title: potassium chloride_3_10d_3pool2_S236

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S236


title: potassium chloride_3_24h_4pool2_S140

status: Public on Feb 17 2025

type: SRA

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S140

library_source: other

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using bcl2fastq v2.20.0.422.
FASTQ files were aligned to the Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences (provided by BioSpyder) using STAR 2.7.8a.
The qCount function from QuasR was used to extract feature counts specified in a GTF file (provided by BioSpyder) from the aligned reads.
Assembly: Human Surrogate+ Tox Panel (S1500+) v2.0 probes reference sequences (provided by BioSpyder)
Supplementary files format and content: Comma-delimited table containing read counts per TempO-Seq probe

molecule: other

organism: Homo sapiens

source_name: liver spheroids

growth_protocol: 3D InSight™ Human Liver Microtissues were purchased from InSphero (Wagistrasse, Schlieren, Switzerland) in a 96-well plate format, with a single spheroid per well. The liver spheroids are a co-culture from ten human liver donors and include primarily hepatocytes and Kupffer cells. Upon receipt of spheroids, media were removed and replaced with fresh media (InSphero Human Liver Maintenance Medium–Tox). The Human Liver Maintenance Medium–Tox is optimized for maintenance of phase I metabolism and does not contain additives or serum. Spheroids were acclimated for 24h prior to chemical exposures.

extract_protocol:
At the 24h and 10d time points media were removed, and spheroids were washed with Dulbecco's phosphate-buffered saline (DPBS; Thermo Fisher Scientific Waltham, MA). Spheroids were lysed by adding 10 µl of 1X TempO-Seq lysis buffer (BioSpyder Technologies Inc Carlsbad, CA) to each well. To ensure complete lysis, spheroids were incubated for approximately 10 minutes at 37°C, pipetted up and down several times, and then frozen at -80 °C until library building.
Lysates and technical RNA were hybridized to the detector oligo mix following the manufacturer's instructions provided in the TEMPO-SEQ Human Tox + Surrogate with Standard Attenuation Transcriptome Kit (96 samples). This was followed by nuclease digestion to eliminate excess oligos, detector oligo ligation, and subsequent amplification of correctly ligated oligos, all performed in accordance with the manufacturer's guidelines.
During the amplification stage, each sample was linked to a sample-specific barcode, enabling the pooling of samples for sequencing purposes. Pooled samples were purified using NucleoSpin Gel and PCR clean-up kits from Takara Bio USA, Inc. (Mountain View, CA). The libraries were sequenced in-house using a NextSeq 500 High-Throughput Sequencing System (Illumina, San Diego, California), employing a 50-cycle protocol from a 75-cycle high-throughput flow cell.

treatment_protocol: Spheroids were cultured under sterile conditions with incubation at 37°C, 5% CO2 as per the manufacturer’s instructions. Liver spheroids were exposed for 24h or 10d to compounds and solvent control (0.1% DMSO or water). Culture media (containing the compounds) were replenished every 3 days. Compound exposure concentrations are in Table 1. Each concentration range was run on four parallel plates (for N = 4).

tag: cell line

value: liver spheroids

tag: chemical

value: potassium chloride

tag: dose

tag: timepoint

tag: replicate


title: sucrose_3_10d_4pool2_S324

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S324

value: sucrose


title: sucrose_3_10d_3pool2_S228

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S228


title: sucrose_3_24h_4pool2_S132

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S132


title: sucrose_3_24h_3pool2_S36

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S36


title: potassium chloride_3_24h_3pool2_S44

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S44


title: acetaminophen_5_24h_3pool2_S5

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S5

value: acetaminophen


title: caffeine_1_10d_4pool2_S316

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S316

value: caffeine


title: cyclosporin A_0.1_24h_4pool2_S116

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S116

value: cyclosporin A


title: cyclosporin A_0.1_10d_3pool2_S212

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S212


title: caffeine_1_24h_4pool2_S124

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S124


title: caffeine_1_10d_3pool2_S220

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S220


title: estradiol_0.0001_10d_3pool2_S252

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S252

value: estradiol


title: cyclosporin A_0.1_24h_3pool2_S20

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S20


title: benzo[a]pyrene_0.03_24h_4pool2_S108

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S108

value: benzo[a]pyrene


title: benzo[a]pyrene_0.03_10d_4pool2_S300

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S300


title: estradiol_0.0001_24h_4pool2_S156

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S156


title: benzo[a]pyrene_0.03_10d_3pool2_S204

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S204


title: troglitazone_0.1_10d_3pool2_S284

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S284

value: troglitazone


title: troglitazone_0.1_24h_3pool2_S92

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S92


title: benzo[a]pyrene_0.03_24h_3pool2_S12

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S12


title: troglitazone_0.1_24h_4pool2_S188

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S188


title: troglitazone_0.1_10d_4pool2_S380

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S380


title: aflatoxin B1_1_10d_4pool2_S364

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S364

value: aflatoxin B1


title: rosiglitazone_0.1_24h_3pool2_S84

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S84

value: rosiglitazone


title: rosiglitazone_0.1_10d_4pool2_S372

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S372


title: aflatoxin B1_1_10d_3pool2_S268

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S268


title: aflatoxin B1_1_24h_4pool2_S172

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S172


title: cyclosporin A_0.1_10d_4pool2_S308

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S308


title: rosiglitazone_0.1_10d_3pool2_S276

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S276


title: acetaminophen_50_24h_4pool2_S100

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S100


title: aflatoxin B1_1_24h_3pool2_S76

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S76


title: acetaminophen_50_10d_3pool2_S196

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S196


title: acetaminophen_50_10d_4pool2_S292

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S292


title: acetaminophen_50_24h_3pool2_S4

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S4


title: WY-14643_10_10d_4pool2_S355

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S355


title: WY-14643_10_24h_4pool2_S163

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S163


title: WY-14643_10_24h_3pool2_S67

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S67


title: WY-14643_10_10d_3pool2_S259

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S259


title: estradiol_0.001_10d_4pool2_S347

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S347


title: estradiol_0.001_24h_4pool2_S155

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S155


title: caffeine_1_24h_3pool2_S28

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S28


title: valproic acid_10_10d_3pool2_S243

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S243

value: valproic acid


title: valproic acid_10_24h_4pool2_S147

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S147


title: estradiol_0.001_24h_3pool2_S59

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S59


title: valproic acid_10_10d_4pool2_S339

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S339


title: valproic acid_10_24h_3pool2_S51

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S51


title: estradiol_0.001_10d_3pool2_S251

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S251


title: potassium chloride_30_10d_4pool2_S331

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S331


title: rosiglitazone_0.1_24h_4pool2_S180

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S180


title: potassium chloride_30_10d_3pool2_S235

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S235


title: potassium chloride_30_24h_4pool2_S139

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S139


title: potassium chloride_30_24h_3pool2_S43

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S43


title: sucrose_30_10d_4pool2_S323

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S323


title: sucrose_30_24h_4pool2_S131

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S131


title: sucrose_30_24h_3pool2_S35

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S35


title: caffeine_10_10d_4pool2_S315

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S315


title: caffeine_10_10d_3pool2_S219

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S219


title: caffeine_10_24h_4pool2_S123

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S123


title: cyclosporin A_1_10d_3pool2_S211

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S211


title: cyclosporin A_1_24h_4pool2_S115

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S115


title: cyclosporin A_1_10d_4pool2_S307

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S307


title: caffeine_10_24h_3pool2_S27

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S27


title: cyclosporin A_1_24h_3pool2_S19

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S19


title: benzo[a]pyrene_0.3_10d_4pool2_S299

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S299


title: benzo[a]pyrene_0.3_10d_3pool2_S203

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S203


title: benzo[a]pyrene_0.3_24h_4pool2_S107

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S107


title: benzo[a]pyrene_0.3_24h_3pool2_S11

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S11


title: troglitazone_1_10d_4pool2_S379

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S379


title: troglitazone_1_10d_3pool2_S283

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S283


title: troglitazone_1_24h_4pool2_S187

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S187


title: rosiglitazone_1_10d_4pool2_S371

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S371


title: rosiglitazone_1_10d_3pool2_S275

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S275


title: troglitazone_1_24h_3pool2_S91

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S91


title: rosiglitazone_1_24h_4pool2_S179

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S179


title: sucrose_30_10d_3pool2_S227

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S227


title: acetaminophen_500_10d_3pool2_S195

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S195


title: aflatoxin B1_10_10d_3pool2_S267

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S267


title: acetaminophen_500_10d_4pool2_S291

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S291


title: aflatoxin B1_10_10d_4pool2_S363

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S363


title: aflatoxin B1_10_24h_3pool2_S75

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S75


title: acetaminophen_500_24h_4pool2_S99

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S99


title: acetaminophen_500_24h_3pool2_S3

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S3


title: aflatoxin B1_10_24h_4pool2_S171

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S171


title: WY-14643_100_10d_4pool2_S354

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S354


title: WY-14643_100_10d_3pool2_S258

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S258


title: WY-14643_100_24h_4pool2_S162

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S162


title: estradiol_0.01_24h_4pool2_S154

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S154


title: WY-14643_100_24h_3pool2_S66

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S66


title: estradiol_0.01_10d_3pool2_S250

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S250


title: estradiol_0.01_24h_3pool2_S58

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S58


title: valproic acid_100_10d_4pool2_S338

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S338


title: valproic acid_100_10d_3pool2_S242

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S242


title: estradiol_0.01_10d_4pool2_S346

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S346


title: valproic acid_100_24h_4pool2_S146

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S146


title: valproic acid_100_24h_3pool2_S50

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S50


title: potassium chloride_300_10d_4pool2_S330

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S330


title: potassium chloride_300_10d_3pool2_S234

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S234


title: rosiglitazone_1_24h_3pool2_S83

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S83


title: potassium chloride_300_24h_3pool2_S42

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S42


title: sucrose_300_10d_3pool2_S226

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S226


title: sucrose_300_24h_3pool2_S34

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S34


title: sucrose_300_10d_4pool2_S322

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S322


title: sucrose_300_24h_4pool2_S130

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S130


title: caffeine_100_10d_3pool2_S218

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S218


title: cyclosporin A_10_10d_3pool2_S210

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S210


title: caffeine_100_10d_4pool2_S314

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S314


title: cyclosporin A_10_24h_4pool2_S114

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S114


title: caffeine_100_24h_4pool2_S122

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S122


title: cyclosporin A_10_10d_4pool2_S306

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S306


title: benzo[a]pyrene_3_10d_4pool2_S298

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S298


title: benzo[a]pyrene_3_24h_4pool2_S106

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S106


title: benzo[a]pyrene_3_24h_3pool2_S10

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S10


title: benzo[a]pyrene_3_10d_3pool2_S202

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S202


title: troglitazone_10_24h_3pool2_S90

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S90


title: troglitazone_10_24h_4pool2_S186

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S186


title: troglitazone_10_10d_3pool2_S282

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S282


title: rosiglitazone_10_10d_3pool2_S274

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S274


title: rosiglitazone_10_10d_4pool2_S370

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S370


title: troglitazone_10_10d_4pool2_S378

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S378


title: rosiglitazone_10_24h_4pool2_S178

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S178


title: potassium chloride_300_24h_4pool2_S138

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S138


title: aflatoxin B1_100_10d_3pool2_S266

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S266


title: aflatoxin B1_100_10d_4pool2_S362

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S362


title: aflatoxin B1_100_24h_4pool2_S170

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S170


title: rosiglitazone_10_24h_3pool2_S82

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S82


title: aflatoxin B1_100_24h_3pool2_S74

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S74


title: caffeine_100_24h_3pool2_S26

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S26


title: media only_0_10d_4pool2_S353

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S353

value: media only


title: acetaminophen_5000_24h_4pool2_S98

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S98


title: acetaminophen_5000_24h_3pool2_S2

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S2


title: acetaminophen_5000_10d_4pool2_S290

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S290


title: acetaminophen_5000_10d_3pool2_S194

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S194


title: cyclosporin A_10_24h_3pool2_S18

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S18


title: media only_0_10d_3pool2_S257

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S257


title: media only_0_24h_4pool2_S161

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S161


title: media only_0_24h_4pool2_S153

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S153


title: media only_0_24h_3pool2_S65

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S65


title: media only_0_24h_3pool2_S57

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S57


title: media only_0_10d_4pool2_S337

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S337


title: media only_0_10d_4pool2_S345

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S345


title: media only_0_10d_3pool2_S241

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S241


title: media only_0_24h_3pool2_S49

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S49


title: DMSO_0_10d_3pool2_S233

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S233

value: DMSO


title: DMSO_0_24h_4pool2_S137

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S137


title: DMSO_0_24h_3pool2_S41

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S41


title: DMSO_0_24h_4pool2_S129

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S129


title: DMSO_0_24h_3pool2_S33

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S33


title: DMSO_0_10d_3pool2_S217

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S217


title: DMSO_0_24h_4pool2_S121

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S121


title: DMSO_0_24h_3pool2_S25

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S25


title: DMSO_0_10d_3pool2_S209

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S209


title: DMSO_0_24h_3pool2_S17

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S17


title: DMSO_0_10d_4pool2_S297

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S297


title: DMSO_0_24h_4pool2_S113

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S113


title: DMSO_0_10d_3pool2_S201

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S201


title: DMSO_0_24h_3pool2_S9

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S9


title: DMSO_0_24h_4pool2_S105

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S105


title: DMSO_0_10d_4pool2_S305

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S305


title: negative control_0_10d_3pool2_S281

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S281

value: negative control


title: media only_0_24h_4pool2_S145

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S145


title: universal human reference RNA_0_10d_4pool2_S369

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S369

value: universal human reference RNA


title: universal human reference RNA_0_10d_3pool2_S273

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S273


title: negative control_0_24h_4pool2_S185

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S185


title: negative control_0_24h_3pool2_S89

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S89


title: media only_0_10d_3pool2_S249

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S249


title: DMSO_0_10d_4pool2_S329

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S329


title: DMSO_0_10d_3pool2_S225

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S225


title: DMSO_0_10d_4pool2_S321

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S321


title: universal human reference RNA_0_24h_3pool2_S81

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S81


title: DMSO_0_10d_4pool2_S313

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S313


title: human brain RNA_0_10d_4pool2_S361

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S361

value: human brain RNA


title: universal human reference RNA_0_24h_4pool2_S177

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S177

value: liver spheroids


title: DMSO_0_10d_4pool2_S289

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S289


title: human brain RNA_0_24h_4pool2_S169

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S169


title: human brain RNA_0_24h_3pool2_S73

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S73


title: DMSO_0_10d_3pool2_S193

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S193


title: DMSO_0_24h_4pool2_S97

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S97


title: negative control_0_10d_4pool2_S377

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S377


title: DMSO_0_24h_3pool2_S1

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S1


title: DMSO_0_10d_2pool1_S360

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S360


title: water_0_10d_1pool1_S256

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S256

value: water


title: DMSO_0_24h_2pool1_S168

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S168


title: water_0_24h_2pool1_S160

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S160


title: water_0_24h_1pool1_S64

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S64


title: DMSO_0_24h_1pool1_S72

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S72


title: water_0_10d_2pool1_S352

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S352


title: DMSO_0_10d_1pool1_S264

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S264


title: water_0_10d_2pool1_S344

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S344


title: human brain RNA_0_10d_3pool2_S265

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S265


title: water_0_10d_2pool1_S336

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S336


title: water_0_24h_1pool1_S56

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S56


title: water_0_24h_1pool1_S48

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S48


title: water_0_10d_1pool1_S232

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S232


title: water_0_10d_1pool1_S248

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S248


title: water_0_10d_1pool1_S240

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S240


title: water_0_24h_1pool1_S40

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S40


title: water_0_10d_2pool1_S328

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S328


title: water_0_10d_2pool1_S320

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S320


title: water_0_24h_2pool1_S144

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S144


title: water_0_10d_1pool1_S224

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S224


title: water_0_24h_2pool1_S128

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S128


title: water_0_10d_1pool1_S216

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S216


title: water_0_10d_2pool1_S312

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S312


title: water_0_24h_2pool1_S120

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S120


title: water_0_24h_1pool1_S32

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S32


title: water_0_10d_2pool1_S304

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S304


title: water_0_10d_1pool1_S208

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S208


title: water_0_24h_1pool1_S24

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S24


title: water_0_24h_2pool1_S112

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S112


title: water_0_24h_1pool1_S16

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S16


title: DMSO_0_10d_1pool1_S288

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S288


title: DMSO_0_24h_2pool1_S192

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S192


title: DMSO_0_10d_2pool1_S376

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S376


title: water_0_24h_2pool1_S152

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S152


title: DMSO_0_10d_2pool1_S384

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S384


title: DMSO_0_24h_2pool1_S184

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S184


title: water_0_24h_2pool1_S136

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S136


title: DMSO_0_10d_1pool1_S272

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S272


title: DMSO_0_24h_2pool1_S176

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S176


title: water_0_10d_2pool1_S296

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S296


title: DMSO_0_24h_1pool1_S80

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S80


title: DMSO_0_24h_1pool1_S88

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S88


title: DMSO_0_10d_1pool1_S280

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S280


title: WY-14643_0.001_10d_2pool1_S359

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S359


title: water_0_10d_1pool1_S200

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S200


title: WY-14643_0.001_10d_1pool1_S263

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S263


title: estradiol_0.0000001_10d_2pool1_S351

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S351


title: water_0_24h_2pool1_S104

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S104


title: estradiol_0.0000001_24h_2pool1_S159

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S159


title: estradiol_0.0000001_24h_1pool1_S63

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S63


title: DMSO_0_24h_1pool1_S96

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S96


title: valproic acid_0.001_10d_2pool1_S343

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S343


title: valproic acid_0.001_10d_1pool1_S247

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S247


title: valproic acid_0.001_24h_2pool1_S151

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S151


title: potassium chloride_0.003_10d_2pool1_S335

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S335

value: potassium chloride


title: potassium chloride_0.003_10d_1pool1_S239

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S239


title: potassium chloride_0.003_24h_2pool1_S143

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S143


title: potassium chloride_0.003_24h_1pool1_S47

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S47


title: DMSO_0_10d_2pool1_S368

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S368


title: valproic acid_0.001_24h_1pool1_S55

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S55


title: sucrose_0.003_10d_2pool1_S327

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S327

value: sucrose


title: sucrose_0.003_10d_1pool1_S231

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S231


title: caffeine_0.001_10d_2pool1_S319

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S319

value: caffeine


title: water_0_24h_1pool1_S8

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S8


title: sucrose_0.003_24h_1pool1_S39

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S39


title: caffeine_0.001_10d_1pool1_S223

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S223


title: WY-14643_0.001_24h_2pool1_S167

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S167


title: WY-14643_0.001_24h_1pool1_S71

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S71


title: caffeine_0.001_24h_1pool1_S31

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S31


title: estradiol_0.0000001_10d_1pool1_S255

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S255


title: cyclosporin A_0.0001_10d_1pool1_S215

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S215

value: cyclosporin A


title: cyclosporin A_0.0001_24h_2pool1_S119

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S119


title: cyclosporin A_0.0001_10d_2pool1_S311

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S311


title: sucrose_0.003_24h_2pool1_S135

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S135


title: benzo[a]pyrene_0.00003_10d_2pool1_S303

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S303


title: benzo[a]pyrene_0.00003_10d_1pool1_S207

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S207


title: caffeine_0.001_24h_2pool1_S127

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S127


title: cyclosporin A_0.0001_24h_1pool1_S23

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S23


title: benzo[a]pyrene_0.00003_24h_2pool1_S111

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S111


title: benzo[a]pyrene_0.00003_24h_1pool1_S15

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S15


title: troglitazone_0.0001_10d_2pool1_S383

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S383


title: troglitazone_0.0001_10d_1pool1_S287

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S287


title: troglitazone_0.0001_24h_2pool1_S191

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S191


title: rosiglitazone_0.0001_10d_2pool1_S375

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S375


title: rosiglitazone_0.0001_24h_2pool1_S183

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S183


title: rosiglitazone_0.0001_24h_1pool1_S87

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S87


title: aflatoxin B1_0.001_10d_2pool1_S367

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S367


title: aflatoxin B1_0.001_10d_1pool1_S271

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S271


title: aflatoxin B1_0.001_24h_2pool1_S175

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S175


title: acetaminophen_0.05_10d_2pool1_S295

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S295

value: acetaminophen


title: aflatoxin B1_0.001_24h_1pool1_S79

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S79


title: acetaminophen_0.05_10d_1pool1_S199

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S199


title: acetaminophen_0.05_24h_2pool1_S103

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S103


title: WY-14643_0.01_10d_2pool1_S358

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S358


title: acetaminophen_0.05_24h_1pool1_S7

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S7


title: WY-14643_0.01_10d_1pool1_S262

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S262


title: WY-14643_0.01_24h_2pool1_S166

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S166


title: troglitazone_0.0001_24h_1pool1_S95

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S95


title: rosiglitazone_0.0001_10d_1pool1_S279

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S279


title: WY-14643_0.01_24h_1pool1_S70

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S70


title: estradiol_0.000001_10d_2pool1_S350

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S350

value: estradiol


title: estradiol_0.000001_10d_1pool1_S254

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S254


title: hiPSCs-CMs LMNA corr.H222P Rep3

city: Paris

first: Marie

last: Kervella

address: 105 boulevard de l'Hôpital

country: France

institute: Inserm

description: Library name: sample 5

library_source: transcriptomic

data_processing:
Reads were pre-processed using fastp module v0.20.0 and aligned on GRCh38 human or GRCm39 mouse reference genome using star v2.7.5a. Pairs of reads aligned were annotated using gtf annotation files provided by ENSEMBL. Genome-aligned reads were indexed with samtools v1.13 and quantified with qualimap v2.2.2b. The number of reads uniquely mapping coding RNA was compiled in a counting matrix using featureCounts v2.0.1. All steps were submitted to quality control using mutliqc v1.13. Differential analysis was performed using the DESeq2 package on R.
Assembly: GRCh38 human or GRCm39 mouse reference genome
Supplementary files format and content: csv files including differential expression analysis data

molecule: total RNA

source_name: cell line

extract_protocol:
Cell pellet were collected and RNA were extracted using following Qiagen Rneasy Mini Kit protocol. RNA were collected from heart sections using trizol/chloroform solution and purified on column.
Library were constructed by iGenSeq Plateform of the Brain Insitute (Paris, France) using the TruSeq stranded total RNA library preparation kit, including depletion of RNA (Illumina Inc.)

tag: tissue

value: cell line

value: hiPSCs-CMs corr.LMNA p.H222P

tag: cell type

value: human induced pluripotent stem cells-derived cardiomyocytes

tag: genotype

value: LMNA corr.H222P


title: hiPSCs-CMs LMNA corr.H222P Rep2

description: Library name: sample 4


title: estradiol_0.000001_24h_2pool1_S158

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S158


title: hiPSCs-CMs LMNA corr.H222P Rep1

description: Library name: sample 3


title: estradiol_0.000001_24h_1pool1_S62

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S62


title: valproic acid_0.01_10d_2pool1_S342

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S342

value: valproic acid


title: hiPSCs-CMs LMNA H222P Rep1

description: Library name: sample 1

value: hiPSCs-CMs LMNA p.H222P

value: LMNA p.H222P


title: valproic acid_0.01_24h_2pool1_S150

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S150


title: Genomic DNA from untreated Jurkat-TetOFF transfected with Tat72 construct replicate 3

type: genomic

city: Majadahonda

first: Ruben

last: Ayala-Suárez

state: Madrid

address: Crta Pozuelo Km 2

department: AIDS Immunopathology Unit

country: Spain

institute: Instituto de Salud Carlos III

hyb_protocol: Bisulfite converted DNA was hybrized to Infinium Methylation EPIC array v 1.0.

scan_protocol: Arrays were imaged in a HISCanSQ Analysis System (Illumina) with standard Illumina recommended settings.

data_processing: Methylation data analysis was performed with the EPIPE methylation analysis pipeline (https://github.com/ijcBIT/epipe). Raw DNA methylation data was processed using the minfi R-package that applies background correction, dye-bias normalization (Noob method selected), and estimates signal detection. Probes with low signal (p-value > 0.01), located in non-CpG methylation positions, positions annotated as single nucleotide polymorphism, or CpG located at sex chromosomes were removed.  Linear models were used for differential methylation analysis using the Limma R package and the Benjamini-Hochberg corrected false discovery rate (FDR) was used to adjust p-values after multiple testing.

label: Cy3 and Cy5

molecule: genomic DNA

source_name: Jurkat TetOFF (Clontech)

label_protocol: 600 ng of DNA quantified by Quant-iT™ PicoGreen™ (Invitrogen) was used for bisulfite conversion with the EZ DNA Methylation kit (Zymo Research). An incubation of 16 cycles of (95ºC 30 + 50ºC 1h) was performed.

growth_protocol: Cells were cultured in RPMI 1640 medium with L-glutamine supplemented with 10 % (v/v) fetal bovine serum (FBS), 100 μg/ml streptomycin, and 100 U/ml penicillin at 37ºC and 5% CO2

extract_protocol: Genomic DNA from the different cell lines was isolated with a QIAamp DNA Mini Kit (Qiagen) following the manufacturer’s instructions.

value: Jurkat TetOFF (Clontech)

tag: transfection

value: pTRE2hyg + Tat72

tag: treatment

value: No


title: Patient 10+Nintedanib

city: Ann Arbor

first: Priyanka

last: Verma

state: MI

address: 2800 Plymouth Rd,

country: USA

institute: University of Michigan

description: Library name: 11979-PV-4

data_processing:
University of Michigan Bioinformatics Core RNA-seq pipeline "Watermelon" version 2.4.4
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt v2.3.
FastQC v0.11.8 was used to ensure the quality of data
Trimmed sequence reads were mapped to GRCh38/hs19 using STAR v2.7.8a
Quantitative count estimates to genes performed with RSEM v1.3.3
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that includes raw count data from each sample

molecule: polyA RNA

source_name: 3D skin orgonids with fibroblast and keratinocytes

growth_protocol: SSc and Healthy fibroblast were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C. Keratinocytes were cultured in Dermal Cell Basal Medium (ATCC PCS-200-030) supplemented with the Keratinocyte Growth Kit (ATCC PCS-200-040). 3D skin orgoinds  were maintained in E  media.

extract_protocol:
RNA was isolated using the Qiagen miRNAeasy Micro Kit
RNA libraries for RNA-seq were prepared using Ilumina paltform via poly A enrichment method following manufacturer's protocols.

treatment_protocol: 3D skin organoids were treated with either Nintedanib (2uM) or vehicle every day.

value: Fibroblast + keratinocytes

value: Patient 10+Nintedanib


title: Genomic DNA from Jurkat TetOFF transfected with Tat72 construct exposed to 48h doxycycline replicate 2

value: Doxycycline 48h


title: Genomic DNA from untreated Jurkat-TetOFF transfected with Tat72 construct replicate 2


title: hiPSCs-CMs LMNA H222P Rep2

description: Library name: sample 2


title: Patient 9+Nintedanib

description: Library name: 11979-PV-2

value: 3D skin orgonids with fibroblast and keratinocytes

value: Patient 9+Nintedanib


title: Genomic DNA from Jurkat TetOFF transfected with Tat72 construct exposed to 48h doxycycline replicate 1


title: valproic acid_0.01_10d_1pool1_S246

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S246

value: liver spheroids


title: Patient 10

description: Library name: 11979-PV-3

value: Patient 10


title: Genomic DNA from untreated Jurkat-TetOFF transfected with Tat72 construct replicate 1


title: Patient 8

description: Library name: 11501-PV-23

value: Patient 8


title: valproic acid_0.01_24h_1pool1_S54

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S54


title: potassium chloride_0.03_10d_2pool1_S334

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S334

value: potassium chloride


title: Patient 9

description: Library name: 11979-PV-1

value: Patient 9


title: potassium chloride_0.03_10d_1pool1_S238

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S238


title: potassium chloride_0.03_24h_1pool1_S46

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S46


title: Genomic DNA from Jurkat TetOFF transfected with Tat101 construct exposed to 48h doxycycline replicate 1

value: pTRE2hyg + Tat101


title: Genomic DNA from untreated Jurkat-TetOFF transfected with Tat101 construct replicate 3


title: Genomic DNA from Jurkat TetOFF transfected with Tat101 construct exposed to 48h doxycycline replicate 3


title: Patient 8+Nintedanib

description: Library name: 11501-PV-24

value: Patient 8+Nintedanib


title: Genomic DNA from Jurkat TetOFF transfected with empty vector exposed to 48h doxycycline replicate 2

value: pTRE2hyg empty plasmid


title: Genomic DNA from untreated Jurkat-TetOFF transfected with Tat101 construct replicate 2


title: potassium chloride_0.03_24h_2pool1_S142

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S142


title: Patient 7+Nintedanib

description: Library name: 11501-PV-22

value: Patient 7+Nintedanib


title: Genomic DNA from untreated Jurkat-TetOFF transfected with Tat101 construct replicate 1

value: Jurkat TetOFF (Clontech)


title: sucrose_0.03_10d_1pool1_S230

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S230

value: sucrose


title: Patient 7

description: Library name: 11501-PV-21

value: Patient 7


title: Genomic DNA from untreated Jurkat TetOFF transfected with empty vector replicate 3

value: No


title: sucrose_0.03_10d_2pool1_S326

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S326


title: Genomic DNA from untreated Jurkat TetOFF transfected with empty vector replicate 2


title: Genomic DNA from Jurkat TetOFF transfected with empty vector exposed to 48h doxycycline replicate 1


title: sucrose_0.03_24h_2pool1_S134

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S134


title: Healthy 6

description: Library name: 11501-PV-19

value: Fibroblast + keratinocytes

value: Healthy 6


title: Healthy 6+ Nintedanib

description: Library name: 11501-PV-20

value: 3D skin orgonids with fibroblast and keratinocytes

value: Healthy 6+ Nintedanib


title: Genomic DNA from untreated Jurkat TetOFF transfected with empty vector replicate 1


title: Genomic DNA from Jurkat TetOFF transfected with Tat101 construct exposed to 48h doxycycline replicate 2

value: Doxycycline 48h


title: sucrose_0.03_24h_1pool1_S38

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S38

value: liver spheroids


title: caffeine_0.01_10d_2pool1_S318

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S318

value: caffeine


title: Healthy 5+ Nintedanib

description: Library name: 11501-PV-18

value: Healthy 5+ Nintedanib


title: Healthy 3

description: Library name: 11501-PV-13

value: Healthy 3


title: caffeine_0.01_24h_2pool1_S126

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S126


title: caffeine_0.01_10d_1pool1_S222

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S222


title: caffeine_0.01_24h_1pool1_S30

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S30


title: Patient 6+Nintedanib

description: Library name: 11501-PV-12

value: Patient 6+Nintedanib


title: Healthy 3+ Nintedanib

description: Library name: 11501-PV-14

value: Healthy 3+ Nintedanib


title: cyclosporin A_0.001_10d_2pool1_S310

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S310

value: cyclosporin A


title: Patient 5+Nintedanib

description: Library name: 11501-PV-10

value: Patient 5+Nintedanib


title: cyclosporin A_0.001_10d_1pool1_S214

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S214


title: Patient 5

description: Library name: 11501-PV-9

value: Patient 5


title: cyclosporin A_0.001_24h_2pool1_S118

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S118


title: cyclosporin A_0.001_24h_1pool1_S22

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S22


title: Patient 4+ Nintedanib

description: Library name: 8827-PV-18

value: Patient 4+ Nintedanib


title: benzo[a]pyrene_0.0003_10d_1pool1_S206

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S206

value: benzo[a]pyrene


title: Patient 4

description: Library name: 8827-PV-17

value: Patient 4


title: Patient 3+ Nintedanib

description: Library name: 8827-PV-16

value: Fibroblast + keratinocytes

value: Patient 3+ Nintedanib


title: Healthy 2+ Nintedanib

description: Library name: 8827-PV-10

value: 3D skin orgonids with fibroblast and keratinocytes

value: Healthy 2+ Nintedanib


title: benzo[a]pyrene_0.0003_24h_1pool1_S14

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S14


title: Patient 3

description: Library name: 8827-PV-15

value: Patient 3


title: troglitazone_0.001_10d_1pool1_S286

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S286

value: liver spheroids

value: troglitazone


title: Healthy 2

description: Library name: 8827-PV-9

value: Healthy 2


title: Healthy 1

description: Library name: 8827-PV-7

value: Healthy 1


title: troglitazone_0.001_24h_2pool1_S190

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S190


title: Patient 6

description: Library name: 11501-PV-11

value: Patient 6


title: Healthy 1+ Nintedanib

description: Library name: 8827-PV-8

value: Healthy 1+ Nintedanib


title: rosiglitazone_0.001_10d_2pool1_S374

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S374

value: rosiglitazone


title: troglitazone_0.001_24h_1pool1_S94

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S94


title: Patient 2

description: Library name: 8827-PV-5

value: Patient 2


title: Patient 1+ Nintedanib

description: Library name: 8827-PV-2

value: Patient 1+ Nintedanib


title: Patient 2+ Nintedanib

description: Library name: 8827-PV-6

value: Patient 2+ Nintedanib


title: rosiglitazone_0.001_24h_2pool1_S182

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S182


title: Patient 1

description: Library name: 8827-PV-1

value: Patient 1


title: benzo[a]pyrene_0.0003_10d_2pool1_S302

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S302

value: benzo[a]pyrene


title: aflatoxin B1_0.01_10d_2pool1_S366

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S366

value: aflatoxin B1


title: DISC1-Z3

city: Shenzhen

first: Shengze

last: Zhang

state: Guangdong

address: No. 66, Gongchang Road

country: China

institute: Sun Yat-sen University

description: Library name: sample6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.26.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with FDR < 0.05  expressed &|log2（foldchange）| ≥1 found by DESeq2 were assigned as differentially
Assembly: GRCh38
Supplementary files format and content: This table contains the RNA count and normalized FPKM values for each sample.

source_name: Brain

extract_protocol:
Total RNA was isolated using TRIZOL reagent. The purity and quantity of the total RNA were assessed using the NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA).The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Brain

value: Pleomorphic/astrocytoid


title: DISC1-Z1

description: Library name: sample4


title: pcDNA-Z2

description: Library name: sample2


title: pcDNA-Z3

description: Library name: sample3


title: aflatoxin B1_0.01_24h_2pool1_S174

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S174


title: aflatoxin B1_0.01_10d_1pool1_S270

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S270


title: benzo[a]pyrene_0.0003_24h_2pool1_S110

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S110


title: aflatoxin B1_0.01_24h_1pool1_S78

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S78


title: acetaminophen_0.5_10d_2pool1_S294

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S294

value: acetaminophen


title: troglitazone_0.001_10d_2pool1_S382

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S382


title: acetaminophen_0.5_24h_1pool1_S6

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S6


title: rosiglitazone_0.001_24h_1pool1_S86

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S86


title: DISC1-Z2

description: Library name: sample5


title: acetaminophen_0.5_10d_1pool1_S198

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S198


title: late stage of differentiation_3D_6

city: Milan

first: Santo

last: Diprima

address: Via Olgettina 58

department: COSR

country: Italy

institute: San Raffaele Hospital

description: Library name: RBC20_3D

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.39)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using featureCounts.
Assembly: UCSC hg38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

source_name: blood

growth_protocol: Samplers were cultured in the presence of Stem Span medium (StemCell Technologies) supplemented with penicillin-streptomycin, L-glutamine, Interleukin-3, erythropoietin, and holo-transferrin.

extract_protocol:
Nucleic acid extraction and purification were performed by RNA Extraction Kit (Qiagen).
500 picogram RNA was used from each sample for cDNA generation using the Takara Smart-Seq v4 Ultra Low Input RNA kit (Takara Bio USA) following manufacturer’s instructions, with 15 cycles of cDNA amplification. Starting from 500 cDNA picogram, libraries were prepared through DNA library prep Illumina kit (Illumina), following manufacturer’s instructions.

value: blood

value: hematopoietic progenitors cells


title: late stage of differentiation_2D_5

description: Library name: RBC20_2D


title: late stage of differentiation_3D_4

description: Library name: RBC17_3D


title: rosiglitazone_0.001_10d_1pool1_S278

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S278

value: liver spheroids


title: late stage of differentiation_2D_3

description: Library name: RBC17_2D


title: pcDNA-Z1

description: Library name: sample1


title: WY-14643_0.1_10d_2pool1_S357

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S357


title: acetaminophen_0.5_24h_2pool1_S102

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S102


title: early stage of differentiation_2D_7

description: Library name: RBC7_2D


title: WY-14643_0.1_10d_1pool1_S261

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S261


title: WY-14643_0.1_24h_2pool1_S165

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S165


title: WY-14643_0.1_24h_1pool1_S69

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S69


title: early stage of differentiation_3D_2

description: Library name: RBC14_3D


title: estradiol_0.00001_10d_2pool1_S349

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S349

value: estradiol


title: early stage of differentiation_3D_8

description: Library name: RBC7_3D


title: estradiol_0.00001_10d_1pool1_S253

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S253


title: estradiol_0.00001_24h_2pool1_S157

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S157


title: neutrophil,HC,biol rep 28

city: Shijiazhuang

first: Huining

address: Academician Building, The Second Hospital of Hebei Medical University, No. 215 West Heping Road, Xinhua District, Shijiazhuang City, Hebei Province, China

description: Library name: H65

data_processing:
Raw FASTQ files were quality-checked using FastQC (v0.11.9).
Adapters and low-quality reads (Q < 20) were removed using Fastp (v0.20.0).
Cleaned reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.9a), and BAM files were generated.
Gene-level quantification was performed using featureCounts (v2.0.1) to generate gene count tables.
Assembly: GRCh38/hg38
Supplementary files format and content: Processed data includes gene count tables stored as tab-delimited text files
Supplementary files format and content: Normalized gene expression data (TPM or FPKM) is provided as tab-delimited text files.

source_name: peripheral blood neutrophils

growth_protocol: Not applicable. This study used peripheral blood neutrophil samples from humans, and no cell or tissue culture was involved.

extract_protocol:
Peripheral blood neutrophils were isolated using density gradient centrifugation. Total RNA was extracted using the TRIzol reagent according to the manufacturer's instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer with RIN ≥7.
Total RNA was enriched for mRNA using Oligo(dT) magnetic beads, and mRNA was fragmented to a suitable size (~300 bp). The fragmented mRNA was reverse-transcribed into cDNA using random primers. Libraries were constructed using the Illumina TruSeq RNA Library Prep Kit. Library fragment sizes were approximately 300 bp. Libraries were quality-checked using the Agilent 2100 Bioanalyzer before sequencing on the Illumina NovaSeq 6000 platform (paired-end).

treatment_protocol: MS patients did not receive any immunosuppressive or disease-modifying therapies, and healthy controls received no treatment

value: peripheral blood neutrophils

value: primary neutrophils

value: healthy control


title: neutrophil,HC,biol rep 29

institute: Second Hospital of Hebei Medical University

description: Library name: H66


title: neutrophil,HC,biol rep 27

description: Library name: H64


title: early stage of differentiation_2D_1

description: Library name: RBC14_2D


title: valproic acid_0.1_10d_2pool1_S341

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S341

value: valproic acid


title: valproic acid_0.1_24h_1pool1_S53

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S53


title: neutrophil,HC,biol rep 25

description: Library name: H62


title: neutrophil,HC,biol rep 24

description: Library name: H59


title: neutrophil,HC,biol rep 21

description: Library name: H53


title: valproic acid_0.1_10d_1pool1_S245

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S245


title: neutrophil,HC,biol rep 26

description: Library name: H63


title: valproic acid_0.1_24h_2pool1_S149

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S149


title: potassium chloride_0.3_24h_2pool1_S141

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S141

value: potassium chloride


title: neutrophil,HC,biol rep 22

description: Library name: H56


title: neutrophil,HC,biol rep 20

description: Library name: H52


title: neutrophil,HC,biol rep 23

description: Library name: H58


title: potassium chloride_0.3_24h_1pool1_S45

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S45


title: potassium chloride_0.3_10d_1pool1_S237

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S237


title: neutrophil,HC,biol rep 19

description: Library name: H50


title: potassium chloride_0.3_10d_2pool1_S333

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S333


title: neutrophil,HC,biol rep 18

description: Library name: H47


title: sucrose_0.3_10d_2pool1_S325

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S325

value: sucrose


title: sucrose_0.3_24h_2pool1_S133

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S133


title: neutrophil,HC,biol rep 17

description: Library name: H41


title: neutrophil,HC,biol rep 16

description: Library name: H39


title: estradiol_0.00001_24h_1pool1_S61

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S61


title: sucrose_0.3_24h_1pool1_S37

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S37


title: neutrophil,HC,biol rep 15

description: Library name: H34


title: caffeine_0.1_10d_2pool1_S317

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S317

value: caffeine


title: neutrophil,HC,biol rep 14

description: Library name: H33


title: neutrophil,HC,biol rep 13

description: Library name: H32


title: caffeine_0.1_10d_1pool1_S221

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S221


title: neutrophil,HC,biol rep 12

description: Library name: H31


title: caffeine_0.1_24h_1pool1_S29

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S29


title: neutrophil,HC,biol rep 11

description: Library name: H30


title: caffeine_0.1_24h_2pool1_S125

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S125


title: neutrophil,HC,biol rep 10

description: Library name: H29


title: cyclosporin A_0.01_24h_2pool1_S117

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S117

value: cyclosporin A


title: cyclosporin A_0.01_10d_1pool1_S213

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S213


title: neutrophil,HC,biol rep 8

description: Library name: H22


title: benzo[a]pyrene_0.003_10d_2pool1_S301

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S301

value: benzo[a]pyrene


title: neutrophil,HC,biol rep 7

description: Library name: H21


title: neutrophil,HC,biol rep 6

description: Library name: H20


title: benzo[a]pyrene_0.003_10d_1pool1_S205

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S205


title: neutrophil,HC,biol rep 9

description: Library name: H25


title: neutrophil,HC,biol rep 5

description: Library name: H19


title: neutrophil,HC,biol rep 2

description: Library name: H14


title: benzo[a]pyrene_0.003_24h_1pool1_S13

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S13


title: troglitazone_0.01_10d_1pool1_S285

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S285

value: troglitazone


title: troglitazone_0.01_10d_2pool1_S381

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S381


title: neutrophil,HC,biol rep 3

description: Library name: H15


title: sucrose_0.3_10d_1pool1_S229

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S229


title: neutrophil,MS,biol rep 8

description: Library name: M10

value: multiple sclerosis


title: troglitazone_0.01_24h_2pool1_S189

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S189


title: neutrophil,MS,biol rep 7

description: Library name: M09


title: cyclosporin A_0.01_10d_2pool1_S309

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S309


title: troglitazone_0.01_24h_1pool1_S93

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S93


title: neutrophil,MS,biol rep 6

description: Library name: M08


title: neutrophil,MS,biol rep 5

description: Library name: M06


title: rosiglitazone_0.01_10d_1pool1_S277

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S277

value: rosiglitazone


title: rosiglitazone_0.01_24h_2pool1_S181

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S181


title: cyclosporin A_0.01_24h_1pool1_S21

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S21


title: neutrophil,MS,biol rep 3

description: Library name: M03


title: aflatoxin B1_0.1_10d_1pool1_S269

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S269

value: aflatoxin B1


title: aflatoxin B1_0.1_10d_2pool1_S365

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S365


title: neutrophil,HC,biol rep 1

description: Library name: H12


title: neutrophil,MS,biol rep 4

description: Library name: M04


title: neutrophil,MS,biol rep 2

description: Library name: M02


title: neutrophil,MS,biol rep 1

description: Library name: M01


title: aflatoxin B1_0.1_24h_2pool1_S173

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S173


title: benzo[a]pyrene_0.003_24h_2pool1_S109

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S109


title: Healthy 5

description: Library name: 11501-PV-17

value: 3D skin orgonids with fibroblast and keratinocytes

value: Fibroblast + keratinocytes

value: Healthy 5


title: neutrophil,HC,biol rep 4

description: Library name: H17


title: acetaminophen_5_10d_1pool1_S197

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S197

value: liver spheroids

value: acetaminophen


title: acetaminophen_5_10d_2pool1_S293

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S293


title: rosiglitazone_0.01_10d_2pool1_S373

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S373


title: acetaminophen_5_24h_2pool1_S101

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S101


title: WY-14643_1_10d_2pool1_S356

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S356


title: rosiglitazone_0.01_24h_1pool1_S85

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S85


title: WY-14643_1_24h_2pool1_S164

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S164


title: aflatoxin B1_0.1_24h_1pool1_S77

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S77


title: acetaminophen_5_24h_1pool1_S5

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S5


title: Human Pre-adipocytes, empty lentivirus+GFP, differentiated-2

city: ANN ARBOR

first: Tae-Hwa

last: Chun

address: 2800 PLYMOUTH RD, NCRC B10-A186, NCRC B10-A186

department: Internal Medicine

description: Library name: 8811-TC-2

data_processing:
The reads were trimmed using Cutadapt v4.8 (Martin, 2011). The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data. Reads were mapped to the reference genome GRCh38 (ENSEMBL 113), using STAR v2.7.8a (Dobin et al., 2013) and assigned count estimates to genes with RSEM v1.3.3 (Li and Dewey, 2011). Alignment options followed ENCODE standards for RNA-seq (Dobin). QC metrics from several different steps in the pipeline were aggregated by multiQC v1.20 (Ewels et al., 2016).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that includes raw count data from each sample

source_name: HPAd

growth_protocol: Human subcutaneous preadipocytes (Cell Applications # 802s-05a) were cultured in high-glucose Dulbecco's modified Eagle's medium (DMEM, Invitrogen) supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine and 10% fetal bovine serum (Invitrogen, A3160402) at 37oC and 5% CO2.

extract_protocol:
RNA extraction was performed using QIAshredder (Qiagen) and RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions.
RNA-Seq libraries were prepared using NEB Kit following the manufacturer's instructions

treatment_protocol: Three days after reaching confluence, the cells were treated with an adipogenic cocktail consisting of 0.25 μM dexamethasone, 1 μg/ml porcine insulin, and 10 μM rosiglitazone (all obtained from Sigma Chemical Co., St. Louis, MO) for two days. This was followed by two days of insulin treatment, and then two days in DMEM with 10% FBS without insulin prior to RNA extraction.

value: HPAd

value: Human subcutaneous preadipocytes

value: adipogenic differentiation


title: Human Pre-adipocytes, control_no-lentivirus, differentiated-3

description: Library name: 8811-TC-12


title: Human Pre-adipocytes, EBF2-full_lentivirus+GFP, differentiated-2

description: Library name: 8811-TC-8


title: Human Pre-adipocytes, empty lentivirus+GFP, differentiated-3

description: Library name: 8811-TC-3


title: Human Pre-adipocytes, EBF2 (1-164)_lentivirus+GFP, differentiated-1

description: Library name: 8811-TC-4


title: WY-14643_1_10d_1pool1_S260

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S260


title: Human Pre-adipocytes, empty lentivirus+GFP, differentiated-1

description: Library name: 8811-TC-1


title: Human Pre-adipocytes, EBF2 (1-164)_lentivirus+GFP, differentiated-3

description: Library name: 8811-TC-6


title: Human Pre-adipocytes, control_no-lentivirus, differentiated-1

description: Library name: 8811-TC-10


title: Human Pre-adipocytes, EBF2-full_lentivirus+GFP, differentiated-1

description: Library name: 8811-TC-7


title: Human Pre-adipocytes, control_no-lentivirus, differentiated-2

description: Library name: 8811-TC-11


title: Human Pre-adipocytes, EBF2 (1-164)_lentivirus+GFP, differentiated-2

description: Library name: 8811-TC-5


title: LC_6

city: Moscow

first: Rustam

last: Heydarov

address: 8-2 Trubetskaya str.

country: Russia

institute: I.M. Sechenov First Moscow State Medical University

description:
Lung carcinoid with ectopic ACTH-secretion 6
ACTH6_S69

data_processing:
Quality of the sequencing reads was assessed using FastQC
Reads were then pre-processed with Trimmomatic to remove adapters and low-quality sections
The trimmed reads were aligned to the reference genome using STAR aligner
Gene-level read counts were obtained using featureCounts from the Subread package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: lung carcinoid

extract_protocol:
RNA was extracted using HiPure FFPE RNA Kit (Magen)
Ribosomal RNA depletion and library construction was performed with KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche). KAPA unique dual-indexed primers (Roche) were used for multiplexing samples in a single sequencing run.

value: lung carcinoid

tag: Sex

value: Male


title: estradiol_0.0001_24h_1pool1_S60

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S60

value: estradiol


title: estradiol_0.0001_10d_2pool1_S348

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S348


title: estradiol_0.0001_10d_1pool1_S252

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S252


title: valproic acid_1_10d_2pool1_S340

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S340

value: valproic acid


title: PNT

description:
Pancreatic neuroendocrine tumor with ectopic ACTH-secretion
ACTH5_S67

source_name: pancreatic neuroendocrine tumor

value: pancreatic neuroendocrine tumor

value: Female


title: LC_4

description:
Lung carcinoid with ectopic ACTH-secretion 4
ACTH1_S75


title: valproic acid_1_10d_1pool1_S244

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S244


title: valproic acid_1_24h_2pool1_S148

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S148


title: LC_3

description:
Lung carcinoid with ectopic ACTH-secretion 3
ACTH3_S68


title: LC_2

description:
Lung carcinoid with ectopic ACTH-secretion 2
ACTH4_S65


title: WY-14643_1_24h_1pool1_S68

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S68


title: LC_1

description:
Lung carcinoid with ectopic ACTH-secretion 1
ACTH7_S70


title: potassium chloride_3_10d_2pool1_S332

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S332

value: potassium chloride


title: valproic acid_1_24h_1pool1_S52

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S52


title: NP_7

description:
Pituitary 7
ACTH_16_S1

source_name: pituitary

value: pituitary


title: potassium chloride_3_10d_1pool1_S236

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S236


title: NP_6

description:
Pituitary 6
ACTH_14_S3


title: NP_2

description:
Pituitary 2
Hy2_S72


title: sucrose_3_10d_2pool1_S324

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S324

value: sucrose


title: estradiol_0.0001_24h_2pool1_S156

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S156


title: PA_22

description:
ACTH-secreting pituitary adenoma 22
ACTH_31_S115

source_name: pituitary adenoma

value: pituitary adenoma


title: PA_21

description:
ACTH-secreting pituitary adenoma 21
ACTH_30_S109


title: caffeine_1_10d_1pool1_S220

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S220

value: caffeine


title: NP_4

description:
Pituitary 4
Hy4_S73


title: potassium chloride_3_24h_2pool1_S140

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S140


title: NP_3

description:
Pituitary 3
Hy3_S76


title: PA_20

description:
ACTH-secreting pituitary adenoma 20
ACTH_29_S111


title: sucrose_3_24h_2pool1_S132

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S132


title: sucrose_3_10d_1pool1_S228

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S228


title: NP_1

description:
Pituitary 1
Hy1_S71


title: caffeine_1_24h_2pool1_S124

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S124


title: PA_19

description:
ACTH-secreting pituitary adenoma 19
ACTH_28_S113


title: PA_18

description:
ACTH-secreting pituitary adenoma 18
ACTH_27_S114


title: cyclosporin A_0.1_10d_2pool1_S308

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S308

value: cyclosporin A


title: LC_5

description:
Lung carcinoid with ectopic ACTH-secretion 5
ACTH2_S66


title: caffeine_1_24h_1pool1_S28

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S28

value: liver spheroids


title: NP_5

description:
Pituitary 5
Hy5_S74


title: PA_17

description:
ACTH-secreting pituitary adenoma 17
ACTH_26_S107


title: PA_15

description:
ACTH-secreting pituitary adenoma 15
ACTH_24_S103


title: PA_16

description:
ACTH-secreting pituitary adenoma 16
ACTH_25_S112


title: potassium chloride_3_24h_1pool1_S44

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S44


title: cyclosporin A_0.1_24h_1pool1_S20

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S20


title: cyclosporin A_0.1_10d_1pool1_S212

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S212


title: benzo[a]pyrene_0.03_10d_2pool1_S300

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S300

value: benzo[a]pyrene


title: caffeine_1_10d_2pool1_S316

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S316


title: PA_14

description:
ACTH-secreting pituitary adenoma 14
ACTH_23_S110


title: sucrose_3_24h_1pool1_S36

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S36


title: benzo[a]pyrene_0.03_10d_1pool1_S204

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S204


title: PA_13

description:
ACTH-secreting pituitary adenoma 13
ACTH_22_S104


title: benzo[a]pyrene_0.03_24h_2pool1_S108

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool1_S108


title: PA_12

description:
ACTH-secreting pituitary adenoma 12
ACTH_21_S108


title: PA_11

description:
ACTH-secreting pituitary adenoma 11
ACTH_20_S106


title: PA_10

description:
ACTH-secreting pituitary adenoma 10
ACTH_19_S8