title: GM00645, Wildtype, biological replicate 2, Input, G4 ChIPseq rep3

city: Tübingen

first: Yingguang Frank

last: Chan

address: Max Planck Ring 9

department: Chan group

institute: Friedrich Miescher Laboratory of the Max Planck Society

description: fastq files are trimmed fastq files; bedgraph files are genrated from the filtered bamfiles

data_processing:
Raw FASTQ reads  were extracted with bcl2fastq (version 2.20). Tn5 and Truseq adapter sequences, G repeats due to sequencing artefacts, and reads shorter than 20 bp were trimmed and removed using cutadapt (version 4.0).  Reads were then aligned to human reference genome version hg38using bwa mem (Version: 0.7.17-r1188). Duplicates were marked and removed using Picard (version 2.18.25). Prior to calling peaks, mitochondrial reads, reads with a mapping quality lower than 20 and reads in hg38 blacklisted regions (downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38human/hg38.blacklist.bed.gz) were discarded.  For each biological replicate, an equal number of reads were subsampled from each technical replicate and pooled to call peaks. Peak calling was performed using MACS2 (version 2.1.1.20160309) with callpeak –format BAM narrowPeak. Peak sets from 2 biological replicates were ranked by their signal values and then filtered based on reproducibility via IDR("Measuring reproducibility of high-throughput experiments" (2011), Annals of Applied Statistics, Vol. 5, No. 3, 1752-1779, by Li, Brown, Huang, and Bickel). The final high confidence peaks for each sample were obtained with the criteria of IDR <0.05. Peaks were also called with input samples using the same parameters, which were used as regions to be excluded in the differential analysis in Diffbind. The analysis was carried out by using default parameters and summits =FALSE, bFullLibSize=FALSE and edgeR normalization.
Assembly: hg38
Supplementary files format and content: bedgraph files generated from the filtered bamfile for each sample
Supplementary files format and content: narrowPeak, G4 ChIPseq peaks called for each biological replicate consisting of 3 technical replicates
Supplementary files format and content: narrowPeak, G4 ChIPseq peaks for WT or BLM-/- sample after filtering on irreproducibility of the ChIPseq peaks in the two biological replicates

growth_protocol: Cell lines derived from Bloom Syndrome and healthy donors were obtained from Coriell Institute (fibroblast cell lines: GM08505, GM00637). LCLs were cultured in RPMI 1640 medium (Gibco, Cat. #21875) supplemented with 15% fetal bovine serum (FBS, Gibco, UK, Cat. #10500), 1% penicillin-streptomycin (P/S, Gibco, US, Cat #15140) and 1% GlutaMAX-I (Gibco, UK, Cat. #35050).  Fibroblast lines were cultured in 1X DMEM (Gibco, UK, Cat. #11960) supplemented with, 1% minimum essential medium non-essential amino acids (MEM NEAA, Gibco, UK, Cat. #11140) and 10% (GM00637) or 15% ( GM08505) fetal bovine serum (FBS, Gibco, UK, Cat. #10500), 1% penicillin-streptomycin (P/S, Gibco, US, Cat #15140) respectively. Cell passaging was performed according to recommendations by Coriell Institute. All cells were cultured at 37°C under 5% CO2.

extract_protocol:
Chromatin preparation essentially follows the previously described protocol in {https://doi.org/10.1038/nprot.2017.150} with a few modifications. Cells cultured in two full 15cm dishes were washed once in 1xPBS and directly fixed in the dish with 1% formaldehyde in cell culture medium at RT for 8.5 min. Nuclei were lysed in 250ul lysis buffer and sheared in small tubes (microTUBE AFA Fiber Pre-Slit Snap-cap 6x16mm, Covaris, Cat. 520045) on Covaris S220 with the following parameter: water level=15, duty cycle=15, intensity =6, cycle per burst =200 for 3min. There was a 30s pause after 1 min of sonication. The IP reaction was performed essentially as described previously in {https://doi.org/10.1038/nprot.2017.150}, with the following modifications. For each sample, 2 biological replicates were prepared, each in turn divided into 3 technical replicates of immune-precipitation (IP), except for the wild-type fibroblasts, for which the second biological replicate was performed with only 2 technical replicates due to the limited amount of BG4 antibody. During BG4 IP, chromatin was incubated with the primary antibody for an extended duration of 2 hours, and a doubled amount of beads was used in pull-down. To purify DNA from both the IP samples (DNA pulled down by the beads) and the input samples (sheared chromatin without going through IP steps), 75 μl of reverse-crosslinking buffer (0.2% SDS, 1x TE, and 50 mM NaCl) was introduced. The samples were incubated at 37°C for one hour, followed by an overnight incubation at 65°C. Following an additional hour of proteinase K digestion at 65°C, DNA purification was carried out using a MinElute kit (QIAGEN).
Library preparation were carried out with the DNA Thruplex kit (Takara, Cat. #R400674, Cat. #R400665) following the manufacturer’s protocols.

value: fibroblast

value: Wildtype

tag: chip antibody

value: absolute antibody, cat.no. Ab00174-30.164


title: primary epithelial stem cells-derived extracellular vesicles (EV), CD9+EV, rep 2

status: Public on Feb 18 2025

type: SRA

city: SKT

first: Sunyoung

last: Park

state: Seoul

country: South Korea

institute: Yonsei university

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Quantile normalization was performed by EdgeR.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Salivary gland

growth_protocol: Human parotid gland derived epithelial cells were cultured in Dermacult with Y27632 (10uM), A83-01 (1 uM), and LDN193189 (0.1 uM).

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small  RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

treatment_protocol: To optain exosomes, we harvested medium from nearly confluent human parotid epithleial cells culture with exosome removed dermacult omitting small molecules.

tag: tissue

value: Salivary gland

tag: cell line

value: primary cell culture

tag: cell type

value: epithelial stem cell

tag: type

value: CD9+ enriched

tag: treatment


title: highly effective DSC ID2

type: RNA

city: Yokohama

first: Yumiko

last: Ishimatsu-Tsuji

address: Nishi-ku

country: Japan

institute: Shiseido

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized toand Agilent SurePrint G3 Human GE 8x60K ver2 microarray (G4858A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (AgilentG3_HiSen_GX_1Color protocol).

data_processing: The scanned images were analyzed with Feature Extraction Software12.1.0.3  (Agilent) using default parameters (protocol GE1-1200_June14 and Grid: 039494_D_F_20190203) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: clinical trial volunteers, Not disclosed

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Freshly isolated dermal sheath cups from clinical trial volunteers were transferred into culture plates and were incubated at 37°C and 5% CO2 in the culture medium for cell expansion.

extract_protocol: Cells were suspended in 1 ml of Isogen (Nippon Gene, Tokyo) and total RNA was extracted according to the instructions for use. RNA purification was performed using the RNeasy Mini Kit (Qiagen, Hilden). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent Tape station (Agilent Technologies, Santa Clara, CA).

tag: group

value: highly effective DSC

value: dermal sheath cup cells


title: ILC2s, VISTA KO rep3

city: Los Angeles

first: Mohammad Hossein

last: Kazemi

state: CA

address: 1450 Biggy St.

department: Microbiology and Molecular Immunology

country: USA

institute: University of Southern California

data_processing:
Partek Flow, version 10.0
Sequence reads were trimmed by quality score (min Phred score 20 from both end, and trimmed reads shorter than 25bp were discarded).
Trimmed reads were mapped to mm10 with GENECODE M25 annotation as a guidance by STAR 2.7.8.
Aligned reads were further quantified to GENCODE M25 with Partek E/M algorithm.
Genes with less than 10 counts in all samples were removed from the analysis. The remaining genes were subjected to differential expression analysis by DESeq2 with median ratio normalization
Assembly: mm10
Supplementary files format and content: Excel file includes raw read counts per gene per sample

organism: Mus musculus

source_name: lung

growth_protocol: Cells were freshly isolated on day 4 from the lungs of mice treated for 3 consecutive days with  0.5µg rmIL-33 intranasally

extract_protocol:
Cultured ILC2s were recovered, lysed in RLT buffer (Qiagen) and RNA was extracted using the MicroRNeasy kit (Qiagen)
For each sample, a total of 10pg of RNA was used to generate cDNA (SMARTer Ultra Low Input RNA v3 kit, Clontech) for library preparation

value: lung

tag: strain

value: BALB/c

tag: genotype

value: VISTA KO


title: highly effective DSC ID5


title: highly effective DSC ID1


title: GM00638, Wildtype, biological replicate 1, IP rep2, G4 ChIPseq rep2

country: Germany

library_source: genomic

molecule: genomic DNA

value: absolute antibody, cat.no. Ab00174-30.157


title: highly effective DSC ID6


title: ILC2s, VISTA KO rep2


title: primary epithelial stem cells-derived extracellular vesicles (EV), CD9-EV, rep 3

value: CD9+ depleted


title: Patient 130 liver scRNA-seq sample

city: Houston

first: Ziyi

last: Li

state: TX

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

library_source: transcriptomic single cell

data_processing:
Processing of raw reads was performed using the Cell Ranger software provided by 10X genomics and the hg38 human reference genome (GRCm38 v86 and corresponding GENCODE annotation file). During read alignment, PCR duplicates were removed. The UMI (unique molecular identifier) for each gene is counted to measure the gene expression levels. The cell doublet status is inferred by the software DoubletFinder. A number of quality-control metrics are evaluated to control the data quality, including the total UMI count, the total number of genes detected, the mitochondrial gene ratio, log10(gene number) per UMI, and the inferred status of cell doublet.  Low-quality cells with a total UMI count smaller than 500, a total number of genes smaller than 200, and a mitochondrial gene ratio greater than 50% are excluded for further analysis.
Assembly: GRCm38 v86
Supplementary files format and content: Filtered bc matrix from CellRanger

source_name: Liver

extract_protocol:
The sample was incubated at 37 °C for 5 min. After dissociation, 2ml of advanced DMEM+10%FBS media was added to the sample and filtered through a 70 μm cell strainer (Fisher Scientific, cat.43-10070-40) into Eppendorf tubes
The filtrate was centrifuged at 500g for 5 min, and the supernatant was removed. If the pellet was bloody, red blood cell (RBC) removal was performed using RBC Lysis Solution (1x) (Miltenyi Biotec, cat. No. 130-094-183) for 10 min at RT. Sample was then centrifuged at 500g for 5 min and pellet was resuspended in 1ml of advanced DMEM, to be combined into one Eppendorf tube.
The single-cell suspension was visualized, counted, and stored at nitrogen until 10x Genomics Single-Cell sequencing was performed.

tag: individual

value: Patient 130

value: Liver

tag: status

value: Progressor

tag: progression time

tag: progression type

value: late progressor

tag: sequencing core_id


title: Patient 99 pleural effusion scRNA-seq sample

source_name: Pleural effusion

value: Patient 99

value: Pleural effusion

value: 9 m


title: GM00640, Wildtype, biological replicate 1, Input, G4 ChIPseq rep3

value: fibroblast

value: Wildtype

value: absolute antibody, cat.no. Ab00174-30.159


title: primary epithelial stem cells-derived extracellular vesicles (EV), total EV, rep 2

value: Salivary gland

value: primary cell culture

value: epithelial stem cell

value: WT


title: primary epithelial stem cells-derived extracellular vesicles (EV), CD9-EV, rep 1


title: primary epithelial stem cells-derived extracellular vesicles (EV), total EV, rep 1

description: whole


title: GM00644, Wildtype, biological replicate 2, IP rep3, G4 ChIPseq rep3

value: absolute antibody, cat.no. Ab00174-30.163


title: primary epithelial stem cells-derived extracellular vesicles (EV), CD9-EV, rep 2


title: Patient 126 liver scRNA-seq sample

value: Patient 126


title: ILC2s, VISTA KO rep1

value: lung

value: BALB/c

value: VISTA KO


title: ILC2s, Wild type rep3

value: Wild type


title: ILC2s, Wild type rep2


title: GM00639, Wildtype, biological replicate 1, IP rep3, G4 ChIPseq rep3

value: absolute antibody, cat.no. Ab00174-30.158


title: Patient 1 pleural effusion scRNA-seq sample

value: Patient 1

value: Progressor

value: late progressor


title: GM00637, Wildtype, biological replicate 1, IP rep1, G4 ChIPseq rep1

value: fibroblast

value: absolute antibody, cat.no. Ab00174-30.156


title: Patient 3 ascites scRNA-seq sample 2

source_name: Ascites

value: Patient 3

value: Ascites


title: GM00643, Wildtype, biological replicate 2, IP rep2, G4 ChIPseq rep2

value: Wildtype

value: absolute antibody, cat.no. Ab00174-30.162


title: GM08505, BLM-/-, biological replicate 2, IP rep2, G4 ChIPseq rep2

value: BLM-/-

value: absolute antibody, cat.no. Ab00174-30.152


title: GM08505, BLM-/-, biological replicate 1, IP rep2, G4 ChIPseq rep2

value: absolute antibody, cat.no. Ab00174-30.147


title: GM08505, BLM-/-, biological replicate 1, Input, G4 ChIPseq rep3

value: absolute antibody, cat.no. Ab00174-30.149


title: GM08505, BLM-/-, biological replicate 1, IP rep3, G4 ChIPseq rep3

value: absolute antibody, cat.no. Ab00174-30.148


title: GM08505, BLM-/-, biological replicate 2, Input, G4 ChIPseq rep3

value: absolute antibody, cat.no. Ab00174-30.154


title: ILC2s, Wild type rep1

value: lung

value: BALB/c

value: Wild type


title: GM08505, BLM-/-, biological replicate 1, IP rep1, G4 ChIPseq rep1

value: absolute antibody, cat.no. Ab00174-30.146


title: DLD-1 LB2-AID, 16hr auxin, replicate 3

status: Public on Feb 17 2025

city: San Francisco

first: Yewande

last: Alabi

state: California

address: 555 Mission Bay Boulevard South Rm 312A

institute: UCSF

description:
Library name: Sample 42
DLD1_LB2_16hr-aux_3

data_processing:
Sequencing reads (fastq files) were mapped to the reference human genome GRCh38 using STAR aligner version 2.7.10a.
The bam files were indexed using samtools version 1.10. RPKM normalized coverage files were generated from the sorted bam files using bamCoverage function of deepTools package version 3.4.5.
A read counts table was generated using featureCounts version 1.6.4.
The read counts table was used as an input for DESeq2 version 1.40.2 to perform differential gene expression analysis.
Assembly: human genome GRCh38
Supplementary files format and content: tab-deliniated text file incliudes raw counts for each sample

growth_protocol: DLD1s were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GenClone 25-501) supplemented with 10% fetal bovine serum. Cells were incubated at 5% CO2 and at 37 °C.

extract_protocol:
DLD1 parental, AID-Lamin A/C, AID-Lamin B1, and AID-Lamin B2 cells were treated with auxin for 0, 16 or 96 hours. Four replicates per condition were used. Each replicate was one well of a 6-well plate (Corning 3516). RNA was extracted using RNeasy Plus Mini Kit (QIAGEN 74136). 500ng of RNA was used for the construction of sequencing libraries.
The libraries were prepped using the Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (Illumina 20040529) following the standard protocol. Each library was given a unique index using IDT for Illumina – DNA/RNA UD indexes Set A (Illumina 20026121). The library was pooled in equimolar amounts. Paired-end sequencing on the pooled library was done using the Illumina NextSeq2000.

treatment_protocol: Auxin (Sigma Aldrich I5148) was dissolved in DMSO and used at a concentration of 1mM.

value: adherant colorectal adenocarcinoma

value: 16hr auxin


title: DLD-1 LB2-AID, 96hr auxin, replicate 3

description:
Library name: Sample 46
DLD1_LB2_96hr-aux_3

value: 96hr auxin


title: DLD-1 LB2-AID, 96hr auxin, replicate 2

description:
Library name: Sample 45
DLD1_LB2_96hr-aux_2


title: DLD-1 LB2-AID, 16hr auxin, replicate 4

description:
Library name: Sample 43
DLD1_LB2_16hr-aux_4


title: GM00642, Wildtype, biological replicate 2, IP rep1, G4 ChIPseq rep1

value: fibroblast

value: absolute antibody, cat.no. Ab00174-30.161


title: DLD-1 LB2-AID, 96hr auxin, replicate 1

description:
Library name: Sample 44
DLD1_LB2_96hr-aux_1


title: DLD-1 LB2-AID, 0hr auxin, replicate 4

description:
Library name: Sample 39
DLD1_LB2_0hr-aux_4

value: 0hr auxin


title: DLD-1 LB2-AID, 0hr auxin, replicate 1

description:
Library name: Sample 36
DLD1_LB2_0hr-aux_1


title: DLD-1 LB1-AID, 96hr auxin, replicate 3

description:
Library name: Sample 34
DLD1_LB1_96hr-aux_3


title: DLD-1 LB2-AID, 16hr auxin, replicate 1

description:
Library name: Sample 40
DLD1_LB2_16hr-aux_1


title: DLD-1 LB1-AID, 96hr auxin, replicate 1

description:
Library name: Sample 32
DLD1_LB1_96hr-aux_1


title: DLD-1 LB1-AID, 96hr auxin, replicate 2

description:
Library name: Sample 33
DLD1_LB1_96hr-aux_2


title: DLD-1 LB2-AID, 0hr auxin, replicate 2

description:
Library name: Sample 37
DLD1_LB2_0hr-aux_2


title: DLD-1 LB2-AID, 0hr auxin, replicate 3

description:
Library name: Sample 38
DLD1_LB2_0hr-aux_3


title: DLD-1 LB1-AID, 96hr auxin, replicate 4

description:
Library name: Sample 35
DLD1_LB1_96hr-aux_4


title: DLD-1 LB1-AID, 16hr auxin, replicate 3

description:
Library name: Sample 30
DLD1_LB1_16hr-aux_3


title: DLD-1 LB1-AID, 16hr auxin, replicate 4

description:
Library name: Sample 31
DLD1_LB1_16hr-aux_4


title: DLD-1 LB1-AID, 16hr auxin, replicate 1

description:
Library name: Sample 28
DLD1_LB1_16hr-aux_1


title: DLD-1 LB1-AID, 16hr auxin, replicate 2

description:
Library name: Sample 29
DLD1_LB1_16hr-aux_2


title: DLD-1 LB2-AID, 16hr auxin, replicate 2

description:
Library name: Sample 41
DLD1_LB2_16hr-aux_2


title: DLD-1 LB1-AID, 0hr auxin, replicate 2

description:
Library name: Sample 26
DLD1_LB1_0hr-aux_2


title: DLD-1 LB1-AID, 0hr auxin, replicate 3

description:
Library name: Sample 27
DLD1_LB1_0hr-aux_3


title: GM08505, BLM-/-, biological replicate 2, IP rep1, G4 ChIPseq rep1

description: fastq files are trimmed fastq files; bedgraph files are genrated from the filtered bamfiles

value: absolute antibody, cat.no. Ab00174-30.151


title: DLD-1 LA/C-AID, 96hr auxin, replicate 4

description:
Library name: Sample 24
DLD1_LAC_96hr-aux_4

value: LA/C-AID


title: DLD-1 LB1-AID, 0hr auxin, replicate 1

description:
Library name: Sample 25
DLD1_LB1_0hr-aux_1


title: DLD-1 LA/C-AID, 96hr auxin, replicate 3

description:
Library name: Sample 23
DLD1_LAC_96hr-aux_3


title: DLD-1 LA/C-AID, 16hr auxin, replicate 2

description:
Library name: Sample 18
DLD1_LAC_16hr-aux_2


title: DLD-1 LA/C-AID, 0hr auxin, replicate 2

description:
Library name: Sample 14
DLD1_LAC_0hr-aux_2


title: DLD-1 LA/C-AID, 16hr auxin, replicate 3

description:
Library name: Sample 19
DLD1_LAC_16hr-aux_3


title: DLD-1 parental, 96hr auxin, replicate 4

description:
Library name: Sample 12
DLD1_96hraux_4

value: WT


title: DLD-1 LA/C-AID, 0hr auxin, replicate 1

description:
Library name: Sample 13
DLD1_LAC_0hr-aux_1


title: DLD-1 LA/C-AID, 16hr auxin, replicate 1

description:
Library name: Sample 17
DLD1_LAC_16hr-aux_1


title: DLD-1 LA/C-AID, 96hr auxin, replicate 2

description:
Library name: Sample 22
DLD1_LAC_96hr-aux_2


title: DLD-1 LA/C-AID, 16hr auxin, replicate 4

description:
Library name: Sample 20
DLD1_LAC_16hr-aux_4


title: DLD-1 parental, 96hr auxin, replicate 3

description:
Library name: Sample 11
DLD1_96hraux_3


title: DLD-1 parental, 96hr auxin, replicate 1

description:
Library name: Sample 9
DLD1_96hraux_1


title: DLD-1 LA/C-AID, 0hr auxin, replicate 4

description:
Library name: Sample 16
DLD1_LAC_0hr-aux_4


title: DLD-1 parental, 16hr auxin, replicate 3

description:
Library name: Sample 7
DLD1_16hraux_3


title: DLD-1 parental, 16hr auxin, replicate 4

description:
Library name: Sample 8
DLD1_16hraux_4


title: DLD-1 parental, 16hr auxin, replicate 2

description:
Library name: Sample 6
DLD1_16hraux_2


title: DLD-1 parental, 16hr auxin, replicate 1

description:
Library name: Sample 5
DLD1_16hraux_1


title: DLD-1 parental, 0hr auxin, replicate 4

description:
Library name: Sample 4
DLD1_0hraux_4


title: DLD-1 parental, 96hr auxin, replicate 2

description:
Library name: Sample 10
DLD1_96hraux_2


title: DLD-1 parental, 0hr auxin, replicate 1

description:
Library name: Sample 1
DLD1_0hraux_1


title: RC17 cells, FGF17, 24h, rep3

city: Copenhagen

first: Erno

last: Hänninen

address: Blegdamsvej 3B

department: reNEW, Novo Nordisk Foundation Center for Stem Cell Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
Genome alingment with nf-core/rnaseq pipeline with skip_trimming=True
Assembly: hg38
Supplementary files format and content: salmon.merged.gene_counts.tsv contains the raw gene counts for each sample

molecule: polyA RNA

source_name: directed to ventral midbrain

growth_protocol: RC17 were cultured in StemMACS iPS Brew XF (Miltenyi Biotec) and passaging was performed using 0.5mM EDTA dissociation at 37°C. For the first 24h after passaging 10µM ROCK inhibitor (Miltenyi Biotec) was included in the media. Specification of hESC towards VM fates was performed in accordance with the Nolbrant et al., 2017 protocol

extract_protocol:
Upon sample collection cells were washed once with cold PBS -/- and lysed in RLT buffer (QIAGEN). RNA was extracted using RNeasy Mini kit (QIAGEN) including on column DNase treatment (QIAGEN).
Libraries were prepared using the NEBNext Poly(A) mRNA magnetic isolation module (NEB #E7490S) in combination with NEBNext Ultra II directional RNA library prep kit for Illumina (NEB #E7765) following manufacturer’s protocol. Libraries were eluted in 17.5ul 0.1X TE after the final clean up.

treatment_protocol: On differentiation day 9, cells were treated with either FGF8b 100 ng/mL or FGF17 100 ng/mL for 15 min, 1 h, 4 h and 24 h.

value: directed to ventral midbrain

value: hESC

value: FGF17 24h


title: RC17 cells, FGF17, 4h, rep3

value: FGF17  4h


title: RC17 cells, FGF8, 1h, rep3

value: FGF8 1h


title: RC17 cells, FGF17, 1h, rep3

value: FGF17 1h


title: DLD-1 LA/C-AID, 96hr auxin, replicate 1

description:
Library name: Sample 21
DLD1_LAC_96hr-aux_1


title: DLD-1 LA/C-AID, 0hr auxin, replicate 3

description:
Library name: Sample 15
DLD1_LAC_0hr-aux_3


title: RC17 cells, FGF8, 15m, rep3

value: FGF8 15m


title: RC17 cells, FGF17, 24h, rep2


title: RC17 cells, FGF17, 15m, rep3

value: FGF17 15m


title: RC17 cells, FGF8, 24h, rep2

value: FGF8 24h


title: RC17 cells, FGF8, 4h, rep2

value: FGF8 4h


title: RC17 cells, FGF17, 4h, rep2

value: FGF17 4h


title: RC17 cells, FGF17, 1h, rep2


title: RC17 cells, FGF17, 15m, rep2


title: RC17 cells, FGF8, 1h, rep2


title: RC17 cells, FGF8, 15m, rep2


title: DLD-1 parental, 0hr auxin, replicate 3

description:
Library name: Sample 3
DLD1_0hraux_3

value: adherant colorectal adenocarcinoma


title: DLD-1 parental, 0hr auxin, replicate 2

description:
Library name: Sample 2
DLD1_0hraux_2


title: RC17 cells, FGF8, 24h, rep3


title: highly effective DSC ID3

value: highly effective DSC

value: dermal sheath cup cells


title: RC17 cells, FGF8, 24h, rep1


title: RC17 cells, FGF17, 4h, rep1


title: RC17 cells, FGF8, 4h, rep1


title: RC17 cells, FGF17, 24h, rep1


title: Patient 5 pleural effusion scRNA-seq sample

value: Patient 5

value: Pleural effusion

value: Baseline

value: on treatment

value: late progressor


title: RC17 cells, FGF17, 1h, rep1

value: directed to ventral midbrain

value: hESC


title: RC17 cells, FGF8, 15m, rep1


title: RC17 cells, FGF8, 1h, rep1

value: FGF8 1h


title: RC17 cells, FGF17, 15m, rep1


title: RC17 cells, FGF8, 4h, rep3


title: cutntag_H3K4me3_2

city: Vienna

first: Thomas

last: Eder

address: Veterinaerplatz 1

department: Department for Biological Sciences and Pathobiology

country: Austria

institute: University of Veterinary Medicine, Vienna

data_processing:
Raw files were preprocessed with prinseq-lite, aligned against the mouse (mm10) or human (hg38) reference genomes with BWA (version 0.7.17-r1188), post-processed and sorted with samtools (version 1.13). The function bamCoverage from Deeptools (version 3.5.1) was then used to create BigWig files with a binSize of 10 and using CPM for normalization. Also tornado -and profile-plots were created with Deeptools (computeMatrix and then plotHeatmap or plotProfile). Peaks were called with macs2 (version 2.1.0) and the --broad option. The R package DiffBind was then used to get differential ChIP-seq regions applying DESeq2. Read counts per genes were obtained with featureCounts from the subread package and all hockey-stick- and scatter-plots were created with ggplot2 in R.
Assembly: Cut&Tag: mm10 and hg38
Supplementary files format and content: Cut&Tag: BigWig files and peak files for all sample except IgG control.

source_name: Bone marrow of NUP98::KDM5A PDX

growth_protocol: All NUP98::KDM5A cell lines were cultured in RPMI 1640 supplemented with 10% FBS, 100 U/ml penicillin and 100 µg/ml streptomycin, 4 mM L-Glutamine, 1 mM Sodium pyruvate, 50 µM 2-Mercaptoethanol and 20 mM HEPES at 37 °C, 5% CO2, and 95% humidity. Primary NUP98::KDM5A PDX AML cells were cultured in IMDM containing 15% BIT 9500 Serum Substitute, 100 ng/ml SCF, 50 ng/ml Flt3-Ligand, 20 ng/ml IL-3, 20 ng/ml G-CSF, 100 µM ß-mercaptoethanol, 50 µg/ml gentamicin, 10 µg/ml ciprofloxacin, 500 nM SR1 and 1 µm UM729 at 37 °C, 5% CO2, and 95% humidity.

extract_protocol:
Cut&Tag: DNA was extracted by column-based DNA purification provided in the iDeal CUT&Tag kit for histones compatible with histones and some non-histone proteins (Diagenode).
Cut&Tag: Sequencing libraries were generated with the iDeal CUT&Tag kit for histones compatible with histones and some non-histone proteins (Diagenode).

treatment_protocol: Cut&Tag: Cells were treated with dTAG13 (35 nM) or DMSO for 8h.

value: Bone marrow of NUP98::KDM5A PDX

value: acute myeloid leukemia cells


title: cutntag_H3K27ac_3


title: cutntag_IgG_1


title: cutntag_H3K27ac_2


title: cutntag_H3K27ac_1


title: cutntag_H3K4me3_1


title: D5 Day 181 Control

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to Mmul_8.0.1 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package using the NCBI Homo sapiens Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+3) CPM

organism: Macaca mulatta

source_name: whole blood PaxGene vacutainer

growth_protocol: in vivo

extract_protocol:
Whole blood was collected in PaxGene vacutainers, and total RNA was isolated using the PreAnalytiX Paxgene kit protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols for the Illumina TruSeq Stranded Total RNA - Globin kit.

treatment_protocol: no treament

tag: donor id

tag: timepoint

value: Day 181

tag: agent

value: Control

tag: virus


title: D4 Day 181 Control


title: D6 Day 181 Control


title: D3 Day 181 Control


title: D7 Day 181 Control


title: D2 Day 181 Control


title: C7 Day 181 Rapamycin

value: Rapamycin


title: C6 Day 181 Rapamycin


title: C5 Day 181 Rapamycin


title: C4 Day 181 Rapamycin


title: C1 Day 181 Rapamycin


title: C3 Day 181 Rapamycin


title: D5 Day 84 Control

value: Day 84


title: D1 Day 84 Control


title: D2 Day 84 Control


title: C2 Day 181 Rapamycin


title: D7 Day 84 Control


title: D6 Day 84 Control


title: D3 Day 84 Control


title: cutntag_H3K4me3_3

tag: tissue


title: C6 Day 84 Rapamycin


title: C5 Day 84 Rapamycin


title: C7 Day 84 Rapamycin


title: C4 Day 84 Rapamycin


title: D1 Day 181 Control


title: C3 Day 84 Rapamycin


title: C2 Day 84 Rapamycin


title: D5 Day 0 Control

value: Day 0


title: D3 Day 0 Control


title: C1 Day 84 Rapamycin


title: D7 Day 0 Control


title: C6 Day 0 Rapamycin


title: D4 Day 0 Control


title: D1 Day 0 Control


title: D2 Day 0 Control


title: C4 Day 0 Rapamycin


title: D4 Day 84 Control


title: C5 Day 0 Rapamycin


title: C7 Day 0 Rapamycin


title: C2 Day 0 Rapamycin


title: C3 Day 0 Rapamycin


title: C1 Day 0 Rapamycin


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen d0-d4, rep2

city: Edinburgh

first: Elisa

last: Barbieri

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tamd0-d4 rep2

data_processing:
Quality of reads was assessed by FastQC (v. 0.11.9), index and adaptor sequences were trimmed using TrimGalore (v. 0.6.6) and Cutadapt (v. 1.9.1) followed by a second quality check with FastQC.
Sequences were aligned to the mm10 mouse reference genome using Burrows-Wheeler Alignment (BWA, v. 0.7.16) tool with the maximal exact matches (MEM) option.
Fragments were quality filtered (>10) with Samtools (v. 1.6) and PCR duplicates were marked with Picard (v. 2.23.3) and removed with Samtools. Mitochondrial fragments were eliminated with Samtools.
Mapped reads were shifted by +4 bp for the forward strand and -5 bp for the reverse strand. Shifted bam files were transformed into BED files for peak calling using MACS2.
Bigwig tracks were generated with the bamCoverage option in the python-based DeepTools  (v. 3.5.1).
Assembly: mm10
Supplementary files format and content: bigwig

growth_protocol: Cells were routinely cultured in Serum/LIF media on gelatin plates. PGCLC differentiation was perfomed as previosly descrbied (Hayashi et al, 2011). Cells were first kept in 2i/LIF (N2B27 supplemented with CHIR99021 and PD0325901 ) for at least three passages prior to EpiLC and PGCLC differentiation. EpiLCs were derived for 44 hours in EpiLC medium (N2B27 supplemented with human Activin A and Fgf) and then cultured in suspension in GK15 (GMEM 15% KOSR) for 6 days. Cultures with cytokines were also supplemented with BMP4, BMP8a, SCF, LIF and EGF.

extract_protocol:
Nuclei were resuspended in Tagmentation Master Mix containing Assembled Trasposomes (Active Motif, cat. 53150). Tagmentation was performed in a thermocycler at 37°C for 20 minutes. Tagmented DNA was recovered using the DNA Clean and Concentration-5 kit (Zymo Research, cat. D4013).
Library was prepared using NEBNext High Fidelity 2x PCR Master Mix and indexed primers reported in Buenrostro et al, 2013, using the following protocol: 72°C for 5 minutes, and 98°C for 30 seconds followed by 9 cycles of : 98°C for 10 seconds, 63°C for 30 seconds, 72°C for 1 minute.

treatment_protocol: Otx2-/- Otx2-ERT2 cells were treated with 1 µM of 4-hydroxytamoxifen for the indicated times. To change tamoxifen containing media, aggregates were collected at day 2, washed, resuspended in GK15 and incubated in 5 mm dishes in rotation until day 4 before collection and analysis.

tag: cell line

value: Otx2-/- OTX2-ERT2

value: PGCLC aggregates

tag: time point

value: day 4

value: plus cytokines, tamoxifen d0-d4


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen 6h, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tam6h rep1

tag: cell type

value: plus cytokines, tamoxifen 6h at day 4


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen 1h, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tam1h rep1

tag: treatment

value: plus cytokines, tamoxifen 1h at day 4


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen 6h, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tam6h rep2


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen 1h, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tam1h rep2


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, untreated, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 noTam rep1

value: plus cytokines


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen d0-d4, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tamd0-d4 rep1


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen d0-d2, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tamd0-d2 rep2

value: plus cytokines, tamoxifen d0-d2


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, Tamoxifen d0-d2, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 Tamd0-d2 rep1


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 2, untreated, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d2 noTam rep2

value: day 2


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 4, Tamoxifen d0-d2, CUT&RUN OTX2 rep2

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd4 Tam CUT_RUN OTX2 rep2

data_processing:
Quality of reads was assessed by FastQC (v. 0.11.9 [36]), index and adaptor sequences were trimmed using TrimGalore (v. 0.6.6 [37]) and Cutadapt (v. 1.9.1 [38]) followed by a second quality check with FastQC.
Sequences were aligned to the mm10 mouse reference genome using Burrows-Wheeler Alignment (BWA, v. 0.7.16 [39]) tool with the maximal exact matches (MEM) option.
Fragments were quality filtered (>10) with Samtools (v. 1.6[40]) and PCR duplicates were marked with Picard (v. 2.23.3 [41]) and removed with Samtools. Reads of OTX2 CUT&RUN in ESCs and EpiLCs were normalized to the number of e.coli reads before further analysis.
Peaks were called with Model-Based Analysis of ChIP-Seq (MACS2, v. 2.1.1 [42]) at 5% FDR using parameter -f BAMPE for paired-end input. Blacklisted regions were subtracted from the peak list using BEDTools (v. 2.27.1 [43]) and reproducible peaks between the 2 biological replicates were identified with IDR (v. 2.0.4.2 [44]).
Bigwig tracks were generated with the bamCoverage option in the python-based DeepTools  (v. 3.5.1).
Assembly: mm10
Supplementary files format and content: bigwigs
Library strategy: CUT&Run

extract_protocol:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN) was performed as previously reported in Skene et al 2018, using 5x105 cells per replicate, 2 biological replicates per sample, 1:100 dilution of anti-OTX2 (R&D systems, cat. AF1979) and homemade pAG-MNase.
Barcoded libraries were generated with the NEBNext Ultra II DNA Library prep kit (E7645S) and NEBNext Multiplex Oligos for Illumina (E7335S, E7500S, E7710S, E7730S) with modifications. 5 ng of DNA was used per library. End-prep and ligation were performed according to the manufacturer’s instructions. 1 µl of USER enzyme was used per sample. For the final PCR step, 1 µl of both universal and indexed primers were used, and the annealing/extension step was decreased to 30 seconds to reduced amplification of large fragments. Clean up steps were performed with home-made PCR purification beads.

value: Otx2-/- ERT2-OTX2


title: ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, Tamoxifen 6h, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 EpiLC Tam6h rep2

value: EpiLC

value: Activin A + bFGF, tamoxifen 6h


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 2, Tamoxifen d0-d2, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d2 Tamd0-d2 rep1


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 2, Tamoxifen d0-d2, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d2 Tamd0-d2 rep2


title: ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, Tamoxifen 1h, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 EpiLC Tam1h rep2

value: Activin A + bFGF, tamoxifen 1h


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 4, untreated, CUT&RUN OTX2 rep2

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd4 noTam CUT_RUN OTX2 rep2


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 4, Tamoxifen d0-d2, CUT&RUN OTX2 rep1

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd4 Tam CUT_RUN OTX2 rep1

tag: antibody


title: D6 Day 0 Control

value: Control


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 2, Tamoxifen d0-d2, CUT&RUN OTX2 rep1

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd2 Tam CUT_RUN OTX2 rep1


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 2, untreated, rep1

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d2 noTam rep1


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 2, untreated, CUT&RUN OTX2 rep1

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd2 noTam CUT_RUN OTX2 rep1


title: Otx2-/- EpiLCs OTX2 CUT&RUN rep2

description:
Library name: Otx2-/- EpiLC OTX2 CUT_RUN rep2
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation

value: Activin A + bFGF


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 2, Tamoxifen d0-d2, CUT&RUN OTX2 rep2

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd2 Tam CUT_RUN OTX2 rep2


title: Otx2-/- 2i/LIF ESCs OTX2 CUT&RUN rep2

description:
Library name: Otx2-/- ESC OTX2 CUT_RUN rep2
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation

value: ESC (2i/LIF)


title: Otx2-/- EpiLCs OTX2 CUT&RUN rep1

description:
Library name: Otx2-/- EpiLC OTX2 CUT_RUN rep1
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation


title: ATAC-seq Otx2-/- OTX2-ERT2 PGCLC aggregates, plus cytokines, day 4, untreated, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 PGCLC d4 noTam rep2


title: Otx2-/- 2i/LIF ESCs OTX2 CUT&RUN rep1

description:
Library name: Otx2-/- ESC OTX2 CUT_RUN rep1
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 2, untreated, CUT&RUN OTX2 rep2

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd2 noTam CUT_RUN OTX2 rep2


title: WT EpiLCs OTX2 CUT&RUN rep2

description:
Library name: WT EpiLC OTX2 CUT_RUN rep2
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation

value: wild-type


title: Mouse platelets, WT, biol rep 3

first: Margaret

last: Goodell

address: One Baylor Plaza, N1030

institute: Baylor College of Medicine

data_processing:
Raw sequencing reads were initially trimmed using cutadapt to remove potential adaptor contamination and low-quality reads based on the default threshold for each RNA-Seq profile
The remaining reads were then aligned to the reference mouse genome (mm10) using the STAR aligner with default settings.
Gene-level counts and transcript levels were quantified in terms of TPM using RSEM.
Lowly expressed genes that expressed 0 in all samples were filtered out, resulting in 18,462 genes kept for further analysis.
Differentially expressed genes between WT and HET samples were identified using the DESeq2 R package
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file contains raw counts for each sample.
Supplementary files format and content: Tab-delimited txt file contains TPM values for each sample.

source_name: Platelets

extract_protocol:
RNA was isolated using the Qiagen RNeasy Mini kit (74104).
Libraries were prepared for sequencing using the Tru-Seq Stranded mRNA kit (Illumina 20020594) according to the manufacturer’s instructions using >200 ng input RNA. Library quality was assessed using a D1000 screentape (Agilent 5067-5584) on the Agilent Tapestation

value: Platelets

value: WT

tag: age

value: 13 weeks

tag: Sex

value: Male


title: Mouse platelets, WT, biol rep 1

tag: genotype


title: WT 2i/LIF ESCs OTX2 CUT&RUN rep2

description:
Library name: WT ESC OTX2 CUT_RUN rep2
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation


title: WT EpiLCs OTX2 CUT&RUN rep1

description:
Library name: WT EpiLC OTX2 CUT_RUN rep1
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation


title: Otx2-/- OTX2-ERT2 PGCLC aggregates,  plus cytokines, day 4, untreated, CUT&RUN OTX2 rep1

description: Library name: Otx2-/- OTX2-ERT2 PGCLCd4 noTam CUT_RUN OTX2 rep1

value: PGCLC aggregates

value: day 4


title: quant_dTAG_8h_1

data_processing:
Raw files were preprocessed with prinseq-lite, aligned against the mouse reference genome (mm10) with STAR (version 2.7.9a), post-processed and sorted with samtools (version 1.4) and the counts per gene were obtained with featureCounts (version 2.0.3) from the subread package. Normalized expression and differentially expressed genes were calculated using the DESeq2 R package. Heatmaps were created with the heatmap.2 function from the gplots R package. The time-series plots were created with the maSigPro R library.
Assembly: RNA-seq: mm10
Supplementary files format and content: RNA-seq: comma-delimited file with normalized counts per gene

extract_protocol:
RNA-seq: RNA was isolated using the NEB Monarch Total RNA Miniprep Kit (NEB).
RNA-seq: Sequencing libraries were generated using the QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina.

treatment_protocol: RNA-seq: Cells were treated with dTAG13 (35 nM) for 8h or 24h; or with BSJ-4-116 (100 nM) for 4h; or with DMSO for 24h.

value: acute myeloid leukemia cells


title: quant_dTAG_24h_3


title: quant_dTAG_24h_4


title: WT 2i/LIF ESCs OTX2 CUT&RUN rep1

description:
Library name: WT ESC OTX2 CUT_RUN rep1
The CUT&RUN bam files have been normalized based on the e.coli reads before bigwig generation


title: quant_dTAG_24h_2


title: Mouse platelets, WT, biol rep 4


title: quant_DMSO_4

value: DMSO


title: ATAC-seq Otx2-/- OTX2-ERT2 EpiLCs, untreated, rep2

description: Library name: ATAC Otx2-/- OTX2-ERT2 EpiLC Tam0h rep2

value: Otx2-/- OTX2-ERT2

value: day 2


title: Mouse platelets, Dnmt3a+/–, biol rep 3


title: quant_DMSO_1


title: quant_DMSO_2


title: Mouse platelets, WT, biol rep 2


title: Mouse platelets, Dnmt3a+/–, biol rep 4


title: quant_BSJ_4h_4


title: quant_BSJ_4h_1


title: Mouse platelets, Dnmt3a+/–, biol rep 2


title: Mouse platelets, Dnmt3a+/–, biol rep 1


title: cutntag_dTAG13_H3K4me3_3


title: cutntag_dTAG13_H3K27ac_2


title: quant_dTAG_8h_4


title: quant_dTAG_8h_3


title: quant_dTAG_8h_2


title: cutntag_DMSO_IgG_1


title: cutntag_DMSO_H3K4me3_2


title: quant_dTAG_24h_1


title: quant_DMSO_3


title: cutntag_DMSO_H3K4me3_1


title: cutntag_DMSO_H3K27ac_2


title: cutntag_DMSO_H3K27ac_3


title: quant_BSJ_4h_2


title: quant_BSJ_4h_3


title: cutntag_dTAG13_H3K4me3_2


title: cutntag_dTAG13_H3K4me3_1


title: cutntag_dTAG13_H3K27ac_3


title: cutntag_dTAG13_H3K27ac_1


title: CoSDC CAR-M, rep2

city: Nanjing

first: Yuxin

last: Wang

address: 163 Xianlin Road

country: China

institute: Nanjing University

description:
Library name: SC4IE2024
10X Genomics

data_processing:
Raw 10X sequencing reads were aligned to the GRCh38 genome using Cell Ranger (v7.2.0).
Assembly: GRCh38
Supplementary files format and content: Tab-separted values files and matrix files

source_name: CAR-M

extract_protocol:
The cocultures were trypsinized, washed and resuspended in PBS buffer. EGFP+ CoSDC CAR-Ms were sorted by FACS. Cells were washed and resuspended in PBS buffer+0.1% FBS.
scRNA-seq library was constructed using the 10X Genomics Chromium system following manufacturer’s instructions. In brief, the suspended cells were loaded into Chromium microfluidic chips and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed. The barcoded cDNA was purified and amplified, followed by fragmenting, A-tailing and ligation with adaptors.

value: CAR-M

value: Antigen encounter


title: cutntag_DMSO_H3K4me3_3


title: CoSDC CAR-M, rep3

description:
Library name: SC4IE3
10X Genomics


title: CAR-CD247, PSMA- stim,  donor1

description: Library name: A1_CD247_KC

data_processing:
Read quality was assessed with FastQC (v0.12.1) and adapters trimmed using Cutadapt (v4.4)
Reads were then aligned to the GRCh38 genome (Ensembl) using HISAT2 (v2.2.1), and counted using featureCounts
Assembly: GRCh38 release 84 (Ensembl)
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: Monocyte-derived macrophages

growth_protocol: Cells were maintained in X-VIVO 15 medium containing 10% FBS at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted from CAR-Ms in vitro, using the TRIzol reagent (Invitrogen).
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

tag: donor

value: Monocyte-derived macrophages

value: PSMA- stim

tag: batch


title: CAR-CD247, PSMA+ stim, donor3

description: Library name: A3_CD247_KP

value: PSMA+ stim


title: CAR-CD247, PSMA+ stim, donor1

description: Library name: A1_CD247_KP


title: CoSDC CAR-M, rep1

description:
Library name: SC4IE
10X Genomics


title: CAR-LY9, PSMA+ stim, donor3

description: Library name: A3_LY9_KP


title: cutntag_DMSO_H3K27ac_1


title: CAR-LY9, PSMA+ stim, donor1

description: Library name: A1_LY9_KP


title: Female WT5

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Sequenced reads were trimmed for adaptor sequence with Trim_Galore v0.6.7, and masked for low-complexity or low-quality sequence, then mapped to Mus_musculus.GRCm39.107  whole genome using star v2.7.10a. BAM and BAI files were generated using SAMtools v1.6. Counts were generated with the subread v2.0.1 and the featureCounts function (-p -t exon -g gene_id -a -o)
The count matrix was then analyzed using DESeq2 v1.38.3 to caculate differentialy expressed genes and normalized counts
DeSeq2 Normalized counts were calcuated by counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene
Assembly: Mus_musculus.GRCm39.107
Supplementary files format and content: txt file with raw transcript counts from featureCounts
Supplementary files format and content: Xlsx file with Normalized_counts for each transcript from DESeq2

source_name: Kidney

extract_protocol:
Zymo Direct-Zol mini prep plus kit
Libraries were prepared for sequencing using standard Illumina protocols, and poly A selection

value: Kidney

value: Female

value: No treatment


title: CAR-CD247, PSMA- stim, donor3

description: Library name: A3_CD247_KC


title: hCD45+ cells, COMB7 CAR-M treatment

description:
Library name: COMB7
10X Genomics

source_name: human CD45+ cells

extract_protocol:
The tumor tissues were isolated from the mice and quickly immersed in PBS buffer. Samples were minced into about 0.5 mm3 pieces and enzymatically digested in digestion medium (PBS supplemented with collagenase I, collagenase II and collagenase IV).  The samples were incubated and digested at 37℃ for 60 min and then filtered using a 40 μm strainer. Cells were washed and resuspended in PBS buffer+0.1% FBS. Human CD45-positive cells were sorted by FACS.
scRNA-seq library was constructed using the 10X Genomics Chromium system following manufacturer’s instructions. In brief, the suspended cells were loaded into Chromium microfluidic chips and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed. The barcoded cDNA was purified and amplified, followed by fragmenting, A-tailing and ligation with adaptors.

value: human CD45+ cells


title: CAR-CD247 PSMA+ stim, donor2

description: Library name: A2_CD247_KP


title: hCD45+ cells, UTD treatment

description:
Library name: UTD
10X Genomics

value: UTD


title: CAR-CD247, PSMA- stim, donor2

description: Library name: A2_CD247_KC


title: CAR-LY9, PSMA- stim, donor3

description: Library name: A3_LY9_KC


title: CAR-LY9, PSMA+ stim, donor2

description: Library name: A2_LY9_KP


title: Male Q5

value: male

value: Q


title: Female Q5


title: Male R4

value: R


title: CAR-LY9, PSMA- stim, donor2

description: Library name: A2_LY9_KC


title: Male WT4

value: WT


title: Male R5


title: Female R2


title: Male WT5


title: Male Q4


title: Female Q3


title: CAR-LY9, PSMA- stim,  donor1

description: Library name: A1_LY9_KC


title: Female Q4


title: Male R2


title: Male Q3


title: Female R3


title: Male R3


title: Male WT2


title: Male WT3


title: Female WT4


title: Female R1


title: Female WT3


title: Female WT1


title: Male Q2


title: Female WT2


title: Female Q1


title: Male WT1


title: L-GMP cells, CX-5461_3

first: Xiangguo

last: Shi

state: Texas

address: 1 Baylor Plz

department: Molecular and Human Genetics

data_processing:
Raw sequencing data was processed following ENCODE consortium's recommended steps for RNA-seq data.
Briefly, we performed quality control with FastQC and reporting with MultiQC, trimming with Trim-Galore, mapping with STAR, quantification with RSEM and differential gene expression analysis with DESeq2.
In addition, data was normalized with ERCC spike-in protein level.
Assembly: mm10
Supplementary files format and content: Tab-delimited files including gene/transcript ID, counts, TPM, and FPKM for all genes
Supplementary files format and content: Tab-delimited files including gene/transcript ID, counts, TPM, and FPKM for all gene isoforms

source_name: Blood

growth_protocol: L-GMP cells were cultured in RPMI1640 supplemented with 20% FBS, 10ng/ml mouse IL3, and 1% Pen/Strep in a humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol:
L-GMP cells were lysed in Trizol, and RNA was extracted following the manufacturer's protocol. Subsequently, the DNase I-treated RNA samples underwent purification using the QIAGEN MinElute kit before being utilized for cDNA synthesis and amplification via the SMART-Seq2 kit.
The cDNA was fragmented and barcoded for sequencing using a Nextera XT kit.

treatment_protocol: L-GMP cells were treated with MMF, CX-5461, Guanosine, or a combination of MMF and Guanosine for 24 hours

value: Blood

value: L-GMP cells

value: AML LSCs


title: L-GMP cells, CX-5461_4


title: Male R1


title: L-GMP cells, CX-5461_2


title: Male Q1


title: Female Q2


title: L-GMP cells, CX-5461_1


title: L-GMP cells, MMF+Guanosine_1

value: MMF+Guanosine


title: L-GMP cells, MMF+Guanosine_4


title: L-GMP cells, MMF+Guanosine_3


title: L-GMP cells, MMF+Guanosine_2


title: L-GMP cells, MMF_3

value: MMF


title: L-GMP cells, MMF_2


title: L-GMP cells, Control_4

value: Control


title: L-GMP, MMF_3

data_processing:
Raw sequencing data was processed following ENCODE consortium's recommended steps for ATAC-seq data with replicates.
Briefly, we performed quality control with FastQC, trimming with Trim-Galore, mapping with bowtie2, peak calling with macs2, quality Control of peaks with ChIPQC, and combined replicates with ChIP-R.
Assembly: mm10
Supplementary files format and content: Tab-delimited narrowPeak text files including genomic position, score, and statistical significance values

extract_protocol:
L-GMP cells were sorted and incubated with ATAC lysis buffer. These cells were then tagmented with Tn5 at 37°C for 30 min. The DNA fragments were purified by a DNA purification kit (Zymo), and amplified with NEBNext Q5 Hot Start HiFi PCR Master Mix.
The DNA fragments were barcoded for sequencing using a Nextera XT kit.

treatment_protocol: L-GMP cells were treated with MMF for 24 hours.


title: L-GMP cells, Control_3


title: L-GMP cells, MMF_1


title: L-GMP cells, Control_2


title: L-GMP cells, MMF_4


title: L-GMP cells, Control_1


title: L-GMP, MMF_1


title: KO_6A, scRNAseq

city: Wuhan

first: Weizhen

last: Chen

state: Hubei

address: 115#, Donghu road

department: Medical Research Institute

institute: Wuhan University

description: 10x Genomics

data_processing:
The raw gene expression matrix generated from each sample were aggregated using CellRanger (v5.0.1) provided on the 10x genomics website (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome). Downstream analysis was done using the R package Seurat (v 3.2.0). Quality control was applied to cells based on number of detected genes and proportion of mitochondrial reads per cell. Specifically, cells with less than 200 detected genes or cells with >90% of the proportion of the maximum genes were filtered out. For the mitochondrial metric, sorted the cells in descending order of mitochondrial read ratio, and filtered out the top 15% of cells. Potential doublets were identified and removed by DoubletDetection. Cell cycle analysis was performed by using CellCycleScoring function in Seurat program. The gene expression dataset was normalized, subsequent principal component (n=15) analysis was conducted using only the 2000 highly variable genes in the dataset. U-MAP was then used for two-dimensional visualization of the resulting clusters. For each cluster, the marker genes were identified using the FindAllMarkers function as implemented in the Seurat package (logfc. threshold >0.25, minPct >0.1 and Padj≤0.05). Then, clusters were remarked to a known cell type by SCSA method. Differently expressed gene across different samples were identified using the FindMarkers function in Seurat with parameters ‘logfc. threshold >0.25, minPct>0.1 and Padj≤0.05’.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: 4th mammary gland

extract_protocol:
4th mammary glands from WT or Gpm6aKO mice were isolated from 6-8 weeks old virgin female mice at specified stages. Minced tissue was placed in culture medium [RPMI 1640 with 25 mM HEPES, 5% FBS, 1% penicillin-streptomycin, 300 U/ml collagenase III (Worthington)] and digested for 2 h at 37◦C with shaking violently every 15 min. The cell pellet was collected by centrifugation at 1000 rpm, 4◦C for 5 min. After lysis of the red blood cells in NH4Cl, a single-cell suspension was obtained by sequential incubation with 0.05% trypsin-EDTA at 37◦C for 5 min and 0.1 mg/ml DNase I (Sigma) for 5 min with gentle pipetting, followed by filtration through 70-µm cell strainers. The total primary mammary epithelial cells (DAPI- cells) were FACS-isolated from three WT and three Gpm6aKO littermates. Cells were examined by microscope after 0.4% Trypan blue coloring. When the viability of cells was higher than 80 percent, the experiment of library construction was performed.
The single-cell library was constructed using the ChromiumTM Controller and ChromiumTM Single Cell 3’ Reagent Version 2 Kit (10x Genomics, Pleasanton, CA). Briefly, single cells, reagents and Gel Beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized GEMs (Gel Bead in emulsion) using the GemCode Technology. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM. Post RT-GEMs were cleaned up and cDNA were amplified. cDNA was fragmented and fragments end were repaired, as well A-tailing was added to the 3’ end. The adaptors were ligated to fragments which were double sided SPRI selected. Another double sided SPRI selecting was carried out after sample index PCR. The final library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe).

value: 4th mammary gland

value: Total mammary primary cells

value: primary cells

value: Gpm6a deletion


title: L-GMP, Control_3


title: WT_6A, scRNAseq

description: 10x Genomics


title: L-GMP, Control_1


title: Jurkat cells, Tat72, biological replicate 3

city: Majadahonda

first: Ruben

last: Ayala-Suárez

state: Madrid

address: Crta Pozuelo Km 2

department: AIDS Immunopathology Unit

country: Spain

institute: Instituto de Salud Carlos III

description: Library name: Tat72_3

data_processing:
Trimming of poor-quality bases and adapters was carried out with the Trimmomatic tool, using a 4-base-wide sliding window to trim the ends when the average quality per base drops below 15 or any base with a Phred quality below 3. The software also cuts adapters from the sequences allowing two seed mismatches. Any sequences shorter than 30 bases were removed from the output.
The alignment was performed by HISAT2 within the RSEM pipeline.
The reads that passed the quality control requirements were aligned to the reference to estimate gene expression abundance in transcripts per million, calculating 95% credibility intervals.
Assembly: GRCH38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Jurkat TetOFF (Clontech)

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

extract_protocol:
Total RNA was isolated with the miRNeasy kit (Qiagen).
Libraries for RNA-Seq were synthesized with the TruSeq Stranded Total RNA library prep kit with the Ribo-Zero Human (Illumina) from 1 µg total RNA following the standard protocol.
The libraries were pooled (n=12) and sequenced with a single NextSeq 500/550 High output kit v2.5 for 75 cycles (Illumina) in a NextSeq 500 sequencer (Illumina)

treatment_protocol: A total of 400.000 Jurkat cells per well with the different HIV-Tat constructs or the empty vector control (3 biological replicates) were retrieved from culture. Doxycycline was added to Tat101-transfected cells at 1 μg/ml for 2 days. Cell pellets were then obtained and frozen.

value: Jurkat TetOFF (Clontech)

value: T lymphocyte cells

tag: transfection

value: pTRE2hyg + Tat72

value: No


title: L-GMP, Control_2


title: Jurkat cells, Tat72, biological replicate 2

description: Library name: Tat72_2


title: Jurkat cells, Tat101, biological replicate 3

description: Library name: Tat101_3

value: pTRE2hyg + Tat101


title: Jurkat cells, Tet OFF, biological replicate 2

description: Library name: TetOFF_2

value: pTRE2hyg empty plasmid


title: Jurkat cells, Tat101, biological replicate 1

description: Library name: Tat101_1


title: Jurkat cells, Tat101, biological replicate 2

description: Library name: Tat101_2


title: Jurkat cells, Tet OFF, biological replicate 1

description: Library name: TetOFF_1


title: DMSO_0_10d_3pool2_S264

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S264

library_source: other

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

molecule: other

source_name: liver spheroids

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

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

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

value: liver spheroids

tag: chemical

value: DMSO

tag: dose

tag: replicate


title: Jurkat cells, Tat101+DOX, biological replicate 2

description: Library name: Tat101DOX_2

value: Doxycycline 48h


title: DMSO_0_24h_4pool2_S168

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S168

tag: timepoint


title: Jurkat cells, Tet OFF, biological replicate 3

description: Library name: TetOFF_3


title: Jurkat cells, Tat72, biological replicate 1

description: Library name: Tat72_1


title: water_0_10d_4pool2_S352

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S352

value: water


title: water_0_10d_3pool2_S256

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S256


title: DMSO_0_10d_4pool2_S360

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S360


title: DMSO_0_24h_3pool2_S72

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S72


title: water_0_10d_3pool2_S248

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S248


title: L-GMP, MMF_2

value: Blood

value: L-GMP cells

value: AML LSCs

value: WT


title: water_0_24h_4pool2_S160

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S160


title: water_0_10d_4pool2_S344

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S344


title: water_0_24h_3pool2_S64

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S64


title: water_0_24h_4pool2_S152

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S152


title: water_0_10d_4pool2_S336

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S336


title: Jurkat cells, Tat101+DOX, biological replicate 3

description: Library name: Tat101DOX_3


title: water_0_24h_3pool2_S56

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S56


title: Jurkat cells, Tat101+DOX, biological replicate 1

description: Library name: Tat101DOX_1


title: water_0_24h_4pool2_S144

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S144


title: water_0_10d_3pool2_S232

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S232


title: water_0_10d_4pool2_S328

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S328


title: water_0_24h_4pool2_S136

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S136


title: water_0_24h_4pool2_S128

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S128


title: water_0_10d_3pool2_S224

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S224


title: water_0_10d_4pool2_S312

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S312


title: water_0_10d_4pool2_S304

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S304


title: water_0_24h_3pool2_S24

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S24


title: water_0_24h_4pool2_S112

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S112


title: water_0_10d_4pool2_S320

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S320


title: water_0_24h_3pool2_S16

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S16


title: water_0_10d_3pool2_S208

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S208


title: water_0_24h_4pool2_S120

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S120


title: DMSO_0_24h_4pool2_S192

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S192


title: DMSO_0_10d_3pool2_S280

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S280


title: DMSO_0_24h_4pool2_S184

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S184


title: DMSO_0_24h_3pool2_S96

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S96


title: DMSO_0_10d_4pool2_S376

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S376


title: water_0_10d_3pool2_S240

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S240


title: DMSO_0_10d_4pool2_S368

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S368


title: DMSO_0_10d_3pool2_S288

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S288


title: water_0_24h_3pool2_S48

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S48


title: DMSO_0_10d_3pool2_S272

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S272


title: water_0_24h_3pool2_S40

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S40


title: water_0_10d_4pool2_S296

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S296


title: DMSO_0_24h_4pool2_S176

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S176


title: DMSO_0_24h_3pool2_S80

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S80


title: water_0_10d_3pool2_S200

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S200


title: water_0_24h_3pool2_S32

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S32


title: water_0_10d_3pool2_S216

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S216


title: WY-14643_0.001_10d_3pool2_S263

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S263


title: water_0_24h_3pool2_S8

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S8


title: WY-14643_0.001_10d_4pool2_S359

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S359


title: water_0_24h_4pool2_S104

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S104


title: DMSO_0_10d_4pool2_S384

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S384


title: estradiol_0.0000001_10d_4pool2_S351

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S351

value: estradiol


title: WY-14643_0.001_24h_4pool2_S167

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S167


title: estradiol_0.0000001_24h_4pool2_S159

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S159


title: valproic acid_0.001_10d_4pool2_S343

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S343

value: valproic acid


title: DMSO_0_24h_3pool2_S88

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S88


title: estradiol_0.0000001_10d_3pool2_S255

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S255


title: WY-14643_0.001_24h_3pool2_S71

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S71


title: valproic acid_0.001_10d_3pool2_S247

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S247


title: valproic acid_0.001_24h_4pool2_S151

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S151


title: valproic acid_0.001_24h_3pool2_S55

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S55


title: potassium chloride_0.003_10d_4pool2_S335

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S335

value: potassium chloride


title: sucrose_0.003_24h_4pool2_S135

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S135

value: sucrose


title: sucrose_0.003_10d_3pool2_S231

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S231


title: potassium chloride_0.003_24h_3pool2_S47

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S47


title: sucrose_0.003_24h_3pool2_S39

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S39


title: sucrose_0.003_10d_4pool2_S327

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S327


title: potassium chloride_0.003_24h_4pool2_S143

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S143


title: caffeine_0.001_24h_4pool2_S127

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S127

value: caffeine


title: potassium chloride_0.003_10d_3pool2_S239

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S239


title: caffeine_0.001_24h_3pool2_S31

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S31


title: caffeine_0.001_10d_3pool2_S223

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S223


title: caffeine_0.001_10d_4pool2_S319

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S319


title: cyclosporin A_0.0001_10d_3pool2_S215

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S215

value: cyclosporin A


title: cyclosporin A_0.0001_10d_4pool2_S311

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S311


title: benzo[a]pyrene_0.00003_10d_4pool2_S303

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S303

value: benzo[a]pyrene


title: benzo[a]pyrene_0.00003_24h_4pool2_S111

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S111


title: benzo[a]pyrene_0.00003_10d_3pool2_S207

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S207


title: estradiol_0.0000001_24h_3pool2_S63

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S63


title: troglitazone_0.0001_10d_4pool2_S383

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S383

value: troglitazone


title: benzo[a]pyrene_0.00003_24h_3pool2_S15

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S15


title: troglitazone_0.0001_10d_3pool2_S287

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S287


title: rosiglitazone_0.0001_10d_3pool2_S279

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S279

value: rosiglitazone


title: rosiglitazone_0.0001_24h_4pool2_S183

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S183

value: liver spheroids


title: troglitazone_0.0001_24h_3pool2_S95

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S95


title: rosiglitazone_0.0001_24h_3pool2_S87

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S87


title: troglitazone_0.0001_24h_4pool2_S191

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S191


title: aflatoxin B1_0.001_10d_4pool2_S367

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S367

value: aflatoxin B1


title: rosiglitazone_0.0001_10d_4pool2_S375

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S375


title: aflatoxin B1_0.001_24h_4pool2_S175

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S175


title: aflatoxin B1_0.001_24h_3pool2_S79

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S79


title: acetaminophen_0.05_10d_4pool2_S295

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S295

value: acetaminophen


title: acetaminophen_0.05_10d_3pool2_S199

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S199


title: WY-14643_0.01_10d_4pool2_S358

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S358


title: acetaminophen_0.05_24h_3pool2_S7

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S7


title: cyclosporin A_0.0001_24h_4pool2_S119

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S119


title: cyclosporin A_0.0001_24h_3pool2_S23

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S23


title: WY-14643_0.01_24h_4pool2_S166

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S166


title: WY-14643_0.01_24h_3pool2_S70

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S70


title: estradiol_0.000001_24h_3pool2_S62

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S62


title: estradiol_0.000001_24h_4pool2_S158

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S158


title: estradiol_0.000001_10d_3pool2_S254

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S254


title: valproic acid_0.01_24h_4pool2_S150

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S150


title: valproic acid_0.01_10d_4pool2_S342

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S342


title: potassium chloride_0.03_10d_3pool2_S238

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S238


title: potassium chloride_0.03_24h_3pool2_S46

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S46


title: caffeine_0.01_10d_3pool2_S222

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S222


title: sucrose_0.03_24h_3pool2_S38

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S38


title: aflatoxin B1_0.001_10d_3pool2_S271

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S271


title: potassium chloride_0.03_10d_4pool2_S334

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S334


title: sucrose_0.03_10d_4pool2_S326

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S326


title: sucrose_0.03_24h_4pool2_S134

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S134


title: valproic acid_0.01_24h_3pool2_S54

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S54


title: potassium chloride_0.03_24h_4pool2_S142

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S142


title: caffeine_0.01_24h_3pool2_S30

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S30


title: benzo[a]pyrene_0.0003_10d_3pool2_S206

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S206


title: sucrose_0.03_10d_3pool2_S230

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S230


title: cyclosporin A_0.001_10d_3pool2_S214

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S214


title: benzo[a]pyrene_0.0003_24h_4pool2_S110

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S110


title: caffeine_0.01_24h_4pool2_S126

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S126


title: cyclosporin A_0.001_10d_4pool2_S310

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S310


title: WY-14643_0.01_10d_3pool2_S262

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S262


title: estradiol_0.000001_10d_4pool2_S350

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S350


title: cyclosporin A_0.001_24h_3pool2_S22

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S22


title: cyclosporin A_0.001_24h_4pool2_S118

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S118


title: benzo[a]pyrene_0.0003_10d_4pool2_S302

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S302


title: troglitazone_0.001_10d_3pool2_S286

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S286


title: valproic acid_0.01_10d_3pool2_S246

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S246


title: acetaminophen_0.05_24h_4pool2_S103

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S103


title: benzo[a]pyrene_0.0003_24h_3pool2_S14

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S14


title: troglitazone_0.001_10d_4pool2_S382

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S382


title: troglitazone_0.001_24h_4pool2_S190

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S190


title: troglitazone_0.001_24h_3pool2_S94

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S94


title: caffeine_0.01_10d_4pool2_S318

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S318


title: rosiglitazone_0.001_10d_3pool2_S278

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S278


title: rosiglitazone_0.001_24h_3pool2_S86

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S86


title: rosiglitazone_0.001_24h_4pool2_S182

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S182


title: aflatoxin B1_0.01_10d_4pool2_S366

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S366


title: aflatoxin B1_0.01_10d_3pool2_S270

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S270


title: aflatoxin B1_0.01_24h_4pool2_S174

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S174


title: acetaminophen_0.5_10d_4pool2_S294

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S294


title: aflatoxin B1_0.01_24h_3pool2_S78

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S78


title: WY-14643_0.1_10d_4pool2_S357

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S357


title: acetaminophen_0.5_24h_4pool2_S102

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S102


title: WY-14643_0.1_24h_4pool2_S165

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S165


title: acetaminophen_0.5_10d_3pool2_S198

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S198


title: WY-14643_0.1_24h_3pool2_S69

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S69


title: estradiol_0.00001_24h_4pool2_S157

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S157


title: estradiol_0.00001_10d_3pool2_S253

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S253


title: estradiol_0.00001_10d_4pool2_S349

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S349


title: estradiol_0.00001_24h_3pool2_S61

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S61


title: valproic acid_0.1_10d_3pool2_S245

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S245


title: valproic acid_0.1_10d_4pool2_S341

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S341


title: valproic acid_0.1_24h_4pool2_S149

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S149


title: potassium chloride_0.3_24h_3pool2_S45

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S45


title: sucrose_0.3_10d_4pool2_S325

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S325


title: valproic acid_0.1_24h_3pool2_S53

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S53


title: potassium chloride_0.3_10d_4pool2_S333

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S333


title: potassium chloride_0.3_24h_4pool2_S141

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S141


title: potassium chloride_0.3_10d_3pool2_S237

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S237


title: rosiglitazone_0.001_10d_4pool2_S374

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S374


title: sucrose_0.3_10d_3pool2_S229

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S229


title: sucrose_0.3_24h_4pool2_S133

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S133


title: caffeine_0.1_10d_4pool2_S317

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S317


title: acetaminophen_0.5_24h_3pool2_S6

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S6


title: caffeine_0.1_10d_3pool2_S221

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S221


title: caffeine_0.1_24h_3pool2_S29

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S29


title: WY-14643_0.1_10d_3pool2_S261

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S261


title: cyclosporin A_0.01_10d_4pool2_S309

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S309


title: sucrose_0.3_24h_3pool2_S37

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S37


title: cyclosporin A_0.01_10d_3pool2_S213

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S213


title: cyclosporin A_0.01_24h_3pool2_S21

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S21


title: benzo[a]pyrene_0.003_10d_4pool2_S301

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S301


title: benzo[a]pyrene_0.003_24h_4pool2_S109

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S109


title: troglitazone_0.01_10d_4pool2_S381

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S381


title: cyclosporin A_0.01_24h_4pool2_S117

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S117


title: benzo[a]pyrene_0.003_10d_3pool2_S205

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S205


title: benzo[a]pyrene_0.003_24h_3pool2_S13

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S13


title: troglitazone_0.01_10d_3pool2_S285

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S285


title: troglitazone_0.01_24h_3pool2_S93

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S93


title: troglitazone_0.01_24h_4pool2_S189

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S189


title: rosiglitazone_0.01_10d_4pool2_S373

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S373


title: rosiglitazone_0.01_10d_3pool2_S277

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S277


title: rosiglitazone_0.01_24h_3pool2_S85

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S85


title: rosiglitazone_0.01_24h_4pool2_S181

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S181


title: aflatoxin B1_0.1_10d_3pool2_S269

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S269


title: aflatoxin B1_0.1_24h_4pool2_S173

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S173


title: acetaminophen_5_10d_4pool2_S293

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S293


title: aflatoxin B1_0.1_24h_3pool2_S77

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S77


title: acetaminophen_5_10d_3pool2_S197

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S197


title: aflatoxin B1_0.1_10d_4pool2_S365

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S365


title: acetaminophen_5_24h_4pool2_S101

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S101


title: caffeine_0.1_24h_4pool2_S125

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S125


title: WY-14643_1_10d_4pool2_S356

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S356


title: WY-14643_1_10d_3pool2_S260

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S260


title: WY-14643_1_24h_4pool2_S164

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S164


title: WY-14643_1_24h_3pool2_S68

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S68


title: estradiol_0.0001_10d_4pool2_S348

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S348


title: estradiol_0.0001_24h_3pool2_S60

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S60


title: valproic acid_1_10d_3pool2_S244

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S244


title: valproic acid_1_10d_4pool2_S340

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S340


title: valproic acid_1_24h_4pool2_S148

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S148


title: potassium chloride_3_10d_4pool2_S332

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S332


title: valproic acid_1_24h_3pool2_S52

description:
Templated oligo sequencing with the Human S1500+ surrogate v2.0 kit (TempO-Seq, BioSpyder, Carlsbad, CA)
pool2_S52