepertoire Inc. The resulting immune receptor sequence data covers the second framework region through the beginning of the constant region, including the CDR3 hypervariable region.

value: B cells

value: WT


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_3_2_D11_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_1_E01_AF03]


title: NHK2 2D (F0750-43a)


title: NHK1 2D (F0750-37a)


title: bulk_BCR_sequences_lymphnode_technical_rep2_biological_rep4

source_name: ear skin

value: ear skin

value: S. epidermidies association


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_1_B11_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_1_A06_AF03]


title: bulk_BCR_sequences_lymphnode_technical_rep1_biological_rep4


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_10_C01_AF03]


title: bulk_BCR_sequences_lymphnode_technical_rep1_biological_rep3


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_100_F09_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_10_B05_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_10_F06_AF03]


title: bulk_BCR_sequences_lymphnode_technical_rep2_biological_rep3


title: TW_PFOA_TERT_OAT1_Basolateral_2

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

data_processing:
The gene count matrices were generated from single-end reads with four lanes per sample with 76 base pairs (bp).
Reads were quality trimmed using Fastp (version 0.21.0) approach using the default settings with the exceptions of adapter trimming being excluded and the reads being trimmed to 50 bp (Chen et al., 2018).
The reads from the four lanes for each sample were combined to generate a single fastq file.
These files were used as input to the TempO-seq analysis pipeline (House et al., 2017) with the human S1500+ probe manifest file to generate a gene count matrix.
Quality control steps were applied to filter the raw counts: (i) exclusion of samples with fewer than 200,000 counts and (ii) removal of genes with average counts lower than 5% of the number in the remaining samples, except for the genes listed in Supplemental Table 2 that were retained for subsequent analyses. For further analyses, a total of 2,311 genes were evaluated. The Bioconductor's DESeq2 package (Love et al., 2014) was utilized to perform differential expression analysis and generate the complete normalized count matrix for all experimental conditions.
Assembly: S1500+ Gene Set
Supplementary files format and content: normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: hash.csv file with meta data of the samples

extract_protocol:
Cell lysates were used for the Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies) assay as mRNA quantitation technology of choice (House et al., 2017). Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported detailed elsewhere (House et al., 2022).
TempO-seq libraries were prepared using the human S1500+ targeted transcriptome panel (Mav et al., 2018) consisting of 2,982 transcripts according to the manufacturer’s instructions. Briefly, hybridization of the mRNA content of cell lysates was achieved by incubation of 2 μL of the lysate with 2 μL hybridization mix as follows: 10 min at 70°C, cooling ramp from 70°C to 45°C for 49 min, and 1 min at 45°C. Excess oligonucleotides were then digested in a nuclease catalyzed reaction for 90 min at 37°C. Next, hybridization products were incubated with DNA ligase for 60 min at 37°C. Nuclease and ligase were then denatured using a heat denaturation step (80°C for 30 min). A total of 10 μl of each ligation product were then mixed with an equal volume of PCR amplification mix and amplified in a LightCycler 96 (Roche, Basel, Switzerland) using the manufacturer recommended settings. Amplicon samples (5 μl) were then pooled and purified using a commercial PCR clean-up kit (Clontech, Mountain View, CA). Pooled libraries were sequenced in 75 single-end read mode dual index run with custom primers using NextSeq 550 sequencing (Illumina, San Diego, CA).

value: PFOA


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_10_C08_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_100_F02_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_100_D02_AF03]


title: bulk_BCR_sequences_postive_control_technical_rep2_biological_rep1


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_10_A04_AF03]


title: TW_PFOA_TERT_OAT1_Basolateral_1


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_100_A02_AF03]


title: TW_PFOA_TERT_OAT1_Basolateral_3


title: TW_PFOA_TERT_OAT1_Apical_2


title: bulk_BCR_sequences_lymphnode_technical_rep2_biological_rep1


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_32_F01_AF03]


title: bulk_BCR_sequences_lymphnode_technical_rep2_biological_rep2


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_100_A01_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_32_G06_AF03]


title: bulk_BCR_sequences_lymphnode_technical_rep1_biological_rep2


title: TW_PFOA_TERT_OAT1_Apical_3


title: bulk_BCR_sequences_lymphnode_technical_rep1_biological_rep1


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_32_C07_AF03]


title: TW_PFOA_TERT_OAT1_Apical_1


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_32_D10_AF03]


title: bulk_BCR_sequences_spleen_technical_rep2_biological_rep4


title: bulk_BCR_sequences_spleen_technical_rep1_biological_rep4


title: TW_Tenofovir_TERT_OAT1_Apical_3

value: Tenofovir


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_1_G01_AF03]

value: FC8diol (DTXSID30396867)


title: TW_Tenofovir_TERT_OAT1_Basolateral_1


title: TW_Tenofovir_TERT_OAT1_Basolateral_2


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_1_C03_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_1_F05_AF03]


title: TW_Tenofovir_TERT_OAT1_Apical_2


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_1_B06_AF03]


title: bulk_BCR_sequences_spleen_technical_rep2_biological_rep3


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_1_A08_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_032_H01_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_032_F04_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_032_B03_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_032_D05_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_3_2_H08_AF03]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF03_FC10diol_FHM.txt
Normalized+1_AF03_FC10diol_FHM_toxic_removed.txt

value: FC10diol (DTXSID50369896)


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_32_A07_AF03]


title: TW_Tenofovir_TERT_OAT1_Apical_1


title: bulk_BCR_sequences_spleen_technical_rep1_biological_rep2


title: TW_Cisplatin_TERT_OAT1_Basolateral_3

value: Cisplatin


title: bulk_BCR_sequences_spleen_technical_rep2_biological_rep2


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_3_2_G05_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_3_2_D12_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC8diol (DTXSID30396867) [AF04_0_032_A09_AF03]


title: TW_Cisplatin_TERT_OAT1_Basolateral_2


title: bulk_BCR_sequences_spleen_technical_rep2_biological_rep1


title: TW_Cisplatin_TERT_OAT1_Basolateral_1


title: TW_Cisplatin_TERT_OAT1_Apical_3


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_3_2_D06_AF03]


title: bulk_BCR_sequences_spleen_technical_rep1_biological_rep3


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_32_F03_AF03]


title: TW_Cisplatin_TERT_OAT1_Apical_1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_32_E08_AF03]


title: bulk_BCR_sequences_skin_technical_rep1_biological_rep4


title: bulk_BCR_sequences_skin_technical_rep2_biological_rep4


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_32_H10_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_3_2_B08_AF03]


title: TW_Cisplatin_TERT_OAT1_Apical_2


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_32_D03_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_32_B12_AF03]


title: bulk_BCR_sequences_skin_technical_rep1_biological_rep3


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_1_E12_AF03]


title: TW_Untreated_TERT_OAT1_Untreated_2

value: Untreated


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_1_E06_AF03]


title: bulk_BCR_sequences_skin_technical_rep2_biological_rep3


title: bulk_BCR_sequences_skin_technical_rep2_biological_rep2


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_1_H07_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_1_F08_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_1_B02_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_10_H09_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_10_E09_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_10_C12_AF03]


title: bulk_BCR_sequences_spleen_technical_rep1_biological_rep1


title: TW_PFOA_TERT_Parent_Basolateral_3


title: bulk_BCR_sequences_skin_technical_rep1_biological_rep1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_100_H11_AF03]


title: bulk_BCR_sequences_skin_technical_rep2_biological_rep1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_10_D09_AF03]


title: TW_PFOA_TERT_Parent_Basolateral_1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_100_G07_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_10_B09_AF03]


title: TW_Untreated_TERT_OAT1_Untreated_3


title: TW_PFOA_TERT_Parent_Apical_3


title: VDJ_Tcells_lane1

description:
Seurat_Tcells_final_object_with_VDJ.rds
clonotypes.csv
consensus_annotations.csv
HTO_features.csv

data_processing:
Data was demultiplexed with cellranger, counted, aggregated and finally analyzed with Seurat.
Assembly: mm10
Supplementary files format and content: Seurat_Tcells_final_object_with_VDJ.rds (R Seurat Object file)
Supplementary files format and content: clonotypes.csv (comma separated values)
Supplementary files format and content: consensus_annotations.csv (comma separated values)
Supplementary files format and content: filtered_feature_bc_matrix.h5 (cellranger output)
Supplementary files format and content: HTO_features.csv (comma separated values)
Library strategy: scTCR-seq

source_name: skin, spleen, LN

extract_protocol:
Mouse ear skin was digested for 1 hours, mechanically dissociated, RBC lysed and washed.
single cell libraries were preapred using a 10X Genomics 5' kit following manufacturer's instructions.
GEX, HTO and VDJ libraries were prepared and sequenced on a NextSeq 2000 platform

value: skin, spleen, LN

value: T cells

value: wild type

value: S. epidermidies

tag: library type

value: VDJ


title: TW_PFOA_TERT_Parent_Apical_2


title: bulk_BCR_sequences_skin_technical_rep1_biological_rep2


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_100_D04_AF03]

value: whole body

value: US EPA GLTED wild type

value: microg/L


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_100_F11_AF03]

value: 5-6 days post fertilization


title: TW_PFOA_TERT_Parent_Apical_1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_100_A12_AF03]


title: HTO_Tcells_lane1

description:
Seurat_Tcells_final_object_with_VDJ.rds
filtered_feature_bc_matrix.h5
HTO_features.csv

data_processing:
Data was demultiplexed with cellranger, counted, aggregated and finally analyzed with Seurat.
Assembly: mm10
Supplementary files format and content: Seurat_Tcells_final_object_with_VDJ.rds (R Seurat Object file)
Supplementary files format and content: clonotypes.csv (comma separated values)
Supplementary files format and content: consensus_annotations.csv (comma separated values)
Supplementary files format and content: filtered_feature_bc_matrix.h5 (cellranger output)
Supplementary files format and content: HTO_features.csv (comma separated values)

value: HTO


title: GEX_Tcells

library_source: transcriptomic single cell

value: mRNA


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_32_G08_AF03]


title: TW_Tenofovir_TERT_Parent_Basolateral_3


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_32_H06_AF03]


title: Skin_LTA_KO_D14_B_Sample3

city: BETHESDA

first: Cihan

last: Oguz

state: MD

address: NIHBC 29B BG RM 1NN20, 9000 ROCKVILLE PIKE

data_processing:
The initial processing of the expression data involved generating fastq files and count matrices using Cell Ranger v7.1.0 (10X Genomics, Pleasanton, CA) that was run with the “Include introns=False” option and the mm10-2020-A transcriptome reference, whereas the TCR data was processed with Cell Ranger v.7.0.0 and the vdj_GRCm38_alts_ensembl-7.0.0 reference.
In the downstream analysis of the expression data, the Cell Ranger output (filtered_feature_bc_matrix.h5 file) of each sequencing library was loaded into Seurat version 3.1/4.1.0 (Hao et al., 2023) using the  CreateSeuratObject function with min.cells=100 and min. features = 200 settings, that retained the genes detected in at least 100 cells with at least 200 genes detected per cell. For filtering out the low-quality cells, we used the isOutlier function of the R package scuttle (v1.4.0) with nmads (number of median absolute deviations) thresholds of 4 for the highest allowed mitochondrial content (percent. mt), and 3 and 2.5 for the lowest and highest gene and UMI counts (nFeature_RNA and nCount_RNA) allowed, respectively. Log-normalization (LogNormalize) of the RNA count data and centered log-ratio transformation (CLR) of the HTO count data were carried out using the NormalizeData function. For HTO demultiplexing the cells into the TSB and TA treatment groups and removing any additional doublets, HTODemux was run with a positive. quantile = 0.99, whereas FindIntegrationAnchors, IntegrateData, RunPCA, RunUMAP, and FindNeighbors functions of Seurat were run with the top 20 dimensionsData was then normalized, scaled and PCA analysis was performed with xyz principal components. FindClusters function of Seurat was used to cluster the default Louvain clustering setting with a resolution of 0.1.
To manually annotate each cluster with a cell type we utilized the cluster-specific genes with a log2 fold-change greater than > 0.25 compared to remaining clusters and a detection rate (fraction of cells expressing a gene) of at least 0.25. TCR repertoire sequencing data were analyzed with the scRepertoire package v1.11.0 (Borcherding et al., 2020) in R v4.1.1 (R Core Team 2017). Starting with the filtered CellRanger contig annotations output, combineTCR, and combineExpression functions were used for combining the TCR data from each sample and for integration of the combined TCR data with the single cell RNA-Seq data, respectively. We, utilized the amino acid sequence of the paired CDR3 regions of the alpha and beta chains as the clonotype definition, whereas. Clonotype abundance and clonotype sharing between the clusters were identified using scRepertoire.
Assembly: mm10
Supplementary files format and content: Cell Ranger scRNA-seq count matrices are in the h5 data format (one h5 file per sample)

extract_protocol:
Ears were excised and separated into the ventral and dorsal sheets. Tissue samples were digested in RPMI containing 55 µM β-mercaptoethanol, 20 µM HEPES (HyClone), 0.25 mg/mL Liberase purified enzyme blend (RocheDiagnostic Corp.), 0.2 mg/mL DNase I (Sigma) and incubated for 1.5 hours at 37°C and 5% CO2. Digested skin sheets were homogenized using the Medicon/Medimachine tissue homogenizer system (Becton Dickinson) and spun down at 500xg for 5min. Cells were stained and CD4 T cells and CD19+B220+ B cells were sorted
Library construction was performed utilizing the 10X Genomics single cell RNA-seq 5' kit according to manufactor's instructions.

value: skin

value: CD19+B220+ B cells

value: Lta-/-

value: 14 days post S. epidermidies topical association


title: Skin_WT_D7_CD4T_Sample2

value: CD4 T cells

value: WT

value: 7 days post S. epidermidies topical association


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_1_G12_AF03]

value: FC10diol (DTXSID50369896)


title: TW_Tenofovir_TERT_Parent_Basolateral_2

value: Tenofovir


title: TW_PFOA_TERT_Parent_Basolateral_2

value: PFOA


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_32_B07_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_032_H12_AF03]


title: TW_Tenofovir_TERT_Parent_Apical_2


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_1_H05_AF03]


title: TW_Tenofovir_TERT_Parent_Basolateral_1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_32_E02_AF03]


title: Skin_WT_D7_CD4T_Sample1


title: TW_Tenofovir_TERT_Parent_Apical_3


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_32_F12_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_032_H04_AF03]


title: TW_Tenofovir_TERT_Parent_Apical_1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_1_E03_AF03]


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_032_G10_AF03]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_3_2_D01_CH06]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF02_PFTrDA_FHM.txt
Normalized+1_AF02_PFTrDA_FHM_regrouped.txt

value: PFTrDA (DTXSID90868151)


title: iPSC-NC_NoRFP-SampleC2

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

country: Netherlands

institute: Utrecht University

data_processing:
The samples’ data is demultiplexed using fqtk with CEL-seq2 read structure, and other settings were set to default (fqtk). Afterward, the data was aligned to the Human (GRCh38) reference genome, and count tables were generated using STARSolo [Kaminow & Yunusov, 2021]. Reads that mapped equally well to multiple locations were discarded
Assembly: GRCh38
Supplementary files format and content: Tab delimited counts
Supplementary files format and content: Tab delimited meta data

source_name: cord blood

growth_protocol: ACAN-2A-mScarlet reporter human iPSCs were maintained in mTeSR-Plus medium (STEMCELL Technologies, #100-0276) on Vitronectin XF coated plates in humidified atmosphere with 5% CO2 and 37 degree for chondrogenic differentiation, and maintained in mTeSR1 (STEMCELL Technologies, #85850) on Matrigel (Corning, #354277) coated plates for notochordal differentiation

extract_protocol:
total RNA was extracted using TRIZOL LS by Single Cell Discoveries B.V.
The sorted cells were lysed in TRIzol LS (Invitrogen, #1029602) and stored at -80℃. After RNA extraction, bulk RNA sequencing was performed using a modified version of the CEL-Seq protocol(Hashimshony et al. 2012) by Single Cell Discoveries B.V. (Utrecht, The Netherlands).  All extracted and purified RNA samples were assessed by Agilent Tapestation and passed the quality control with high quantity and quality (with RNA integrity number (RIN) scores > 6). Subsequently, these mRNA samples were barcoded with CEL-seq primers during reverse transcription after which they were pooled for second strand synthesis. Resulting cDNA were pooled into one library and amplified using in vitro transcription reaction (IVT). The amplified RNA sequencing libraries were prepared with Illumina TruSeq small RNA primers (Illumina), for paired-end sequencing on the Illumina Novaseq™ X Plus, with a 10B 100 cycles Illumina kit (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles). Read 1 was used to identify the Illumina library index and CEL-seq2 sample barcode.

treatment_protocol: iPSCs were seeded on Laminin 521 (Corning, #354223) coated plates at 20.000 cells/cm2 in mTeSR1 medium supplemented with ROCK inhibitor on Day -2. After two days recovery, iPSCs were cultured in N2B27 medium (detailedly described in Table S1) supplemented with 3 µM CHIR99021 (Axon, #1386) from Day 0 to Day 2 to activate WNT pathway and drove iPSCs to mesendoderm progenitor cells (MEPCs). The MEPCs were dissociated by TrypLE (Gibco, #12604-013) and transfected with Lipofectamine RNAiMAX (Invitrogen, #13778075) and human NOTO synthetic mRNA (volume ratio is 1:5 and 156 ng/ cm2) in a single cell suspension, and seeded on new Laminin521-coated plates at 160.000 cells/ cm2 on Day 2. The NOTO mRNA transfected cells were maintained in N2B27 medium supplemented with 3 µM CHIR99021 complemented with 100 ng/mL recombinant human Noggin (Miltenyi Biotec, #130-103-456) for 3 days allowing the emergence of embryonic iPSC-derived NLCs. A further 3D culture step was performed to mature the differentiated NLCs, with day 5 monolayer cells dissociated and spun down (1200 rpm, 5 mins) in round bottom 96-well plates (Costar, #7007) at 200.000 cells per pellet. Pellets were maintained in disc medium (hgDMEM + Glutamax (Invitrogen, #31966) with 1% ITS Premix (Corning, #354352), 1% MEM Non-essential amino acids (NEAA) (Gibco, #11140050), 40 μg/ml L-Proline (Sigma, #P5607), 0.1 mM ascorbic acid 2-phosphate (Asap) (Sigma-Aldrich, #A8960)) together with 10 ng/mL TGFβ1 (R&D Systems, #240-B-010) for 14 days. The differentiation process was performed in 37 degree incubator with 5% CO2 and 20% O2. Medium was refreshed daily. When iPSCs reached 50% confluence, the culture medium was switched to mesodermal differentiation medium composed of IMDM GlutaMAX (IMDM; ThermoFisher Scientific, #31980030) and Ham’s F12 Nutrient Mix (F12; ThermoFisher Scientific, #11765) with 1% chemically defined lipid concentrate (Gibco, #11905), 1% insulin/human transferrin/selenous acid (ITS+; Corning, #354352), 1% penicillin/streptomycin (P/S; Gibco, #15140), and 450μM 1-thioglycerol (Sigma-Aldrich, #M6145). For induction of anterior primitive streak (day 0), human iPSCs were rinsed with wash medium consisting of IMDM/F12 and 1% P/S, and then fed with mesodermal differentiation medium supplemented with 30 ng/ml of Activin  A  (Stemgent, #03-0001), 4μM of CHIR99021 (CHIR; Stemgent, #04-0004), and 20 ng/ml human fibroblast growth factor (FGF; R&D Systems, Minneapolis, MN) for 24 hours. For induction of paraxial mesoderm (day 1), cells were briefly washed with wash medium and were fed with mesodermal differentiation medium supplemented with 2μM SB-505124 (SB5; Tocris, #3263), 3μM CHIR99021, 20 ng/ml FGF, 4μM dorsomorphin (DM; Stemgent, #04-0024) for 24 hours. For induction of early somite (day 2), after a brief wash with wash medium, cells were fed with mesodermal differentiation medium supplemented with 2μM SB5, 4μM DM, 1μM WNT-C59 (C59; Cellagen Technology, #C7641-2S), and 500 nM PD173074 (PD17; Tocris, #3044) for 24 hours. For induction of sclerotome (day 3–5), after a brief wash with DMEM/F12 (Gibco, #31331028), cells were fed with mesodermal differentiation medium supplemented with 2μM purmorphamine (Pur; Stemgent, #04-0009) and 1μM WNT-C59 for 3 days. Medium was changed daily. For induction of chondroprogenitor cells (day 6 to days 14), cells were fed with mesodermal differentiation medium supplemented with 20 ng/ml human bonemorphogenetic protein 4 (BMP-4; R&D Systems, #314-BP). On day 14, chondroprogenitor cell aggregates were collected for chondrogenesis by washing with wash medium, manually picking, and centrifuging aggregates for 4 min at 1200 rpm. Cell aggregates were maintained in DMEM/F-12 supplemented with 1% ITS-plus, β-mercaptoethanol (55 μM; Gibco, #31350010), dexamethasone  (100 nM), 1% non-essential amino acids (NEAA; Gibco, 11140050), L-ascorbate-2-phosphate (50 μg/ml), L-proline (40 μg/ml), TGF-β1 (10 ng/ml), and antibiotics, for up to 28 days while refreshing medium every 3–4 days.

value: cord blood

value: induced pluripotent stem cells

value: notochrdal differentiation day 14 pellet


title: TW_Cisplatin_TERT_Parent_Basolateral_2

value: Cisplatin


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_1_B10_AF03]

value: whole body

value: US EPA GLTED wild type

value: microg/L

value: 5-6 days post fertilization


title: iPSC-CLC_NoRFP-SampleC 2

value: chondrogenic differentiation, day 28 pellet


title: iPSC-NC_NoRFP-SampleC1


title: TW_Cisplatin_TERT_Parent_Apical_3


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_032_C11_AF03]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_32_G04_CH06]


title: TW_Cisplatin_TERT_Parent_Apical_1


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_32_G03_CH06]


title: iPSC-NC_RFP-SampleC1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_032_E10_AF03]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_3_2_D11_CH06]


title: iPSC-CLC_NoRFP-SampleC1


title: iPSC-NC_RFP-SampleC2


title: TW_Cisplatin_TERT_Parent_Basolateral_3


title: iPSC-CLC_RFP-SampleC1


title: TempO-Seq larval whole body after 24 h exposure to FC10diol (DTXSID50369896) [AF03_0_1_G02_AF03]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_3_2_C09_CH06]


title: iPSC-CLC_RFP-SampleC2


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_1_E11_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_3_2_A05_CH06]


title: TW_Untreated_TERT_Parent_Untreated_1

value: Untreated


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_32_B01_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_3_2_C06_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_32_D07_CH06]


title: TW_Untreated_TERT_Parent_Untreated_3


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_1_B11_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_32_A03_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_1_E07_CH06]


title: Reference sample 75%

city: College Park

first: Shaik

middle: Ohidar

last: Rahaman

state: Maryland

address: 4300 Chapel Lane, Skinner Building, Room #3108

department: Nutrition and Food Science

institute: University of Maryland, College Park

library_source: genomic

data_processing:
FASTQ files from the Ion Torrent S5 server were aligned to a local reference database using the open-source Bismark Bisulfite Read Mapper program (v0.12.2) with the Bowtie2 alignment algorithm (v2.2.3). Methylation levels were calculated in Bismark by dividing the number of methylated reads by the total number of reads. An R-squared value (RSQ) was calculated from the controls set at known methylation levels to test for PCR bias.
Assembly: Bismark Bisulfite Read Mapper program (v0.12.2) with the Bowtie2 alignment algorithm (v2.2.3)
Supplementary files format and content: Comma separated values files containing chromosome, start position, end position, methylation β-value, methylated reads, and total reads for each sample

molecule: genomic DNA

organism: synthetic construct

source_name: 75% methylated DNA

growth_protocol: WT and TRPV4KO thio peritoneal macrophages were cultured in 10% FBS containing DMEM containing 1X anti-anti at 37C and 5% CO2.

extract_protocol:
Cell pellet samples were lysed based on the total cell count per sample and total volume received using M-digestion Buffer (ZymoResearch; Irvine, CA; cat# D5021-9) and 5-10μL of protease K (20mg/mL), with a final M-digestion concentration of 2X. The samples were incubated at 65°C for a minimum of 2 hours.20μL of the supernatant from the sample extracts were bisulfite modified using the EZ-96 DNA Methylation-Direct Kit™ (ZymoResearch; Irvine, CA; cat# D5023) as per the manufacturer’s protocol with minor modification. The bisulfite modified DNA samples were eluted using M-elution buffer in 46μL.All bisulfite modified DNA samples were amplified using separate multiplex or simplex PCRs. PCRs included 0.5 units of HotStarTaq (Qiagen; Hilden, Germany; cat# 203205), 0.2μM primers, and 3μL of bisulfite-treated DNA in a 20μL reaction. All PCR products were verified using the Qiagen QIAxcel Advanced System (v1.0.6). Prior to library preparation, PCR products from the same sample were pooled and then purified using the QIAquick PCR Purification Kit columns or plates (cat# 28106 or 28183). ii. Recommended PCR cycling conditions: 95°C 15 min; 45 x (95°C 30s; Ta°C 30 s; 68°C 30 s); 68°C 5 min; 4°C ∞ iii. Customer samples were run alongside established reference DNA samples with a range of methylation. They were created by mixing high- and low-methylated DNA to obtain samples with 0, 5, 10, 25, 50, 75, and 100% methylation. The high-methylated DNA is in vitro enzymatically methylated genomic DNA with >85% methylation. The low-methylated DNA is chemically and enzymatically treated with <5% methylation. They are first tested on numerous gene-specific and global methylation assays using pyrosequencing.
Libraries were prepared using a custom Library Preparation method created by EpigenDx. Next, library molecules were purified using Agencourt AMPure XP beads (Beckman Coulter; Brea, CA; cat# A63882). Barcoded samples were then pooled in an equimolar fashion before template preparation and enrichment were performed on the Ion Chef™ system using Ion 520™ & Ion 530™ ExT Chef reagents (Thermo Fisher; Waltham, MA; cat# A30670). Following this, enriched, template-positive library molecules were sequenced on the Ion S5™ sequencer using an Ion 530™ sequencing chip (cat# A27764).

treatment_protocol: Cells were treated with 100ng/ml of eLPS for 24 hours in 1% BSA containing DMEM with 1X anti-anti at 37C and 5% CO2.

value: reference control sample


title: TW_Cisplatin_TERT_Parent_Apical_2


title: Reference sample 50%

source_name: 50% methylated DNA


title: Reference sample 100%

source_name: 100% methylated DNA


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_1_E01_CH06]


title: CN_PFOA_TERT_OAT1_Basolateral_3


title: Reference sample 10%

source_name: 10% methylated DNA


title: CN_PFOA_TERT_OAT1_Basolateral_1


title: Reference sample 25%

source_name: 25% methylated DNA


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_10_C01_CH06]


title: CN_PFOA_TERT_OAT1_Basolateral_2


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_10_C08_CH06]


title: CN_PFOA_TERT_OAT1_Apical_3


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_10_A04_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_10_F06_CH06]


title: TW_Untreated_TERT_Parent_Untreated_2


title: Reference sample 5%

source_name: 5% methylated DNA


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_10_B05_CH06]


title: CN_PFOA_TERT_OAT1_Apical_2


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_100_F09_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_100_F02_CH06]


title: CN_PFOA_TERT_OAT1_Apical_1


title: Reference sample 0%

source_name: 0% methylated DNA


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_100_D02_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_100_A02_CH06]


title: Nasal, OVA+CSJ, 300mg/kg, rep1

city: Daejeon

first: Su-Jin

last: Baek

address: 1672, Yuseong-daero

country: South Korea

institute: KOREA INSTITUTE of ORIENTAL MEDICINE

data_processing:
Quality of raw sequence data was checked via the FastQC and adapter or low quality bases were trimmed with TrimGalore
After trimming, the reads were aligned to the mouse reference genome (mm10) using the STAR aligner
Read count was calculated as gene expression abundance using the RSEM and gene annotation mm10 (refGene) Gene Transfer Format (GTF) file
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include count values for each sample

source_name: Nasal

extract_protocol:
Total RNAs were isolated from OVA-induced AR mouse model treated with CSJ 100 mg/kg/mice and CSJ 300 mg/kg/mice using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA)
Library was quantified by QauntiFluor ssDNA System (Promega, WI, USA).

treatment_protocol: The control mice (non-sensitized) administered only saline. Next, on day 21, the mice were randomly divided into five groups (n = 6–8 mice per group) namely, a CON group (control), an OVA group (AR model treated with OVA), a CSJ100 group (AR model treated with CSJ100 mg/kg/mice), a CSJ300 group (AR model treated with CSJ300 mg/kg/mice), and a DEX group (AR model treated with dexamethasone 1 mg/kg/mice).

value: Nasal

tag: strain

value: BALB/c

value: OVA+CSJ, 300mg/kg


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_1_A06_CH06]


title: Nasal, OVA+CSJ, 100mg/kg, rep3

value: OVA+CSJ, 100mg/kg


title: CN_Tenofovir_TERT_OAT1_Basolateral_3

value: Tenofovir


title: Nasal, OVA+CSJ, 300mg/kg, rep3


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_100_A01_CH06]

value: PFTrDA (DTXSID90868151)


title: Nasal, OVA+CSJ, 100mg/kg, rep1


title: Ga-269 trt3

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Morway RD

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina NovaSeq 6000-S4 was used to sequence the libraries for 2 x 150 cycles
Illumina bcl2fastq conversion software
The genome of Muscadine noble was used as the reference sequences for RNA-seq analysis
Reads were individually mapped to the reference genome using the STAR package (Spliced Transcripts Alignment to a Reference, v2.7.9a)
The mapping results were processed with the HTSeq (High-Throughput Sequence Analysis in Python, v0.11.2), samtools, and scripts developed in house at ICBR of UF to remove potential PCR duplicates, choose and count uniquely mapped reads for gene expression analysis
Assembly: The counted reads of each gene were analyzed by a DESeq2-based R pipeline. Differentially expressed (DE) genes were analyzed in a pairwise comparison between genotypes samples. Transcripts per million (TPM) counts were averaged across biological replicates and genes were filtered for moderate expression (TPM ≥ 100) in at least one genotype.
Supplementary files format and content: tab-delimited text files include the mapped read counts for each Sample

organism: Vitis rotundifolia

source_name: pedicel

growth_protocol: Eighteen muscadine genotypes ranging in mature fruit size and color were grown at the University of Florida’s Plant Science Research and Education Unit in Citra, FL

extract_protocol:
Total RNA was isolated from each sample using the Nucleospin RNA Plant and Fungi Mini kit (Macherey-Nagel, PA, USA) following the manufacturer's protocol. To remove all DNA, the total RNA was treated with DNase using the PureLinkTM Dnase Set (InvitrogenTM, CA, USA). To selectively precipitate RNA, a lithium chloride (LiCl) precipitation step was performed
RNA-seq libraries were constructed at the ICBR Gene Expression and Genotyping Core Lab using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, United States) following the manufacturer’s recommendations. A total of 1000 ng samples of RNA with RNA integrity numbers (RIN) greater than 5.6 were used

treatment_protocol: Pedicel tissue from two muscadine genotypes, Ga. 12-3-22 (weakly attached) and Ga. 6-1-269 (strongly attached), was collected at two developmental stages (pea-size and maturity). Pedicel tissue was harvested at the Plant Science Research and Education Unit in Citra, Florida where it was flash frozen in liquid nitrogen and stored at -80°C until further use

value: pedicel

tag: tissue type

value: mature

tag: phenotype

value: strongly attached

tag: developmental stage

value: maturity

value: flash frozen in nitrogen


title: CN_Tenofovir_TERT_OAT1_Basolateral_1


title: Ga-269 trt1


title: Nasal, OVA+dexamethasone, rep1

value: OVA+dexamethasone


title: Ga-269 trt2


title: Nasal, OVA+dexamethasone, rep3


title: Loc1p IP (2)

type: RNA

city: Guildford

first: André

middle: P.

last: Gerber

state: Surrey

address: Stag Hill Campus

department: Microbial Sciences

country: United Kingdom

institute: University of Surrey

description: ProtA Loc1 tagged cells were grown to OD=0.6. Loc1-zz immunoprecipitation and TEV elution. N9/oligo-dT and aminoallyl labeled.

hyb_protocol: annotation not provided

scan_protocol: annotation not provided

data_processing: annotation not provided

organism: Saccharomyces cerevisiae

source_name: Loc1 tot. RNA (extract)

label_protocol: N9/oligo dT primed, amino-allyl labeled.

extract_protocol: annotation not provided

value: yeast cell

source_name: Loc1 RNA-IP


title: Loc1p IP (1)

description: ProtA-tagged Loc1 grown to mid-log in YPD. RNA-IP, TEV-eluate; oligo-dT/N9 primed, amino-allyl label.

source_name: Loc1 tot. RNA (ex)

source_name: Loc1-zz RNA-IP


title: CN_PFOA_TERT_Parent_Basolateral_1

value: PFOA


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_32_G06_CH06]

source_name: whole body

value: whole body

value: US EPA GLTED wild type

value: microg/L

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_1_G01_CH06]


title: CN_Untreated_TERT_OAT1_Untreated_1

value: Untreated


title: Nasal, OVA+dexamethasone, rep2

value: Nasal

value: BALB/c


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_32_D10_CH06]


title: CN_PFOA_TERT_Parent_Basolateral_3


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_32_C07_CH06]


title: Loc1p IP (3)

description: Loc1-protA grown in YPD to mid-log phase. IP and elution with TEV. N9/oligo-dT, amino-allyl labeled.

source_name: tot. RNA Loc1 (ex)

source_name: IP RNA Loc1 (3)


title: Ga-22 trt3

value: weakly attached


title: Ga-269 ctr3

value: pea-size


title: Ga-269 ctr2

value: pedicel


title: CN_PFOA_TERT_Parent_Basolateral_2


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_1_C03_CH06]

value: PFTrDA (DTXSID90868151)


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_1_F05_CH06]


title: Nasal, OVA-induced model, rep3

value: OVA-induced model


title: Ga-269 ctr1

value: mature

value: strongly attached


title: CN_PFOA_TERT_Parent_Apical_3


title: Nasal, OVA-induced model, rep2


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_1_B06_CH06]


title: Ga-22 ctr3

value: flash frozen in nitrogen


title: Nasal, OVA+CSJ, 100mg/kg, rep2

value: OVA+CSJ, 100mg/kg


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_032_H01_CH06]


title: W22, tassel, biol rep 3

city: St Paul

first: Nathan

last: Springer

address: 1479 Gortner Ave

department: Plant and Microbial Biology

institute: University of Minnesota

data_processing:
nf-core RNA-seq pipeline Nextflow v20.10.0 for initial QC and raw read counting
Reads were trimmed using Trim Galore! v0.6.5 and aligned to the W22 reference genome using Hisat2 v2.1.0 with default parameters (hisat2 -x $db $input -p 12 --met-stderr --new-summary). Uniquely aligned reads were counted per feature by featureCounts v2.0.1.
Raw read counts were normalized by library size and corrected for library composition bias using the TMM normalization approach in edgeR v3.28.0 to give CPM (Counts Per Million reads) for each gene in each sample. CPM values were normalized by W22 gene CDS lengths to give FPKM (Fragments Per Kilobase of exon per Million reads) values.
Genes were considered expressed if their CPM was ≥ 1 in at least one sample per tissue
Assembly: Zea mays W22
Supplementary files format and content: Tab-delimited text file includes raw read counts, TMM normalized CPM values, FPKM values for each W22 gene in every sample. The B73v4 gene ID is recorded for W22 genes with one-to-one gene models between W22 and B73v4. The expressed column indicates if the W22 gene was considered expressed in our experiment (TRUE or FALSE). The filtered_DE column indicates if the gene was filtered from the differential expression analysis (TRUE = filtered out, FALSE = included). See Materials and Methods: Identification of TF mutant allele DE genes for further description.

organism: Zea mays

source_name: tassel

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Plant Mini Kit
Paired-end libraries were prepared from a minimum of 500 ng of total RNA using the standard Illumina TruSeq Stranded mRNA library protocol. Single-end libraries were prepared from 2 µg of total RNA using the Illumina TruSeq RNA Sample Prep Kit

value: tassel

value: VT

value: 80 days after sowing

tag: uniformmu id

value: not applicable

value: control


title: CN_Tenofovir_TERT_OAT1_Basolateral_2

value: Tenofovir


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_032_F04_CH06]

value: whole body

value: US EPA GLTED wild type

value: microg/L

value: 5-6 days post fertilization


title: CN_PFOA_TERT_Parent_Apical_2

value: PFOA


title: Nasal, OVA-induced model, rep1

value: Nasal

value: BALB/c


title: Ga-22 trt2

value: pedicel

value: mature

value: weakly attached

value: maturity


title: ILD436

city: VANCOUVER

last: He

address: 1081 Burrard St Room 166

institute: University Of British Columbia

scan_protocol: Nano string

data_processing: Sample quality was confirmed via manufacturer recommended quality control assessments, then normalized according to housekeeping genes

source_name: Whole Blood

extract_protocol: RNA was extracted from PAXgene samples using the PAXgene Blood miRNA Kit (PreAnalytiX, Hombrechtikon, Switzerland), and RNA quality was confirmed by the RNA 6000 Nano Kit (Agilent, Santa Clara, California, USA) via RNA integrity numbers obtained from Bioanalyzer analysis. Blood gene expression was profiled using 100 ng of purified RNA with a custom NanoString nCounter Elements assay (NanoString Technologies, Seattle, WA) that measures 166 transcripts.

tag: diagnosis

value: SSc-ILD

tag: Sex

value: F

tag: fvc

tag: dlco

value: AntiInflammatory

tag: race

value: Asian


title: Nasal, Saline, rep2

tag: tissue

value: Saline


title: ILD428

value: IPF

value: M

tag: treatment

value: AntiFibrotic

value: White


title: Nasal, Saline, rep3


title: CN_Tenofovir_TERT_Parent_Basolateral_3

tag: cell type

tag: cell line

value: Tenofovir


title: Nasal, Saline, rep1


title: CN_PFOA_TERT_Parent_Apical_1

value: PFOA


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_1_A08_CH06]

value: whole body

tag: genotype

value: US EPA GLTED wild type

value: PFTrDA (DTXSID90868151)

tag: conc.

tag: conc. units

value: microg/L

tag: exposure duration

value: 5-6 days post fertilization


title: CN_Tenofovir_TERT_Parent_Basolateral_2


title: Ga-22 ctr2

value: pedicel

tag: tissue type

value: mature

value: weakly attached

value: pea-size

value: flash frozen in nitrogen


title: Ga-22 ctr1

tag: phenotype


title: W22, tassel, biol rep 2

value: tassel

tag: developmental stage

value: VT

tag: age

value: 80 days after sowing

value: not applicable

value: control


title: ILD400

tag: diagnosis

value: IPAF

value: M

value: AntiInflammatory

value: White


title: CN_Tenofovir_TERT_Parent_Apical_3

value: Tenofovir


title: hsf24-m4, tassel, biol rep 1

tag: uniformmu id

value: mutant


title: CN_Tenofovir_TERT_Parent_Apical_2


title: W22, tassel, biol rep 1


title: ILD387

value: HP

tag: Sex

tag: fvc


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_032_D05_CH06]

value: whole body

value: US EPA GLTED wild type

value: PFTrDA (DTXSID90868151)

value: microg/L

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_032_A09_CH06]


title: CN_Tenofovir_TERT_Parent_Apical_1


title: hsf24-m4, tassel, biol rep 2

value: tassel


title: CN_Tenofovir_TERT_Parent_Basolateral_1


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_3_2_D01_CH03]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF01_PFOS_FHM.txt

value: PFOS (DTXSID8037706)


title: CN_Cisplatin_TERT_Parent_Basolateral_3

value: Cisplatin


title: hsf24-m3, tassel, biol rep 2

value: VT

value: 80 days after sowing


title: hsf24-m4, tassel, biol rep 3


title: ILD381

value: IPF

value: F

tag: dlco

tag: race


title: CN_Cisplatin_TERT_Parent_Apical_2

tag: treatment


title: ILD386

value: IPAF

value: Asian


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_32_F01_CH06]

tag: tissue

tag: cell type


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_3_2_D11_CH03]

tag: cell line

tag: genotype


title: Nasal, OVA+CSJ, 300mg/kg, rep2

value: Nasal

tag: strain

value: BALB/c

value: OVA+CSJ, 300mg/kg


title: hsf24-m3, tassel, biol rep 3

value: mutant


title: ILD378

value: SSc-ILD

value: M

value: AntiInflammatory

value: White


title: CN_Cisplatin_TERT_Parent_Basolateral_1


title: ILD383


title: CN_Cisplatin_TERT_Parent_Apical_3


title: hsf24-m3, tassel, biol rep 1

value: tassel


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_032_B03_CH06]

value: whole body

value: US EPA GLTED wild type

value: PFTrDA (DTXSID90868151)

tag: conc.

tag: conc. units

value: microg/L

tag: exposure duration

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_32_G04_CH03]

value: PFOS (DTXSID8037706)


title: ILD370

value: F


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_3_2_C09_CH03]


title: ILD374

value: HP

value: Native Hawaiian or Other Pacific Islander


title: Ga-22 trt1

value: pedicel

tag: tissue type

value: mature

tag: phenotype

value: weakly attached

tag: developmental stage

value: maturity

value: flash frozen in nitrogen


title: CN_Cisplatin_TERT_Parent_Apical_1

value: Cisplatin


title: CN_Cisplatin_TERT_Parent_Basolateral_2


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_3_2_C06_CH03]

tag: age


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_32_G03_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_3_2_A05_CH03]