title: Female Liver, 10 mg/kg/day MOPA, Animal 195

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_195l

value: Female

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Female Liver, 10 mg/kg/day MOPA, Animal 193

status: Public on Mar 05 2024

type: SRA

city: RTP

first: Logan

middle: J

last: Everett

state: North Carolina

address: 109 T.W. Alexander Dr

department: Office of Research and Development

country: USA

institute: U.S. Environmental Protection Agency

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_193l

library_source: transcriptomic

data_processing:
Raw sequencing reads (FASTQ files) were aligned to known probe sequences listed in the TempO-Seq probe manifest using HISAT2 to compute a matrix of read counts for each probe in each sample.
Assembly: TempO-seq Rat S1500+ v1.2
Supplementary files format and content: Count table CSV files contain a row for each known probe and a column for each sample. Each cell contains the number of reads from a single cell uniquely aligned to a single probe sequence
Supplementary files format and content: Probe manifest CSV file contains a row for each known probe with the probe name, sequence, and target gene

molecule: total RNA

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Male and female Sprague Dawley (Crl:CD IGS, Charles River Laboratory) rats are purchased at 6 – 8 weeks of age. Upon receipt, the animals are placed on a standard, purified laboratory diet and reverse osmosis treated drinking water ad libitum. The specific brand and type of food and source of the water should be noted in Appendix II (Detailed Animal Study Report) of the individual assessment. After a 7- to 14-day quarantine and acclimation period, the animals are weighed and randomly assigned by weight to chemical exposure and control groups. Only clinically healthy animals are used in the study. The target age for initiating exposure is 8 - 10 weeks.

extract_protocol:
Treated and control animals are necropsied approximately 24 hours after the last exposure. Carbon dioxide asphyxiation is used as the method of euthanasia, with death confirmed by a secondary method such as exsanguination or cervical dislocation. The following tissues were dissected from each animal: kidney, liver, adrenal gland, brain, heart, lung, ovary (females), spleen, testis (males), thyroid, thymus, and uterus (females). Tissue samples were collected within ten minutes of termination. The left liver lobe, right kidney, left lung, both testis, uterus, heart, spleen, thymus and whole brain were sectioned into 5mm^3 pieces. Samples from these larger tissues were then individually divided into at least 3 cryovials. At least two of the samples from each tissue in each animal were preserved in RNAlater™ (Thermo Fisher Scientific) at 4°C overnight and then frozen at approximately -20°C for up to 3 weeks before transferring to approximately -80°C. At least one sample from each larger tissue is frozen immediately in liquid nitrogen and stored at approximately -80°C.   The smaller bilateral tissues: adrenal glands, thyroid gland, and ovaries (female) are placed into two cryovials and preserved in RNALater with the left side of the tissue or gland going into the first cryovial and the right side going into the second cryovial. The first tube of RNALater preserved tissue is submitted for sequencing. For each tissue undergoing transcriptomic analysis, total RNA is extracted from one of the aliquots stored in RNAlater™.
The isolated total RNA is used to perform targeted RNA sequencing (RNA-seq) using the BioSpyder TempO-Seq rat S1500+ assay (v1.2) according to manufacturer’s instructions. No specific RNA purity or integrity criteria are applied to the RNA samples as the TempO-Seq assay has been designed to provide high quality gene expression measurements on whole cell lysates, purified RNA, and formalin-fixed paraffin embedded tissue.

treatment_protocol: For oral gavage studies, at least four male and four female rats per dose group receive the vehicle alone or test article in vehicle via gavage (5 or 10 ml/kg) for five days. Animals are weighed daily prior to administration and are observed twice daily, once during administration and once in the late afternoon, at least six hours apart, for assessment of moribundity and mortality. Formal clinical observations are performed on the first day post-dosing and prior to necropsy. Moribund animals or animals exhibiting overt clinical toxicity are removed from the study. The temperature in the experimental animal room is maintained at a target of 22°C (± 3°C) with a relative humidity that is ideally between 50-60% but is at least 30% and preferably not to exceed 70% other than during room cleaning. Lighting is artificial with a sequence of 12 hours light, 12 hours dark. Animals are housed individually or caged in small groups of no more than three animals of the same sex in accordance with local institutional animal care and use requirements.

tag: Sex

tag: tissue

tag: strain

tag: age

tag: treatment

value: 10 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:10 mg/kg/day

value: dose group:6

value: route of_exposure:Oral gavage

tag: sample qc_issue

value: No Issue


title: GEN_TC00503572_H23

description:
GEN
TC00503572_H23

data_processing:
Each FASTQ file was aligned to the probe sequences in the hWTv1 assay using HISAT2 v2.1.0 with spliced alignment disabled.
Aligned reads in SAM format were processed with SAMtools v1.9 to compute the number of uniquely aligned reads for each probe. Probe counts and associated meta-data for each well were stored for analysis using MongoDB v3.6.14.
Assembly: hWTv1
Supplementary files format and content: Processed data provided as a single table of counts for all probes x all samples

organism: Homo sapiens

source_name: MCF7 Cells

growth_protocol: Experiments were performed using MCF7 breast adenocarcinoma cells (ATCC® HTB-22) cultured in Dulbecco’s Modified Eagle Medium (DMEM) + 10% heat-inactivated fetal bovine serum (FBS) containing 1× Gibco® penicillin-streptomycin-glutamine (PSG). For each independent culture, a single vial of MCF7 cells was thawed, subject to a uniform expansion and passaging schedule to generate enough cells for seeding in 384-well plates and to ensure that cells were tested at a consistent passage number across all replicate cultures. At the time of seeding into assay plates (Corning 3985BC), cell suspensions were volumetrically adjusted with growth media to a concentration of 2.5x10^2 cells / µL. Forty microliters of cell suspension was then dispensed into each assay well using a MultiFlo FX multi-mode dispenser equipped with a 10 µL dispensing cassette (BioTek, Winooski, VT) in order to achieve an initial seeding density of 10,000 live cells / well. Cells were dispensed into all wells of the HTTr assay plates except column 1 to allow for addition of transcriptomic reference samples to be added to each HTTr assay plate following lysate preparation. After seeding, assay plates were placed in a humidified incubator (37°C) with 5% CO2 atmosphere for 24 h prior to treatment.

extract_protocol:
Six hours after water extract treatment, HTTr assay plates were removed from the incubator and media in each assay well drained to a residual volume of 10 µL. A 10 µL volume of 2× BioSpyder lysis buffer was dispensed into each assay well. Then, 20 µL volumes of Universal Human Reference RNA (UHRR), Human Brain Reference RNA (HBRR), bulk lysates from MCF7 cells treated with 0.5% DMSO (BL DMSO) or 1 µM trichostatin A (BL TSA), and lysis buffer blans were dispensed into the first column of each assay plate. The plates were sealed with an adhesive aluminum plate cover and incubated at room temperature, protected from light, for 30 min. The plates were then stored at -80°C prior to shipment to BioSpyder, Inc.
Samples were analyzed by BioSpyder using a custom-attenuated version of the TempO-Seq human whole transcriptome version 1 (hWTv1) assay, which includes 21,111 probes covering 19,287 genes. In brief, 2 µL of each lysate was hybridized with 2 µL of detector oligos from the hWTv1 assay using the following thermal cycler protocol: 10 min at 70°C, followed by gradual decrease to 45°C over 49 min, terminating with 45°C incubation for 16-24 hours. Excess oligos were then removed via nuclease digestion (90 min at 37°C) and hybridized detector oligos were ligated (60 min at 37°) following respective additions of 24 µL TempO-Seq nuclease and ligation mixes. RNA/DNA duplexes were then heat-denatured and 10 µL of each ligation product was transferred to an amplification microplate containing 10 µL of PCR master mix per well. Ligation products were then uniquely labeled during product amplification (10 min at 37°C, 2 min at 95°C, 6 cycles of 95°C for 30 s, 54°C for 30 s, 72°C for 120 s, 16 cycles of 95°C for 30s and 72°C for 120s, followed by 72°C for 60 s) with well coordinate-specific “barcoded” primer pairs containing universal adaptors for sequencing. Samples were then pooled into a series of three sequencing libraries (1 for each plate). Pooled sequencing libraries were then distributed across multiple lanes of a HiSeq dual flow cell and analyzed on a HiSeq 2500 Ultra-High-Throughput Sequencing System (Illumina, San Diego, CA).

treatment_protocol: DMSO-solubilized water extracts collected from each sampling site were shipped frozen to US EPA and stored at  80°C prior to dose plate preparation. Eight-point dilution series (1/2 log10 spacing) of each stock sample was prepared in a LabCyte Echo-qualified 384-well low dead volume (384LDV) plate. Transcriptomics reference chemicals for MCF7 cells (genistein, trichostatin A, sirolimus) were solubilized as 200× dosing solutions corresponding to nominal test concentrations of 10, 1 and 0.1 µM, respectively. Triplicate wells of dosing solutions for each of the reference chemicals were added to the dose plates along with quadruplicate wells of pure DMSO as a vehicle control. The dose plate was then sealed with a Nunc aluminum adhesive plate cover and stored at -80°C until use. On the first day of dosing, the dose plate was thawed to room temperature inside a desiccator, centrifuged briefly to ensure even distribution of the dose solution in each well and unsealed. A LabCyte Echo 550 acoustic dispenser was then used to transfer 200 nL of dosing solutions to the assay plates containing 40 uL of culture media. The final DMSO concentration was 0.5% for all treatment, reference treatment and vehicle control wells. Well coordinates were uniquely randomized on each assay plate with respect to treatment so that any potential edge-well effects were distributed in an unbiased manner across all possible treatment conditions.

tag: cell line

value: 6h exposure of 10 uM of Genistein

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

value: Genistein

tag: chemical sample_id

tag: chemical concentration

value: 10 uM

tag: dose level

tag: exposure time

tag: assay plate

tag: assay plate_well

tag: water type


title: EP000004A06_5_1.473477CF_TC00503572_H12

description:
EP000004A06_5_1.473477CF
TC00503572_H12

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_6

value: Drinking Water


title: Female Liver, 3 mg/kg/day MOPA, Animal 192

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_192l

value: 3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:3 mg/kg/day

value: dose group:5


title: SIRO_TC00503572_H20

description:
SIRO
TC00503572_H20

value: 6h exposure of 0.1 uM of Sirolimus

value: Sirolimus


title: Female Liver, 3 mg/kg/day MOPA, Animal 191

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_191l

value: Female

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: EP000004B02_4_0.497018CF_TC00503572_H07

description:
EP000004B02_4_0.497018CF
TC00503572_H07

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_14

value: Blank


title: Female Liver, 3 mg/kg/day MOPA, Animal 189

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_189l

value: route of_exposure:Oral gavage

value: No Issue


title: Female Liver, 3 mg/kg/day MOPA, Animal 190

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_190l


title: BL_TSA_TC00503572_H01

description:
BL_TSA
TC00503572_H01

value: 6h exposure of 0 uM of Trichostatin A

value: Trichostatin A

value: 0 uM


title: Female Liver, 3 mg/kg/day MOPA, Animal 188

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_188l

value: 3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage


title: EP000004B04_2_0.049970CF_TC00503572_G24

description:
EP000004B04_2_0.049970CF
TC00503572_G24

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_16

value: DMEM + 10% HI-FBS

value: Reclaimed Water


title: Untrtd_TC00503572_H04

description:
Untrtd
TC00503572_H04

value: untreated


title: Female Liver, 1 mg/kg/day MOPA, Animal 187

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_187l

value: Female

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:1 mg/kg/day

value: dose group:4


title: EP000004A07_7_12.711864CF_TC00503572_G23

description:
EP000004A07_7_12.711864CF
TC00503572_G23

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_7


title: EP000004B04_3_0.149731CF_TC00503572_G19

description:
EP000004B04_3_0.149731CF
TC00503572_G19

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_16


title: Female Liver, 10 mg/kg/day MOPA, Animal 196

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_196l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: 10 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:10 mg/kg/day

value: dose group:6

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Female Liver, 1 mg/kg/day MOPA, Animal 185

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_185l

value: route of_exposure:Oral gavage

value: No Issue


title: EP000004B04_7_12.711864CF_TC00503572_G22

description:
EP000004B04_7_12.711864CF
TC00503572_G22

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_16

value: DMEM + 10% HI-FBS

value: Reclaimed Water


title: Female Liver, 1 mg/kg/day MOPA, Animal 184

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_184l

value: Female

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage


title: Female Liver, 1 mg/kg/day MOPA, Animal 186

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_186l

value: dose:1 mg/kg/day

value: dose group:4


title: Female Liver, 10 mg/kg/day MOPA, Animal 194

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_194l


title: EP000004A08_7_12.711864CF_TC00503572_G15

description:
EP000004A08_7_12.711864CF
TC00503572_G15

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_8

value: Wastewater


title: EP000004B05_8_50.000000CF_TC00503572_G09

description:
EP000004B05_8_50.000000CF
TC00503572_G09

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_17

value: 50 CF

value: Drinking Water


title: Female Liver, 0.3 mg/kg/day MOPA, Animal 180

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_180l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: 0.3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.3 mg/kg/day

value: dose group:3


title: EP000004B03_3_0.149731CF_TC00503572_G11

description:
EP000004B03_3_0.149731CF
TC00503572_G11

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_15

value: DMEM + 10% HI-FBS


title: EP000004A10_2_0.049970CF_TC00503572_H19

description:
EP000004A10_2_0.049970CF
TC00503572_H19

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_10

value: Blank


title: Female Liver, 0.3 mg/kg/day MOPA, Animal 182

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_182l

value: Female

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: Female Liver, 0.3 mg/kg/day MOPA, Animal 179

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_179l


title: EP000004A01_3_0.149731CF_TC00503572_G03

description:
EP000004A01_3_0.149731CF
TC00503572_G03

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_1

value: Reclaimed Water


title: Female Liver, 0.3 mg/kg/day MOPA, Animal 181

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_181l


title: BL_TSA_TC00503572_G01

description:
BL_TSA
TC00503572_G01

value: 6h exposure of 0 uM of Trichostatin A

value: Trichostatin A

value: 0 uM


title: EP000004B01_6_4.716981CF_TC00503572_G07

description:
EP000004B01_6_4.716981CF
TC00503572_G07

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_13

value: Wastewater


title: Female Liver, 0.3 mg/kg/day MOPA, Animal 178

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_178l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: 0.3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.3 mg/kg/day


title: EP000004A04_5_1.473477CF_TC00503572_F23

description:
EP000004A04_5_1.473477CF
TC00503572_F23

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_4

value: DMEM + 10% HI-FBS

value: Drinking Water


title: Female Liver, 0.1 mg/kg/day MOPA, Animal 176

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_176l

value: Female

value: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.1 mg/kg/day

value: dose group:2

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage


title: EP000004B06_4_0.497018CF_TC00503572_F13

description:
EP000004B06_4_0.497018CF
TC00503572_F13

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_18

value: Surface Water


title: EP000004B04_8_50.000000CF_TC00503572_F16

description:
EP000004B04_8_50.000000CF
TC00503572_F16

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_16

value: 50 CF

value: Reclaimed Water


title: Female Liver, 0.1 mg/kg/day MOPA, Animal 175

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_175l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: No Issue


title: Female Liver, 0.1 mg/kg/day MOPA, Animal 174

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_174l


title: Female Liver, 0.1 mg/kg/day MOPA, Animal 177

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_177l


title: EP000004A09_8_50.000000CF_TC00503572_F12

description:
EP000004A09_8_50.000000CF
TC00503572_F12

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_9

value: DMEM + 10% HI-FBS

value: Blank


title: Female Liver, 0.1 mg/kg/day MOPA, Animal 173

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_173l

value: Female

value: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage


title: Female Liver, 0.01 mg/kg/day MOPA, Animal 172

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_172l

value: 0.01 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.01 mg/kg/day

value: dose group:1


title: Female Liver, 1 mg/kg/day MOPA, Animal 183

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_183l

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:1 mg/kg/day

value: dose group:4

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage


title: EP000004B04_4_0.497018CF_TC00503572_F11

description:
EP000004B04_4_0.497018CF
TC00503572_F11

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_16

value: Reclaimed Water


title: EP000004A06_6_4.716981CF_TC00503572_F06

description:
EP000004A06_6_4.716981CF
TC00503572_F06

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_6

value: Drinking Water


title: Female Liver, 0.01 mg/kg/day MOPA, Animal 171

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_171l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: No Issue


title: EP000004A05_5_1.473477CF_TC00503572_F08

description:
EP000004A05_5_1.473477CF
TC00503572_F08

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_5

value: DMEM + 10% HI-FBS

value: Surface Water


title: EP000004B04_5_1.473477CF_TC00503572_F05

description:
EP000004B04_5_1.473477CF
TC00503572_F05

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_16


title: Female Liver, 0.01 mg/kg/day MOPA, Animal 170

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_170l

value: Female

value: 0.01 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.01 mg/kg/day

value: dose group:1


title: Female Liver, 0.01 mg/kg/day MOPA, Animal 169

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_169l

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage


title: BL_DMSO_TC00503572_F01

description:
BL_DMSO
TC00503572_F01

value: untreated

value: 0 uM


title: Female Liver, 0.01 mg/kg/day MOPA, Animal 168

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_168l


title: Female Liver, Vehicle Control, Animal 166

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_166l

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: dose group:0


title: Female Liver, Vehicle Control, Animal 167

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_167l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation


title: Female Liver, Vehicle Control, Animal 165

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_165l

value: No Issue


title: EP000004A02_2_0.049970CF_TC00503572_E21

description:
EP000004A02_2_0.049970CF
TC00503572_E21

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_2

value: DMEM + 10% HI-FBS

value: Wastewater


title: EP000004A12_8_50.000000CF_TC00503572_E24

description:
EP000004A12_8_50.000000CF
TC00503572_E24

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_12

value: 50 CF

value: Surface Water


title: Female Liver, Vehicle Control, Animal 164

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_164l

value: Female

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: EP000004A02_6_4.716981CF_TC00503572_F21

description:
EP000004A02_6_4.716981CF
TC00503572_F21

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_2


title: EP000004A09_3_0.149731CF_TC00503572_E17

description:
EP000004A09_3_0.149731CF
TC00503572_E17

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_9

value: Blank


title: Female Liver, Vehicle Control, Animal 163

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_163l

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: route of_exposure:Oral gavage


title: EP000004A06_8_50.000000CF_TC00503572_E16

description:
EP000004A06_8_50.000000CF
TC00503572_E16

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_6

value: Drinking Water


title: EP000004A08_1_0.014967CF_TC00503572_E15

description:
EP000004A08_1_0.014967CF
TC00503572_E15

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_8


title: EP000004A02_4_0.497018CF_TC00503572_E13

description:
EP000004A02_4_0.497018CF
TC00503572_E13

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_2


title: Female Liver, Vehicle Control, Animal 162

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_162l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: dose group:0

value: No Issue


title: Female Liver, Vehicle Control, Animal 161

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_161l

value: Female


title: Female Liver, Vehicle Control, Animal 160

description:
etap_mopa_liver_female_counts.csv
Plate_23_MOPA_liverf_160l

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Male Liver, 300 mg/kg/day MOPA, Animal 159

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_159l

value: Male

value: 300 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:300 mg/kg/day

value: dose group:9


title: Male Liver, 300 mg/kg/day MOPA, Animal 157

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_157l


title: EP000004B02_1_0.014967CF_TC00503572_F03

description:
EP000004B02_1_0.014967CF
TC00503572_F03

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_14

value: DMEM + 10% HI-FBS

value: Blank


title: Male Liver, 300 mg/kg/day MOPA, Animal 158

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_158l

value: route of_exposure:Oral gavage


title: EP000004A07_5_1.473477CF_TC00503572_E10

description:
EP000004A07_5_1.473477CF
TC00503572_E10

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_7

value: Reclaimed Water


title: BL_DMSO_TC00503572_E01

description:
BL_DMSO
TC00503572_E01

value: untreated

value: 0 uM


title: Male Liver, 300 mg/kg/day MOPA, Animal 156

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_156l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation


title: EP000004A12_3_0.149731CF_TC00503572_D23

description:
EP000004A12_3_0.149731CF
TC00503572_D23

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_12

value: Surface Water


title: EP000004B02_2_0.049970CF_TC00503572_E02

description:
EP000004B02_2_0.049970CF
TC00503572_E02

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_14


title: EP000004B01_5_1.473477CF_TC00503572_E07

description:
EP000004B01_5_1.473477CF
TC00503572_E07

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_13

value: Wastewater


title: Male Liver, 100 mg/kg/day MOPA, Animal 154

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_154l

value: Male

value: 100 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:100 mg/kg/day

value: dose group:8

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: No Issue


title: Male Liver, 300 mg/kg/day MOPA, Animal 155

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_155l

value: 300 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:300 mg/kg/day

value: dose group:9

value: route of_exposure:Oral gavage


title: EP000004A04_3_0.149731CF_TC00503572_D19

description:
EP000004A04_3_0.149731CF
TC00503572_D19

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_4

value: DMEM + 10% HI-FBS

value: Drinking Water


title: Male Liver, 100 mg/kg/day MOPA, Animal 153

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_153l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation


title: EP000004A09_4_0.497018CF_TC00503572_D20

description:
EP000004A09_4_0.497018CF
TC00503572_D20

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_9

value: Blank


title: EP000004A06_7_12.711864CF_TC00503572_D17

description:
EP000004A06_7_12.711864CF
TC00503572_D17

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_6


title: Male Liver, 100 mg/kg/day MOPA, Animal 152

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_152l

value: Male

value: 100 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:100 mg/kg/day


title: Male Liver, 100 mg/kg/day MOPA, Animal 150

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_150l

value: dose group:8

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: No Issue


title: Male Liver, 100 mg/kg/day MOPA, Animal 151

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_151l


title: Male Liver, 30 mg/kg/day MOPA, Animal 149

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_149l

value: 30 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:30 mg/kg/day

value: dose group:7


title: EP000004B05_4_0.497018CF_TC00503572_D16

description:
EP000004B05_4_0.497018CF
TC00503572_D16

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_17

value: DMEM + 10% HI-FBS


title: EP000004B03_4_0.497018CF_TC00503572_E11

description:
EP000004B03_4_0.497018CF
TC00503572_E11

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_15

value: Wastewater


title: Male Liver, 30 mg/kg/day MOPA, Animal 147

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_147l

value: Liver

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: route of_exposure:Oral gavage


title: Male Liver, 30 mg/kg/day MOPA, Animal 146

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_146l

value: Male


title: Male Liver, 30 mg/kg/day MOPA, Animal 145

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_145l


title: R1267Q, day45, rep1

city: Saint-Petersburg

first: Margarita

last: Sorokina

address: Akkuratova 2

country: Russia

institute: Almazov National Medical Research Centre

data_processing:
Read quality was checked for each sample using FastQC v0.11.9.
Sequenced reads were mapped to the mouse genome using mapper STAR v2.7 with rat reference genome GRCh38.p13 and annotation GENCODE (gencode.v41.primary_assembly)
Aligned reads were count with featureCounts program v1.6.4.
Further analysis were made using DESeq2, fgsea и clusterProfiler R packages, as well as MSigDB and phantasus online tools.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file includes matrix of raw counts for each of 9 Samples

molecule: polyA RNA

source_name: hiPSC-CMs

growth_protocol: hiPSC cell line we obtained from PBMCs of two patients with FLNC mutation using CytoTune-iPS 2.0 Sendai Reprogramming Kit (Thermo Fisher Scientific)

extract_protocol:
Total RNA was isolated from the cells with an Extract RNA kit (Evrogen, Russia)
Libraries were constructed using TruSeq Stranded mRNA library prep kit

treatment_protocol: hiPSC differentiation in CMs was performed by modulating Wnt pathway, applying small molecules (Lian et al. 2012) with modifications.

value: hiPSC-CMs

tag: cell type

value: cardiomyocytes from hiPSC

tag: genotype/status

value: FLNC mutation R1267Q

tag: day of_cardio_differentiation


title: R1267Q, day45, rep2

tag: tissue


title: R1267Q, day45, rep3


title: V2264M, day45, rep3

value: FLNC mutation V2264M


title: Male Liver, 10 mg/kg/day MOPA, Animal 143

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_143l

tag: Sex

tag: strain

tag: age

value: 10 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:10 mg/kg/day

value: dose group:6

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: No Issue


title: Male Liver, 10 mg/kg/day MOPA, Animal 141

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_141l

tag: treatment

tag: sample qc_issue


title: Male Liver, 10 mg/kg/day MOPA, Animal 140

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_140l


title: EP000004A10_3_0.149731CF_TC00503572_D09

description:
EP000004A10_3_0.149731CF
TC00503572_D09

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_10

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

value: Blank


title: V2264M, day45, rep2


title: Male Liver, 10 mg/kg/day MOPA, Animal 144

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_144l

value: Liver


title: EP000004A11_1_0.014967CF_TC00503572_D13

description:
EP000004A11_1_0.014967CF
TC00503572_D13

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_11

tag: chemical sample_id

tag: chemical concentration

tag: dose level


title: Donor, day45, rep3

value: Healthy Donor


title: EP000004A10_6_4.716981CF_TC00503572_D08

description:
EP000004A10_6_4.716981CF
TC00503572_D08

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_10

tag: exposure time

tag: assay plate

tag: assay plate_well


title: EP000004A02_3_0.149731CF_TC00503572_D15

description:
EP000004A02_3_0.149731CF
TC00503572_D15

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_2

tag: water type

value: Wastewater


title: Male Liver, 3 mg/kg/day MOPA, Animal 138

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_138l

value: Male

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: 3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:3 mg/kg/day

value: dose group:5

value: route of_exposure:Oral gavage


title: Male Liver, 3 mg/kg/day MOPA, Animal 137

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_137l

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: No Issue


title: Donor, day45, rep2

value: hiPSC-CMs

tag: cell type

value: cardiomyocytes from hiPSC

tag: genotype/status

tag: day of_cardio_differentiation


title: Male Liver, 3 mg/kg/day MOPA, Animal 136

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_136l

tag: Sex

tag: tissue

value: Liver

tag: strain


title: EP000004A05_6_4.716981CF_TC00503572_D07

description:
EP000004A05_6_4.716981CF
TC00503572_D07

tag: treatment

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_5

value: DMEM + 10% HI-FBS

value: Surface Water


title: Male Liver, 3 mg/kg/day MOPA, Animal 135

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_135l

tag: age

tag: sample qc_issue


title: EP000004B06_1_0.014967CF_TC00503572_D05

description:
EP000004B06_1_0.014967CF
TC00503572_D05

tag: cell line

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_18

tag: media

tag: chemical name


title: Male Liver, 1 mg/kg/day MOPA, Animal 134

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_134l

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:1 mg/kg/day

value: dose group:4


title: GEN_TC00503572_D14

description:
GEN
TC00503572_D14

value: 6h exposure of 10 uM of Genistein

value: Genistein

tag: chemical sample_id

tag: chemical concentration

value: 10 uM

tag: dose level


title: Male Liver, 1 mg/kg/day MOPA, Animal 133

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_133l

value: Male

value: Sprague Dawley

value: 10-12 weeks post acclimation


title: Male Liver, 1 mg/kg/day MOPA, Animal 131

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_131l

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: HBRR_TC00503572_D01

description:
HBRR
TC00503572_D01

source_name: Human Brain Reference RNA

value: NA (Universal Human Reference RNA)

value: untreated

tag: exposure time

tag: assay plate

tag: assay plate_well


title: Male Liver, 10 mg/kg/day MOPA, Animal 142

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_142l

value: Liver

value: 10 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:10 mg/kg/day

value: dose group:6


title: V2264M, day45, rep1

value: hiPSC-CMs

tag: cell type

value: cardiomyocytes from hiPSC

tag: genotype/status

value: FLNC mutation V2264M


title: TSA_TC00503572_C22

description:
TSA
TC00503572_C22

value: 6h exposure of 1 uM of Trichostatin A

value: DMEM + 10% HI-FBS

value: Trichostatin A

value: 1 uM

tag: water type


title: Male Liver, 0.3 mg/kg/day MOPA, Animal 129

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_129l

tag: Sex

value: Male

tag: tissue

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: 0.3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.3 mg/kg/day

value: dose group:3


title: Male Liver, 0.3 mg/kg/day MOPA, Animal 128

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_128l

value: Liver

tag: strain

tag: treatment

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: EP000004A10_8_50.000000CF_TC00503572_C19

description:
EP000004A10_8_50.000000CF
TC00503572_C19

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_10

value: 50 CF

value: Blank


title: Male Liver, 0.3 mg/kg/day MOPA, Animal 127

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_127l

tag: age

tag: sample qc_issue


title: Male Liver, 3 mg/kg/day MOPA, Animal 139

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_139l

value: 3 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:3 mg/kg/day

value: dose group:5


title: Male Liver, 0.3 mg/kg/day MOPA, Animal 126

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_126l


title: Male Liver, 0.3 mg/kg/day MOPA, Animal 125

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_125l


title: EP000004A06_3_0.149731CF_TC00503572_C15

description:
EP000004A06_3_0.149731CF
TC00503572_C15

tag: cell line

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_6

tag: media

value: DMEM + 10% HI-FBS

value: Drinking Water


title: Male Liver, 0.1 mg/kg/day MOPA, Animal 123

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_123l

value: Male

value: Sprague Dawley

value: 10-12 weeks post acclimation

value: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.1 mg/kg/day

value: dose group:2


title: EP000004A11_5_1.473477CF_TC00503572_C17

description:
EP000004A11_5_1.473477CF
TC00503572_C17

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_11

tag: chemical name

tag: chemical sample_id


title: EP000004B05_7_12.711864CF_TC00503572_C13

description:
EP000004B05_7_12.711864CF
TC00503572_C13

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_17

tag: chemical concentration

tag: dose level


title: EP000004A05_8_50.000000CF_TC00503572_C08

description:
EP000004A05_8_50.000000CF
TC00503572_C08

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_5

tag: exposure time

tag: assay plate

value: Surface Water


title: Donor, day45, rep1

value: hiPSC-CMs

tag: cell type

value: cardiomyocytes from hiPSC

value: Healthy Donor

tag: day of_cardio_differentiation


title: Male Liver, 0.1 mg/kg/day MOPA, Animal 121

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_121l

value: Liver

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)

value: route of_exposure:Oral gavage

value: No Issue


title: Male Liver, 0.1 mg/kg/day MOPA, Animal 122

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_122l

value: Male


title: Male Liver, 0.01 mg/kg/day MOPA, Animal 117

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_117l

value: Sprague Dawley

value: 0.01 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.01 mg/kg/day

value: dose group:1


title: EP000004A11_2_0.049970CF_TC00503572_D02

description:
EP000004A11_2_0.049970CF
TC00503572_D02

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_11

value: DMEM + 10% HI-FBS

tag: assay plate_well

tag: water type

value: Blank


title: Male Liver, 0.1 mg/kg/day MOPA, Animal 120

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_120l

tag: Sex

tag: tissue

value: 10-12 weeks post acclimation

value: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.1 mg/kg/day

value: dose group:2


title: EP000004A04_6_4.716981CF_TC00503572_C04

description:
EP000004A04_6_4.716981CF
TC00503572_C04

tag: treatment

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_4

value: Drinking Water


title: Male Liver, 0.01 mg/kg/day MOPA, Animal 119

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_119l

value: Liver

tag: strain

tag: age

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Male Liver, 1 mg/kg/day MOPA, Animal 132

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_132l

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:1 mg/kg/day

value: dose group:4

value: route of_exposure:Oral gavage

tag: sample qc_issue

value: No Issue


title: Male Liver, Vehicle Control, Animal 114

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_114l

value: Male

value: Sprague Dawley

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: dose group:0


title: Male Liver, 0.01 mg/kg/day MOPA, Animal 118

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_118l

value: 10-12 weeks post acclimation

value: 0.01 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.01 mg/kg/day

value: dose group:1


title: SIRO_TC00503572_C02

description:
SIRO
TC00503572_C02

tag: cell line

value: 6h exposure of 0.1 uM of Sirolimus

tag: media

value: DMEM + 10% HI-FBS

value: Sirolimus


title: Male Liver, 0.01 mg/kg/day MOPA, Animal 116

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_116l

value: Liver

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: Male Liver, Vehicle Control, Animal 112

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_112l


title: Male Liver, 1 mg/kg/day MOPA, Animal 130

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_130l

value: 1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:1 mg/kg/day

value: dose group:4


title: Male Liver, 0.01 mg/kg/day MOPA, Animal 115

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_115l

value: Male

value: route of_exposure:Oral gavage

value: No Issue


title: Male Liver, Vehicle Control, Animal 113

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_113l

value: Sprague Dawley

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day


title: EP000004A09_6_4.716981CF_TC00503572_B17

description:
EP000004A09_6_4.716981CF
TC00503572_B17

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_9

tag: chemical name

tag: chemical sample_id

value: Blank


title: HBRR_TC00503572_C01

description:
HBRR
TC00503572_C01

value: NA (Universal Human Reference RNA)

value: untreated

tag: chemical concentration

tag: dose level


title: Male Liver, Vehicle Control, Animal 110

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_110l

value: 10-12 weeks post acclimation

value: dose group:0


title: Male Liver, 0.1 mg/kg/day MOPA, Animal 124

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_124l

value: Liver

value: 0.1 mg/kg/day MOPA, 5-day repeat exposure, oral gavage

value: dose:0.1 mg/kg/day

value: dose group:2


title: Male Liver, Vehicle Control, Animal 111

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_111l

value: chemical name:Perfluoro-3-methoxypropanoic acid (MOPA)


title: EP000004B01_7_12.711864CF_TC00503572_B16

description:
EP000004B01_7_12.711864CF
TC00503572_B16

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_13

value: DMEM + 10% HI-FBS

tag: exposure time

tag: assay plate

value: Wastewater


title: Male Liver, Vehicle Control, Animal 108

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_108l

value: Male

value: Sprague Dawley

value: route of_exposure:Oral gavage

value: < 50% reads aligned


title: EP000004A08_4_0.497018CF_TC00503572_B12

description:
EP000004A08_4_0.497018CF
TC00503572_B12

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_8


title: Male Liver, Vehicle Control, Animal 109

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_109l

value: Deionized water control, 5-day repeat exposure, oral gavage

value: dose:0 mg/kg/day

value: No Issue


title: EP000004A07_8_50.000000CF_TC00503572_B15

description:
EP000004A07_8_50.000000CF
TC00503572_B15

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_7

value: 50 CF

value: Reclaimed Water


title: Male Liver, Vehicle Control, Animal 107

description:
etap_mopa_liver_male_counts.csv
Plate_22_MOPA_liverm_107l

value: Liver

value: 10-12 weeks post acclimation

value: dose group:0


title: EP000004B05_2_0.049970CF_TC00503572_B11

description:
EP000004B05_2_0.049970CF
TC00503572_B11

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_17

value: Drinking Water


title: athero_mouse_20

city: Stockholm

first: Michael

last: Vanlandewijck

address: Blickagången 6

department: Department of Medicine

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic single cell

data_processing:
Demultiplexing with bcl2fastq
Removal of adapter sequencing with TrimGalore
Alignment against the mouse GRCm38 build using Bowtie2
Removal of duplets using samtools
Generation of a count matrix with FeatureCounts from the SubRead package
Assembly: GRCm38
Supplementary files format and content: Count files, with every column a cell and every row a gene.

organism: Mus musculus

source_name: Aortic Arch

extract_protocol:
FACS into 384well plate of single cells from dissociation of human carotid atherosclerotic plaque
RNA libraries were prepared using standard SmartSeq2 protocol

value: Aortic Arch

tag: genotype

tag: time point

value: Early Stage(20 weeks)


title: EP000004A04_4_0.497018CF_TC00503572_B08

description:
EP000004A04_4_0.497018CF
TC00503572_B08

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_4

value: DMEM + 10% HI-FBS

tag: assay plate_well

tag: water type


title: athero_mouse_21

tag: tissue


title: athero_mouse_19


title: athero_mouse_17

value: Advanced Stage (60 weeks)


title: EP000004B03_5_1.473477CF_TC00503572_B06

description:
EP000004B03_5_1.473477CF
TC00503572_B06

tag: treatment

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_15

value: Wastewater


title: athero_mouse_18


title: athero_mouse_16


title: athero_mouse_14


title: EP000004B01_8_50.000000CF_TC00503572_B03

description:
EP000004B01_8_50.000000CF
TC00503572_B03

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_13


title: athero_mouse_15


title: EP000004A05_4_0.497018CF_TC00503572_B02

description:
EP000004A05_4_0.497018CF
TC00503572_B02

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_5

value: Surface Water


title: athero_mouse_13

value: Advanced Stage (45 weeks)


title: athero_mouse_12


title: EpiLC_4h_clone4_ATAC-seq

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

country: Denmark

institute: Copenhagen University

library_source: genomic

data_processing:
Raw reads were processed with bcl2fastq, adapters were trimmed with cutadapt, reads were mapped to mm10 using bowtie2. ChrM, duplicate reads and reads in blacklisted regions were removed. Peaks were called using macs2 (v 2.2.7.1) (--broad -f BAMPE --qvalue 0.001).
Assembly: mm10
Supplementary files format and content: bigwig files

molecule: genomic DNA

growth_protocol:
CRAFR26 mESCs were cultured in 2i/LIF media consisting of N2B27 media supplemented with 3 μM of the GSK3 inhibitor Chir (Axon, CHIR99021), 1 μM of the MEKi PD03 (PD0325901, Sigma PZ0162) and 1000 U/ml of LIF (prepared in house).
CRAFR26 RSCs were cultured in N2B27 media supplemented with 2 µM IWP2 (Millipore, 681671), 1 µM of the MEKi PD03 (PD0325901, Sigma, PZ0162) and 1000 U/ml of LIF (prepared in house).
CRAFR26 ESCs were differentiated into EpiLCs by plating into N2B27 media supplemented with 12 ng/ml bFGF (Peprotech, 450-33-100µG), 20 ng/ml Activin A (Peprotech, 120-14E-200µG) and 1 µM XAV939 (Sigma,  X3004) for 48 h.

extract_protocol:
50,000 cells were collected in a 1.5 ml DNA LoBind tube (Eppendorf, 0030108051), and lysed for 3 minutes on ice in 0.1% IGEPAL, 0.1% Tween-20, 0.01% Digitonin (Promega, G9441). Nuclei were washed and pelleted for 10 minutes at 500g, and then treated for 30 minutes at 37ºC with Tn5 transposase (Illumina, 20034197).
DNA was extracted using DNA Clean and Concentrator 5-kit (Zymo Research, D4014), and libraries were prepared according to Buenrostro et al. 2013.

treatment_protocol: For ERK induction, mESCs were cultured for 48h (2h for EpiLCs) before the experiment in 250 nM of the FGFRi PD17 (PD173074, Sigma, P2499). Then, the c-RAF kinase construct was induced by adding 250 nM 4OHT (4-Hydroxytamoxifen, Sigma, H7904).

tag: cell type

value: EpiLC

tag: clone

value: clone 4

tag: time

value: PD17 2h, 4OHT 4h


title: athero_mouse_11


title: athero_mouse_10


title: EpiLC_4h_clone8_ATAC-seq

tag: cell line

value: clone 8


title: athero_mouse_23


title: athero_mouse_9


title: athero_mouse_22


title: EpiLC_0h_clone8_ATAC-seq

value: PD17 2h


title: EpiLC_0h_clone4_ATAC-seq


title: athero_mouse_8

value: Early Stage(30 weeks)


title: athero_mouse_6

value: Aortic Arch


title: EP000004A06_1_0.014967CF_TC00503572_A22

description:
EP000004A06_1_0.014967CF
TC00503572_A22

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_6

tag: media

value: Drinking Water


title: athero_mouse_7


title: UHRR_TC00503572_B01

description:
UHRR
TC00503572_B01

source_name: Universal Human Reference RNA

value: NA (Universal Human Reference RNA)

value: untreated

tag: chemical name


title: RSC_4h_clone8_ATAC-seq

value: RSC

value: PD17 48h, 4OHT 4h


title: EP000004A03_4_0.497018CF_TC00503572_A19

description:
EP000004A03_4_0.497018CF
TC00503572_A19

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_3

value: DMEM + 10% HI-FBS

tag: chemical sample_id


title: RSC_4h_clone4_ATAC-seq


title: EP000004A12_5_1.473477CF_TC00503572_A17

description:
EP000004A12_5_1.473477CF
TC00503572_A17

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_12

tag: chemical concentration

value: Surface Water


title: athero_mouse_4

value: Wt

value: Baseline(10 weeks)


title: athero_mouse_3


title: RSC_0h_clone8_ATAC-seq


title: athero_mouse_2


title: EP000004A06_4_0.497018CF_TC00503572_A15

description:
EP000004A06_4_0.497018CF
TC00503572_A15

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_6

tag: dose level


title: NPC_input

city: LOS ANGELES

first: Chia-ho

last: Lin

state: CA

address: 6577 MRL. 675 CHARLES E YOUNG DR. SOUTH

institute: UCLA

data_processing:
Reads were aligned to mm10 using STAR.  Peak calling was performed using Homer findpeaks  with -style factor -center -strand both -fdr 0.01. Bigwig files were generaed using deeptools bamCoverage (--outFileFormat bigwig --binSize 10 --normalizeUsing RPKM -p 20).
Assembly: mm10
Supplementary files format and content: bigwig

source_name: HBG3 ES cell line-derived NPC

extract_protocol: NOT PROVIDED

value: HBG3 ES cell line-derived NPC

value: Neural  Progenitor Cell (NPC)

value: WT

value: Differentiation to NPC


title: athero_mouse_1

value: Aortic Arch


title: RSC_0h_clone4_ATAC-seq

value: clone 4


title: NPC_E7KI-3 (ChIP-seq rep-3)

value: Dpf2 E7-KI


title: ESC_4h_clone8_ATAC-seq

value: ESC

value: clone 8


title: EP000004A01_2_0.049970CF_TC00503572_A14

description:
EP000004A01_2_0.049970CF
TC00503572_A14

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_1

tag: exposure time

value: Reclaimed Water


title: EP000004A05_2_0.049970CF_TC00503572_A12

description:
EP000004A05_2_0.049970CF
TC00503572_A12

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_5

value: DMEM + 10% HI-FBS

tag: assay plate


title: NPC_E7KO-2 (ChIP-seq rep-2)

tag: genotype

value: Dpf2 E7-KO


title: NPC_E7KI-2 (ChIP-seq rep-2)


title: EP000004A09_7_12.711864CF_TC00503572_A20

description:
EP000004A09_7_12.711864CF
TC00503572_A20

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_9

value: Blank


title: ESC_4h_clone4_ATAC-seq

value: PD17 48h, 4OHT 4h


title: ESC_0h_clone8_ATAC-seq


title: NPC_E7KO-1 (ChIP-seq rep-1)

value: HBG3 ES cell line-derived NPC


title: NPC_WT-3 (ChIP-seq rep-3)

value: Neural  Progenitor Cell (NPC)


title: NPC_E7KO-3 (ChIP-seq rep-3)


title: ESC_0h_clone4_ATAC-seq


title: EP000004A02_5_1.473477CF_TC00503572_A11

description:
EP000004A02_5_1.473477CF
TC00503572_A11

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_2

value: Wastewater


title: EP000004A07_4_0.497018CF_TC00503572_A08

description:
EP000004A07_4_0.497018CF
TC00503572_A08

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_7


title: EP000004A12_1_0.014967CF_TC00503572_A07

description:
EP000004A12_1_0.014967CF
TC00503572_A07

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_12

value: Surface Water


title: NPC_WT-1 (ChIP-seq rep-1)

value: WT

value: Differentiation to NPC


title: miRNA CB_tg_crush_146

city: Würzburg

first: Chi Wang

last: Ip

address: Josef-Schneider-Strasse 11

department: Neurology

country: Germany

institute: Neurologische Klinik und poliklinik

description: cerebellum, nerve-injured, miRNA, biol rep6

data_processing:
R version 4.1.0
Sequence reads were annoted, adapter-trimmed and mapped using miRge3.0
Read counts were summarized for each gene using featureCounts version 1.6.4
Assembly: miRge3.0
Supplementary files format and content: tab-delimited text files include raw count and r-log transformed count for each sample, as well as log2Foldchange, pvalue and p.adjust vlaue

source_name: Right cerebellum

growth_protocol: Mice were housed in the animal facility of the University Hospital of Würzburg and kept in standard condition (21°C, 12-h light/dark cycle)

extract_protocol:
miRNA was harvested using miRneasy mini kit(Qiagen) for the cerebellum and miRNeasy micro kit (Qiagen) for cortex and striatum . 500 ng of total RNA was used for the construction of sequencing libraries.
DNA libraries for miRNA-seq were prepared using QIASeq miRNA UDI Library Kit following manufacturer's protocols.

treatment_protocol: A right sciatic nerve crush injury was performed for 1 minute on isoflurane- anesthetized 12 week-old wt and DYT1KI mice

value: Right cerebellum

tag: Sex

value: male

value: right sciatic nerve crush

value: 12 weeks post injury


title: ESC_input

source_name: HBG3 ES cell line

value: HBG3 ES cell line

value: Embryonic stem cell (ESC)

value: Stem cell maintenance


title: EP000004A03_7_12.711864CF_TC00503572_A05

description:
EP000004A03_7_12.711864CF
TC00503572_A05

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_3

value: DMEM + 10% HI-FBS

tag: assay plate_well


title: miRNA CB_tg_crush_145

description: cerebellum, nerve-injured, miRNA, biol rep5


title: ESC_E7KI-3 (ChIP-seq rep-3)

value: Dpf2 E7-KI


title: ESC_E7KI-2 (ChIP-seq rep-2)


title: EP000004A03_8_50.000000CF_TC00503572_A04

description:
EP000004A03_8_50.000000CF
TC00503572_A04

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_3

value: 50 CF

tag: water type


title: ESC_E7KO-3 (ChIP-seq rep-3)

value: Dpf2 E7-KO


title: athero_mouse_5

tag: tissue

value: Aortic Arch

tag: time point

value: Early Stage(30 weeks)


title: miRNA CB_tg_crush_127

description: cerebellum, nerve-injured, miRNA, biol rep4

tag: treatment


title: NPC_E7KI-1 (ChIP-seq rep-1)

value: HBG3 ES cell line-derived NPC

tag: cell type

value: Neural  Progenitor Cell (NPC)


title: ESC_E7KO-2 (ChIP-seq rep-2)


title: ESC_E7KO-1 (ChIP-seq rep-1)


title: EP000004B05_6_4.716981CF_TC00503572_A03

description:
EP000004B05_6_4.716981CF
TC00503572_A03

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_17

value: Drinking Water


title: UHRR_TC00503572_A01

description:
UHRR
TC00503572_A01

value: NA (Universal Human Reference RNA)

value: untreated


title: ESC_WT-3 (ChIP-seq rep-3)

value: HBG3 ES cell line

value: WT


title: EP000004A06_4_0.497018CF_TC00284699_P24

description:
EP000004A06_4_0.497018CF
TC00284699_P24

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_6


title: ESC_WT-2 (ChIP-seq rep-2)

value: Embryonic stem cell (ESC)

value: Stem cell maintenance


title: miRNA CB_tg_crush_26

description: cerebellum, nerve-injured, miRNA, biol rep2

value: Right cerebellum

value: male

value: right sciatic nerve crush

tag: time

value: 12 weeks post injury


title: NPC_WT-2 (ChIP-seq rep-2)

tag: cell line

value: Differentiation to NPC


title: ESC_WT-1 (ChIP-seq rep-1)


title: KZ2658-GC4680008_DNase_WT_Th1_2uM_BRM014_inhibitor_12h_2

city: Bethesda

first: Keji

last: Zhao

state: MD

address: Building 10 Room 7B06A

department: National Heart, Lung, and Blood Institute

institute: national Institute of Health

description: Dnase-seq

data_processing:
Basecalls performed
Reads from Pro-seq, DNase-seq and ChIC-seq were mapped to mouse genome (mm10) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed. Reads from RNA-seq data were mapped to mouse genome (mm10) using Bowtie.
Paired-end sequencing reads for MNase-seq were mapped to mouse genome (mm10) using Bowtie2. Discordantly aligned reads, reads with mapping quality (MAPQ) ≤10, and redundant reads were removed from further analysis. We selected the fragments with range of 140-180bp as canonical nucleosomes for further analysis. The midpoints of nucleosomes were defined as their positions. We used center-weighted occupancy score to plot aggregated nucleosome profiles at single base resolution. Specifically, we defined the nucleosome center positioning (NCP) score S_k at position k, as the normalized nucleosome count with center at position k. We defined center-weighted occupancy score at position k as∑_(j=-73)^(j=73)▒S_(k+j)  w_j, where w_j is the Gaussian weight equal to e^(-(j/20)^2/2).
Assembly: mm10
Supplementary files format and content: bedgraph files for Pro-seq, DNase-seq and ChIC-seq::
Supplementary files format and content: bedgraph files for RNA-seq:: normlized by the library size and using a window size of 200bp
Supplementary files format and content: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: normlized by the library size and using a window size of 20bp
Supplementary files format and content: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both WT replicates

source_name: CD4 Th1 cells

extract_protocol:
Briefly, 10,000 cells from each cell type were collected by FACS sorting. 0.3 unit of DNase I (Roche) was added to each cell type and incubated at 37°C for 5 minutes. Reactions were stopped by adding 80 μl of stop buffer (10 mM Tris-HCl, 10 mM NaCl, 0.1% SDS, 10 mM EDTA) containing 1 μl of 20 mg/ml proteinase K. Samples were incubated at 55°C overnight, and DNAs were purified by using MinElute reaction cleanup kit following the manufacturer's protocol.
Purified DNA was end-repaired using end-repair kit (ER81050, Epicentre), followed by A-addition using Klenow fragment (3’ to 5’ exo minus) and dATP. The Y-shaped adaptors were then ligated to DNA ends using T4 DNA ligase. Libraries were amplified with Illumina primers for 16 cycles and library fragments from 150bp to 300bp were isolated for sequencing on Illumina HiSeq or NovaSeq platforms.

tag: cell lines

value: In vitro cultured mouse primery CD4+ T cells


title: KZ2658-GC4680007_DNase_WT_Th1_2uM_BRM014_inhibitor_12h_1

description: Dnase-seq


title: EP000004B02_4_0.497018CF_TC00284699_P23

description:
EP000004B02_4_0.497018CF
TC00284699_P23

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_14

tag: media

value: DMEM + 10% HI-FBS

tag: chemical name

value: Blank


title: miRNA CB_tg_crush_17

description: cerebellum, nerve-injured, miRNA, biol rep1


title: KZ2658-GC4680005_DNase_WT_Th1_Control_1

description: Dnase-seq


title: miRNA CB_tg_naive_140

description: cerebellum, naive, miRNA, biol rep6

value: naive


title: KZ2658-GC4680006_DNase_WT_Th1_Control_2

description: Dnase-seq


title: KZ2658-GC4680004-Pro-seq_WT_Th1_2uM_BRM014_inhibitor_12h_2

description: Pro-seq

extract_protocol:
PRO-seq (precision nuclear run-on sequencing) assays were performed as previously reported {Mahat, 2016 #10} with some modifications. Briefly, 500,000 cells were sorted from both Brg1-AID and control mice and permeabilized with ice-cold permeabilization buffer (1x106 cells/ml) on ice for 5 minutes. Then, the nuclear run-on reaction was carried out in the presence of biotin-dATP and unlabeled dCTP, dATP, dGTP, dUTP and sarkosyl. The nascent RNAs were extracted, fragmented, and purified by streptavidin pull-down. Next, 3' adapters were ligated directly to the purified nascent RNA. Following streptavidin purification, 5' ends were repaired using TAP and PNK and then ligated to 5' adapters. The adapter-containing RNA fragments are enriched by streptavidin pull-down, followed by reverse transcription
Reverse transcripted cDNA were PCR amplified with Illumina primers for 18 cycles, The fragments from 150bp to 700bp were isolated from E-gel and sequenced on Illumina NovaSeq.


title: ESC_E7KI-1 (ChIP-seq rep-1)

value: Dpf2 E7-KI


title: miRNA CB_tg_naive_139

description: cerebellum, naive, miRNA, biol rep5


title: KZ2658-GC4680003-Pro-seq_WT_Th1_2uM_BRM014_inhibitor_12h_1

description: Pro-seq


title: miRNA CB_tg_naive_133

description: cerebellum, naive, miRNA, biol rep4


title: miRNA CB_tg_naive_60

description: cerebellum, naive, miRNA, biol rep3


title: TSA_TC00284699_P12

description:
TSA
TC00284699_P12

value: 6h exposure of 1 uM of Trichostatin A

value: Trichostatin A

tag: chemical sample_id

tag: chemical concentration

value: 1 uM


title: KZ2658-GC4680002-Pro-seq_WT_Th1_Control_2

description: Pro-seq


title: EP000004A06_2_0.049970CF_TC00284699_P20

description:
EP000004A06_2_0.049970CF
TC00284699_P20

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_6

tag: dose level

tag: exposure time

value: Drinking Water


title: Mice fibroblast-H3K27ac-CHIC-AID-with TSA-2#-New cells

description: ChIC-seq

source_name: Fibroblasts

value: Fibroblasts


title: KZ2658-GC4680001-Pro-seq_WT_Th1_Control_1

description: Pro-seq


title: Mice fibroblast-H3K27ac-CHIC-AID-with TSA-1#-New cells

description: ChIC-seq

extract_protocol:
cells for ChIC-seq were fixed for 10 minutes with 1% formaldehyde and permeabilized with RIPA buffer (10 mM Tris-Cl, 150 mM NaCl, 0.1% SDS, 0.1% NaDOC, 1% Triton X-100) for 10 minutes at RT. Antibodies (anti-H3K4me3 (17-614, Millipor and protein A-MNase fusion protein were mixed well and incubated at 4°C for 30 minutes. Next, the antibody-pA-Mnase complex was added to the permeabilized cells and incubated at 4°C for 1 hour. Then, the cells were washed with 600 μl RIPA buffer four times and rinsed once with 200 μl rinsing buffer (10 mM Tris-Cl and 10 mM NaCl, 0.1% Triton X-100). The MNase digestion was initiated by re-suspending rinsed cells in 40 μl reaction solution buffer (10 mM Tris-Cl, 10 mM NaCl, 0.1% Triton X-100, 2 mM CaCl2) and incubated at 37°C for 3 minutes. The reaction was stopped by adding 80 μl stop buffer (20 mM Tris-Cl, 10 mM EGTA, 20 mM NaCl, 0.2% SDS) and 1 μl proteinase K, then incubated at 65°C for overnight. DNAs were purified by using MinElute reaction cleanup kit.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. The ligation reaction was performed by adding 2 μM Illumina's adapters to each sample and incubated at RT one hour. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments from 180bp to 300bp were isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Hi-seq3000 following the manufacturer's protocols.


title: EP000004A02_3_0.149731CF_TC00284699_P11

description:
EP000004A02_3_0.149731CF
TC00284699_P11

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_2

tag: assay plate

value: Wastewater


title: Mice fibroblast-H3K27ac-CHIC-AID-without TSA-2#-New cells

description: ChIC-seq


title: miRNA CB_tg_crush_37

description: cerebellum, nerve-injured, miRNA, biol rep3

value: Right cerebellum

tag: Sex

value: male

tag: genotype

value: right sciatic nerve crush


title: Mice fibroblast-H3K27ac-CHIC-AID-without TSA-1#-New cells

description: ChIC-seq


title: EP000004A11_2_0.049970CF_TC00284699_P07

description:
EP000004A11_2_0.049970CF
TC00284699_P07

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_11

tag: assay plate_well

tag: water type


title: miRNA CB_tg_naive_27

description: cerebelum, naive, miRNA, biol rep1

tag: tissue

value: 12 weeks post injury


title: TGN_6_BST2_3

city: Kaifeng, Henan Province

first: Yanqing

last: Li

address: Jinming Avenue

country: China

institute: Henan University

description:
processed data file:
mTGNs_BST2_gene_expression.xls

data_processing:
Base calling and the quality score of each base are calculated based on the phred-33 quality score standard by the sub-Pixel Registration algorithm according to the optical signal intensity of each lane
This project uses the filtering software SOAPnuke (Versionv1.5.2) developed by BGI independently for filtering. SOAPnuke   Official Websitehttps://github.com/BGI-flexlab/SOAPnuke The specific steps are as follows: 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).
Hierarchical Indexing for Spliced Alignment of Transcripts (HISTAT) is software for mapping RNA-seq reads. HISAT will use the global FM index to anchor the position of partial sequences in each read on the genome; then, use the partial genome indexes of these alignment positions to align the remaining sequences of each read to extend the alignment area. Software information:HISAT2 (Version：v2.0.4) ,Official Website：http://www.ccb.jhu.edu/software/hisat
Bowtie2 (v2.2.5) was used to compare clean reads to reference sequences for gene alignment with -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200. And then RSEM (v1.2.8) was used to calculate gene and transcript expression levels with -p 8 --forward-prob 0.5 --paired-end.
Genome_build: GCF_000001635.26_GRCm38.p6 for Mus musculus GCF_000001405.39_GRCh38.p13 for Homo sapiens
Supplementary_files_format_and_content: FPKM values, Reads Count for each Sample

growth_protocol: phKCs were seeded into 24 well plates and cultured in KBM-Gold medium with KBM Gold SingleQuot KC supplement (Lonza, Basel, Switzerland). Cells were maintained in the above medium for 3 days before use.     Mouse trigeminal neurons (mTGNs) were isolated from postnatal d5 C57BL/6 mice after the mice after being deeply anesthetized by i.p. injection of a mixture of 0.2% xylazine, 1% ketamine, and 0.9% NaCl. The harvested ganglia were incubated with Hank’s balanced salt solution (HBSS) using collagenase I (10 mg/mL, Sigma) and dispase II (5 mg/mL, Sigma) for 30 minutes. Digests were washed with DMEM and the cell suspension was filtered through a 100-μm cell strainer and cultured in 24-well plates pre-coated with poly-L-lysine (Sigma) and laminin (Sigma) in medium consisting DMEM supplemented with 5% (v/v) FBS (Sigma), 100 U/ml penicillin, 100 μg/ml streptomycin in the presence of cytosine β-d-arabinofuranoside (Sigma) 10 µM, 1xB27, and nerve growth factor 50 ng/ml (Sigma) for 7 days

extract_protocol:
Remove the upper medium and wash it twice with cold PBS, frozen on ice, and RNA was harvested using Trizol reagent.The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on DNBSeq platform (BGI-Shenzhen, China)

treatment_protocol: phKCs were treated with IL-27(100 ng/ml) for 6h or BST2(250 ng/ml) for 24h; mTGNs were treated with IL-27(100 ng/ml) or BST2(500 ng/ml) for 6h

value: mouse trigeminal ganglion neurons

tag: treatment

value: BST2 (500 ng/ml) treated


title: TGN_6_BST2_2

tag: cell type


title: Mice fibroblast-H3K27ac-CHIC-WT-with TSA-1#-New cells

description: ChIC-seq


title: EP000004B05_3_0.149731CF_TC00284699_P10

description:
EP000004B05_3_0.149731CF
TC00284699_P10

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_17

value: DMEM + 10% HI-FBS


title: Mice fibroblast-H3K27ac-CHIC-WT-with TSA-2#-New cells

description: ChIC-seq


title: EP000004A05_1_0.014967CF_TC00284699_P04

description:
EP000004A05_1_0.014967CF
TC00284699_P04

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_5

value: Surface Water


title: EP000004A01_6_4.716981CF_TC00284699_P22

description:
EP000004A01_6_4.716981CF
TC00284699_P22

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_1

value: Reclaimed Water


title: miRNA CB_wt_crush_154

value: WT

tag: time


title: miRNA CB_wt_crush_156


title: Mice fibroblast-H3K27ac-CHIC-WT-without TSA-2#-New cells

description: ChIC-seq

value: Fibroblasts


title: EP000004B06_2_0.049970CF_TC00284699_P03

description:
EP000004B06_2_0.049970CF
TC00284699_P03

tag: cell line

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_18


title: miRNA CB_wt_crush_128


title: TGN_6h_Ctrl3

value: untreated


title: Mice fibroblast-H3K27ac-CHIC-WT-without TSA-1#-New cells

description: ChIC-seq

tag: cell lines


title: EP000004A07_5_1.473477CF_TC00284699_P02

description:
EP000004A07_5_1.473477CF
TC00284699_P02

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_7

tag: media


title: TGN_6h_Ctrl2


title: miRNA CB_wt_crush_29

value: Right cerebellum

value: male


title: miRNA CB_tg_naive_39

description: cerebellum, naive, miRNA, biol rep2

value: naive


title: Mice fibroblast-DNase-AID-with TSA-2#-New cells

description: Dnase-seq


title: EP000004B06_6_4.716981CF_TC00284699_O23

description:
EP000004B06_6_4.716981CF
TC00284699_O23

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_18

tag: chemical name


title: TGN_6h_Ctrl1

value: mouse trigeminal ganglion neurons


title: Mice fibroblast-DNase-AID-with TSA-1#-New cells

description: Dnase-seq


title: mTGN_IL27_3

description:
processed data file:
mTGNs_IL27_gene_expression.xls

value: IL-27(100 ng/ml) treated


title: miRNA CB_wt_naive_160

description: cerebellum, naive, miRNA, biol rep6

value: 12 weeks post injury


title: Mice fibroblast-DNase-AID-without TSA-2#-New cells

description: Dnase-seq


title: EP000004B04_7_12.711864CF_TC00284699_O20

description:
EP000004B04_7_12.711864CF
TC00284699_O20

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_16

value: DMEM + 10% HI-FBS

tag: chemical sample_id


title: mTGN_IL27_2


title: Mice fibroblast-DNase-AID-without TSA-1#-New cells

description: Dnase-seq


title: TGN_6_BST2_1

value: BST2 (500 ng/ml) treated


title: miRNA CB_wt_naive_159

description: cerebellum, naive, miRNA, biol rep5


title: EP000004A03_4_0.497018CF_TC00284699_O17

description:
EP000004A03_4_0.497018CF
TC00284699_O17

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_3

tag: chemical concentration

value: Surface Water


title: Mice fibroblast-DNase-WT-with TSA-2#-New cells

description: Dnase-seq


title: EP000004A03_1_0.014967CF_TC00284699_O16

description:
EP000004A03_1_0.014967CF
TC00284699_O16

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_3

tag: dose level


title: Mice fibroblast-DNase-WT-with TSA-1#-New cells

description: Dnase-seq

value: Fibroblasts


title: mTGN_Ctrl_3


title: miRNA CB_wt_naive_158

description: cerebellum, naive, miRNA, biol rep4

value: WT


title: mTGN_IL27_1


title: EP000004A08_1_0.014967CF_TC00284699_O14

description:
EP000004A08_1_0.014967CF
TC00284699_O14

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_8

tag: exposure time

value: Wastewater


title: miRNA CB_wt_naive_138

description: cerebellum, naive, miRNA, biol rep2

value: Right cerebellum


title: mTGN_Ctrl_2

value: untreated


title: miRNA CB_wt_naive_157

description: cerebellum, naive, miRNA, biol rep3

value: male

value: naive


title: Mice fibroblast-DNase-WT-without TSA-2#-New cells

description: Dnase-seq


title: miRNA CB_wt_crush_28

value: right sciatic nerve crush


title: mTGN_Ctrl_1

value: mouse trigeminal ganglion neurons


title: EP000004B06_1_0.014967CF_TC00284699_O21

description:
EP000004B06_1_0.014967CF
TC00284699_O21

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_18

tag: assay plate


title: miRNA CB_wt_naive_31

description: cerebelum, naive, miRNA, biol rep1

tag: Sex

value: 12 weeks post injury


title: EP000004A09_5_1.473477CF_TC00284699_O12

description:
EP000004A09_5_1.473477CF
TC00284699_O12

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_9

value: DMEM + 10% HI-FBS

value: Blank


title: EP000004A11_1_0.014967CF_TC00284699_O09

description:
EP000004A11_1_0.014967CF
TC00284699_O09

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_11


title: miRNA STR_tg_crush_146

description: striatum, nerve-injured, miRNA, biol rep6

source_name: Left striatum

value: Left striatum

tag: genotype


title: Mice fibroblast-DNase-WT-without TSA-1#-New cells

description: Dnase-seq

value: Fibroblasts


title: Mice fibroblast-Brg1-CHIC-AID-with TSA-2#

description: ChIC-seq


title: day235_CapIGseq_BCL2+CK_rep4

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

data_processing:
Raw data was processed following the MiXCR pipeline (DOI: 10.1038/nmeth.3364).  the diversity of BCR repertoire, we used the iNEXT (version 3.0.0) R package.
Assembly: mm10
Supplementary files format and content: csv file including unique clone number, Shannon diversity score/group, Simpson clonality score/group for each sample
Library strategy: CapIG-seq (aka, B cell receptor sequencing)

source_name: Spleen

extract_protocol:
Genomic DNA was extracted using the PureLink genomic DNA mini kit (Invitrogen, cat# K182002) following the manual.
Briefly, 250 ng of DNA per sample was sheared to 250 bp segments using the Covaris LE220 and then subject to DNA library construction using the KAPA HyperPrep kit (Roche, cat# KK8502). We next followed the IDT xGen hybridization capture of DNA libraries protocol to capture the BCR VDJ fragments from the library using a custom probe set designed through the IDT xGen Hyb Panel design tool.

value: Spleen

value: Germinal center B cell


title: day235_CapIGseq_BCL2+CK_rep3


title: miRNA STR_tg_crush_145

description: striatum, nerve-injured, miRNA, biol rep5


title: Mice fibroblast-Brg1-CHIC-AID-with TSA-1#

description: ChIC-seq


title: miRNA STR_tg_crush_127

description: striatum, nerve-injured, miRNA, biol rep4


title: day235_CapIGseq_BCL2+CK_rep2


title: Mice fibroblast-Brg1-CHIC-AID-without TSA-2#

description: ChIC-seq


title: EP000004A04_3_0.149731CF_TC00284699_O05

description:
EP000004A04_3_0.149731CF
TC00284699_O05

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_4

tag: assay plate_well

value: Drinking Water


title: day235_CapIGseq_BCL2+CK_rep1


title: day235_CapIGseq_BCL2+K_rep4


title: Mice fibroblast-Brg1-CHIC-AID-without TSA-1#

description: ChIC-seq


title: EP000004A04_2_0.049970CF_TC00284699_O02

description:
EP000004A04_2_0.049970CF
TC00284699_O02

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_4

tag: water type


title: miRNA STR_tg_crush_37

description: striatum, nerve-injured, miRNA, biol rep3

tag: tissue

value: male


title: Mice fibroblast-Brg1-CHIC-WT-with TSA-2#

description: ChIC-seq


title: EP000004A06_6_4.716981CF_TC00284699_N20

description:
EP000004A06_6_4.716981CF
TC00284699_N20

tag: treatment

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_6


title: day235_CapIGseq_BCL2+K_rep3

tag: cell type


title: miRNA STR_tg_crush_17

description: striatum, nerve-injured, miRNA, biol rep1

value: right sciatic nerve crush

tag: time


title: EP000004A01_5_1.473477CF_TC00284699_N18

description:
EP000004A01_5_1.473477CF
TC00284699_N18

tag: cell line

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_1

value: Reclaimed Water


title: Mice fibroblast-Brg1-CHIC-WT-with TSA-1#

description: ChIC-seq

tag: cell lines


title: Mice fibroblast-Brg1-CHIC-WT-without TSA-2#

description: ChIC-seq


title: EP000004B03_5_1.473477CF_TC00284699_N17

description:
EP000004B03_5_1.473477CF
TC00284699_N17

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_15

tag: media

value: Wastewater


title: miRNA STR_tg_naive_140

description: striatum, naive, miRNA, biol rep6

value: naive

value: 12 weeks post injury


title: miRNA STR_tg_naive_139

description: striatum, naive, miRNA, biol rep5


title: day235_CapIGseq_BCL2+K_rep2


title: EP000004A11_5_1.473477CF_TC00284699_O08

description:
EP000004A11_5_1.473477CF
TC00284699_O08

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_11

value: DMEM + 10% HI-FBS

tag: chemical name

value: Blank


title: Mice fibroblast-Brg1-CHIC-WT-without TSA-1#

description: ChIC-seq

value: Fibroblasts


title: day235_CapIGseq_BCL2+K_rep1

value: Spleen

value: Germinal center B cell


title: miRNA STR_tg_naive_133

description: striatum, naive, miRNA, biol rep4

value: Left striatum


title: day235_CapIGseq_BCL2+C_rep4


title: Fibroblast from BRG1-AID mice-proseq-replicate-2#

description: Pro-seq


title: EP000004A02_5_1.473477CF_TC00284699_N15

description:
EP000004A02_5_1.473477CF
TC00284699_N15

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_2

tag: chemical sample_id


title: EP000004A10_6_4.716981CF_TC00284699_O07

description:
EP000004A10_6_4.716981CF
TC00284699_O07

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_10

tag: chemical concentration


title: day235_CapIGseq_BCL2+C_rep3


title: Fibroblast from BRG1-AID mice-proseq-replicate-1#

description: Pro-seq


title: miRNA STR_tg_naive_60

description: striatum, naive, miRNA, biol rep3

value: male


title: miRNA STR_tg_crush_26

description: striatum, nerve-injured, miRNA, biol rep2

value: right sciatic nerve crush


title: EP000004B04_5_1.473477CF_TC00284699_N13

description:
EP000004B04_5_1.473477CF
TC00284699_N13

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_16

tag: dose level


title: day235_CapIGseq_BCL2+C_rep2


title: Fibroblast from WT mice-proseq-replicate-2#

description: Pro-seq


title: EP000004A04_1_0.014967CF_TC00284699_N11

description:
EP000004A04_1_0.014967CF
TC00284699_N11

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_4

tag: exposure time

value: Drinking Water


title: miRNA STR_tg_naive_39

description: striatum, naive, miRNA, biol rep2


title: day235_CapIGseq_BCL2+C_rep1


title: Fibroblast from WT mice-proseq-replicate-1#

description: Pro-seq


title: EP000004A10_3_0.149731CF_TC00284699_N16

description:
EP000004A10_3_0.149731CF
TC00284699_N16

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_10

tag: assay plate


title: miRNA STR_tg_naive_27

description: striatum, naive, miRNA, biol rep1

tag: Sex

value: naive


title: EP000004A02_4_0.497018CF_TC00284699_N08

description:
EP000004A02_4_0.497018CF
TC00284699_N08

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_2

value: Wastewater


title: day235_CapIGseq_BCL2_rep4

tag: genotype


title: miRNA STR_wt_crush_154

value: WT

value: 12 weeks post injury


title: DMSO_TC00284699_N04

description:
DMSO
TC00284699_N04

value: 0.5% DMSO vehicle control

value: DMEM + 10% HI-FBS

value: DMSO

value: 0 uM

tag: assay plate_well


title: Hepatocyte from BRG1-AID mice-proseq-replicate-1#

description: Pro-seq

source_name: Hepatocytes

value: Hepatocytes


title: day235_CapIGseq_BCL2_rep2

value: Spleen

value: Germinal center B cell


title: day235_CapIGseq_BCL2_rep3


title: miRNA STR_wt_crush_156

value: Left striatum

value: male

value: right sciatic nerve crush


title: Hepatocyte from WT mice-proseq-replicate-2#

description: Pro-seq


title: EP000004B01_1_0.014967CF_TC00284699_M22

description:
EP000004B01_1_0.014967CF
TC00284699_M22

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_13

tag: water type


title: miRNA STR_wt_crush_128

tag: tissue


title: miRNA STR_wt_crush_29

tag: treatment


title: EP000004A01_8_50.000000CF_TC00284699_N07

description:
EP000004A01_8_50.000000CF
TC00284699_N07

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_1

value: 50 CF

value: Reclaimed Water


title: BRG1-AID mice AID hepatocytes P300.R2

description: ChIC-seq


title: miRNA STR_wt_crush_28


title: Untrtd_TC00284699_M16

description:
Untrtd
TC00284699_M16

value: untreated


title: CC_WT_rep3

data_processing:
nfcore atac seq version 1.2.1
Assembly: mm10
Supplementary files format and content: Consensus Peak Counts

source_name: spleen

extract_protocol:
60,000 freshly sorted live cells were washed in cold PBS, lysed in 60 ul cold lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) for 3 min on ice, followed by addition of 1 ml wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Tween-20) and centrifugation to pellet nuclei.
Bulk ATAC-seq libraries were prepared following the Omni-ATAC protocol. Briefly, nuclei were resuspended in a transposition reaction mix prepared using the Illumina Tagment DNA Enzyme and Buffer Kit (Illumina, 20034197) and incubated at 37 ºC for 30 minutes on thermomixer at 1,000 rpm to allow for transposition-based DNA fragmentation and adapter ligation. Tagged DNA fragments were purified using the Clean & Concentrator-5 Kit (ZYMO, D4014), then subjected to PCR amplification and double-sided bead purification (to remove primer dimers and larger than 1,000 bp fragments) using the AMPure XP beads (Beckman Coulter, A63881).

treatment_protocol: Mice (WT, C, K, and CK) were immunized with SRBC for 10 days before sorting GC B cells.

value: spleen

tag: cell type

value: CC

value: WT


title: CB_WT_rep3

value: CB


title: miRNA STR_wt_crush_19

tag: time

value: 12 weeks post injury


title: EP000004B03_6_4.716981CF_TC00284699_M10

description:
EP000004B03_6_4.716981CF
TC00284699_M10

tag: cell line

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_15

value: DMEM + 10% HI-FBS

value: Wastewater


title: miRNA STR_wt_naive_160

description: striatum, naive, miRNA, biol rep6

value: naive


title: BRG1-AID mice WT hepatocytes P300.R2

description: ChIC-seq

tag: cell lines

value: Hepatocytes


title: CC_WT_rep4


title: Hepatocyte from BRG1-AID mice-proseq-replicate-2#

description: Pro-seq


title: day235_CapIGseq_BCL2_rep1

value: Spleen

value: Germinal center B cell


title: EP000004A09_1_0.014967CF_TC00284699_M08

description:
EP000004A09_1_0.014967CF
TC00284699_M08

value: 6h exposure of 0.01496735 uM of MCF7_HTTr_Water_Sample_9

tag: media

value: Blank


title: GEN_TC00284699_M17

description:
GEN
TC00284699_M17

value: 6h exposure of 10 uM of Genistein

tag: chemical name

value: Genistein

value: 10 uM


title: EP000004A05_2_0.049970CF_TC00284699_M03

description:
EP000004A05_2_0.049970CF
TC00284699_M03

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_5

tag: chemical sample_id

value: Surface Water


title: miRNA STR_wt_naive_158

description: striatum, naive, miRNA, biol rep4

value: Left striatum

value: male

value: WT


title: EP000004B06_4_0.497018CF_TC00284699_M06

description:
EP000004B06_4_0.497018CF
TC00284699_M06

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_18

tag: chemical concentration


title: CC_WT_rep2

value: spleen

value: CC


title: BRG1-AID mice AID hepatocytes H3K27ac.R2

description: ChIC-seq


title: BRG1-AID mice WT hepatocytes P300.R1

description: ChIC-seq


title: CC_WT_rep1


title: CB_WT_rep2

value: CB


title: Hepatocyte from WT mice-proseq-replicate-1#

description: Pro-seq

value: Hepatocytes


title: BRG1-AID mice WT hepatocytes H3K27ac.R2

description: ChIC-seq


title: EP000004A05_8_50.000000CF_TC00284699_L21

description:
EP000004A05_8_50.000000CF
TC00284699_L21

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_5

value: DMEM + 10% HI-FBS

value: 50 CF

tag: dose level


title: CB_WT_rep1


title: miRNA STR_wt_naive_138

description: striatum, naive, miRNA, biol rep2

value: naive

value: 12 weeks post injury


title: miRNA STR_wt_naive_157

description: striatum, naive, miRNA, biol rep3


title: miRNA STR_wt_naive_31

description: striatum, naive, miRNA, biol rep1


title: EP000004A07_6_4.716981CF_TC00284699_L18

description:
EP000004A07_6_4.716981CF
TC00284699_L18

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_7

tag: exposure time

value: Reclaimed Water


title: day235_BCL2+CK_rep4

data_processing:
BWA was utilized to map the paired-end clean reads to the mouse reference genome mm10. SNPs and InDels were detected and filtered (total counts ≥ 10) using GATK software.
Assembly: mm10
Supplementary files format and content: xlsx file summarizing variants called in each sample, the values represent VAF (variant allele frequency).
Library strategy: WES-seq (whole exome sequencing)

extract_protocol:
Genomic DNA was extracted using the PureLink genomic DNA mini kit (Invitrogen, cat# K182002) following the manual.
Sequencing libraries were generated using the Agilent SureSelectXT Mouse All Exon kit (cat# 5190-4641) following the manual.

value: Spleen

value: Germinal center B cell


title: day235_BCL2+CK_rep3


title: BRG1-AID mice WT hepatocytes H3K27ac.R1

description: ChIC-seq


title: DMSO_TC00284699_L15

description:
DMSO
TC00284699_L15

value: 0.5% DMSO vehicle control

value: DMSO

value: 0 uM

tag: assay plate


title: miRNA CX_tg_crush_146

description: cortex, nerve-injured, miRNA, biol rep6

source_name: Left cortex

value: Left cortex

tag: Sex

value: male

value: right sciatic nerve crush


title: BRG1-AID mice hepatocytes AID 1:6000 R2

description: MNase-seq

extract_protocol:
MNase-seq assays were performed as described bellow. Briefly, 10,000 CD4+ T cells from both Brg1-AID GFP+ (KO BRG1) and control mice (WT BRG1 GFP+) were sorted by flow cytometer and deposited directly into 1.5 ml Eppendorf tubes, which contained 32 μl of cell lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 2 mM CaCl2, 0.1% Triton X-100). For MNase digestion, 8 μl diluted MNase (1:4000 in lysis buffer) was added to the cells and incubated at 37°C for 5 minutes. The reaction was stopped by adding 80 μl stop buffer (10mM Tris-HCl, pH 7.5, 10mM NaCl, 0.15% SDS, 10mM EGTA), and 2 μl of 20 mg/ml Proteinase K. Following incubation at 65°C overnight,
libraries prepared and sequenced as described for the DNase-seq assays


title: day235_BCL2+CK_rep2

tag: genotype


title: EP000004B05_2_0.049970CF_TC00284699_L12

description:
EP000004B05_2_0.049970CF
TC00284699_L12

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_17

tag: assay plate_well

value: Drinking Water


title: miRNA CX_tg_crush_145

description: cortex, nerve-injured, miRNA, biol rep5


title: BRG1-AID mice hepatocytes WT 1:6000 R2

description: MNase-seq

value: Hepatocytes


title: EP000004B03_2_0.049970CF_TC00284699_L11

description:
EP000004B03_2_0.049970CF
TC00284699_L11

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_15

value: DMEM + 10% HI-FBS

tag: water type

value: Wastewater


title: miRNA STR_wt_naive_159

description: striatum, naive, miRNA, biol rep5

tag: tissue

value: Left striatum

value: WT

value: naive

value: 12 weeks post injury


title: day235_BCL2+K_rep4

value: Spleen

value: Germinal center B cell


title: BRG1-AID mice hepatocytes AID 1:6000 R1

description: MNase-seq


title: day235_BCL2+K_rep3


title: miRNA CX_tg_crush_37

description: cortex, nerve-injured, miRNA, biol rep3

tag: treatment


title: BRG1-AID mice hepatocytes WT 1:6000 R1

description: MNase-seq


title: MNase_Brg1_KO CD4+ Th1 cell 10hs G+ Rep.2 4000

data_processing:
Basecalls performed
Reads from Pro-seq, DNase-seq and ChIC-seq were mapped to mouse genome (mm10) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed. Reads from RNA-seq data were mapped to mouse genome (mm10) using Bowtie.
Paired-end sequencing reads for MNase-seq were mapped to mouse genome (mm10) using Bowtie2. Discordantly aligned reads, reads with mapping quality (MAPQ) ≤10, and redundant reads were removed from further analysis. We selected the fragments with range of 140-180bp as canonical nucleosomes for further analysis. The midpoints of nucleosomes were defined as their positions. We used center-weighted occupancy score to plot aggregated nucleosome profiles at single base resolution. Specifically, we defined the nucleosome center positioning (NCP) score S_k at position k, as the normalized nucleosome count with center at position k. We defined center-weighted occupancy score at position k as∑_(j=-73)^(j=73)▒S_(k+j)  w_j, where w_j is the Gaussian weight equal to e^(-(j/20)^2/2).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for Pro-seq, DNase-seq and ChIC-seq: normalized by the library size and using a window size of 200bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: bedgraph files for RNA-seq: normalized by the library size and using a window size of 20bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both WT replicates; irst column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both KO replicates; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density

tag: cell type

value: In vitro cultured mouse primary CD4+ T cells


title: BRG1-AID mice AID hepatocytes H3K27ac.R1

description: ChIC-seq


title: day235_BCL2+K_rep2


title: miRNA CX_tg_crush_127

description: cortex, nerve-injured, miRNA, biol rep4

tag: time


title: EP000004A01_2_0.049970CF_TC00284699_L07

description:
EP000004A01_2_0.049970CF
TC00284699_L07

tag: cell line

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_1

value: Reclaimed Water


title: miRNA CX_tg_crush_26

description: cortex, nerve-injured, miRNA, biol rep2

value: Left cortex

value: male


title: miRNA CX_tg_crush_17

description: cortex, nerve-injured, miRNA, biol rep1

value: right sciatic nerve crush


title: EP000004A03_3_0.149731CF_TC00284699_L09

description:
EP000004A03_3_0.149731CF
TC00284699_L09

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_3

value: Surface Water


title: MNase_Brg1_KO CD4+ Th1 cell 10hs G+ Rep.1 4000

description: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz


title: EP000004B01_6_4.716981CF_TC00284699_L06

description:
EP000004B01_6_4.716981CF
TC00284699_L06

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_13


title: day235_BCL2+K_rep1


title: day235_BCL2+C_rep4


title: EP000004B01_5_1.473477CF_TC00284699_L02

description:
EP000004B01_5_1.473477CF
TC00284699_L02

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_13

value: DMEM + 10% HI-FBS


title: MNase_Brg1_WT CD4+ Th1 cell 10hs G+ Rep.2 4000

description: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz


title: EP000004A07_2_0.049970CF_TC00284699_L03

description:
EP000004A07_2_0.049970CF
TC00284699_L03

value: 6h exposure of 0.04997 uM of MCF7_HTTr_Water_Sample_7


title: MNase_Brg1_WT CD4+ Th1 cell 10hs G+ Rep.1 4000

value: WT


title: miRNA CX_tg_naive_133

description: cortex, naive, miRNA, biol rep4

value: naive


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs P300 rep.2

data_processing:
Library strategy: ChIC-seq
Basecalls performed
Reads from Pro-seq, DNase-seq and ChIC-seq were mapped to mouse genome (mm10) using Bowtie2. Reads with MAPQ ≤ 10 or redundant reads that mapped to the same location and orientation were removed. Reads from RNA-seq data were mapped to mouse genome (mm10) using Bowtie.
Paired-end sequencing reads for MNase-seq were mapped to mouse genome (mm10) using Bowtie2. Discordantly aligned reads, reads with mapping quality (MAPQ) ≤10, and redundant reads were removed from further analysis. We selected the fragments with range of 140-180bp as canonical nucleosomes for further analysis. The midpoints of nucleosomes were defined as their positions. We used center-weighted occupancy score to plot aggregated nucleosome profiles at single base resolution. Specifically, we defined the nucleosome center positioning (NCP) score S_k at position k, as the normalized nucleosome count with center at position k. We defined center-weighted occupancy score at position k as∑_(j=-73)^(j=73)▒S_(k+j)  w_j, where w_j is the Gaussian weight equal to e^(-(j/20)^2/2).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files for Pro-seq, DNase-seq and ChIC-seq: normalized by the library size and using a window size of 200bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: bedgraph files for RNA-seq: normalized by the library size and using a window size of 20bp; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: WT_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both WT replicates; irst column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density
Supplementary_files_format_and_content: KO_4000_3lanes.bed.140180.chr10_11.begraph_kernal20bp.txt.gz: combine both KO replicates; first column is for chromsome, second column is for start site, and third column is for end site, the forth column is for density


title: day235_BCL2+C_rep3


title: EP000004B05_8_50.000000CF_TC00284699_L10

description:
EP000004B05_8_50.000000CF
TC00284699_L10

value: 6h exposure of 50 uM of MCF7_HTTr_Water_Sample_17

value: 50 CF

value: Drinking Water


title: EP000004A06_5_1.473477CF_TC00284699_K23

description:
EP000004A06_5_1.473477CF
TC00284699_K23

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_6


title: day235_BCL2+CK_rep1

value: Spleen

value: Germinal center B cell


title: day235_BCL2+C_rep2


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs P300 rep.1

value: In vitro cultured mouse primary CD4+ T cells


title: day235_BCL2+C_rep1


title: miRNA CX_tg_naive_39

description: cortex, naive, miRNA, biol rep2

value: Left cortex

value: male

value: 12 weeks post injury


title: miRNA CX_tg_naive_60

description: cortex, naive, miRNA, biol rep3


title: miRNA CX_tg_naive_27

description: cortex, naive, miRNA, biol rep1


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs P300 rep.2


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs P300 rep.1


title: EP000004A03_5_1.473477CF_TC00284699_K19

description:
EP000004A03_5_1.473477CF
TC00284699_K19

value: 6h exposure of 1.4734774 uM of MCF7_HTTr_Water_Sample_3

value: Surface Water


title: EP000004A03_6_4.716981CF_TC00284699_K14

description:
EP000004A03_6_4.716981CF
TC00284699_K14

value: 6h exposure of 4.71698115 uM of MCF7_HTTr_Water_Sample_3


title: miRNA CX_tg_naive_140

description: cortex, naive, miRNA, biol rep6


title: miRNA CX_tg_naive_139

description: cortex, naive, miRNA, biol rep5


title: day235_BCL2_rep3


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs H3K27AC rep.2


title: miRNA CX_wt_crush_154

description: cortex, nerve-injured, miRNA, biol rep5

value: right sciatic nerve crush


title: ChIC-seq_Brg1-AID CD4+ Th1 cell 10hs H3K27AC rep.1


title: DMSO_TC00284699_K13

description:
DMSO
TC00284699_K13

value: 0.5% DMSO vehicle control

value: DMEM + 10% HI-FBS

value: DMSO

value: 0 uM


title: day235_BCL2_rep1


title: day235_BCL2_rep2


title: miRNA CX_wt_crush_128

description: cortex, nerve-injured, miRNA, biol rep4

value: WT


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs H3K27AC rep.2


title: EP000004A04_7_12.711864CF_TC00284699_K20

description:
EP000004A04_7_12.711864CF
TC00284699_K20

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_4

value: Drinking Water


title: miRNA CX_wt_crush_29

description: cortex, nerve-injured, miRNA, biol rep3


title: EP000004B06_7_12.711864CF_TC00284699_K11

description:
EP000004B06_7_12.711864CF
TC00284699_K11

value: 6h exposure of 12.7118644 uM of MCF7_HTTr_Water_Sample_18


title: ChIC-seq_Brg1-WT CD4+ Th1 cell 10hs H3K27AC rep.1


title: EP000004A08_4_0.497018CF_TC00284699_K17

description:
EP000004A08_4_0.497018CF
TC00284699_K17

value: 6h exposure of 0.4970179 uM of MCF7_HTTr_Water_Sample_8

value: Wastewater


title: day235_BCL2_rep4

value: Spleen

value: Germinal center B cell


title: DNAse_NC Brgf/f mice hepatocytes Dnase #6 KO Rep.3

value: Hepatocytes

value: Brg1f/f, Alb-Cre


title: miRNA CX_wt_crush_156

description: cortex, nerve-injured, miRNA, biol rep6

value: Left cortex

value: male

value: 12 weeks post injury


title: EP000004A06_3_0.149731CF_TC00284699_K05

description:
EP000004A06_3_0.149731CF
TC00284699_K05

value: 6h exposure of 0.1497305 uM of MCF7_HTTr_Water_Sample_6