title: FJ03_HIRA knockout

city: La Jolla

first: Xue

last: Lei

address: 10901 N Torrey Pines Rd

institute: SBP medical discovery institute

data_processing:
A novel mm10 reference genome including sequences for tdTom and Cre was created as per the 10X genomics guidelines.
Count matrices were produced for each sample using Cellranger software version 2.2.0 with the following parameters: --transcriptome=./refdata-cellranger-mm10-1.2.0.Cre-tdTom --localcores=58 --localmem=112GB
Genome_build: mm10
Supplementary_files_format_and_content: barcode, genes and matrix files per sample

source_name: HIRA knockout_E15.5 Skin

extract_protocol:
Tissue harvesting: Embryos were harvested at E15.5 then washed in ice cold HBSS. Trunk skin was then removed, rinsed in HBSS and digested in 300ul of 0.2 U/ml dispase and 0.5mg/ml DnaseI in HBSS for 45 minutes at 37 degrees celcius. Digestion was halted by the addition of 5mM EDTA/PBS.
dissociation protocol: Skin suspensions were dissociated by passing through 18G then 21G needles, then filtered through 50 um filter membranes. Cell suspensions were centrifuged at 300g for 5 minutes at 4 degrees celcius, before being resuspended in sorting buffer (1% FBS, 5mM EDTA and 25mM HEPES in PBS).
cell sorting protocol: tdTomato negative skins were used as a negative control for gating and 1 ug/ml DAPI was used as a dead cell marker prior to sorting. TdTomato positive live cells were sorted using a BD FACSAria cell sorter.
Approximately 7000-10000 cells per sample were used for single cell RNA isolation, cDNA synthesis and library preparation using a 10X Genomics Chromium Single Cell 3’ Reagent kit as per the manufacturer’s protocol. Libraries were sequenced using an Illumina HiSeq4000 sequencer.

tag: strain background

value: mixed; close (~99.9%) to C57BL/6J

tag: genotype/variation

value: HIRA knockout

tag: developmental stage

value: skin


title: Mouse_Ulix_1_2

status: Public on Jun 11 2025

type: SRA

city: Cambridge

first: Loke CTR

last: Bioinformatics

address: Downing Street

department: Physiology building

country: United Kingdom

institute: Loke Centre for Trophoblast Research

description: Library name: SIM5111A2

library_source: transcriptomic single cell

data_processing:
Raw sequencing was processed according to a modified nf-core/scrnaseq pipeline
Reads were trimmed to remove adapter sequences and aligned to the mouse GRCm38 reference genomes using STAR aligner
Transcript abundances, using the Ensembl gene annotations (versions 102 for mouse) were estimated using STAR quantmode, converted into a count matrix and further processed using scanpy. No computational doublet detection was performed. We excluded samples in which more than 15% of total reads aligning to the mitochondrial genome.
Assembly: Mouse GRCm38
Supplementary files format and content: tab delimited .h5ad file

molecule: polyA RNA

organism: Mus musculus

source_name: Mouse pre-implantation embryo

growth_protocol: Embryos were cultured in Global Media + 10% Human serum albumin (Cooper Surgical) .

extract_protocol:
Single-cell cDNA synthesis was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) according to the manufacturer’s instrictions. Briefly, single-cells were manually picked after dissociation and snap frozen on dry ice in reaction buffer in low-bind 0.2 ml PCR tubes and stored at -80°C until processing. Samples were subject to first strand cDNA synthesis, then cDNA was amplified by LD-PCR for 23 cycles. Amplified cDNA was purified on AMPure XP beads, using a 96-well magnetic stand (ThermoFisher), and eluted in 17 µl of elution buffer.
The libraries were prepared using the Nextera XT DNA Library Preparation Kit (Illumina) according to the manufacturer’s protocol. Sequencing was carried out as paired-end 50bp read on a Novaseq 6000 sequencer.

treatment_protocol: Day 3.25 mouse embryos were treated for 24 hours with 5µM Ulixertinib (Cambridge Bioscience) or 0.1% DMSO and collected at day 4.25. Mouse embryos were subject to immunosurgery to remove outer trophectoderm cells and isolate the inner cell mass. The zona pellucida was removed by washing embryos through drops of Acidic Tyrode’s solution (Merck) pre-warmed to 37°C and overlaid with mineral oil. Embryos were then washed briefly and incubated at 37°C for 30 min in 20% anti-mouse serum antibody (Sigma) or 20% anti-human serum antibody (Sigma), depending on the species, in Global media + 10% HSA. Embryos were then washed briefly in Global Media + 10% HSA, before incubation with 20% Guinea Pig Serum Complement (Merck) at 37°C for 10-15 min until trophectoderm cell began to lyse. Embryos were then moved to a drop of medium and triturated with 100 µm STRIPPER tip (Cooper Surgical) to remove lysed trophectoderm cells and to isolate the inner cell mass. Isolated inner cell mass were then briefly washed, then incubated at 37°C for 3 min in 0.5% Trypsin, 1 mM EDTA in PBS (Fisher Scientific). Then, were transferred to 4% BSA, 0.5 mM EDTA in PBS for fine manual dissociation into single cells with pulled (Sutter Instruments) glass capillaries (World Precision Instruments). Cells were then picked manually with pulled glass capillaries for downstream single-cell RNA-seq.

tag: tissue

value: Mouse pre-implantation embryo

tag: cell type

value: Embryo

tag: treatment

value: Ulixertinib

tag: time point

value: day 4.25 (24hrs treatment)


title: FJ04_Wild type

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

source_name: WT_E15.5 Skin

value: Wild type


title: Human_DMSO_5_12

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

institute: The Babraham Institute

description: Library name: Sample52

data_processing:
Raw sequencing was processed according to a modified nf-core/scrnaseq pipeline
Reads were trimmed to remove adapter sequences and aligned to the human GRCh38 reference genomes using STAR aligner
Transcript abundances, using the Ensembl gene annotations (versions 110 for human) were estimated using STAR quantmode, converted into a count matrix and further processed using scanpy. No computational doublet detection was performed. We excluded samples in which more than 30% of total reads aligning to the mitochondrial genome and fewer than 8,000 unique genes were detected.
Assembly: Human GRCh38
Supplementary files format and content: tab delimited .h5ad file

organism: Homo sapiens

source_name: day 6.5 (36hrs treatment)

growth_protocol: Embryos were cultured in GT-L culture media (Vitrolife).

extract_protocol:
Single-cell cDNA synthesis was performed using SMART-Seq mRNA (Takara) according to the manufacturer’s instrictions. Briefly, single-cells were manually picked after dissociation and snap frozen on dry ice in 10.5µl 1x reaction buffer in low-bind 0.2 ml PCR tubes and stored at -80°C until processing. Samples were subject to first strand cDNA synthesis, then cDNA was amplified by LD-PCR for 18 cycles. Amplified cDNA was purified on AMPure XP beads, using a 96-well magnetic stand (ThermoFisher), and eluted in 17 µl of elution buffer.
The libraries were prepared using the SMART-Seq mRNA LP kit (Takara) according to the manufacturer’s protocol. Sequencing was carried out as paired-end 150bp read on an AVITI sequencer.

treatment_protocol: Day 5 human embryos were treated with 5µM Ulixertinib (Cambridge Bioscience) or 0.1% DMSO for either 36 hours and collected at day 6.5. Human embryos were then microdissected for single-cell RNA-seq and subjected to laser dissection (Saturn 5 Laser) to remove the mural trophectoderm. Isolated inner cell mass and polar trophectoderm cells were then briefly washed, then incubated at 37°C for 3 min in 0.5% Trypsin, 1 mM EDTA in PBS (Fisher Scientific). Then, were transferred to 4% BSA, 0.5 mM EDTA in PBS for fine manual dissociation into single cells with pulled (Sutter Instruments) glass capillaries (World Precision Instruments). Cells were then picked manually with pulled glass capillaries for downstream single-cell RNA-seq.

value: Human pre-implantation embryo

value: DMSO


title: Human_DMSO_5_13

description: Library name: Sample53


title: 170207-14, NPDR

city: Changchun

first: Peng

last: Chen

address: Xinmin Street 126

department: Department of genetics

country: China

institute: Jilin University

data_processing:
After sequencing, the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads. The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left. miRDeep2 software was used to predict the novel miRNAs with these trimmed reads. Then, the trimmed reads were aligned to merged pre-miRNA databases (known pre-miRNA from miRBase v21 plus the newly predicted pre-miRNAs) using Novoalign software (v2.07.11) with at most one mismatch. Reads (counts < 2) were discarded when calculating the miRNA expression. In order to characterize the isomiR variability, sequences that matched the miRNA precursors in the mature miRNAs region ±4 nt (no more than 1 mismatch) were accepted as mature miRNA isomiRs, which were grouped according to the 5-prime (5p) or 3-prime (3p) arm of the precursor hairpin. The numbers of mapped tags that were defined as the raw expression levels of that miRNA. To correct for the difference in tag counts between samples, the tag counts were scaled to TPM (the copy number of transcripts per million) based on the total number of tag aligned. Choosing a different isomiR sequence for measuring miRNA expression can affect the ability to detect differential miRNA expression. We use the most abundant isomiR, the mature miRNA annotated in miRBase and all isoforms of miRNA(5p or 3p) to calculate the miRNAs expression.
Assembly: miRBASE v21
Supplementary files format and content: The processed file is a tab-deliminated text file and contains the miRNA read counts of all samples, with miRNA names in rows and sample names in columns.

source_name: peripheral blood serum

extract_protocol:
Participants were instructed to fast for 8-12 hours, and approximately 5ml of venous blood was collected using vacuum tubes containing citrate anticoagulant at room temperature in the early morning. The whole blood was centrifuged at 1000g for 10 minutes, and the plasma was collected and stored at -80°C for further use.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps:  1) 3'-adaptor ligation;  2) 5'-adaptor ligation;  3) cDNA synthesis;  4) PCR amplification;  5) size selection of ~135-155 bp PCR amplified fragments (corresponding to ~15-35 nt small RNAs).  The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina NextSeq 500 per the manufacturer's instructions.

value: peripheral blood serum

tag: disease

value: NPDR

tag: batch

tag: Sex

value: female

tag: age

tag: bmi


title: FJ01_Wild type


title: FJ02_HIRA knockout


title: Mouse_DMSO_1_11

description: Library name: SIM5110A23


title: 170205-03, NPDR

value: male


title: Human_DMSO_5_11

description: Library name: Sample51


title: 170106-01, NPDR


title: Mouse_DMSO_1_10

description: Library name: SIM5110A22


title: S2_FJ_HIRA knockout


title: Human_DMSO_5_18

description: Library name: Sample58


title: Human_DMSO_5_9

description: Library name: Sample49


title: Mouse_DMSO_1_12

description: Library name: SIM5110A24


title: 170412-07, T2D


title: Mouse_DMSO_1_9

description: Library name: SIM5110A21


title: 170411-15, T2D


title: siCTCF, replicate 3

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

institute: South China Agricultural University

description: Library name: siCTCF3

data_processing:
Clean reads were mapped to mouse genome (UCSC hg19) by using HISAT v2.2.1
Mapped reads were assembled by using Cufflinks v2.2.1
Assembly: hg19
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample

source_name: primary human endometrial stromal cells

extract_protocol:
TRIzol reagent (Invitrogen) was used to extract total RNAs according to manufacturers’ instructions.
RNA-seq libraries were created by using the TruSeq RNA sample preparation kit (Illumina).

treatment_protocol: primary human endometrial stromal cells (hESCs) were treated with siCTCF or siNC for 48h.

value: primary human endometrial stromal cells


title: Mouse_DMSO_1_8

description: Library name: SIM5110A20


title: Human_DMSO_5_8

description: Library name: Sample48


title: Human_DMSO_5_10

description: Library name: Sample50


title: Human_DMSO_5_7

description: Library name: Sample47


title: siCTCF, replicate 2

description: Library name: siCTCF2


title: 170329-08, T2D


title: S1_FJ_Wild type


title: Mouse_DMSO_1_7

description: Library name: SIM5110A19


title: 170205-11, NPDR


title: 170315-10, T2D


title: Mouse_DMSO_1_6

description: Library name: SIM5110A18


title: siCTCF, replicate 1

description: Library name: siCTCF1


title: siNC, replicate 3

description: Library name: siNC3


title: Human_DMSO_5_6

description: Library name: Sample46


title: Human_DMSO_5_5

description: Library name: Sample45


title: 170314-12, T2D


title: Mouse_DMSO_1_5

description: Library name: SIM5110A17


title: 170307-04, T2D


title: siNC, replicate 1

description: Library name: siNC1


title: Human_DMSO_5_4

description: Library name: Sample44


title: 170226-04, T2D


title: Mouse_DMSO_1_4

description: Library name: SIM5110A16


title: Mouse_DMSO_1_3

description: Library name: SIM5110A15


title: 170104-14, T2D


title: Human_DMSO_5_3

description: Library name: Sample43


title: Human_DMSO_5_2

description: Library name: Sample42


title: Human_DMSO_5_1

description: Library name: Sample41


title: VCaP cells, R1881+RBN2397, 18h, biol rep 2

city: Charlottesville

first: Krzysztof

last: Wierbiłowicz

state: VA

address: 1400 Jefferson Park Ave, PO Box 800577

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Reads were pseudoaligned to the hg38 genome (ENSEMBL GRCh38.89) using kallisto.
The transcript-level abundance estimates were summarized to gene-level counts using tximport.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: VCaP

growth_protocol: VCaP cells were maintained in DMEM media supplemented with 10% fetal bovine serum (FBS) in a humidified environment in the presence of 5% CO2, and at 37 °C.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit.
Library preparation and sequencing were performed by Hudson Alpha. In brief, a fluorometric assay was used to assess the RNA concentration and integrity; the standard polyA method was used to make indexed libraries; size and concentration were determined using quality control.

treatment_protocol: VCaP cells were plated in the phenol-free DMEM media supplemented with 10% charcoal-stripped (depleted of androgens) FBS and treated with R1881, RBN2397, and R1881+RBN2397 and corresponding vehicles (ethanol for R1881 and DMSO for RBN2397) for 18 hr in biological triplicates

tag: cell line

value: VCaP

value: metastatic prostate cancer

tag: genotype

value: WT.


title: siNC, replicate 2

description: Library name: siNC2


title: Mouse_DMSO_1_2

description: Library name: SIM5110A14


title: 161215-02, T2D


title: Mouse_DMSO_1_1

description: Library name: SIM5110A13


title: VCaP cells, R1881+RBN2397, 18h, biol rep 3


title: VCaP cells, R1881+RBN2397, 18h, biol rep 1


title: Human_Ulix_6_40

description: Library name: Sample40


title: 161206-09, T2D


title: DM-1

city: hangzhou city

first: liu

middle: guo

last: xuan

address: No. 182 Tianmushan Road, Hangzhou City, Zhejiang Province

institute: Hangzhou Medical College

description: Library name: sample2

data_processing:
The demuitiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software  v2.1.1.
Assembly: Mouse mm10
Supplementary files format and content: non
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
The isolated  cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+supplemented with 2 mg/ ml collagenase type l and 40 U/ml DNase l) and incubated at 37 ℃ for 30 min. Cells were washed and re-suspended in PBS and stained w ith a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive cells were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Cells were washed inHBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, Cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an llumina R1 primer sequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRlselect reagent for subsequent library construction. During the library construction llumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: heart

value: typical T2DM model


title: VCaP cells, RBN2397, 18h, biol rep 3


title: Human_Ulix_6_39

description: Library name: Sample39


title: VCaP cells, RBN2397, 18h, biol rep 2


title: Ctrl-1

description: Library name: sample1

value: WT


title: 161128-03, T2D


title: Human_Ulix_6_38

description: Library name: Sample38

value: Embryo


title: 170419-16, NPDR


title: VCaP cells, RBN2397, 18h, biol rep 1


title: Human_Ulix_6_37

description: Library name: Sample37

value: Ulixertinib


title: VCaP cells, R1881, 18h, biol rep 3


title: 170315-03, NPDR


title: Human_Ulix_6_36

description: Library name: Sample36


title: 170308-08, NPDR


title: D4 ES RNA-seq, rep1

city: Boston

first: Hyun Jung

last: Oh

state: MA

address: 185 Cambridge St.

institute: MGH

description: Library name: d4 RNA-seq R1

data_processing:
!Sample_data_processing = RNA-seq: RNA-seq reads were processed for adaptor sequence trimming and PCR duplicate removal using Trim Galore (v0.4.1; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a stringency of 12 allowed error rate 0.2. Prior to genome alignment, a preliminary alignment step was conducted using STAR aligner80 (v2.7.3) to remove reads aligning to rDNA sequences. The unmapped reads from this rDNA alignment were then aligned to the mouse genome (GRCm38/mm10) using STAR with the parameters ?--outSAMprimaryFlag AllBestScore --outMultimapperOrder Random --outSAMtype BAM Unsorted --outFilterMultimapNmax 200 --outFilterMismatchNoverLmax 0.3 --seedSearchStartLmax 50 --outSAMattributes NH HI NM MD --outSAMunmapped Within --outReadsUnmapped Fastx.? All unmapped reads were subsequently filtered out. Allele parsing was performed using SNPsplit (https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit) with SNP VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf.gz) obtained from ftp://ftp-mouse.sanger.ac.uk/current_snps/. Reads aligned to either cas (CAST/EiJ) or mus (129S1/SvImJ) alleles were distinguished based on known SNP positions. To prepare RNA-seq data for generating signal summaries over genes, we utilized the HOMER (v4.10)76 toolkit with the parameters ?makeTagDirectory -removeSpikes 10000 8 -sspe -flip?. To obtain the counts of reads mapped to exons, we employed the Homer script ?analyzeRepeats.pl? with the parameters ?rna mm10 -count genes -dfile OrderSet1 -noadj -norm 0 -condenseGenes -strand +?. Gene expression counts from HOMER-processed BAM files were imported into R and organized into a DGEList object using the edgeR package. Genes were filtered using the filterByExpr function with default parameters, retaining 15,333 out of 24,940 genes based on sufficient raw count expression across samples, as determined by the experimental groups (d0, d4, d7, each with two replicates). Library sizes were recalculated from filtered counts, and normalization was performed using the Trimmed Mean of M-values (TMM) method (calcNormFactors, method="TMM") to adjust for differences in library composition, yielding a normalized DGEList object. Dispersions were estimated in three sequential steps: common dispersion (estimateCommonDisp), trended dispersion (estimateGLMTrendedDisp), and tagwise dispersion (estimateTagwiseDisp), capturing gene-specific variability and generating pseudo-counts that reflect normalized expression adjusted for dispersion.  A design matrix was constructed without an intercept to model the three conditions (d0, d4, d7), each with two replicates.To further account for potential batch effects and unmodeled sources of variation, surrogate variable analysis (SVA) was applied using the sva package. The normalized counts were used as input, with the design matrix defined by the experimental group labels. Surrogate variables estimated by SVA were appended to the design matrix and incorporated into the linear modeling framework. Precision weights were calculated using the voom function from the limma package, and the resulting expression matrix was further adjusted using removeBatchEffect to regress out the surrogate variables while preserving the primary group structure. For downstream analysis and visualization, these values were transformed to transcripts per million (TPM). We selected 372 X-linked genes based on exonic allelic read counts with a minimum of 45 (sum of Castaneus and Musculus reads > 45) in at least one of the libraries across all libraries. Allelic ratios were calculated by computing the Xi proportion [mus/(mus+cas)] of read counts between mus and cas alleles for each replicate at each time point.
Assembly: mm10
Supplementary files format and content: Allelic read counts, allelic proportions, and gene expression levels in TPM (xlsx)

growth_protocol: Undifferentiated female mouse embryonic stem cells were grown on the irradiated MEF feeders in regular DMEM medium (high-glucose) with 15% FBS and LIF. For differentiation, cells were trypsinizied and incubated in the medium at 37 °C for at least 40 min. After separation of ES cells from attached feeders, ES cells were re-plated on non-gelatinized petri dishes in the complete DMEM medium without LIF. Embryoid bodies (EB) formed from ES cells were transferred to the gelatinized cell culture plates on day 4 of differentiation. Cells were harvested on indicated days.

extract_protocol:
Total RNA was extracted using TRIzol, depleted of ribosomal RNA and then treated with DNase. The rRNA-depleted RNA was selected by size greater than 200nt, fragmented to a mediam size of about 200nt and then subjected to RT reaction. The subsequent first-strand cDNA was subjected to second strand cDNA synthesis using NEBNext Ultra Directional RNA Second Strand Synthesis Module (NEB, #E7550S).
After second strand cDNA synthesis, the resulting double-stranded DNA was subjected to library construction using  NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.

value: Differentiating mESC (day 4)


title: D0 ES RNA-seq, rep2

description: Library name: d0 RNA-seq R2

data_processing:
RNA-seq: RNA-seq reads were processed for adaptor sequence trimming and PCR duplicate removal using Trim Galore (v0.4.1; https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with a stringency of 12 allowed error rate 0.2. Prior to genome alignment, a preliminary alignment step was conducted using STAR aligner80 (v2.7.3) to remove reads aligning to rDNA sequences. The unmapped reads from this rDNA alignment were then aligned to the mouse genome (GRCm38/mm10) using STAR with the parameters ?--outSAMprimaryFlag AllBestScore --outMultimapperOrder Random --outSAMtype BAM Unsorted --outFilterMultimapNmax 200 --outFilterMismatchNoverLmax 0.3 --seedSearchStartLmax 50 --outSAMattributes NH HI NM MD --outSAMunmapped Within --outReadsUnmapped Fastx.? All unmapped reads were subsequently filtered out. Allele parsing was performed using SNPsplit (https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit) with SNP VCF file (mgp.v5.merged.snps_all.dbSNP142.vcf.gz) obtained from ftp://ftp-mouse.sanger.ac.uk/current_snps/. Reads aligned to either cas (CAST/EiJ) or mus (129S1/SvImJ) alleles were distinguished based on known SNP positions. To prepare RNA-seq data for generating signal summaries over genes, we utilized the HOMER (v4.10)76 toolkit with the parameters ?makeTagDirectory -removeSpikes 10000 8 -sspe -flip?. To obtain the counts of reads mapped to exons, we employed the Homer script ?analyzeRepeats.pl? with the parameters ?rna mm10 -count genes -dfile OrderSet1 -noadj -norm 0 -condenseGenes -strand +?. Gene expression counts from HOMER-processed BAM files were imported into R and organized into a DGEList object using the edgeR package. Genes were filtered using the filterByExpr function with default parameters, retaining 15,333 out of 24,940 genes based on sufficient raw count expression across samples, as determined by the experimental groups (d0, d4, d7, each with two replicates). Library sizes were recalculated from filtered counts, and normalization was performed using the Trimmed Mean of M-values (TMM) method (calcNormFactors, method="TMM") to adjust for differences in library composition, yielding a normalized DGEList object. Dispersions were estimated in three sequential steps: common dispersion (estimateCommonDisp), trended dispersion (estimateGLMTrendedDisp), and tagwise dispersion (estimateTagwiseDisp), capturing gene-specific variability and generating pseudo-counts that reflect normalized expression adjusted for dispersion.  A design matrix was constructed without an intercept to model the three conditions (d0, d4, d7), each with two replicates.To further account for potential batch effects and unmodeled sources of variation, surrogate variable analysis (SVA) was applied using the sva package. The normalized counts were used as input, with the design matrix defined by the experimental group labels. Surrogate variables estimated by SVA were appended to the design matrix and incorporated into the linear modeling framework. Precision weights were calculated using the voom function from the limma package, and the resulting expression matrix was further adjusted using removeBatchEffect to regress out the surrogate variables while preserving the primary group structure. For downstream analysis and visualization, these values were transformed to transcripts per million (TPM). We selected 372 X-linked genes based on exonic allelic read counts with a minimum of 45 (sum of Castaneus and Musculus reads > 45) in at least one of the libraries across all libraries. Allelic ratios were calculated by computing the Xi proportion [mus/(mus+cas)] of read counts between mus and cas alleles for each replicate at each time point.
Assembly: mm10
Supplementary files format and content: Allelic read counts, allelic proportions, and gene expression levels in TPM (xlsx)

value: Undifferentiated mESC (day 0)


title: Human_Ulix_6_35

description: Library name: Sample35

value: Human pre-implantation embryo


title: VCaP cells, R1881, 18h, biol rep 2


title: Human_Ulix_6_34

description: Library name: Sample34


title: Human_Ulix_6_33

description: Library name: Sample33


title: CTCF Late2C_GFP_control_for_ADNP_OE

city: Beijing

first: Wei

last: Xie

state: Beijing

address: Qinghuayuan

department: School of Life Science

institute: Tsinghua University

library_source: genomic

data_processing:
The paired-end CUT&RUN reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.RNA-seq reads were aligned to the mouse reference genome (mm9) by STAR (Dobin et al., 2013) with the following parameters: --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate -outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was normalized to FPKM values using Cufflinks (Trapnell et al., 2012).
For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized.
To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values for 100-bp bins of the genome.
Narrow peaks were called using MACS2 with the parameters -g mm -nomodel -nolambda and broad peaks were called using MACS2 with the parameters -g mm -broad --broad-cutoff 0.05 -nomodel -nolambda.
RNA-seq reads were aligned to the mouse reference genome (mm9) by STAR (Dobin et al., 2013) with the following parameters: --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate - outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was normalized to FPKM values using Cufflinks (Trapnell et al., 2012).
Assembly: mm9
Supplementary files format and content: Processed data files in BigWig format containg the RPKM-normarlized signal values for 100-bp bins of the genome (for CUT&RUN) or the FPKM values for each gene.
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol: CUT&RUN was conducted following the published protocol (Skene et al., 2018) with modifications. Oocytes or embryos removed zona pellucida were transferred into 0.2mL conventional, non-low-binding PCR tube (Axygen). Cells were attached to a solid support using concanavalin A–coated magnetic beads to allow simple handling. Following in situ binding of the antibody and pA-MN specifically to the target protein, pA-MN was activated by calcium at 0 °C. Cleaved fragments released with two cuts were free to diffuse out of the nuclei. After removing the intact nuclei by centrifugation, the supernatant containing released chromatin fragments were used to extract DNA directly for library construction. Purified DNA was subjected to Tru-seq library construction using either KAPA Hyper Prep Kit (KAPA biosystems, KK8502) or NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

treatment_protocol: Control

tag: strain

value: GFP injection


title: 170204-10, NPDR

value: peripheral blood serum


title: 170111-06, NPDR

value: NPDR


title: 170302-05, NPDR

value: female


title: CTCF Late2C_ADNP_OE_rep2

treatment_protocol: ADNP OE

value: ADNP OE


title: VCaP cells, vehicle, 18h, biol rep 3

value: vehicle


title: 161222-04, NPDR

value: male


title: VCaP cells, vehicle, 18h, biol rep 2

value: VCaP

value: metastatic prostate cancer


title: D0 ES RNA-seq, rep1

description: Library name: d0 RNA-seq R1


title: D4 ES RNA-seq, rep2

description: Library name: d4 RNA-seq R2


title: CTCF Late2C_ADNP_OE_rep1


title: Human_Ulix_6_31

description: Library name: Sample31


title: VCaP cells, R1881, 18h, biol rep 1

value: WT.


title: Human_Ulix_6_32

description: Library name: Sample32


title: VCaP cells, vehicle, 18h, biol rep 1


title: SMC3_DRB_4h

data_processing:
The paired-end CUT&RUN reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.RNA-seq reads were aligned to the mouse reference genome (mm9) by STAR (Dobin et al., 2013) with the following parameters: --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate -outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was normalized to FPKM values using Cufflinks (Trapnell et al., 2012).
For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized.
To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values for 100-bp bins of the genome.
Narrow peaks were called using MACS2 with the parameters -g mm -nomodel -nolambda and broad peaks were called using MACS2 with the parameters -g mm -broad --broad-cutoff 0.05 -nomodel -nolambda.
Assembly: mm9
Supplementary files format and content: Processed data files in BigWig format containg the RPKM-normarlized signal values for 100-bp bins of the genome.
Library strategy: CUT&RUN

treatment_protocol: For DRB treatment, 8-cell embryos (68-70 h after hCG injection) were collected and cultured in CZB medium supplemented with DRB (final concentration 120 μM) for 2 or 4 hours.

value: embryo

tag: Stage

value: DRB for 4 hours


title: Aur-Kang-CMTM6sh-HCT-3

city: Austin

first: Ningling

last: Kang

state: MN

address: 801 16th Ave NE

institute: Hormel Institute

data_processing:
Illumina Real time Analysis and CASAVA software 1.8.2 were used for basecalling.
Raw reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control checks on raw sequence data for each sample were performed with FastQC.  Read mapping was performed via Bowtie (v2.2.4.0) using the Human genome (hg19) as reference
Raw reads for each gene generated from the HiSeq2500 sequencer were subjected to statistical analysis using the edgeR package and cuffdiff2 package based on two selection criteria (fold change ≥ 2 & FDR < 0.05, and fold change ≥ 1.5 & FDR < 0.01).  The overlap of these four criteria was used to identify genes.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Colon Cancer Cells

growth_protocol: Cells obtained from ATCC were cultured with DMEM supplemented with 10% FBS, streptomycin and penicillin.

extract_protocol:
RNA samples were isolated from the cells by using RNeasy Plus Mini kit (Qiagen, 74134) and gDNA Eliminator Columns were used to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing by using standard Illumina protocols

value: Colon Cancer Cells

value: Cell expressing CMTM6 shRNA


title: 161130-06, NPDR


title: Human_Ulix_6_30

description: Library name: Sample30

value: Embryo

value: Ulixertinib


title: Aur-Kang-CMTM6sh-HCT-2


title: 161128-18, NPDR


title: SMC3_DRB_2h

value: WT

value: DRB for 2 hours


title: 161123-06, NPDR

value: peripheral blood serum


title: Aur-Kang-CMTM6sh-HCT-1


title: SMC3_DMSO_control_for_DRB

value: DMSO for 4 hours


title: Human_Ulix_6_29

description: Library name: Sample29

value: Human pre-implantation embryo


title: Glaucoma PBMC, sample 5, scRNAseq

first: Emil

last: Kriukov

address: 20 Staniford St

institute: Schepens Eye Research Institute

description: 10x Genomics

data_processing:
The demultiplexing, barcoding, gene counting and aggregation were performed using Cell ranger v. 7.0.1. Further downstream analysis was performed using R- and Python- dependent tools described in the manuscript.
Assembly: GRCh38 (cell ranger GRCh38-2020-A)
Supplementary files format and content: Tab-separated values files and matrix file for each dataset

source_name: PBMC

extract_protocol:
Whole blood of control and patients with POAG was collected using BD Vacutainer tubes. PBMC were isolated according to the manufactuer's protocol and stored in Recovery Cell Culture Freezing Medium in liquid nitrogen until use.
Single-cell library preparation with 10× Chromium Next GEM Single Cell 5′ Kit v2 (NovaSeq:S4 150PE) (10× genomics) according to the manufacturer’s instructions. The single-cell cDNA libraries were sequenced by NexSeq500 (Illumina).

value: PBMC

value: Immune

tag: disease state

value: Primary open-angle glaucoma

tag: unique donor id

value: Female

tag: ethnicity

value: White


title: Human_Ulix_6_28

description: Library name: Sample28


title: SMC3_8C_heatshock_control

treatment_protocol: Mouse 8-cell embryos were collected in G1 medium (Vitrolife). Heat shock was induced by placing the embryos or mESCs at 43 °C for 60 minutes, followed by a recovery at 37 °C for 30 minutes. Cell division did not occur in these embryos or mESCs during the treatment or the recovery time. Control embryos or mESCs were maintained at 37 °C throughout culture and were harvested at the same time with heat shock samples. Blastomere numbers and cell numbers are counted to allow downstream spike-in normalization.

value: untreated


title: Aur-Kang-NT-HCT-3

value: Cell expressing control shRNA


title: Glaucoma PBMC, sample 4, scRNAseq

description: 10x Genomics


title: Aur-Kang-NT-HCT-2


title: SMC3_8C_heatshock

value: embryo

value: Heatshock at 43C for 30min then recover at 37C for 30min


title: RNA_8C_heatshock_control

data_processing:
The paired-end CUT&RUN reads were aligned with the parameters: -t –q –N 1 –L 25 –X 1000 --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.RNA-seq reads were aligned to the mouse reference genome (mm9) by STAR (Dobin et al., 2013) with the following parameters: --quantMode GeneCounts --outSAMtype BAM SortedByCoordinate -outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was normalized to FPKM values using Cufflinks (Trapnell et al., 2012).
For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized.
To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values for 100-bp bins of the genome.
Narrow peaks were called using MACS2 with the parameters -g mm -nomodel -nolambda and broad peaks were called using MACS2 with the parameters -g mm -broad --broad-cutoff 0.05 -nomodel -nolambda.
Assembly: mm9
Supplementary files format and content: Processed data files in BigWig format containg the RPKM-normarlized signal values for 100-bp bins of the genome.

extract_protocol: Total RNA-seq libraries were prepared as previously described (Brind'Amour et al., 2018). Briedly, RNA was extracted from mouse embryos or cells using TRIzol (Thermo, 10296028). Ribosomal RNA was then depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S). NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S) were used to synthesize cDNA. Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instructions. All libraries were sequenced by Illumina Hi-Seq Xten or Novaseq 6000 according to the manufacturer’s instructions.


title: Human_Ulix_6_27

description: Library name: Sample27


title: Glaucoma PBMC, sample 3, scRNAseq

description: 10x Genomics


title: RNA_8C_heatshock_rep2


title: Human_Ulix_6_24

description: Library name: Sample24


title: Glaucoma PBMC, sample 1, scRNAseq

description: 10x Genomics

value: Male


title: RNA_8C_heatshock_rep1


title: Aur-Kang-NT-HCT-1

value: Colon Cancer Cells


title: Human_Ulix_6_23

description: Library name: Sample23

value: Embryo

value: Ulixertinib


title: Glaucoma PBMC, sample 2, scRNAseq

description: 10x Genomics


title: Healthy PBMC, sample 3, scRNAseq

description: 10x Genomics

value: Healthy


title: Control,replica 2,scRNAseq

city: Tainan

first: Chunwei

last: Lin

address: No. 1, Daxue Rd., East Dist.

country: Taiwan

institute: National Cheng Kung University

data_processing:
Sequencing data were imported to Cellranger (version 6.0.1) for further analysis. We used the cellranger mkfastq function to demultiplex base-call files into FASTQ files, followed by the cellranger count function to perform alignment, filtering, barcode counting, and Unique Molecular Identifier counting.
Assembly: rn6
Supplementary files format and content: Tab-separated values files and metrics

organism: Rattus norvegicus

source_name: skeleton muscle

extract_protocol:
Single-cell suspensions were obtained from rat skeletal muscle using the Skeletal Muscle Dissociation Kit (MACS 130-098-305) and subsequently incubated with 1 ml RBC lysis buffer for 2 min in room temperature. Cells were then centrifuged at 500G for 5 min and resuspended in Dulbecco’s modified Eagle’s medium (Hyclone) supplemented with 10% fetal bovine serum (Hyclone). An aliquot of the single cell suspension was stained with the trypan blue (Invitrogen) and measured cell viability and number with TC20TM automated cell counted (Bio-rad) to ensure cell viability was greater than 80%.
scRNA-seq libraries were prepared with Chromium Single cell 5’ Reagent Kits v2 (10X Genomics, USA) following the manufacturer’s protocol. In brief, 10,000 cells which mixed with reverse transcription reagent, gel beads and partitioning oil were loaded into a Chromium Next GEM Chip K. Then, Chip K was subsequently loaded into a Chromium Controller to generate gel bead-in-emulsions and follow by reverse transcripts (53°C for 45 min; 85°C for 5 min) to produced cDNA. cDNA were then cleanup with Dynabeads and followed by cDNA amplification [98°C for 45 sec; (98°C for 20 sec, 63°C for 30 sec and 72°C for 1 min) × 11 cycles; 72°C for 1 min]. The amplified cDNA was then fragmented, ligated with adapter and sample index, and performed double sided selection with SPRI beads (Beckman) according to manufacturer’s protocol. Finally, the libraries were quantified with Qubit dsDNA HS assay kit (ThermoFisher), and the libraries average fragment size were measured with 4150 Tapestation system (Agilent). Finally, libraries were sequenced on an Illumina NextSeq 2000 platform. A total of 2 x 150 bp paired-end runs of Illumina NextSeq 2000 were performed according to manufacturer’s protocol.

value: skeleton muscle

value: Control


title: SMC3, mESC

data_processing:
The paired-end CUT&RUN reads were aligned with the parameters: -t -q -N 1 -L 25 -X 1000 --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
For downstream analysis, we normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome. To minimize the batch and cell type variation, RPKM values across whole genome were further Z-score normalized.
To visualize the CUT&RUN signals in the UCSC genome browser, we generated the RPKM values for 100-bp bins of the genome.
Narrow peaks were called using MACS2 with the parameters -g mm -nomodel -nolambda and broad peaks were called using MACS2 with the parameters -g mm -broad --broad-cutoff 0.05 -nomodel -nolambda.
Assembly: mm9
Supplementary files format and content: Processed data files in BigWig format containg the RPKM-normarlized signal values for 100-bp bins of the genome.
Library strategy: CUT&RUN

source_name: R1 mESC

extract_protocol: CUT&RUN was conducted following the published protocol (Skene et al., 2018) with modifications. Oocytes or embryos removed zona pellucida were transferred into 0.2mL conventional, non-low-binding PCR tube (Axygen). Cells were attached to a solid support using concanavalin A-coated magnetic beads to allow simple handling. Following in situ binding of the antibody and pA-MN specifically to the target protein, pA-MN was activated by calcium at 0 °C. Cleaved fragments released with two cuts were free to diffuse out of the nuclei. After removing the intact nuclei by centrifugation, the supernatant containing released chromatin fragments were used to extract DNA directly for library construction. Purified DNA was subjected to Tru-seq library construction using either KAPA Hyper Prep Kit (KAPA biosystems, KK8502) or NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).

treatment_protocol: No treatment

value: WT

value: embryonic stem cell

tag: antibody


title: E-stim,replica 2,scRNAseq

tag: tissue

value: E-stim


title: Human_Ulix_6_22

description: Library name: Sample22

value: Human pre-implantation embryo

tag: cell type


title: Naïve,replica 1,scRNAseq

tag: treatment

value: Naïve


title: Human_Ulix_6_21

description: Library name: Sample21


title: SMC3, EPI, rep2

source_name: E6.5 Epiblast

value: PWK/PhJ (Pat) x C57BL/6J (Mat)

value: E6.5 Epiblast


title: Healthy PBMC, sample 2, scRNAseq

description: 10x Genomics

value: PBMC

value: Immune

value: Female

value: White


title: Healthy PBMC, sample 1, scRNAseq

description: 10x Genomics


title: Control,replica 1,scRNAseq


title: Human_Ulix_6_25

description: Library name: Sample25


title: melb-a cells, lenti- shHIRA II biol rep4

data_processing:
FASTQs were generated using bcl2fastq.
Read pseudo-alignment was completed with Kallisto read-mapping software v0.46.2.
Transcript-level counts and abundance data were imported into R using the TxImport package
TPM normalized using the package edgeR.
Assembly: mm10
Supplementary files format and content: File includes raw counts for each sample
Supplementary files format and content: File includes TPM values for each sample

source_name: melb-a cells

growth_protocol: melb-a cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine, 10ng/ml SCF, 40 pM Fgf2, 25U/ml penicillin, and 25 μg/ml streptomycin in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted from cells using TRIzol and Direct-zol RNA MiniPrep Plus kit (Zymo R2072).
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina® (NEB, Ipswich MA).

treatment_protocol: melb-a cells were splitted to a confluency of ~50%. Lentivirus was diluted in 1 ml growth medium per 3.5 cm well and incubated with 8 μg/ml polybrene for 16 hours. The infected cells were selected using 1 μg/ml puromycin.

value: melb-a cells

value: melanoblasts

value: wt

value: lenti- shHIRA II


title: SMC3, 8C, rep2

value: untreated


title: Human_Ulix_6_20

description: Library name: Sample20

value: Embryo

value: Ulixertinib


title: melb-a cells, lenti- shHIRA II biol rep3


title: Human_Ulix_6_19

description: Library name: Sample19


title: Naïve,replica 2,scRNAseq

value: skeleton muscle


title: Human_Ulix_6_26

description: Library name: Sample26


title: E-stim,replica 1,scRNAseq

value: E-stim


title: E9.5 lambdoidal junctions epithelia

city: New York

first: Louis

last: Faure

state: NY

address: 321 E 61st Street

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ML11

data_processing:
Initial processing of raw sequencing reads was conducted using the Cell Ranger v2.2.0 pipeline from 10X Genomics, which involved demultiplexing, aligning to the mouse genome (mm10 1.2.0)
The main subsequent analyses were mainly performed using pagoda2 R package. Additional filtering was performed based on gene/molecule dependency (pagoda2, gene.vs.molecule.cell.filter), with cells having more that 1x105 transcripts, less than 1000 transcripts or more than 10% of mitochondrial proportion being filtered out. Genes with less than 10 total transcripts overall were discarded.
Assembly: mm10
Supplementary files format and content: raw count matrices generated by cellranger

source_name: lambdoidal junctions

growth_protocol: Mouse embryos were generated using previously described mutant alleles and genotyping methods for conditional and constitutive alleles of Zfhx3, Pbx1, Pbx2, p63, and transgenes such as CrectCre, Pitx2Cre, Wnt4Cre, Ai14(RCL-tdT)-D12, and FUCCI2a13. In Fucci2a mice, G1 phase cells are marked by mCherry-hCdt1, which accumulates during G1 and is degraded at the transition to S. Cells in G2/M are highlighted by mVenus-hGem, which builds up during the S/G2/M phases and rapidly degrades before cytokinesis. Wild-type Swiss Webster mice, sourced from Charles River Laboratories, were bred via natural timed mating using female mice over 6 weeks of age. Embryos were collected between gestational days E9.5 to E12.5, with E0.5 defined as noon on the day a vaginal plug was detected, following euthanasia of the pregnant females. All mouse embryonic stages are indicated in figures and/or figure legends. Due to genetic complexity, genotyping of mice and embryos was necessary before proceeding with analyses. Both male and female embryos were analyzed without sex discrimination, as the observed phenotypes in Pbx1/2 and p63 mutants are fully penetrant across all specimens.

extract_protocol:
Embryonic litters were collected and staged based on somite count and limb morphology on designated days of development and then dissected in ice-cold PBS. At E9.5, embryonic faces were isolated from the heads by dissecting the frontonasal and maxillary prominences, carefully avoiding the forebrain and developing eye placode. By E10.5 and E11.5, entire midfaces were dissected to include the MNP, LNP, and MxP, while avoiding eye and brain tissues. The lambdoidal junction was specifically isolated using surgical scalpels to dissect the upper halves of the LNP and MNP at the horizontal midline of the nasal pits, and the lower half of the MxP at the horizontal midpoint, ensuring the lambdoidal junction remained intact without separating the individual prominences. For wild-type (Swiss Webster) scRNAseq, samples were pooled for dissociation into single cell suspensions. A fresh cocktail of 1X Liberase TL (Roche #05401020001) and 1X DNAseI Grade II (Roche #10104159001) was prepared. Tissue samples were then incubated in this enzymatic cocktail at 37°C without agitation for 10-13 minutes, with gentle pipetting every 5 minutes to facilitate tissue breakdown. The enzymatic reaction was stopped with ice-cold PBS, and cells were centrifuged at 300 RCF for 10 minutes and resuspended in ice-cold cell staining buffer (0.5% Bovine Serum Albumin, 2mM EDTA in PBS). Cells were stained with 1.25μL of anti-EpCAM-APC (Invitrogen 17-5791-82) antibody for 15 minutes at 4°C in the dark, followed by centrifugation and resuspension in FACS buffer (5% FBS, 5mM EDTA in PBS). To identify dead cells, DAPI was added to the cell suspension at a 1:1000 ratio. Cells were kept on ice and sorted using a Sony SH800S sorter, with gating strategies to exclude doublets and dead cells. DAPI negative, EpCAM positive cells were collected.
RNA libraries were prepared according to 10X protocol.

value: lambdoidal junctions

value: Mouse stem cells

value: Epithelial cells

value: WT


title: Human_Ulix_6_18

description: Library name: Sample18

value: Human pre-implantation embryo


title: Human_Ulix_6_17

description: Library name: Sample17


title: SMC3, Early2C, rep2

source_name: Early 2-cell

value: PWK/PhJ (Pat) x C57BL/6J (Mat)

value: Early 2-cell


title: melb-a cells, lenti- shHIRA II biol rep1


title: E10.5 lambdoidal junctions epithelia

description: Library name: ML10


title: SMC3, Early2C, rep1


title: melb-a cells, lenti- shHIRA I biol rep4

value: lenti- shHIRA I


title: SMC3, 8C, rep1


title: E11.5 lambdoidal junctions epithelia replicate 2

description: Library name: ML9


title: SMC3, PN3, rep2

source_name: PN3 zygote

value: PN3 zygote


title: SMC3, PN3, rep1


title: Human_Ulix_6_15

description: Library name: Sample15


title: SMC3, EPI, rep1

value: E6.5 Epiblast


title: E10.5 WT lambdoidal junctions epithelia

description: Library name: ML7


title: Human_Ulix_6_14

description: Library name: Sample14


title: melb-a cells, lenti- shHIRA I biol rep3

value: melb-a cells

value: melanoblasts

value: wt


title: melb-a cells, lenti- shHIRA I biol rep2


title: CTCF, mESC, rep2

value: untreated

value: embryonic stem cell

value: CTCF


title: melb-a cells, lenti- shHIRA I biol rep1


title: Human_Ulix_6_13

description: Library name: Sample13

value: Embryo

value: Ulixertinib


title: melb-a cells, lenti- shHIRA II biol rep2

value: lenti- shHIRA II


title: CTCF, mESC, rep1


title: Human_Ulix_6_12

description: Library name: Sample12


title: D7 CTCF-degron (dTAG-13) ES CHART-seq input, rep2

description: Library name: dTAG Jpx CHART-seq input R2

data_processing:
CHART-Seq:  CHART-seq reads were aligned to the mm10 genome using the same parameters as those applied to RNA-seq, with the additional parameter “--alignIntronMax 1.”  Sequencing depth was increased by combining the bam files from two biological replicates. The merged bam files were used to generate input-subtracted Jpx coverage using the function “get.smoothed.tag.density” from SPP software with the parameters “bandwidth=500, step=100, tagshift.” To enable comparison across conditions, Jpx CHART profiles were normalized by equalizing coverage integrated over the Jpx locus ± 3 kb (chrX:103490558-103509425).
Assembly: mm10
Supplementary files format and content: Input-normalized coverage files (bedGraph).

growth_protocol: Undifferentiated female mouse embryonic stem cells were grown on the irradiated MEF feeders in regular DMEM medium (high-glucose) with 15% FBS and LIF. For differentiation, cells were trypsinizied and incubated in the medium at 37 °C for at least 40 min. After separation of ES cells from attached feeders, ES cells were re-plated on non-gelatinized petri dishes in the complete DMEM medium without LIF. Embryoid bodies (EB) formed from ES cells were transferred to the gelatinized cell culture plates on day 4 of differentiation. Cells were harvested on day 7.

extract_protocol:
CHART-seq: Cells were crosslinked with 1% formaldehyde and nuclei were further crosslinked with 3% formaldehyde. Nuclei chromatin was sheared by sonication to yield the majority of fragments with approximately 3kb. The resulting extracts were hybridized with either Jpx CHART probes (biotinylated DNA oligonucleotides that were complementary to Jpx) and captured by streptavidin beads. After washes, DNA was eluted in the elution buffer with RNase H.
CHART enriched DNA was further sonicated and subjected to library construction steps including end-repair, dA-tailing, adaptor ligation, double-size selection and PCR amplification using NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S) for Illumina.

value: Differentiating mESC (day 7)

value: CTCF degron


title: Human_Ulix_6_11

description: Library name: Sample11

data_processing:
Raw sequencing was processed according to a modified nf-core/scrnaseq pipeline
Reads were trimmed to remove adapter sequences and aligned to the human GRCh38 reference genomes using STAR aligner
Transcript abundances, using the Ensembl gene annotations (versions 110 for human) were estimated using STAR quantmode, converted into a count matrix and further processed using scanpy. No computational doublet detection was performed. We excluded samples in which more than 30% of total reads aligning to the mitochondrial genome and fewer than 8,000 unique genes were detected.
Assembly: Human GRCh38
Supplementary files format and content: tab delimited .h5ad file

value: Human pre-implantation embryo


title: melb-a cells, lenti- shScramble biol rep4

value: lenti- shScramble


title: Human_Ulix_6_10

description: Library name: Sample10


title: CTCF, EPI, rep2

value: PWK/PhJ (Pat) x C57BL/6J (Mat)

value: WT


title: D7 CTCF-degron (dTAG-13) ES Jpx CHART-seq, rep2

description:
Library name: dTAG Jpx CHART-seq R2
Processed data: Xic.dTAG.input-normalized Jpx CHART.comp.bedGraph


title: Human_Ulix_6_16

description: Library name: Sample16


title: melb-a cells, lenti- shScramble biol rep2


title: CTCF, EPI, rep1


title: D7 CTCF-degron (dTAG-13) ES Jpx CHART-seq, rep1

description:
Library name: dTAG Jpx CHART-seq R1
Processed data: Xic.dTAG.input-normalized Jpx CHART.comp.bedGraph


title: melb-a cells, lenti- shScramble biol rep3


title: Human_Ulix_6_9

description: Library name: Sample9


title: melb-a cells, lenti- shScramble biol rep1


title: E11.5 lambdoidal junctions epithelia replicate 1

description: Library name: ML8

value: lambdoidal junctions

value: Mouse stem cells

value: Epithelial cells


title: CTCF, ICM, rep2

source_name: ICM of E3.5 blastocyst

value: ICM of E3.5 blastocyst


title: D7 CTCF-degron (DMSO) ES CHART-seq input, rep2

description: Library name: DMSO Jpx CHART-seq input R2

value: DMSO


title: Human_Ulix_6_8

description: Library name: Sample8


title: D7 CTCF-degron (DMSO) ES Jpx CHART-seq, rep2

description:
Library name: DMSO Jpx CHART-seq R2
Processed data: Xic.DMSO.input-normalized Jpx CHART.comp.bedGraph


title: CTCF, 8C, rep2

value: untreated


title: CTCF, ICM, rep1


title: melb-a cells, lenti- shLuciferase biol rep3

value: melb-a cells

value: melanoblasts

value: wt

value: lenti- shLuciferase


title: Human_Ulix_6_7

description: Library name: Sample7

value: Embryo

value: Ulixertinib


title: E10.5 Mutant lambdoidal junctions epithelia

description: Library name: ML6

value: Pbx1 mutant


title: D7 CTCF-degron (DMSO) ES CHART-seq input, rep1

description: Library name: DMSO Jpx CHART-seq input R1

value: Differentiating mESC (day 7)

value: CTCF degron


title: Human_Ulix_6_6

description: Library name: Sample6

value: Human pre-implantation embryo


title: melb-a cells, lenti- shLuciferase biol rep2


title: CTCF, Late2C, rep2

source_name: Late 2-cell

value: PWK/PhJ (Pat) x C57BL/6J (Mat)

value: WT

value: Late 2-cell

value: CTCF


title: D7 CTCF-degron (dTAG-13) ES CHART-seq input, rep1

description: Library name: dTAG Jpx CHART-seq input R1


title: Human_Ulix_6_5

description: Library name: Sample5


title: melb-a cells, lenti- shLuciferase biol rep1


title: Human_Ulix_6_4

description: Library name: Sample4


title: Human_Ulix_6_3

description: Library name: Sample3


title: D7 WT ES CHART-seq input, rep2

description: Library name: WT Jpx CHART-seq input R2


title: melb-a cells, lenti- shLuciferase biol rep4


title: CTCF, Late2C, rep1


title: melb-a cells, parental biol rep4

value: parental


title: Human_Ulix_6_2

description: Library name: Sample2


title: CTCF, PN3, rep2

value: PN3 zygote


title: CTCF, Early2C, rep2

value: untreated

value: Early 2-cell


title: melb-a cells, parental biol rep1

value: melb-a cells

value: melanoblasts


title: D7 WT ES CHART-seq input, rep1

description: Library name: WT Jpx CHART-seq input R1


title: melb-a cells, parental biol rep3

value: wt


title: D7 WT ES Jpx CHART-seq, rep1

description:
Library name: WT Jpx CHART-seq R1
Processed data: Xic.WT.input-normalized Jpx CHART.comp.bedGraph


title: CTCF, 8C, rep1


title: Human_Ulix_6_1

description: Library name: Sample1

value: Embryo


title: CTCF, PN3, rep1


title: D7 CTCF-degron (DMSO) ES Jpx CHART-seq, rep1

description:
Library name: DMSO Jpx CHART-seq R1
Processed data: Xic.DMSO.input-normalized Jpx CHART.comp.bedGraph

value: DMSO


title: Etoposide|25.0uM|DTXSID5023035|24h|S40_S23-etopiside-25-24-1

status: Public on Jun 10 2025

city: Research Triangle Park

first: Imran

last: Shah

state: NC

address: Mail Code: D143-02

department: Office of Research and Development

institute: US Environmental Protection Agency

description:
Library name: S40_S23-etopiside-25-24-1
TempO-LINC

data_processing:
To generate the TempO-LINC® single-cell expression data, barcoded reads were demultiplexed using an in-house developed software. Briefly, reads were scanned to find the sequences of the barcodes, allowing an offset of up to 3 nucleotides from their expected positions and 1 mismatch from their expected sequence to allow for gaps and variations due to minor sequencing errors. Reads featuring the same barcode combination were pooled together into barcode-associated clusters. A cell calling read threshold was set at 10,000 reads/cell based on inflection point analysis of a ranked barcode distribution plot (knee plot). Cell-associated reads were then aligned to the reference human whole transcriptome TempO-Seq probe sequences using bwa v. 0.7.17 (mem algorithm, parameters: -v 1 -c 2 -L 100). UMIs were used to collapse the reads originating from the same transcript and remove any PCR duplicates. The probes featuring a UMI count >0 for each single-cell alignment indicated an expressed/detected gene. Cell count tables were generated using the software featureCount v 2.0.1 (BioSpyder human transcriptome probes v2.1).
Assembly: BioSpyder human transcriptome probes v2.1 (GRCh38)
Supplementary files format and content: AnnData single-cell format using gzip compression. Created using scanpy v1.10.3

source_name: liver

growth_protocol: Terminally differentiated human hepatic cells (NoSpin HepaRG™) provided directly from the distributer (Lonza, Morrisville, NC) were seeded at 3X10^3 cells/cm2 in 24-well plates coated with rat tail collagen (Sigma-Aldrich, Saint Louis, MO) at a density of approximately 5 µg/cm2. After dispersion and seeding, cells were allowed to settle in the plate at room temperature for ~2 hrs in a biosafety cabinet before being transferred to an incubator set at 37°C, 5% CO2. Cells were incubated for 7 days in HepaRG Base Medium with Supplement (MH100; Lonza) plus Thawing and Plating additive (MHTAP; Lonza) before treatments, changing the media every 48-72 hrs. During cellular treatment, 0.1% DMSO was used as a vehicle control, corresponding to the final vehicle percentage for all solubilized chemicals. Treatments were carried out for 24 hrs before termination.

extract_protocol:
Following treatment, cells were dissociated into a single cell suspension, cell counts and viability were determined with a fluorometric Nexcelom Cellometer automated cell counter (Nexcelom Biosciences, Lawrence, MA) using Acridine Orange (AO)/Propidium Iodide (PI) stain (Perkin Elmer, Inc., Waltham, MA), following manufacturer’s instructions, and then the cells were fixed and processed for single-cell library construction. Cells were initially incubated for 11 min at 37°C in 0.25% Trypsin-EDTA (Thermo Fisher Scientific) with 40 mM DTT, 0.1 mg/ml actinomycin D, 1 mg/ml anisomycin, and 6 mM RNaseOUT recombinant ribonuclease inhibitor (Thermo Fisher Scientific, Waltham, MA) in 250 µl volume, followed by an additional 15 min 37°C incubation after adding 250 µl 0.5% Collagenase Type 1 (Worthington, Lakewood, NJ) in EBSS (Earle's Balanced Salt Solution) and DTT (Dithiothreitol) 40mM  DTT (Dithiothreitol) and 6mM RNaseOUT. Using a wide-bore pipette tip, cells were then dissociated by gentle pipetting for 10 min, 2 ml of 37°C HepaRG Base Medium was added to stop enzymatic activity, and cells were pelleted at 200 xg for 3 min at 4°C. After media removal, cells were resuspended in 1 ml cell suspension media (1X PBS, 0.5% Opti-Prep Density Gradient Medium (Sigma-Aldrich), 0.1% Bovine Serum Albumin Fraction V (Thermo Fisher Scientific, Waltham, MA), 6 mM RNaseOUT) pre-chilled to 4°C. The cells were pelleted twice more at 200 xg for 3 min at 4°C, washing each time with fresh Cell Suspension Media. After the final wash, cells were filtered through a 40 µm nylon cell strainer, transferred, and stored in a Lo-Bind tube. For the TempO-LINC® assay samples, dissociated cells were fixed in 1% paraformaldehyde solution in 1 X PBS at room temp for 25 min with slow rocking, then quenched in 1:1 volume of 10 mM Tris 0.1% Pluronic F-68 (Thermo Fisher Scientific). Cells were then pelleted at 500xg for 5 min at 4°C and washed in 0.1% Pluronic F-68, 0.1% BSA Bovine Serum Albumin Fraction V, 0.1 U/µl Superase*In (Thermo Fisher Scientific) and 0.1 U/µl Enzymatics (Qiagen, Germantown, MD) ribonuclease inhibitors, and 40 mM DTT. After a final spin, most of the supernatant was removed, and cells were frozen at -20°C overnight, then stored at -80°C until library prep.
TempO-LINC® single-cell sequencing libraries were prepared using the TempO-LINC v1.0 protocol (BioSpyder, Carlsbad, CA) by BioSpyder. Briefly, saponin permeabilized cells from each sample were first hybridized with BioSpyder TempO-Seq whole transcriptome WT v2.1 Detector Oligos (DOs) that had been 5’ phosphorylated. Following hybridization, excess DOs were washed away, and the remaining DOs hybridized to target mRNA were ligated at 37°C for 1 hr. Samples were then labeled by distributing them into 48 wells of a microplate. Each well contained fixed cells from one of the treatment samples and one of 48 unique molecular barcodes (“barcode 1”) Then the barcodes were ligated to the 5’ phosphorylated detector oligos - still hybridized to mRNA within the fixed cells. This first barcode not only comprised a portion of each cell-specific barcode but since each treatment sample was placed into a unique well for ligating on barcode 1, barcode 1 also identified the treatment condition. Cells were pooled following the first sample barcode ligation and then redistributed into wells of a plate containing 48 additional barcodes (“barcode 2”) were ligated onto barcode 1. Following pooling and a third round of barcode addition by ligation (“barcode 3”), after which unique molecular indexes (UMIs) were also added, cells were pooled once again and then distributed into 12 PCR tubes, and the fully barcoded DOs were amplified with indexed primers, a separate unique index being added to each PCR tube. Combining these barcodes and UMIs allows single-cell RNA sequencing to efficiently process large numbers of cells from multiple samples, allowing for comprehensive analysis of cellular heterogeneity and gene expression patterns (Eastburn et al. 2024). Amplified DNA was pooled, purified, and quantified before paired-end sequencing on an Illumina NovaSeq 6000 using a S4 flow cell.

treatment_protocol: A set of 8 chemicals (including DMSO control) was tested to investigate distinct mechanisms of cellular stress responses. Chemical concentrations were selected to ensure that they did not induce significant cell dealth in HepaRG cells by keeping them below the AC50 for cytotoxicity.   Brefeldin A, recognized for its role in inducing the unfolded protein response (UPR) by disrupting ER-to-Golgi protein transport, was used at concentrations ranging from 0.001, 0.01, and  0.100 µM. Etoposide, a well-known DNA damage response (DDR) activator and a topoisomerase II inhibitor, was included at doses of 0.25, 2.5, and 25 µM to assess DDR activation and cytotoxicity. For investigating oxidative stress response (OSR), tert-butylhydroquinone was chosen for its ability to activate the NRF2 pathway, a key player in cellular defense against oxidative stress, and was tested at concentrations of 3, 30, and 300 µM. Rotenone, known to induce mitochondrial stress by inhibiting the mitochondrial electron transport chain, was tested at concentrations of 0.2, 0.4, and 0.8 µM. Cycloheximide, a protein synthesis inhibitor impacting many cellular processes, was tested at concentrations of 0.200, 2.000, and 20.000 µM. Tunicamycin, another UPR inducer known for inhibiting N-linked glycosylation, was tested at concentrations of 0.001, 0.010, and 0.100 µM. Lastly, troglitazone, a PPARγ agonist influencing lipid metabolism and mitochondrial function and can modulate PPARα pathway activity, was tested at concentrations of 0.001, 0.010, and 0.100 µM. 0.1% dimethyl sulfoxide (DMSO) was used as the vehicle control for all treatments. These test chemicals, spanning a range of concentrations, were selected to provide a comprehensive view of transcriptional concentration responses across different cellular stress pathways without reaching a concentration level of each producing significant cell loss.

value: liver

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

tag: timeh

tag: chem name

value: Etoposide

tag: conc

tag: dtxsid


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S40_S21-brefeldin-a-0.1-24-1

description:
Library name: S40_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A

tag: batch


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S40_S20-tBHQ-300-24-1

description:
Library name: S40_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S40_S24-tuncamycin-0.1-24-1

description:
Library name: S40_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S40_S22-cycloheximide-20-24-1

description:
Library name: S40_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S40_S16-cycloheximide-2-24-1

description:
Library name: S40_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S40_S17-etopiside-2.5-24-1

description:
Library name: S40_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S40_S18-tuncamycin-0.01-24-1

description:
Library name: S40_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells


title: CTCF, Early2C, rep1

value: PWK/PhJ (Pat) x C57BL/6J (Mat)

value: WT

value: untreated

value: Early 2-cell

value: CTCF


title: D7 WT ES Jpx CHART-seq, rep2

description:
Library name: WT Jpx CHART-seq R2
Processed data: Xic.WT.input-normalized Jpx CHART.comp.bedGraph

value: Differentiating mESC (day 7)


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S39_S24-tuncamycin-0.1-24-1

description:
Library name: S39_S24-tuncamycin-0.1-24-1
TempO-LINC

value: liver

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S40_S15-brefeldin-a-0.01-24-1

description:
Library name: S40_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: Troglitazone|0.01uM|DTXSID8023719|24h|S40_S13-troglitazone-0.01-24-1

description:
Library name: S40_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S40_S14-tBHQ-30-24-1

description:
Library name: S40_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S39_S22-cycloheximide-20-24-1

description:
Library name: S39_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: melb-a cells, parental biol rep2

value: melb-a cells

value: melanoblasts

value: wt

value: parental


title: Etoposide|25.0uM|DTXSID5023035|24h|S39_S23-etopiside-25-24-1

description:
Library name: S39_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S39_S21-brefeldin-a-0.1-24-1

description:
Library name: S39_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: liver

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S39_S20-tBHQ-300-24-1

description:
Library name: S39_S20-tBHQ-300-24-1
TempO-LINC

value: HepaRG

value: differentiated HepaRG hepatocyte-like cells

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S39_S15-brefeldin-a-0.01-24-1

description:
Library name: S39_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S39_S14-tBHQ-30-24-1

description:
Library name: S39_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S39_S18-tuncamycin-0.01-24-1

description:
Library name: S39_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Etoposide|2.5uM|DTXSID5023035|24h|S39_S17-etopiside-2.5-24-1

description:
Library name: S39_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S39_S19-troglitazone-0.1-24-1

description:
Library name: S39_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S39_S16-cycloheximide-2-24-1

description:
Library name: S39_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells

value: Cycloheximide


title: Troglitazone|0.01uM|DTXSID8023719|24h|S39_S13-troglitazone-0.01-24-1

description:
Library name: S39_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S40_S19-troglitazone-0.1-24-1

description:
Library name: S40_S19-troglitazone-0.1-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S38_S22-cycloheximide-20-24-1

description:
Library name: S38_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S38_S19-troglitazone-0.1-24-1

description:
Library name: S38_S19-troglitazone-0.1-24-1
TempO-LINC

value: liver


title: Etoposide|2.5uM|DTXSID5023035|24h|S38_S17-etopiside-2.5-24-1

description:
Library name: S38_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S38_S21-brefeldin-a-0.1-24-1

description:
Library name: S38_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: HepaRG

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S38_S18-tuncamycin-0.01-24-1

description:
Library name: S38_S18-tuncamycin-0.01-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S38_S16-cycloheximide-2-24-1

description:
Library name: S38_S16-cycloheximide-2-24-1
TempO-LINC


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S38_S14-tBHQ-30-24-1

description:
Library name: S38_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone


title: Troglitazone|0.01uM|DTXSID8023719|24h|S38_S13-troglitazone-0.01-24-1

description:
Library name: S38_S13-troglitazone-0.01-24-1
TempO-LINC


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S37_S21-brefeldin-a-0.1-24-1

description:
Library name: S37_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A


title: Etoposide|25.0uM|DTXSID5023035|24h|S37_S23-etopiside-25-24-1

description:
Library name: S37_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S37_S20-tBHQ-300-24-1

description:
Library name: S37_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S37_S22-cycloheximide-20-24-1

description:
Library name: S37_S22-cycloheximide-20-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S37_S24-tuncamycin-0.1-24-1

description:
Library name: S37_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S38_S15-brefeldin-a-0.01-24-1

description:
Library name: S38_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S37_S18-tuncamycin-0.01-24-1

description:
Library name: S37_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S37_S16-cycloheximide-2-24-1

description:
Library name: S37_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S37_S17-etopiside-2.5-24-1

description:
Library name: S37_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S38_S24-tuncamycin-0.1-24-1

description:
Library name: S38_S24-tuncamycin-0.1-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S38_S23-etopiside-25-24-1

description:
Library name: S38_S23-etopiside-25-24-1
TempO-LINC


title: Troglitazone|0.01uM|DTXSID8023719|24h|S37_S13-troglitazone-0.01-24-1

description:
Library name: S37_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S37_S15-brefeldin-a-0.01-24-1

description:
Library name: S37_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: liver


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S36_S24-tuncamycin-0.1-24-1

description:
Library name: S36_S24-tuncamycin-0.1-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S36_S23-etopiside-25-24-1

description:
Library name: S36_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S38_S20-tBHQ-300-24-1

description:
Library name: S38_S20-tBHQ-300-24-1
TempO-LINC

value: HepaRG


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S36_S20-tBHQ-300-24-1

description:
Library name: S36_S20-tBHQ-300-24-1
TempO-LINC


title: Troglitazone|0.1uM|DTXSID8023719|24h|S36_S19-troglitazone-0.1-24-1

description:
Library name: S36_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S36_S16-cycloheximide-2-24-1

description:
Library name: S36_S16-cycloheximide-2-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Cycloheximide


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S36_S18-tuncamycin-0.01-24-1

description:
Library name: S36_S18-tuncamycin-0.01-24-1
TempO-LINC


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S36_S14-tBHQ-30-24-1

description:
Library name: S36_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Etoposide|2.5uM|DTXSID5023035|24h|S36_S17-etopiside-2.5-24-1

description:
Library name: S36_S17-etopiside-2.5-24-1
TempO-LINC


title: Troglitazone|0.1uM|DTXSID8023719|24h|S37_S19-troglitazone-0.1-24-1

description:
Library name: S37_S19-troglitazone-0.1-24-1
TempO-LINC


title: Troglitazone|0.01uM|DTXSID8023719|24h|S36_S13-troglitazone-0.01-24-1

description:
Library name: S36_S13-troglitazone-0.01-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S35_S24-tuncamycin-0.1-24-1

description:
Library name: S35_S24-tuncamycin-0.1-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S35_S23-etopiside-25-24-1

description:
Library name: S35_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S35_S20-tBHQ-300-24-1

description:
Library name: S35_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S35_S19-troglitazone-0.1-24-1

description:
Library name: S35_S19-troglitazone-0.1-24-1
TempO-LINC


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S35_S18-tuncamycin-0.01-24-1

description:
Library name: S35_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin


title: Etoposide|2.5uM|DTXSID5023035|24h|S35_S17-etopiside-2.5-24-1

description:
Library name: S35_S17-etopiside-2.5-24-1
TempO-LINC


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S37_S14-tBHQ-30-24-1

description:
Library name: S37_S14-tBHQ-30-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S34_S24-tuncamycin-0.1-24-1

description:
Library name: S34_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S36_S22-cycloheximide-20-24-1

description:
Library name: S36_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Etoposide|25.0uM|DTXSID5023035|24h|S34_S23-etopiside-25-24-1

description:
Library name: S34_S23-etopiside-25-24-1
TempO-LINC


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S35_S15-brefeldin-a-0.01-24-1

description:
Library name: S35_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells

value: Brefeldin A


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S35_S14-tBHQ-30-24-1

description:
Library name: S35_S14-tBHQ-30-24-1
TempO-LINC


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S36_S21-brefeldin-a-0.1-24-1

description:
Library name: S36_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S35_S16-cycloheximide-2-24-1

description:
Library name: S35_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Troglitazone|0.01uM|DTXSID8023719|24h|S35_S13-troglitazone-0.01-24-1

description:
Library name: S35_S13-troglitazone-0.01-24-1
TempO-LINC

value: liver

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S34_S21-brefeldin-a-0.1-24-1

description:
Library name: S34_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: HepaRG


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S34_S22-cycloheximide-20-24-1

description:
Library name: S34_S22-cycloheximide-20-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S34_S20-tBHQ-300-24-1

description:
Library name: S34_S20-tBHQ-300-24-1
TempO-LINC


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S34_S18-tuncamycin-0.01-24-1

description:
Library name: S34_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S34_S17-etopiside-2.5-24-1

description:
Library name: S34_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Troglitazone|0.1uM|DTXSID8023719|24h|S34_S19-troglitazone-0.1-24-1

description:
Library name: S34_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S36_S15-brefeldin-a-0.01-24-1

description:
Library name: S36_S15-brefeldin-a-0.01-24-1
TempO-LINC


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S34_S16-cycloheximide-2-24-1

description:
Library name: S34_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S34_S15-brefeldin-a-0.01-24-1

description:
Library name: S34_S15-brefeldin-a-0.01-24-1
TempO-LINC


title: Troglitazone|0.01uM|DTXSID8023719|24h|S34_S13-troglitazone-0.01-24-1

description:
Library name: S34_S13-troglitazone-0.01-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S33_S22-cycloheximide-20-24-1

description:
Library name: S33_S22-cycloheximide-20-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S33_S24-tuncamycin-0.1-24-1

description:
Library name: S33_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S35_S22-cycloheximide-20-24-1

description:
Library name: S35_S22-cycloheximide-20-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S33_S23-etopiside-25-24-1

description:
Library name: S33_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S35_S21-brefeldin-a-0.1-24-1

description:
Library name: S35_S21-brefeldin-a-0.1-24-1
TempO-LINC


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S34_S14-tBHQ-30-24-1

description:
Library name: S34_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S33_S21-brefeldin-a-0.1-24-1

description:
Library name: S33_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A


title: Troglitazone|0.1uM|DTXSID8023719|24h|S33_S19-troglitazone-0.1-24-1

description:
Library name: S33_S19-troglitazone-0.1-24-1
TempO-LINC


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S33_S18-tuncamycin-0.01-24-1

description:
Library name: S33_S18-tuncamycin-0.01-24-1
TempO-LINC


title: Etoposide|2.5uM|DTXSID5023035|24h|S33_S17-etopiside-2.5-24-1

description:
Library name: S33_S17-etopiside-2.5-24-1
TempO-LINC


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S33_S15-brefeldin-a-0.01-24-1

description:
Library name: S33_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S33_S16-cycloheximide-2-24-1

description:
Library name: S33_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Troglitazone|0.01uM|DTXSID8023719|24h|S33_S13-troglitazone-0.01-24-1

description:
Library name: S33_S13-troglitazone-0.01-24-1
TempO-LINC

value: liver


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S32_S24-tuncamycin-0.1-24-1

description:
Library name: S32_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S33_S14-tBHQ-30-24-1

description:
Library name: S33_S14-tBHQ-30-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S32_S23-etopiside-25-24-1

description:
Library name: S32_S23-etopiside-25-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S32_S22-cycloheximide-20-24-1

description:
Library name: S32_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S32_S21-brefeldin-a-0.1-24-1

description:
Library name: S32_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: HepaRG

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S32_S20-tBHQ-300-24-1

description:
Library name: S32_S20-tBHQ-300-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S32_S18-tuncamycin-0.01-24-1

description:
Library name: S32_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S32_S19-troglitazone-0.1-24-1

description:
Library name: S32_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S32_S14-tBHQ-30-24-1

description:
Library name: S32_S14-tBHQ-30-24-1
TempO-LINC


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S32_S15-brefeldin-a-0.01-24-1

description:
Library name: S32_S15-brefeldin-a-0.01-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S31_S24-tuncamycin-0.1-24-1

description:
Library name: S31_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S32_S16-cycloheximide-2-24-1

description:
Library name: S32_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide


title: Troglitazone|0.01uM|DTXSID8023719|24h|S32_S13-troglitazone-0.01-24-1

description:
Library name: S32_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S33_S20-tBHQ-300-24-1

description:
Library name: S33_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S31_S22-cycloheximide-20-24-1

description:
Library name: S31_S22-cycloheximide-20-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S31_S23-etopiside-25-24-1

description:
Library name: S31_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S31_S21-brefeldin-a-0.1-24-1

description:
Library name: S31_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S31_S20-tBHQ-300-24-1

description:
Library name: S31_S20-tBHQ-300-24-1
TempO-LINC

value: liver


title: Etoposide|2.5uM|DTXSID5023035|24h|S31_S17-etopiside-2.5-24-1

description:
Library name: S31_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S31_S19-troglitazone-0.1-24-1

description:
Library name: S31_S19-troglitazone-0.1-24-1
TempO-LINC


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S31_S16-cycloheximide-2-24-1

description:
Library name: S31_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S31_S14-tBHQ-30-24-1

description:
Library name: S31_S14-tBHQ-30-24-1
TempO-LINC

value: HepaRG

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Troglitazone|0.01uM|DTXSID8023719|24h|S31_S13-troglitazone-0.01-24-1

description:
Library name: S31_S13-troglitazone-0.01-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S30_S24-tuncamycin-0.1-24-1

description:
Library name: S30_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: Etoposide|25.0uM|DTXSID5023035|24h|S30_S23-etopiside-25-24-1

description:
Library name: S30_S23-etopiside-25-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S30_S22-cycloheximide-20-24-1

description:
Library name: S30_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S30_S19-troglitazone-0.1-24-1

description:
Library name: S30_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S30_S17-etopiside-2.5-24-1

description:
Library name: S30_S17-etopiside-2.5-24-1
TempO-LINC


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S30_S20-tBHQ-300-24-1

description:
Library name: S30_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S30_S16-cycloheximide-2-24-1

description:
Library name: S30_S16-cycloheximide-2-24-1
TempO-LINC


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S30_S21-brefeldin-a-0.1-24-1

description:
Library name: S30_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S30_S15-brefeldin-a-0.01-24-1

description:
Library name: S30_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S30_S18-tuncamycin-0.01-24-1

description:
Library name: S30_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Etoposide|2.5uM|DTXSID5023035|24h|S32_S17-etopiside-2.5-24-1

description:
Library name: S32_S17-etopiside-2.5-24-1
TempO-LINC


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S30_S14-tBHQ-30-24-1

description:
Library name: S30_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone


title: Troglitazone|0.01uM|DTXSID8023719|24h|S30_S13-troglitazone-0.01-24-1

description:
Library name: S30_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S29_S22-cycloheximide-20-24-1

description:
Library name: S29_S22-cycloheximide-20-24-1
TempO-LINC

value: liver

value: Cycloheximide


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S29_S24-tuncamycin-0.1-24-1

description:
Library name: S29_S24-tuncamycin-0.1-24-1
TempO-LINC


title: Etoposide|25.0uM|DTXSID5023035|24h|S29_S23-etopiside-25-24-1

description:
Library name: S29_S23-etopiside-25-24-1
TempO-LINC

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S29_S20-tBHQ-300-24-1

description:
Library name: S29_S20-tBHQ-300-24-1
TempO-LINC

value: HepaRG


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S29_S21-brefeldin-a-0.1-24-1

description:
Library name: S29_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Brefeldin A


title: Troglitazone|0.1uM|DTXSID8023719|24h|S29_S19-troglitazone-0.1-24-1

description:
Library name: S29_S19-troglitazone-0.1-24-1
TempO-LINC


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S31_S18-tuncamycin-0.01-24-1

description:
Library name: S31_S18-tuncamycin-0.01-24-1
TempO-LINC


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S29_S18-tuncamycin-0.01-24-1

description:
Library name: S29_S18-tuncamycin-0.01-24-1
TempO-LINC


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S29_S16-cycloheximide-2-24-1

description:
Library name: S29_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S29_S15-brefeldin-a-0.01-24-1

description:
Library name: S29_S15-brefeldin-a-0.01-24-1
TempO-LINC


title: Etoposide|2.5uM|DTXSID5023035|24h|S29_S17-etopiside-2.5-24-1

description:
Library name: S29_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S29_S14-tBHQ-30-24-1

description:
Library name: S29_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S28_S24-tuncamycin-0.1-24-1

description:
Library name: S28_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: Etoposide|25.0uM|DTXSID5023035|24h|S28_S23-etopiside-25-24-1

description:
Library name: S28_S23-etopiside-25-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S28_S22-cycloheximide-20-24-1

description:
Library name: S28_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide|20.0uM|DTXSID6024882 for 24h in HepaRG cells


title: Troglitazone|0.01uM|DTXSID8023719|24h|S29_S13-troglitazone-0.01-24-1

description:
Library name: S29_S13-troglitazone-0.01-24-1
TempO-LINC


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S28_S21-brefeldin-a-0.1-24-1

description:
Library name: S28_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: Brefeldin A|0.1uM|DTXSID00880041 for 24h in HepaRG cells


title: Troglitazone|0.1uM|DTXSID8023719|24h|S28_S19-troglitazone-0.1-24-1

description:
Library name: S28_S19-troglitazone-0.1-24-1
TempO-LINC

value: Troglitazone|0.1uM|DTXSID8023719 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S28_S17-etopiside-2.5-24-1

description:
Library name: S28_S17-etopiside-2.5-24-1
TempO-LINC


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S28_S18-tuncamycin-0.01-24-1

description:
Library name: S28_S18-tuncamycin-0.01-24-1
TempO-LINC

value: Tunicamycin|0.01uM|DTXSID8036730 for 24h in HepaRG cells

value: Tunicamycin


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S28_S15-brefeldin-a-0.01-24-1

description:
Library name: S28_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A|0.01uM|DTXSID00880041 for 24h in HepaRG cells


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S28_S16-cycloheximide-2-24-1

description:
Library name: S28_S16-cycloheximide-2-24-1
TempO-LINC

value: liver


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S28_S20-tBHQ-300-24-1

description:
Library name: S28_S20-tBHQ-300-24-1
TempO-LINC

value: tert-Butylhydroquinone|300.0uM|DTXSID6020220 for 24h in HepaRG cells

value: tert-Butylhydroquinone


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S28_S14-tBHQ-30-24-1

description:
Library name: S28_S14-tBHQ-30-24-1
TempO-LINC


title: Cycloheximide|20.0uM|DTXSID6024882|24h|S27_S22-cycloheximide-20-24-1

description:
Library name: S27_S22-cycloheximide-20-24-1
TempO-LINC

value: Cycloheximide


title: Brefeldin A|0.1uM|DTXSID00880041|24h|S27_S21-brefeldin-a-0.1-24-1

description:
Library name: S27_S21-brefeldin-a-0.1-24-1
TempO-LINC

value: HepaRG


title: Etoposide|25.0uM|DTXSID5023035|24h|S27_S23-etopiside-25-24-1

description:
Library name: S27_S23-etopiside-25-24-1
TempO-LINC

value: differentiated HepaRG hepatocyte-like cells

value: Etoposide|25.0uM|DTXSID5023035 for 24h in HepaRG cells

value: Etoposide


title: Troglitazone|0.01uM|DTXSID8023719|24h|S28_S13-troglitazone-0.01-24-1

description:
Library name: S28_S13-troglitazone-0.01-24-1
TempO-LINC

value: Troglitazone|0.01uM|DTXSID8023719 for 24h in HepaRG cells

value: Troglitazone


title: Brefeldin A|0.01uM|DTXSID00880041|24h|S31_S15-brefeldin-a-0.01-24-1

description:
Library name: S31_S15-brefeldin-a-0.01-24-1
TempO-LINC

value: Brefeldin A


title: Troglitazone|0.1uM|DTXSID8023719|24h|S27_S19-troglitazone-0.1-24-1

description:
Library name: S27_S19-troglitazone-0.1-24-1
TempO-LINC


title: tert-Butylhydroquinone|300.0uM|DTXSID6020220|24h|S27_S20-tBHQ-300-24-1

description:
Library name: S27_S20-tBHQ-300-24-1
TempO-LINC


title: Tunicamycin|0.1uM|DTXSID8036730|24h|S27_S24-tuncamycin-0.1-24-1

description:
Library name: S27_S24-tuncamycin-0.1-24-1
TempO-LINC

value: Tunicamycin|0.1uM|DTXSID8036730 for 24h in HepaRG cells


title: Etoposide|2.5uM|DTXSID5023035|24h|S27_S17-etopiside-2.5-24-1

description:
Library name: S27_S17-etopiside-2.5-24-1
TempO-LINC

value: Etoposide|2.5uM|DTXSID5023035 for 24h in HepaRG cells


title: Tunicamycin|0.01uM|DTXSID8036730|24h|S27_S18-tuncamycin-0.01-24-1

description:
Library name: S27_S18-tuncamycin-0.01-24-1
TempO-LINC


title: Cycloheximide|2.0uM|DTXSID6024882|24h|S27_S16-cycloheximide-2-24-1

description:
Library name: S27_S16-cycloheximide-2-24-1
TempO-LINC

value: Cycloheximide|2.0uM|DTXSID6024882 for 24h in HepaRG cells


title: tert-Butylhydroquinone|30.0uM|DTXSID6020220|24h|S27_S14-tBHQ-30-24-1

description:
Library name: S27_S14-tBHQ-30-24-1
TempO-LINC

value: tert-Butylhydroquinone|30.0uM|DTXSID6020220 for 24h in HepaRG cells


title: Troglitazone|0.01uM|DTXSID8023719|24h|S27_S13-troglitazone-0.01-24-1

description:
Library name: S27_S13-troglitazone-0.01-24-1
TempO-LINC