title: CD4 CROP-seq well16

description: 10X Genomics V2 3' kit

data_processing:
CellRanger + scanpy
Assembly: hg19
Supplementary files format and content: h5ad file containing gene expression counts, cell barcodes, feature names, experimental covariates

source_name: CD4+ T cells

extract_protocol:
Primary human CD4+ T cells were isolated from peripheral blood mononuclear cells (PBMCs) by magnetic negative selection using the EasySep Human CD4+ T Cell Isolation Kit (STEMCELL, Cat #17952).
Cells were cultured in X-Vivo media, consisting of X-Vivo15 medium (Lonza, Cat #04- 418Q) with 5\% Fetal Calf Serum, 50mM 2-mercaptoethanol, and 10mM N-Acetyl L-Cysteine. On the day of isolation (Day 1), cells were rested in media without stimulation for 24 hours. The day after isolation (Day 2), cells were stimulated with ImmunoCult Human CD3/CD28 T Cell Activator (STEMCELL, Cat #10971) and IL-2 at 50U/mL. 24 hours post stimulation (Day 3), 1 uL of lentivirus was added directly to cultured T cells and gently mixed. Following 24 hours (Day 4), cells were collected, pelleted, and washed in PBS twice. Then, cells were resuspended in Lonza electroporation buffer P3 (Lonza, Cat #V4XP-3032). Cas9 protein (MacroLab, Berkeley, 40mM stock) was added to the cell suspension at a 1:10 v/v ratio. Cells were transferred to a 96 well electroporation cuvette plate (Lonza, cat #VVPA-1002) for nucleofection using the Lonza Nucleofector 96-well Shuttle System and pulse code EH115 (Lonza, cat #VVPA-1002). Immediately after electroporation, pre-warmed media was added to each electroporation well, and 96-well plate was placed at 37 degrees for 20 minutes. Cells were then transferred to culture vessels in X-Vivo media containing 50U/mL IL-2 at 1e6 cells /mL in appropriate tissue culture vessels. Two days later, 1.5ug/mL Puromycin was added in culture media for selection. Cells were expanded every two days, adding fresh media with IL-2 at 50U/mL. Cells were maintained at a cell density of 1e6 cells /mL. On the final day (Day 13) of the experiment, cells from each of the nine donors were counted using Vi-CELL XR and pooled at equal numbers to obtain a final 180,000 cells in 60 uL of PBS. The pooled cells were then processed by UCSF Institute for Human Genetics (IHG) Genomics Core using 16 wells of 10X Chromium Single Cell v2 (PN-120237), as per manufacturer’s protocol, with each well being separately index.

value: CD4+ T cells


title: PM1_MLN_B_2L RNA

status: Public on Oct 24 2024

type: SRA

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E 69th St

department: Drukier Institute

country: USA

institute: Weill Cornell Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: GRCh38
Supplementary files format and content: Comma-separated files and fasta files
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format

molecule: total RNA

organism: Homo sapiens

source_name: Human Mediastinal LN 2L

extract_protocol:
10x Genomics CG000424_C
10x Genomics CG000424_C

tag: tissue

value: Human Mediastinal LN 2L

tag: cell type

value: B cell


title: LB, 10min, Rep2

city: Basel

first: Knut

last: Drescher

state: BS

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description: data for chromosome I and II

library_source: transcriptomic

data_processing:
Sequencing of the cDNA libraries was performed by MPGC
cDNA reads were imported into CLC Genomics Workbench v11.0 and analyzed using mostly standard parameters.
The reads were checked for quality and mapped to the V. cholerae reference genomes: NCBI Acc.number: AE003852 and AE003853 using the default settings in CLC Genomics Workbench v11.0.
Reads mapping in CDS were counted, and read counts were normalized (TPM), and transformed (log2). Differential expression was tested using the built in tool with CLC Genomics Workbench v11.0. Genes with a FDR adjusted p-value < 0.05 were considered to be differentially expressed.
Assembly: AE003852, AE003853; Vibrio cholerae O1 biovar eltor str. N16961 chromosome I and II, complete genome
Supplementary files format and content: Read count table by TPM normalization

organism: Vibrio cholerae

source_name: Biofilm cells collected from microfluidics

growth_protocol: Bacterial cells in exponential phase (OD600=0.4) were inoculated in microfluidic flow chambers and supplied with LB or LB+peptidolgycan (300 µg/mL) for 10 min.

extract_protocol:
RNA was isolated by the hot phenol method (Jahn et al, J Microbiol Methods,2008) with some modifications. Prepared RNA was DNase-digested and cleaned up using RNACleanXP. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Libary Prep Kit for Illumina (NEB E7760) according to the manufacturers instructions. Quality of the prepared libraries was tested using a TapeStation.

treatment_protocol: Bacterial cells were collected from microfluidic flow chambers in a 1:1 mixture of PBS and RNAstop solution (a mixture of 95% (vol/vol) EtOH and 5% (vol/vol) phenol). After centrifugation and removal of the supernatant, the cells were resuspended in 50 μL of lysozyme buffer, which consisted of TE (10 mM Tris, adjusted to pH 8.0 with HCl), 1 mM EDTA, and 20 U μL-1 Ready-lyse lysozyme (Lucigen, R1804M) and immediately snap frozen in liquid nitrogen until further processing.

tag: strain

value: bacterial cell

tag: condition

value: Grown with LB for 10 min

tag: replicate

value: rep 2


title: PM1_MLN_B_12R VDJ

description: 10x Genomics

source_name: Human Mediastinal LN 12R

value: Human Mediastinal LN 12R


title: LB, 10min, Rep1

description: data for chromosome I and II

value: rep 1


title: CD4 CROP-seq well15

city: San Francisco

first: Min Cheol

last: Kim

state: CA

address: 505 Parnassus Ave

institute: University of California, San Francisco

description: 10X Genomics V2 3' kit

molecule: polyA RNA


title: Arabidopsis Col-0 grown in temperate climate mock treated replicate 2

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

description:
Mock treatment - Plants grown in temperate climate
Col-0_cont_Cl1_2

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Reads QC was performed using spiked-PhiX in-lane controls yielding Q30 error rate <0.4% for all lanes
Basecalling was performed with the HiSeq Control Software 2.2.58, RTA 1.18.64.0 and CASAVA-1.8.2
Paired-end reads were trimmed and mapped to the TAIR10.0 reference genome using the RNA-seq analysis tool of the CLC Genomics Workbench 11.0.1 software (Qiagen). The following mapping parameters were used: mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.8, both strands mapping, and 10 hits maximum per read
Assembly: Arabidopsis thaliana TAIR10.0
Supplementary files format and content: tab-delimited text files include Expression values; Transcripts annotated; Detected transcripts; Exon length; Unique gene reads; Total gene reads; Unique exon reads; Total exon reads; Ratio of unique to total (exon reads); Unique exon-exon reads; Total exon-exon reads; Unique intron reads; Total intron reads; Ratio of intron to total gene reads; Exons; RPKM; Chromosome; Chromosome region start; Chromosome region end per gene

organism: Arabidopsis thaliana

source_name: leaves of 5-week old plants

growth_protocol: Plants were grown in jiffy pots for 35 or 70 days in Percival E41-L3 and E41-L2PLT growth cabinets at day temperatures of 23°C (mediterranean), 20°C (temperate) or 10°C (continental), night temperatures of 7°C (mediterranean), 9°C (temperate) and 1°C (continental), with a 13 hour light period (temperate and mediterranean climate) or 14 hour light period (continental climate) at intensity of 120 μmol/m²/s.

extract_protocol:
The border (ring of ~5mm wide) of disease lesions were collected with a scalpel at 30 hours post inoculation (hpi) for temperate and mediterranean acclimation and 48 hpi for continental acclimation,  and frozen in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min). RNA was extracted using the RNAplus kit (Macherey Nagel) following the manufacturer’s instructions. A Turbo DNAse treatment (Ambion) was applied to remove genomic DNA. The quality and concentrations of RNAs preparations were assessed with an Agilent Bioanalyzer using the Agilent RNA 6000 Nano kit
HiSeq SBS Kit v4

treatment_protocol:
S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed on the adaxial surface of leaves on 5-week old plants. Inoculations were performed on detached leaves under constant 21°C temperature, constant light (120 μmol/m²/s) and 90% relative humidity.
Temperate acclimation consisted in growth for 35 days under cycles of 13 hours at 20°C (day) followed by 11 hours at 9°C (night); mediterranean acclimation consisted in growth for 35 days under cycles of 13 hours at 23°C (day) followed by 11 hours at 7°C (night); continental acclimation consisted in growth for 70 days under cycles of 14 hours at 10°C (day) followed by 10 hours at 1°C (night).

value: leaves of 5-week old plants

tag: cell line

value: A. thaliana Col-0

tag: genotype

tag: treatment 1_(inoculation)

value: mock

tag: treatment 2_(acclimation)

value: temperate


title: PG, 10min, Rep1

description: data for chromosome I and II

value: Grown with LB+PG for 10 min


title: CD4 CROP-seq well14

description: 10X Genomics V2 3' kit


title: HTEC HTO sample 2-1

description:
10X Genomics V2 3' kit
feature_reference.csv
HTEC_counts.h5ad

library_source: other

data_processing:
CellRanger + scanpy
Assembly: GRCh38
Supplementary files format and content: h5ad file containing gene expression counts, cell barcodes, feature names, experimental covariates

molecule: protein

source_name: HTEC

extract_protocol:
Human tracheal epithelial cells were harvested from deceased organ donors according to established protocols (PMID: 1616056). Frozen cell aliquots were reactivated and cultured in epithelial growth media (EGM) [3:1 (v/v) F-12 Nutrient Mixture (Gibco)–Dulbecco's modified Eagle's medium (Invitrogen), 5\% fetal bovine serum (Gibco), 0.4 ug/mL hydrocortisone (Sigma-Aldrich), 5 ug/mL insulin (Sigma-Aldrich), 8.4 ng/mL cholera toxin (Sigma-Aldrich), 10 ng/mL epidermal growth factor (Invitrogen), 24 ug/mL adenine (Sigma-Aldrich), and 10 uM Y-27632 (Enzo Life Sciences)] on 10 mm dishes coated with rat tail collagen (Sigma-Aldrich). EGM was changed three times a week until dishes were confluent, at which point the cells were passaged with 0.25\% trypsin for 30 minutes. For air liquid interface culture, expanded basal cells were plated at 50,000 cells per 6.5 mm transwell insert (Corning 3470) coated with human placental collagen (Sigma-Aldrich) and cultured with Pneumacult ALI (StemCell) for 21-28 days according to the manufacturer’s instructions.
Starting on day 27, interferon stimulation (IFN-beta: 10 ng/ml, IFN-alpha2: 10 ng/ml, IFN-gamma: 10 ng/ml, IFN-lambda2: 10 ng/ml) was added at hours 0, 24, 39, 42, and 45 prior to harvesting (For final timepoints 3, 6, 9, 24, and 48 hours). On the day of harvest, basal media was aspirated and both basal and apical chambers were rinsed twice with PBS. Following two washes, trypsin-EDTA (0.25% Fisher cat. 25200072) was added to both the basal and apical chambers (300 ul basal, 100 ul apical) and incubated for 30 minutes at 37degree C while pipette mixing every 10 minutes. Trypsinization was quenched with 300 ul of maintenance media and transferred to a 1.5ml eppendorf tube (eppendorf cat. 022431021) and centrifuged at 350xg for 5 minutes at 4degree C. Cells were resuspended in 94 ul of cell staining buffer (Biolegend cat. 420201) and blocked with 5 ul of TruStain FcX (Biolegend cat. 422302) for 10 minutes on ice. Blocked cells were stained with 1 ul of Biolegend Totalseq-B hashtags (Biolegend Totalseq-B hashtags 1-11) for 30 minutes on ice. Staining was quenched with 1 ml of cell staining buffer and spun at 300xg for 5 minutes at 4degree C prior to two more washes with 1 ml of cell staining buffer. Cells were resuspended in 100 ul of 0.05% BSA in PBS and counted via Countess II (Fisher cat. A27977). Counted cells were pooled equally into two pools and spun at 300xg for 5 minutes at 4degree C.

value: HTEC

tag: treatment

value: interferons

tag: library type

value: HTO


title: Arabidopsis Col-0 grown in temperate climate mock treated replicate 3

description:
Mock treatment - Plants grown in temperate climate
Col-0_cont_Cl1_3


title: Arabidopsis Col-0 grown in temperate climate mock treated replicate 1

description:
Mock treatment - Plants grown in temperate climate
Col-0_cont_Cl1_1


title: Arabidopsis Col-0 grown in temperate climate infected by S. sclerotiorum replicate 3

description:
Front zone of lesion - Plants grown in temperate climate
Col-0_Fr_Cl1_3

value: A. thaliana Col-0 - Sclerotinia sclerotiorum 1980

value: inoculated


title: PID 14

city: Shatin

first: Yidan

last: ZOU

state: State

address: Rm902, LKS medical Sciences Bldg, PWH, Shatin , HK, 902

country: Hong Kong

institute: The Chinese university of Hong Kong

data_processing:
Cell Ranger (10× Genomics, US)
Seurat suite (version 3.0.1) in R (version 3.5.1)
clustering
t-SNE, cluster visualization
DEG, GO
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Mus musculus

source_name: spinal cord

extract_protocol:
Spinal cords were harvested from sham or SNI mice at PID 3, PID 7 and PID 14 in ice-cold PBS solution. Cells in the ipsilateral L4-L6 spinal cord dorsal horns were isolated, homogenized using loose and tight pestles in 1 mL ice-cold Ca2+/Mg2+-free HBSS for 15-20 times by simultaneously rotation. The homogenate was passed through a pre-wet 70 μm mesh cell strainer (BD Biosciences, USA) and spun down at 300 g for 5 min at 4 °C. The cell pellet was resuspended in 40% Percoll solution (GE Healthcare #GE17-0891-01) and centrifuged at 500 g for 15 min at 4 °C. Cells in pellet resuspended and incubated in ice-cold FACS buffer and then incubated in ice-cold FACS buffer containing Cd11b-PE (BioLegend, #101208) at a final dilution of 1:300 for 30 min. The cells were then washed with 1 mL of ice-cold FACS buffer. After centrifuging at 800 g for 5 min, the pellet was resuspended in ice-cold FACS buffer. Living cells exhibiting high fluorescence levels of Cd11b were sorted by FACS using a 70 μm chip on the FACSAriaTM Fusion Platform (BD Biosciences, Carlsbad, CA, USA) with Purity mode.
Single-cell RNA-Seq libraries was prepared using Chromium Single Cell 3’ Library and Gel Bead Kit v3.0 (10X Genomics #PN-1000075), Chromium Single Cell 3′ Library Construction Kit v3.0 (10X Genomics #PN-1000078), Chromium Chip B Single Cell kit (10X Genomics #PN-1000154), Chromium i7 Multiplex Kit (10X Genomics #PN-120262) and chromium controller, following manufacturer’s instruction. The samples were sequenced on an DNBSEQ-T7 sequencer.

treatment_protocol: Spared nerve injury (SNI; PID 3, PID 7, PID 14) or sham surgeries were conducted.

value: spinal cord

value: microglia

value: wild type

value: SNI


title: PID 7


title: PM1_MLN_B_12L RNA

description: 10x Genomics

source_name: Human Mediastinal LN 12L

value: Human Mediastinal LN 12L

value: B cell


title: PM1_MLN_B_12L VDJ

description: 10x Genomics


title: PM1_MLN_B_12R RNA

description: 10x Genomics

value: Human Mediastinal LN 12R


title: PID 0

value: sham


title: CD4 CROP-seq well11

description: 10X Genomics V2 3' kit

value: CD4+ T cells


title: CD4 CROP-seq well13

description: 10X Genomics V2 3' kit


title: PM1_MLN_B_10R RNA

description: 10x Genomics

source_name: Human Mediastinal LN 10R

value: Human Mediastinal LN 10R


title: PID 3


title: CD4 CROP-seq well12

description: 10X Genomics V2 3' kit


title: PM1_MLN_B_10R VDJ

description: 10x Genomics


title: PM1_MLN_B_10L VDJ

description: 10x Genomics

source_name: Human Mediastinal LN 10L

value: Human Mediastinal LN 10L


title: CD4 CROP-seq well9

description: 10X Genomics V2 3' kit


title: CD4 CROP-seq well10

description: 10X Genomics V2 3' kit


title: time series teratoma wk10 2 replicate 2

city: La Jolla

first: Prashant

last: Mali

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

data_processing:
Align mRNA fastq files to genome and generate gene expression matrices with 10X genomics cellranger count with default parameters
Assembly: hg38_and_mm10
Supplementary files format and content: Files ending in "_matrix.mtx.gz" are counts matrices output by 10X CellRanger in sparse matrix format
Supplementary files format and content: Files ending in "_barcode.tsv.gz" are cell barcodes output by 10X CellRanger
Supplementary files format and content: Files ending in "_features.tsv.gz" are gene features output by 10X CellRanger

molecule: cytoplasmic RNA

growth_protocol: H1, H9, HUES62, and PGP1 PSC cell lines were maintained under feeder-free conditions in mTeSR1 medium (Stem Cell Technologies 85850). Prior to passaging, tissue-culture plates were coated with growth factor-reduced Matrigel (Corning 356230) diluted in DMEM/F-12 medium (Thermo Fisher Scientific 11320033) and incubated for 30 minutes at 37 ⁰C, 5% CO2. Cells were dissociated and passaged using the dissociation reagent Versene (Thermo Fisher Scientific 15040066).

extract_protocol:
To extract nuclei, teratoma tissues frozen in OCT were processed as previously described (dx.doi.org/10.17504/protocols.io.5qpvoby69l4o/v2). Extracted nuclei were passed through a 50 𝜇m filter, followed by a 30 𝜇m filter and pelleted by spinning at 900 rcf at 4 ºC for 10 minutes. Resuspended nuclei in PBS + 1% BSA solution were stained for DAPI and viable nuclei were collected via FACS. Sorted nuclei were pelleted under the same condition and resuspended in PBS + RNase Inhibitors for generating single nucleus sequencing libraries using Chromium Single Cell 3ʹ Reagent Kits v3 (10x Genomics).
Nuclei were passed through a 30 𝜇m filter, spun down at 900 rcf for 5 minutes, and resuspended in 1% BSA solution. Nuclei were sorted for viable singlets and were then loaded into the Chromium Chip B (10x Genomics) and single cell libraries were made using Chromium Single Cell 3ʹ Reagent Kits v3 workflow (10x Genomics). Fastq files were aligned to a hg38 reference and expression matrices were generated using the count command in cellranger v3.0.1 (10X Genomics).


title: Gastroc_glucose_injected_M14

city: Nuthetal

first: Maximilian

last: Kleinert

address: Arthur-Scheunert-Allee 114-116, , Arthur-Scheunert-Allee 114-116

department: Molecular Physiology of Exercise and Nutrition

country: Germany

institute: German Institute of Human Nutrition

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.11a
Read count extraction via STRINGTIE v2.2.1 and prepDE.py (following Protocol stringtie webpage)
Assembly: GRCm39.110
Supplementary files format and content: excel file includes raw counts for each sample

source_name: Gastrocnemius

extract_protocol:
RNA was isolated following a Trizol-Chloroform (peqGOLD TriFastTM, 30-2010P, VWR)  extraction and a DNase digest following manufacturer instructions (Fisher Scientific, #EN0521)
done by BGI (Yantian District, Shenzhen, China)

value: Gastrocnemius

tag: Sex

value: male

value: PanK4 mKO

value: 4-h fast then glucose injection


title: CD4 CROP-seq well8

description: 10X Genomics V2 3' kit


title: time series teratoma wk10 2 replicate 1


title: Gastroc_glucose_injected_M12


title: time series teratoma wk10 1 replicate 3


title: PM1_MLN_B_10L RNA

description: 10x Genomics


title: Gastroc_glucose_injected_M11

value: PanK4 WT


title: Arabidopsis Col-0 grown in temperate climate infected by S. sclerotiorum replicate 2

description:
Front zone of lesion - Plants grown in temperate climate
Col-0_Fr_Cl1_2

value: leaves of 5-week old plants

value: A. thaliana Col-0 - Sclerotinia sclerotiorum 1980

value: inoculated

value: temperate


title: TS1; Tonsil B Cell Fraction C VDJ

description: 10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger (v7.1.0) functions (mkfastq, count, vdj)
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of cell barcode sequences
Supplementary files format and content: features.tsv.gz: list of gene IDs + names
Supplementary files format and content: matrix.mtx.gx: gene expression count data in Market Exchange Format
Supplementary files format and content: consenus.fasta: the consensus sequence of each assembled contig in FASTA format
Supplementary files format and content: filtered_contig_annotations.csv: high-level annotations of each high-confidence contigs from cell associated barcodes

source_name: Tonsil

extract_protocol: 10x Genomics CG000424_C

value: Tonsil


title: time series teratoma wk10 1 replicate 2


title: Gastroc_glucose_injected_M10


title: CD4 CROP-seq well6

description: 10X Genomics V2 3' kit


title: TS1; Tonsil B Cell Fraction B VDJ

description: 10X Genomics


title: time series teratoma wk10 1 replicate 1


title: CD4 CROP-seq well5

description: 10X Genomics V2 3' kit


title: CD4 CROP-seq well7

description: 10X Genomics V2 3' kit


title: Arabidopsis Col-0 grown in temperate climate infected by S. sclerotiorum replicate 1

description:
Front zone of lesion - Plants grown in temperate climate
Col-0_Fr_Cl1_1


title: TS1; Tonsil B Cell Fraction C RNA

description: 10X Genomics


title: CD4 CROP-seq well4

description: 10X Genomics V2 3' kit


title: Gastroc_glucose_injected_M9


title: TS1; Tonsil B Cell Fraction B RNA

description: 10X Genomics


title: time series teratoma wk8 1 replicate 2


title: time series teratoma wk8 2 replicate 1


title: Gastroc_glucose_injected_M8


title: CD4 CROP-seq well3

description: 10X Genomics V2 3' kit


title: Gastroc_glucose_injected_M13


title: Gastroc_glucose_injected_M7


title: time series teratoma wk8 1 replicate 1


title: TS1; Tonsil B Cell Fraction A VDJ

description: 10X Genomics


title: Gastroc_glucose_injected_M6


title: CD4 CROP-seq well2

description: 10X Genomics V2 3' kit


title: Gastroc_glucose_injected_M5


title: time series teratoma wk6 1 replicate 2


title: time series teratoma wk6 2 replicate 1


title: dwarfing Apple rootstock M9_1 phloem 60dabb

city: Qingdao

first: Yanjing

last: Shi

state: Shandong

address: 53# Zhengzhou Road

country: China

institute: Qingdao university of Science & Technology

description: FPKM of 4 samples -64DABB.TXT

data_processing:
Raw data (raw reads) were processed using Trimmomatic， . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads
clean reads were mapped to reference genome using hisat2
FPKM[3] value of each gene was calculated using cufflinks[4]
, and the read counts of each gene
were obtained by htseq-count，
Assembly: https://data.jgi.doe.gov/refine-download/phytozome?genome_id=491
Supplementary files format and content: tabdelimited text files include FPKM of each sample

organism: Malus pumila

source_name: phloem

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion)
The libraries  were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego,  CA, USA) according to the manufacturer’s instruction

value: phloem

tag: phenotype

value: dwarfing


title: time series teratoma wk6 1 replicate 1


title: Gastroc_glucose_injected_M2


title: dwarfing Apple rootstock B9_2 phloem 60dabb

description: FPKM of 4 samples -63DABB.TXT


title: time series teratoma wk4 2 replicate 1


title: dwarfing Apple rootstock M9_2 phloem 60dabb

description: FPKM of 4 samples -65DABB.TXT


title: Gastroc_glucose_injected_M1


title: dwarfing Apple rootstock B9_1 phloem 60dabb

description: FPKM of 4 samples -62DABB.TXT


title: TS1; Tonsil B Cell Fraction A RNA

description: 10X Genomics

value: B cell


title: time series teratoma wk4 1 replicate 1


title: pre-miR-141-3_C [253949444636-4]

type: RNA

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: TRI reagent (Merck)

value: human primary keratinocytes

tag: amount in (microg)

tag: rin number


title: Gastroc_glucose_injected_M3


title: CD4 CROP-seq well1

description: 10X Genomics V2 3' kit

value: CD4+ T cells


title: time series teratoma wk4 1 replicate 2


title: pre-miR-141-3_B [253949444635-4]


title: pre-miR-ctrl_B [253949444635-1]


title: pre-miR-ctrl_C [253949444636-1]


title: Genomic DNA from spinal ependymoma 90

status: Public on Oct 23 2024

type: genomic

city: Graz

first: Lara

last: Engertsberger

address: Auenbruggerplatz 34/2

department: Division of Pediatric Hemato-Oncology

country: Austria

institute: Medical University of Graz

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and the standard recommended Illumina scanner setting.

data_processing:
Statistical analysis was performed using the minfi package version 1.43.1 with the statistical programming language R version 4.3.0.
Average beta-values after combining arrays and normalization using the Noob method.

label: Cy3 and Cy94

molecule: genomic DNA

source_name: spinal ependymomas

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from FFPE tissue using the ReliaPrep™ FFPE gDNA Miniprep System (Promega, Madison, WI) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research, Irvine, CA). The DNA Clean & Concentrator-5 (Zymo Research, Irvine, CA) and the Infinium HD FFPE DNA Restore Kit (Illumina, San Diego, CA) were employed to clean and restore the converted DNA.

value: M

tag: age

tag: localization

value: coccygeal

tag: extent of resection

value: <GTR

tag: who tumor grade

value: myxopapillary WHO grade non-myxopapillary WHO grade 2

tag: classification result v12.5

value: MPE

tag: classification score

tag: OS status

tag: os [days]

tag: pfs status

tag: pfs [days]

tag: material

value: FFPE

value: spinal ependymomas


title: Genomic DNA from spinal ependymoma 86

label: Cy3 and Cy90

value: thoracolumbar

value: WHO grade 3

tag: tissue


title: pre-miR-141-3_A [253949444634-4]

tag: cell type


title: pre-miR-ctrl_A [253949444634-1]


title: Monocytes/macrophages With MEC1 21d rep2

city: Houston

first: Maria Teresa

middle: Sabrina

last: Bertilaccio

state: Texas

address: 1901 East Road

department: Leukemia

institute: The University of Texas MD Anderson Cancer Center

description: monocytes/macrophages from mouse 9

hyb_protocol: The fragmented and labeled sscDNA (5.2 µg) was  hybridized to the mouse Affimetrix GeneChip Clariom D (Mouse Transcriptome 1.0) array at 45ºC for 16 hours, washed and stained using the ThermoFisher proprietary reagents in the GeneChip Fluidics Station 450 (FS450)

scan_protocol: GeneChip Scanner 3000 7G (ThermoFisher Scientific)

data_processing:
CEL files generated after the GeneChip microarrays scanning were uploaded onto the Expression Console software for analysis with SST-RMA algorithm (ThermoFisher)).
Standard expression microarray analysis consisted of normalizing the signal intensity distributions of all probe features on all arrays. A probe feature is a location on the array that contains many copies of the same 25-mer DNA sequence. Normalizing these distributions enabled the comparison of probe signals between groups.
Next, the signal intensities for all probes in a probe set that defined a gene or exon were aggregated into a single value for each array or sample. The aggregate signal value was used to compare gene-level or exon-level expression changes between sample groups or conditions.
The SST-RMA analysis algorithm incorporated pre-processing steps into the CEL files before normalization and summarization with RMA. This algorithm reduced fold change compression by applying a GC correction and by transforming the microarray data signal to a similar signal space of other methods such as RT-PCR or RNA-Seq.

label: biotin

source_name: Murine bone marrow

label_protocol: Biotinylated sense-strand cRNA was prepared according to manufacturer's standard protocol (ThermoFisher Scientific)

extract_protocol: QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit

tag: strain

value: Rag2-/-gamma c-/- on BALB/c background

value: 11 weeks

value: Bone marrow


title: Monocytes/macrophages With MEC1 31d rep3

description: monocytes/macrophages from mouse 16

value: 13 weeks


title: Monocytes/macrophages With MEC1 21d rep3

description: monocytes/macrophages from mouse 10


title: Monocytes/macrophages No MEC1 31d rep2

description: monocytes/macrophages from mouse 12


title: Genomic DNA from spinal ependymoma 85

description: Relation GSM7776604, GSM7781546

label: Cy3 and Cy89

tag: Sex

value: cervical

value: non-myxopapillary WHO grade 2

value: SP-EPN

tag: reanalysis of


title: Genomic DNA from spinal ependymoma 84

description: Relation GSM7776623, GSM7781526

label: Cy3 and Cy88


title: MDA-LM-2 A3

city: Bangkok

first: Penchatr

last: Diskul-Na-Ayudthaya

country: Thailand

institute: Chulabhorn Research Institute/Soonchunhyang Institute of MEDI-BIO science

data_processing:
Quality control of RNA-Seq reads was performed using FastQC (v0.11.9)
The cleaned reads were then ready for alignment to the human reference genome (HG19).
The reads were normalized according to relative logarithmic expression using DESeq2 (Genome Biology Unit; European Molecular Biology Laboratory, Heidelberg, Germany).
Assembly: HG19
Supplementary files format and content: FPKM and normalized counts for each sample

source_name: Breast

growth_protocol: MDA-LM-2 cells were cultured in DMEM medium, supplemented with 10% FBS, antimicrobial agents (100 U/ml penicillin, 100 μg/ml streptomycin) in a humidified 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using  RNeasy mini kit (Qiagen)
RNA libraries for RNA sequencing using the Human TruSeq standard mRNA protocol (Illumina, Inc.) .

value: Breast

tag: cell line

value: epithelial cell

tag: genotype


title: MDA-LM-2 A1

value: control


title: Monocytes/macrophages No MEC1 21d rep3

description: monocytes/macrophages from mouse 3

tag: age


title: Monocytes/macrophages With MEC1 21d rep1

description: monocytes/macrophages from mouse 6


title: Genomic DNA from spinal ependymoma 81

label: Cy3 and Cy85

value: M

tag: localization

tag: extent of resection

value: GTR


title: Genomic DNA from spinal ependymoma 82

description: Relation GSM7776670, GSM7781521

label: Cy3 and Cy86

value: cervicothoracic

value: <GTR

tag: who tumor grade

tag: classification result v12.5


title: Monocytes/macrophages No MEC1 21d rep1

description: monocytes/macrophages from mouse 1


title: MDA-LM-2 A2


title: Genomic DNA from spinal ependymoma 62

description: Relation GSM5600006

label: Cy3 and Cy66

value: lumbosacral

value: MPE

tag: classification score

tag: OS status

value: FFPE

value: spinal ependymomas


title: Monocytes/macrophages No MEC1 31d rep1

description: monocytes/macrophages from mouse 11

value: Rag2-/-gamma c-/- on BALB/c background


title: Monocytes/macrophages With MEC1 31d rep1

description: monocytes/macrophages from mouse 14

value: Bone marrow


title: Monocytes/macrophages With MEC1 31d rep2

description: monocytes/macrophages from mouse 15

value: 13 weeks


title: Monocytes/macrophages No MEC1 31d rep3

description: monocytes/macrophages from mouse 13


title: Monocytes/macrophages No MEC1 21d rep2

description: monocytes/macrophages from mouse 2

value: 11 weeks


title: Genomic DNA from spinal ependymoma 80

description: Relation GSM5600091

label: Cy3 and Cy84

value: thoracolumbar

value: myxopapillary WHO grade non-myxopapillary WHO grade 2

tag: os [days]

tag: pfs status


title: Genomic DNA from spinal ependymoma 51

label: Cy3 and Cy55

value: lumbar

tag: pfs [days]

tag: material


title: Genomic DNA from spinal ependymoma 36

label: Cy3 and Cy40

value: sacral

value: SP-EPN

tag: tissue


title: Genomic DNA from spinal ependymoma 74

label: Cy3 and Cy78

value: F

value: no match


title: Genomic DNA from spinal ependymoma 78

description: Relation GSM5600088

label: Cy3 and Cy82

value: M

value: GTR


title: Genomic DNA from spinal ependymoma 83

description: Relation GSM5600095

label: Cy3 and Cy87

value: non-myxopapillary WHO grade 2


title: Genomic DNA from spinal ependymoma 55

label: Cy3 and Cy59

value: coccygeal

value: MPE


title: Genomic DNA from spinal ependymoma 56

label: Cy3 and Cy60

value: cervical

value: FFPE

value: spinal ependymomas


title: Genomic DNA from spinal ependymoma 28

description: Relation GSM7776627, GSM7781519

label: Cy3 and Cy32

value: cervicomedullary


title: Genomic DNA from spinal ependymoma 19

description: Relation GSM5600087

label: Cy3 and Cy23


title: Genomic DNA from spinal ependymoma 26

description: Relation GSM7776599, GSM6629552

label: Cy3 and Cy30

value: biopsy


title: Genomic DNA from spinal ependymoma 22

description: Relation GSM5600061

label: Cy3 and Cy26


title: Genomic DNA from spinal ependymoma 32

label: Cy3 and Cy36


title: Genomic DNA from spinal ependymoma 30

description: Relation GSM7776731

label: Cy3 and Cy34


title: Genomic DNA from spinal ependymoma 14

description: Relation GSM6629442

label: Cy3 and Cy18


title: Genomic DNA from spinal ependymoma 20

description: Relation GSM5600093

label: Cy3 and Cy24


title: Genomic DNA from spinal ependymoma 13

description: Relation GSM7781419

label: Cy3 and Cy17

value: cervicothoracic

value: SP-EPN-MYCN


title: Genomic DNA from spinal ependymoma 23

description: Relation GSM5600044, GSM6629549

label: Cy3 and Cy27

value: thoracic

value: <GTR

value: myxopapillary WHO grade non-myxopapillary WHO grade 2


title: Genomic DNA from spinal ependymoma 18

description: Relation GSM5600086

label: Cy3 and Cy22

value: lumbar

value: WHO grade 3


title: Genomic DNA from spinal ependymoma 6

description: Relation GSM5600045

label: Cy3 and Cy10

value: M

value: not specified


title: Genomic DNA from spinal ependymoma 9

description: Relation GSM7776601, GSM7781416

label: Cy3 and Cy13

value: GTR

value: non-myxopapillary WHO grade 2

value: SP-EPN


title: Genomic DNA from spinal ependymoma 31

description: Relation GSM5600042

label: Cy3 and Cy35

value: MPE


title: Genomic DNA from spinal ependymoma 2

label: Cy3 and Cy6

value: FFPE


title: Genomic DNA from spinal ependymoma 1

label: Cy3 and Cy5

value: lumbosacral

value: spinal ependymomas


title: Genomic DNA from spinal ependymoma 16

description: Relation GSM5600043, GSM6629961

label: Cy3 and Cy20

value: thoracolumbar


title: Genomic DNA from spinal ependymoma 15

description: Relation GSM6629547

label: Cy3 and Cy19


title: Genomic DNA from spinal ependymoma 34

label: Cy3 and Cy38

value: F


title: HCT116_Cl3_shD1_Dox_dblUIM_D14

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina Protocol

data_processing: Raw IDAT files for each sample were processed using the Bioconductor package “SeSAMe” (Version 1.14.2) for extraction of probe signal intensity values, normalization of probe signal intensity values, and calculation of β-values from the normalized probe signal intensity values. CpG probes with a detection p-value > 0.05 in any one sample were excluded from the analysis.

label: Cy5 and Cy3

source_name: HCT116 Colorectal Carcinoma epithelial cells

growth_protocol: HCT116 colon cancer cell line was purchased from ATCC and maintained according to ATCC recommendations in McCoy's (Gibco 16600-082) media supplemented with 10% Fetal Bovine Serum (Millipore Sigma F0926) and 1% penicillin/streptomycin (Life Technologies, 15140-122) at 5% CO2 and 37C.

extract_protocol: Cells were lysed overnight at 37°C in 2 mls of TE-SDS buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 0.5% SDS), supplemented with 100 μl of 20 mg/ml proteinase K. DNA was purified by phenol:chloroform extraction in three phases: (1) 100% phenol, (2) phenol:chloroform:isoamyl alcohol (25:24:1), and (3) chloroform:isoamyl alcohol (24:1). For each phase, the aqueous layer was combined with the organic layer in a 1:1 ratio. Samples were quickly shaken, allowed to sit on ice for approximately 5 minutes, and then separated by centrifugation at 1,693 RCF for 5 minutes at 4°C. The top aqueous layer was then transferred to a new tube for the next organic phase. Following extraction, DNA was precipitated with 1/10 volume 3 M sodium acetate pH 4.8 and 2.5 volumes 100% ethanol and stored overnight at -20°C. Precipitated DNA was pelleted by centrifugation at 17,090 RCF for 30 minutes at 4°C. The pelleted DNA was washed twice with 70% ethanol, allowed to dry for 15 minutes, and resuspended in TE buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA). Samples were then treated with 1 mg/ml RNAse A at 37°C for 30 minutes and then re-purified by ethanol precipitation as described.

treatment_protocol: In all cases, Baseline (or NoDox) samples were grown in culture for 2 weeks in the absence of doxycycline, and serve as the baseline methylome control for Knockdown and Recovery samples. Knockdown samples were treated with doxycycline (10 ng/mL) for two weeks to induce expression of the shRNA. Recovery samples were treated with doxycycline for two weeks (to induce knockdown of the target protein), and then doxycycline was removed for an additional two weeks to measure recovery methylation dynamics with re-expression of the either UHRF1 or DNMT1. Transgenes for WT and mutant UHRF1 and DNMT1 were stably introduced into the clonally expanded Cl9 shUHRF1 and Cl3 shDNMT1 cell lines, respectively. Doxycycline treatment (10 ng/mL) over 2 weeks depleted the endogenous enzyme in the presence of the transgene protein cover.

tag: cell population

value: Doxycycline-inducible shDNMT1 cells Clone 3

tag: doxycycline treatment

value: Dox

tag: time (days)

tag: transgene cover


title: HCT116_Cl3_shD1_NoDox_dblUIM_D14

value: NoDox


title: Gastroc_glucose_injected_M4

value: Gastrocnemius

tag: Sex

value: male

tag: strain

tag: genotype

value: PanK4 WT

tag: treatment

value: 4-h fast then glucose injection


title: Genomic DNA from spinal ependymoma 7

description: Relation GSM7776603, GSM6629678

label: Cy3 and Cy11

value: M

tag: age

tag: localization

tag: extent of resection

tag: who tumor grade

tag: reanalysis of


title: HCT116_Cl3_shD1_Dox_UIM1_D14

value: DNMT1 P378A/L381A


title: Genomic DNA from spinal ependymoma 3

description: Relation GSM5600092

label: Cy3 and Cy7

value: lumbar

value: GTR

value: myxopapillary WHO grade non-myxopapillary WHO grade 2

tag: classification result v12.5

tag: classification score

tag: OS status

tag: os [days]

tag: pfs status


title: HCT116_Cl8_shD1_Recovery_D28

tag: cell population

value: Doxycycline-inducible shDNMT1 cells Clone 8

tag: doxycycline treatment

value: Dox; NoDox


title: HCT116_Cl3_shD1_NoDox_UIM2_D14

tag: time (days)

tag: transgene cover

value: DNMT1 I442A/I487A


title: HCT116_Cl3_shD1_NoDox_UIM1_D14


title: HCT116_Cl3_shD1_Dox_WT_D14

value: DNMT1 WT


title: HCT116_Cl3_shD1_Knockdown_D14


title: HCT116_Cl3_shD1_NoDox_WT_D14


title: HCT116_Cl3_ShD1_Dox_CatX_D14

value: DNMT1 C1226S


title: HCT116_Cl3_shD1_NoDox_EV_D14

value: Doxycycline-inducible shDNMT1 cells Clone 3

value: Empty vector


title: HCT116_Cl9_shU1_Dox_F59V_D14

value: Doxycycline-inducible shUHRF1 cells Clone 9

value: Dox

value: UHRF1 59V


title: HCT116_Cl9_shU1_Dox_WT_D14

value: UHRF1 WT


title: HCT116_Cl9_shU1_Dox_F46V_D14

value: UHRF1 F46V


title: HCT116_Cl9_shU1_NoDox_F59V_D14

value: NoDox


title: Genomic DNA from spinal ependymoma 10

description: Relation GSM7776607, GSM7781417

label: Cy3 and Cy14

tag: Sex

value: M

value: cervical

value: non-myxopapillary WHO grade 2

value: SP-EPN

tag: pfs [days]

tag: material

value: FFPE

tag: tissue

value: spinal ependymomas


title: HCT116_Cl9_shU1_Dox_RING_D14

value: UHRF1 H741A


title: HCT116_Cl9_shU1_Dox_EV_D14


title: HCT116_Cl3_shD1_Dox_UIM2_D14

value: DNMT1 I442A/I487A


title: HCT116_Cl9_shU1_NoDox_EV_D14


title: HCT116_Cl9_shU1_Knockdown_D14


title: HCT116_Cl9_shU1_NoDox_TTD_D14

value: UHRF1 Y188A


title: HCT116_Cl8_shD1_Knockdown_D14

value: Doxycycline-inducible shDNMT1 cells Clone 8


title: HCT116_Cl9_shU1_NoDox_SRA_D14

value: UHRF1 G448D


title: HCT116_Cl9_shU1_Dox_SRA_D14

value: Doxycycline-inducible shUHRF1 cells Clone 9


title: HCT116_Cl8_shD1_Baseline_D14


title: HCT116_Cl9_shU1_Dox_TTD_D14

value: Dox


title: HCT116_Cl3_shD1_Recovery_D28

value: Doxycycline-inducible shDNMT1 cells Clone 3

value: Dox; NoDox


title: HCT116_Bulk_shD1_Baseline_D14_r2

value: Doxycycline-inducible shDNMT1 cells Bulk


title: HCT116_Cl3_shD1_NoDox_CatX_D14

value: NoDox

value: DNMT1 C1226S


title: HCT116_Cl9_shU1_Baseline_D14


title: HCT116_Bulk_shU1_Baseline_D14

value: Doxycycline-inducible shUHRF1 cells Bulk


title: HCT116_Cl9_shU1_NoDox_RING_D14


title: HCT116_Cl6_shU1_Knockdown_D2

value: Doxycycline-inducible shUHRF1 cells Clone 6


title: HCT116_Bulk_shD1_Knockdown_D14_r1


title: HCT116_Bulk_shD1_Knockdown_D14_r2


title: HCT116_Cl9_shU1_NoDox_WT_D14

value: UHRF1 WT


title: HCT116_Cl9_shU1_NoDox_F46V_D14

value: UHRF1 F46V


title: HCT116_Bulk_shU1_Knockdown_D14


title: HCT116_Cl3_shU1_Recovery_D21

value: Doxycycline-inducible shUHRF1 cells Clone 3


title: HCT116_Bulk_shGFP_Dox_D14

value: Doxycycline-inducible shGFP cells Bulk


title: HCT116_Bulk_shGFP_NoDox_D14


title: HCT116_Cl3_shU1_Recovery_D58


title: HCT116_Cl3_shU1_Knockdown_D14


title: HCT116_Cl3_shU1_Recovery_D17


title: HCT116_Cl6_shU1_Recovery_D28


title: HCT116_Cl3_shU1_Recovery_D28


title: HCT116_Cl6_shU1_Recovery_D58


title: HCT116_Cl3_shU1_Baseline_D14


title: HCT116_Cl6_shU1_Recovery_D17


title: HCT116_Cl6_shU1_Recovery_D21


title: HCT116_Bulk_shD1_Baseline_D14_r1


title: HCT116_Cl6_shU1_Knockdown_D7


title: HCT116_Cl6_shU1_Knockdown_D14


title: HCT116_Cl6_shU1_Baseline_D14


title: TRPV4KO Thioglycolate induced peritoneal macropahges treated with 100ng/ml of eLPS.

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

source_name: Thioglycolate induced peritoneal macrophages

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.

tag: cell type

tag: genotype

value: TRPV4 Knock out

tag: treatment

value: 100ng/ml eLPS treatment


title: TRPV4KO  untreated Thioglycolate induced peritoneal macrophages.

value: Untreated


title: Wild type(WT) Thioglycolate induced peritoneal macropahges treated with 100ng/ml of eLPS.

value: Thioglycolate induced peritoneal macrophages

value: Wild type


title: Wild type(WT) untreated Thioglycolate induced peritoneal macrophages.


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_H03_CH07]

city: Duluth

first: Daniel

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH11_PFTeDA_FHM.txt
Normalized+1_CH07_PFUdA_FHM.txt
Normalized+1_CH11_PFTeDA_FHM_regrouped.txt

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).

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.

value: whole body

tag: cell line

value: US EPA GLTED wild type

value: control

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 control water (PFTrDA and PFNA plates) [control_H03_CH06]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF02_PFTrDA_FHM.txt
Normalized+1_CH06_PFNA_FHM.txt
Normalized+1_AF02_PFTrDA_FHM_regrouped.txt


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_H03_CH09]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH08_PFPB_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_H03_CH03]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF01_PFOS_FHM.txt
Normalized+1_CH03_PFOA_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_H03_CH04]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF09_FHxSA_FHM.txt
Normalized+1_CH04_N-EtFOSA-M_FHM.txt
Normalized+1_CH04_N-EtFOSA-M_FHM_toxic_removed.txt


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_H03_CH05]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF06_PFHpA_FHM.txt
Normalized+1_CH05_PFPeA_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_H03_AF03]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF03_FC10diol_FHM.txt
Normalized+1_AF04_FC8diol_FHM.txt
Normalized+1_AF04_FC8diol_FHM_onesamp_removed.txt
Normalized+1_AF03_FC10diol_FHM_toxic_removed.txt


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_H03_CH01]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH10_82FTS_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_H03_AF05]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF05_PFHxS_FHM.txt
Normalized+1_AF11_FC8DoD_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_H03_AF07]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF07_PFTP_FHM.txt
Normalized+1_AF10_PF4OPeA_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_H03_CH02]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH02_62FTS_FHM.txt
Normalized+1_AF08_42FTS_FHM.txt


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_H02_CH09]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_H02_CH05]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_H02_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_H02_CH04]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTrDA and PFNA plates) [control_H02_CH06]


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_H02_CH01]


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_H02_CH03]


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_H02_CH02]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_H02_AF07]


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_H02_AF03]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_F10_CH05]


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_F10_CH04]


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_F10_CH03]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_H02_AF05]


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_F10_CH09]


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_F10_AF03]


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_C10_CH04]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTrDA and PFNA plates) [control_F10_CH06]


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_C10_CH03]


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_C10_CH09]


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_F10_CH01]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_F10_AF05]


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_C10_CH01]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_C10_AF07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_F10_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_C05_CH09]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTrDA and PFNA plates) [control_C10_CH06]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_F10_AF07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_C10_CH05]


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_F10_CH02]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTrDA and PFNA plates) [control_C05_CH06]


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_C05_CH04]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_C10_AF05]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_C05_AF07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_C05_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_C04_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_C05_CH05]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_C10_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_C10_AF03]


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_C10_CH02]


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_C05_CH03]


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_C05_CH01]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_C05_AF05]


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_C04_AF03]


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_C05_AF03]


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_A11_CH09]


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_C04_CH09]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTrDA and PFNA plates) [control_A11_CH06]


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_C05_CH02]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_C04_CH05]


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_A11_CH04]


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_C04_CH04]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTrDA and PFNA plates) [control_C04_CH06]


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_A11_CH01]


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_C04_CH03]


title: HCT116_Cl6_shU1_Knockdown_D4

value: Dox


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_A11_AF03]


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_C04_CH02]


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_C04_CH01]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_C04_AF05]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_A11_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (FHxSA and N-EtFOSA-M plates) [control_A10_CH04]


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_A10_CH02]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_A11_CH05]


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_A11_CH03]


title: TempO-Seq larval whole body after 24 h exposure control water (6:2FTS and 4:2FTS plates) [control_A11_CH02]


title: TempO-Seq larval whole body after 24 h exposure control water (FC8diol, FC10diol plates) [control_A10_AF03]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_A11_AF05]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_A11_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_3_2_D11_CH07]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH11_PFTeDA_FHM.txt
Normalized+1_CH11_PFTeDA_FHM_regrouped.txt

value: PFTeDA (DTXSID70379295)


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_3_2_D01_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_C04_AF07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFPB plates) [control_A10_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_3_2_C06_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTrDA and PFNA plates) [control_A10_CH06]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTeDA and PFUdA plates) [control_A10_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHpA, PFPeA plates) [control_A10_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_32_B01_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_32_A03_CH07]


title: HCT116_Cl3_shD1_Dox_EV_D14

value: Doxycycline-inducible shDNMT1 cells Clone 3

value: Empty vector


title: TempO-Seq larval whole body after 24 h exposure control water (PFOS and PFOA plates) [control_A10_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_1_E11_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (8:2FTS plate) [control_A10_CH01]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_1_E01_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFTP, PF4OPeA plates) [control_A10_AF07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_3_2_C09_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_3_2_A05_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_32_G04_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_32_D07_CH07]


title: TempO-Seq larval whole body after 24 h exposure control water (PFHxS and FC8DoD plates) [control_A10_AF05]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_1_A06_CH07]


title: HCT116_Cl3_shD1_Baseline_D14

value: NoDox


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_1_E07_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_32_G03_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_100_F09_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_10_C01_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_10_C08_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_1_B11_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_32_D10_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_32_C07_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_10_F06_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_32_A07_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_10_B05_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_10_A04_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_100_F02_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_100_A01_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_100_D02_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_100_A02_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_1_A08_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_32_G06_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_032_D05_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_32_F01_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_032_B03_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_1_G01_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_1_F05_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_1_C03_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_1_B06_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_032_F04_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_032_H01_CH07]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_1_E11_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_32_A03_CH01]


title: TempO-Seq larval whole body after 24 h exposure to PFTeDA (DTXSID70379295) [CH11_0_032_A09_CH07]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_3_2_D11_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_1_E07_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_3_2_D01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_1_E01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_3_2_C09_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_10_F06_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_3_2_C06_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_32_G04_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_32_G03_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_3_2_A05_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_32_D07_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_32_B01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_1_B11_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_100_F02_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_10_C01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_10_C08_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_1_A06_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_32_G06_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_10_B05_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_100_F09_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_100_D02_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_1_F05_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_032_H01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_100_A02_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_32_D10_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_32_C07_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_32_A07_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_032_B03_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_100_A01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_032_A09_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_1_C03_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_1_B06_CH01]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_3_2_D11_CH09]

value: PFPB (DTXSID60663110)


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_3_2_C06_CH09]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_032_D05_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_10_A04_CH01]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_032_F04_CH01]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_3_2_D01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_3_2_C09_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_32_D07_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_3_2_A05_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_32_G04_CH09]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_1_G01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_1_E11_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_1_E01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_32_F01_CH01]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_32_G03_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_1_E07_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_32_B01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_32_A03_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_1_B11_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_1_A06_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_10_C08_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_10_B05_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_100_F02_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_10_C01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_10_A04_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_100_F09_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_100_A01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_32_G06_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_32_F01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_100_D02_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_100_A02_CH09]


title: TempO-Seq larval whole body after 24 h exposure to 8:2FTS (DTXSID00192353) [CH10_0_1_A08_CH01]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_32_D10_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_32_C07_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_1_A08_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_32_A07_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_1_C03_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_032_D05_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_1_F05_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_3_2_H08_CH07]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH07_PFUdA_FHM.txt

value: PFUdA (DTXSID8047553)


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_032_H01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_1_B06_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_032_A09_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_3_2_G05_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_032_F04_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_3_2_D06_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_32_F03_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_10_F06_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_3_2_D12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_32_H10_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_3_2_B08_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_1_G01_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_1_H07_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_32_D03_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_32_E08_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_1_F08_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_32_B12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_1_B02_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFPB (DTXSID60663110) [CH08_0_032_B03_CH09]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_1_E06_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_10_C12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_10_E09_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_10_H09_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_10_D09_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_10_B09_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_100_H11_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_32_B07_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_100_D04_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_100_G07_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_100_F11_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_032_H12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_100_A12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_32_G08_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_32_F12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_32_E02_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_032_E10_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_1_G02_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_3_2_H08_CH06]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH06_PFNA_FHM.txt

value: PFNA (DTXSID8031863)


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_1_E12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_1_G12_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_1_B10_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_1_E03_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_032_H04_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_032_G10_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_032_C11_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_1_H05_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_3_2_D12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFUdA (DTXSID8047553) [CH07_0_32_H06_CH07]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_3_2_B08_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_3_2_D06_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_32_E08_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_32_H10_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_32_F03_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_32_D03_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_1_E12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_3_2_G05_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_1_B02_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_10_H09_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_10_E09_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_10_D09_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_1_F08_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_1_E06_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_10_B09_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_10_C12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_100_G07_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_100_F11_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_100_H11_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_100_D04_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_32_B12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_32_H06_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_32_F12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_32_B07_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_1_H07_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_1_G12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_32_E02_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_1_H05_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_1_G02_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_032_H12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_032_E10_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_032_C11_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_3_2_D12_CH05]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH05_PFPeA_FHM.txt

value: PFPeA (DTXSID6062599)


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_3_2_H08_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_3_2_B08_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_32_H10_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_100_A12_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_32_F03_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_32_E08_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_32_B12_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_32_D03_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_1_H07_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_1_F08_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_1_B02_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_1_E03_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_1_B10_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_32_G08_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_10_E09_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_10_H09_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_1_E12_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_10_D09_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_1_E06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_032_H04_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_10_C12_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_100_H11_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFNA (DTXSID8031863) [CH06_0_032_G10_CH06]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_3_2_G05_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_100_G07_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_3_2_D06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_100_F11_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_10_B09_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_32_H06_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_100_D04_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_32_F12_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_32_G08_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_32_E02_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_1_H05_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_32_B07_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_1_G02_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_1_E03_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_1_G12_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_032_H12_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_032_C11_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_1_B10_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_032_G10_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_032_H04_CH05]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_3_2_D12_CH04]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH04_N-EtFOSA-M_FHM.txt
Normalized+1_CH04_N-EtFOSA-M_FHM_toxic_removed.txt

value: N-EtFOSA-M (DTXSID1032646)


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_0_032_E10_CH05]


title: TempO-Seq larval whole body after 24 h exposure to PFPeA (DTXSID6062599) [CH05_100_A12_CH05]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_32_D03_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_32_F03_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_32_B12_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_3_2_D06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_1_H07_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_3_2_H08_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_1_F08_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_3_2_B08_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_1_E06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_1_B02_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_3_2_G05_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_1_E12_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_10_H09_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_32_E08_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_10_D09_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_10_C12_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_10_E09_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_10_B09_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_100_G07_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_100_F11_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_100_A12_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_32_H10_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_32_G08_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_32_F12_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_32_H06_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_32_B07_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_32_E02_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_1_H05_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_1_G02_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_1_E03_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_1_B10_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_1_G12_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_032_G10_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_032_H12_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_3_2_H08_CH03]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_CH03_PFOA_FHM.txt

value: PFOA (DTXSID8031865)


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_032_C11_CH04]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_032_E10_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_3_2_G05_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_3_2_D12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_100_H11_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_3_2_B08_CH03]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_100_D04_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_32_E08_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_1_H07_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_32_H10_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_1_F08_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_1_E12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_10_H09_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_10_E09_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_10_D09_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_10_C12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to N-EtFOSA-M (DTXSID1032646) [CH04_0_032_H04_CH04]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_1_B02_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_1_E06_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_10_B09_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_100_H11_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_100_F11_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_32_G08_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_100_A12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_32_E02_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_32_H06_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_3_2_D06_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_100_D04_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_1_H05_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_32_B12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_1_G12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_32_B07_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_32_F03_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_32_F12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_1_G02_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_032_H04_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_032_H12_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_32_D03_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_1_B10_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOA (DTXSID8031865) [CH03_0_032_G10_CH03]