title: WT_LW,scRNA

city: Chengdu

first: Xinhui

address: No.14,3Rd Section Of Ren Min Nan Rd.ChengDu,SiChuan 610041,China

institute: Sichuan university

description: 10x Genomics

data_processing:
The cell suspension was loaded into Chromium microfluidic chips with 3’ (v2 or v3, depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq , depends on project) according to the manufacturer’s instructions (Illumina).
Qualitycontrol: Weuse fastp to perform basic statistics on the quality of the raw reads. Generally, cellranger count support FASTQ files from raw base call (BCL) files generated by Illumina sequencers as input file. 10x Genomics® not recommend additional processing of the sequence
Generation and Analysis of Single-Cell Transcriptomes： Raw reads were demultiplexed and mapped to the reference genome by 10X Genomics Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is-cell-ranger) using default parameters. All downstream single-cell analyses were performed using Cell Ranger and Seurat ( (Macosko et al., 2015; Satija et al., 2015) unless mentioned specifically. In brief, for each gene and each cell barcode (filtered by CellRanger), unique molecule identifiers were counted to construct digital expression matrices. Secondary filtration by Seurat : Agene with expression in more than 3 cells was considered as expressed, and each cell was required to have at least 200 expressed genes. And filter out some of the foreign cells.
Secondary Analysis of Gene Expression：The Seurat package was used to normalise data, dimensionality reduction,  clustering,differential expression. we used Seurat alignment method canonical  correlation analysis (CCA) [Nat. Biotechnol. 36, 411–420 (2018).] for integrated  analysis of datasets. For clustering, highly variable genes were selected and the  principal components based on those genes used to build a graph, which was  segmented with a resolution of 0.6
Assembly: mm9
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
Dorsal skin healed from large circular wound (diameter=1.8cm) and sprayed with PBS or  ODN2395 at Day 0,3,6 post wound were collected for the scRNA-seq at 2 days post scab detachment.
The cell suspension was loaded into Chromium microfluidic chips with 3’ (v2 or v3, depends on project) chemistry and barcoded with a 10× Chromium Controller (10X Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ v2(v2 or v3, depends on project) reagent kit (10X Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (HiSeq 2000 or NovaSeq , depends on project) according to the manufacturer’s instructions (Illumina).

treatment_protocol: Dorsal skin healed from large circular wound (diameter=1.8cm) and sprayed with PBS at Day 0,3,6 post wound.

value: Skin


title: dR 2

status: Public on Jul 24 2024

type: SRA

city: Oeiras

first: Vânia

last: Pobre

address: Av. da República

country: Portugal

institute: Instituto de Tecnologia Química e Biológica

library_source: transcriptomic

data_processing:
The quality of the RNA-Seq data was confirmed using the fastQC program. Contaminant adapters and low-quality reads were removed with cutadapt
Reads were mapped against S. pneumoniae TIGR4 genome (NC_003028.3, downloaded from NCBI genome database) using Bowtie2 program
Samtools was used to sort the mapping files by genomic position and quantification of RNA-Seq data was performed using FeatureCounts
Transcripts expression was calculated using the RPKM normalization method
Assembly: NC_003028.3
Supplementary files format and content: tab-delimited file with read counts for each sample

molecule: total RNA

organism: Streptococcus pneumoniae

source_name: culture cell

growth_protocol: S. pneumoniae strains were grown in Todd Hewitt medium, supplemented with 0.5% yeast extract (THY) at 37°C without aeration, or in THY agar medium supplemented with 5% sheep blood (Thermo Scientific) at 37°C in a 5% CO2 atmosphere. When required growth medium was supplemented with 3 μg/mL chloramphenicol (Cm), 1 μg/mL erythromycin (Ery) or 150 μg/mL kanamycin (Km) as specified.

extract_protocol:
Overnight cultures of S. pneumoniae TIGR4 WT and derivatives were diluted in pre-warmed THY to a final OD600 of 0.05 and incubated at 37°C until OD600 ≈ 0.3. 25 mL of culture was collected, mixed with 1 volume of stop solution (10 mM Tris pH 7.2, 25 mM NaNO3, 5 mM MgCl2, 500 µg/mL Cm) and harvested by centrifugation (10 min, 6000 x g, 4°C). For mRNA decay studies, transcription was stopped by addition of rifampicin (0.5 mg/mL) and nalidixic acid (20 µg/mL) to growing cells (OD600 ≈ 0.3). At the indicated times, 25 mL of culture was collected, mixed with 1 volume of stop solution and harvested by centrifugation in the conditions described above. In both cases, total RNA was extracted using Trizol reagent (Ambion)
rRNA was depleted from the samples with the RiboZero kit and sequencing libraries were constructed with the TruSeq kit (Illumina) for bacteria.

tag: strain background

tag: genotype

value: RNase R deletion mutant

tag: cell type

value: culture cell


title: Hep_LPCs rep 2

city: Shanghai

first: hexin

last: Yan

address: Pujian Road

country: China

institute: Shanghai Reji Hospital

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing poly-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks
and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include raw counts of each gene.

organism: Mus musculus

source_name: liver

growth_protocol: 8-week-old of lineage tracing models including tdTomato mice with AAV8-TBG-Cre and AlbCreERT/R26GFP were purified for hepatocytes and non-parenchymal cells respectively, and cultured for transition to progenitor-like cells in transition and expansion media. The differences between these two were clarified by RNA sequencing.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA).
The paired-end libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Cultured in Transition and Expansion Medium (TEM).

tag: tissue

value: liver

value: liver progenitor cells (derived from hepatocytes)

tag: strain

tag: age

value: 6-8 weeks

tag: condition

value: cultured in Transition and Expansion Medium (TEM)


title: MO_MCC_072, skin  - gd VDJ

city: Chicago

first: Jaehyuk

last: Choi

state: Illinois

address: 303 E. Superior St. 5-220

department: Dermatology

country: USA

institute: Northwestern University

library_source: transcriptomic single cell

data_processing:
scRNA-seq Pre-processing: The GRCh38.p13 primary assembly from Ensembl Release 98 and the GENCODE v32 primary assembly were modified as follows. The sequence headers in the Ensembl FASTA were modified to match the primary assembly from GENCODE, by replacing metadata with original contig names, appending "chr" to names of autosomes and sex chromosomes, and handle the mitochondrial chromosome. The GTF file was modified to remove the version suffixes from transcript, gene, and exon IDs to match Previous CellRanger references. The GTF file was further filtered to include genes passing one or more of allowable gene_type, allowable transcript_type, no "PAR" tag, or no "readthrough_transcript" tag. Cellranger 6.1.0 was used to create a reference for scRNA-seq alignment. The MCPyV sequence was added to the primary assembly and to the final GTF file.
FASTQ files containing gene exPression and feature barcodes were aligned to the human hg38 genome and MCPyV genome using CellRanger 6.1.0. Ambient RNA was removed using the CellBender pipeline. Processed read counts for each sample were imported as a Seruat object after which TCR-seq data was added. We then filtered the data based on mitochondrial reads (25% cutoff) and minimum RNA genes (200 genes). Doublets were removed using DoubletFinder, and cells were annotated with ProjectTILS and SingleR, using Monaco and HPCA reference datasets. The data were merged into a single Seurat object. We performed standard Seurat (4.0) clustering, Harmony batch correction, and manual cell cluster annotation based on marker genes, including transcription factors, effector molecules, and Previously annotated cell types. The data were subset by major cell types and subclustered. Contaminating cells were filtered out based on marker gene exPression. Differential gene exPression, gene enrichment, and GSVA were performed, followed by comparison of cell type proportions, analysis of TCR clonotype exPression, and TCR linkage analysis.

organism: Homo sapiens

source_name: skin

extract_protocol: CryoPreserved digested MCC tumor samples were thawed and processed following a modified version of the 10x Demonstrated Protocol "Thawing Dissociated Tumor Cells for Single Cell RNA Sequencing" and BioLegend TotalSeq C protocol. The protocol aimed to maintain high cell viability, decrease background, and reduce costs. Samples were thawed, labeled with TotalSeq C antibodies, and stained with 7-AAD viability staining solution. Cells were then subjected to FACS to sort CD45+ and CD45- cell populations for target enrichment of 2/3 CD45+ cells. After sorting, the final cell Preparation was resuspended in RPMI + 10% FBS + RNase Inhibitor, filtered, and counted to ensure the optimal concentration of 1e6 cells/mL. Finally, the cell suspension was processed for encapsulation and reverse transcription using the 10x 5’ v2 Chromium platform according to manufacture instructions.

treatment_protocol: Tissue dissociation: Human skin tumor biopsies (4mm punch) were dissociated into single-cell suspensions using the Miltenyi Biotec human tumor dissociation kit. Tissue punches were received on ice in biopsy transport media (PBS + FBS + antibiotics). Enzymes H, R, and A were reconstituted following the manufacturer's instructions and mixed with Pre-warmed RPMI 1640 medium. Biopsies were minced into 1-2mm pieces, transferred to enzyme mix, and incubated at 37°C for 30 minutes at 800 rpm in a thermomixer. Following incubation, samples were pipetted to break up clumps and filtered through a 70µm cell strainer into a 50ml conical tube. Tubes were centrifuged at 1500 rpm for 10 minutes at 4°C, and cells were resuspended in cold PBS. Cell viability and concentration were assessed using trypan blue and a cell counting slide. Cells were pelleted again and resuspended in a 1:1 mixture of FBS and FBS + 20% DMSO for cryoPreservation. Cryovials were stored at -80°C overnight before transferring to liquid nitrogen storage.

tag: library type

value: gd VDJ

value: skin

value: Merkel Cell Carcinoma (MCC) cell


title: MO_MCC_072, skin  - ab VDJ

value: ab VDJ


title: Unlesioned WM, BCG_1_4_54_rep1

city: Munich

first: Vini

last: Tiwari

address: Feodor Lynen Straße 17

country: Germany

institute: Technical University Munich, (TUM), Deutsches Zentrum für Neurodegenerative Erkrankungen

data_processing:
Low-quality reads and adapters were trimmed using Trim Galore using the following parameters (reads <20 bp with quality cutoff 20).
The trimmed FASTQ files were mapped to the mm10 reference genome using STAR. The mapped reads (of lesion tissue sections) belonging to the same slide were merged using the merge BAM files tool in Galaxy.(https://usegalaxy.eu/)
To quantify the number of reads mapping to the exons of each gene, Feature counts was used. Differential analysis was performed using Deseq2.
Assembly: mm10
Supplementary files format and content: text files of count values (feature counts) for each sample analyzed

source_name: WM, Brain

extract_protocol:
RNA was isolated from PFA-fixed OCT-embedded frozen brain sections using the method that digest proteins to free cross-linked RNA (Ji et al., 2023).Five WM tissue sections were scratched from each slide and condition.
1 ng mRNA from each sample was taken and continued with the Smart-seq2 protocol as described in (Safaiyan et al., 2021) (Kaya et al., 2022).

treatment_protocol: 200ul of reconstituted BCG containing 8x105-12x106 CFU was injected i.v in aged mice whereas the control mice received Saline

value: WM, Brain

tag: Sex

value: male

tag: treatment

value: BCG

value: 12 months


title: MO_MCC_072, skin  - ADT

value: ADT


title: blood, CAF09hi, immu2, rep 1 CGC010.2019.07.23

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

data_processing:
Emsembl 109
Assembly: tab-separated values (tsv). The first row stores the sample same. The first column stores the ENSEMBL gene id. Counts were stored  in the matrix.
Supplementary files format and content: The file can be read into R by the command `read.table(file = "count_matrix.tsv", sep = "\t")`

molecule: polyA RNA

organism: Macaca fascicularis

source_name: blood

extract_protocol:
RNA was extracted using QIAsymphony PAXgene Blood RNA Kit following manufacturer's instructions.
The library was constructed using NEBnext ultra II RNA library preparation kit with rRNA and globin depletion.
We processed the raw RNA-seq data by nf-core rnaseq (version 3.12.0) (doi: 10.1038/s41587-020-0439-x), a community-curated best practice workflow. In brief, the sequence read quality was checked by fastqc. Then, the adapter and low-quality reads were trimmed by “Trim Galore!”. The reads were mapped to Macaca fascicularis reference genome 6.0 by HISAT2 (doi: 10.1038/s41587-019-0201-4), and annotated by Emsembl 109. The mapped counts were counted by Salmon (doi: 10.1038/s41587-019-0201-4).

treatment_protocol: Blood samples were stored in PAXGene tubes.

value: blood

tag: vaccine

tag: sampling


title: blood, CAF09hi, baseline, rep 1 CGC010.2019.06.24


title: dR 1


title: Hep_LPCs rep 1


title: MO_MCC_072, skin  - RNA

value: RNA


title: MO_MCC_071, skin  - gd VDJ


title: NPC_LPCs rep 2

value: liver progenitor cells (derived from non-parenchymal cells)


title: WT 1

value: Wild-type

value: culture cell


title: NPC_LPCs rep 1

value: liver


title: MO_MCC_071, skin  - ab VDJ


title: blood, CAF10b, immu2, rep 1 CGB104.2019.07.23


title: MO_MCC_071, skin  - ADT


title: LesionWM, Control, 43727_P8D8, rep6

data_processing:
Low-quality reads and adapters were trimmed using Cutadapt using the following parameters (reads <20 bp with quality cutoff 20).
The trimmed FASTQ files were mapped to the mm10 reference genome using STAR. The mapped reads (of lesion tissue sections) belonging to the same slide were merged using the merge BAM files tool in Galaxy.(https://usegalaxy.eu/)
To quantify the number of reads mapping to the exons of each gene, Feature counts was used. Differential analysis was performed using Deseq2.
Assembly: mm10
Supplementary files format and content: text files of count values (feature counts) for each sample analyzed

source_name: LesionWM, Brain

extract_protocol:
RNA was isolated from PFA-fixed OCT-embedded frozen brain sections using the method that digest proteins to free cross-linked RNA (Ji et al., 2023).Four lesion tissue sections were scratched from each slide and condition.
1 ng mRNA from each sample was taken and continued with the Smart-seq2 protocol as described in (Safaiyan et al., 2021) (Kaya et al., 2022).

value: LesionWM, Brain

value: Saline


title: TLR9agonist_LW,scRNA

last: Li

description: 10x Genomics

source_name: SKin

treatment_protocol: Dorsal skin healed from large circular wound (diameter=1.8cm) and sprayed with TLR9agonist ODN2395 at Day 0,3,6 post wound.

value: SKin

value: WT


title: MO_MCC_071, skin  - RNA

value: skin

value: Merkel Cell Carcinoma (MCC) cell


title: blood, CAF10b, baseline, rep 1 CGB104.2019.06.24


title: Replicate 12, dialout library

city: Madison

first: Max

last: Frenkel

address: 433 babcock drive

institute: UW Madison

library_source: genomic

data_processing:
For scATAC/Spear-ATAC libraries: Sequencing data was converted to fastq files using cellranger-atac mkfastq (10x Genomics, version 2.1.0). Reads were then aligned to the hg38 reference genome and quantified using cellranger-atac count. The current version of Cell Ranger can be accessed here:https://support.10xgenomics.com/single-cell-atac/software/downloads/latest
For dialout libraries: To filter for reads that contain the correct structure of amplicon, we grepped for 4 constants sequences that flanked the barcodes: “AAATCCAAGC”, “CCAGAGCATG”, “CAAGGTGGTT”, and “ATACTGATTC”. . We then matched each of the supposed hardcoded barcodes to one of the known hardcoded barcodes from the list that we intended to synthesize by identifying a closest match using a maximum restricted Damerau-Levenshtein distance of 3. We then generated a list of unique hardcoded barcode – random barcode pairs. We restricted that list to pairs to those that were seen more than once. Finally, we required that, for a given random barcode, more than 95% of the reads had to match to the same hardcoded barcode.
Assembly: hg38
Supplementary files format and content: Tab separated values
Library strategy: Spear-ATAC

molecule: genomic DNA

extract_protocol:
Nuclei were prepared according to 10X Genomics’ Nuclear Isolation for Single Cell ATAC Sequencing protocol with the following notes. IGEPAL CA-630 was used for the lysis buffer a 10% solution of which was prepared fresh on the day of nuclear isolation using 100% stock (Sigma i8896). After trypsinization and pelleting, cells were washed twice with ice cold PBS + 0.04% BSA before following the remainder of the nuclear isolation protocol. Lysis occurred for 4 minutes which previously was found to be appropriate time for cytoplasmic removal while retaining nuclear membrane architecture by DIC microscopy. Cells were resuspended in diluted nuclei buffer and triplicates were counted before proceeding with Spear-ATAC sequencing as previously published.
Library construction was performed according to 10X Genomics scATAC-seq v2 Chemistry and Spear-ATAC with the following modifications and notes. 10,000 nuclei were targeted for capture per 10X chip lane. Spear-ATAC included the following changes to the 10X scATAC library preparation protocol: the 1.2 uL per reaction of 50 uM oSP1735 oligonucleotide is spiked into the GEM generation master mix and the in-GEM PCR was increased from 12 to 15 cycles. Single-cell ATAC library fragment size distribution was analyzed by Tapestation prior to preparing enriched dial-out libraries for perturbation genotyping. The dial-out libraries were again prepared according to the Spear-ATAC protocol with the following changes: linear PCR with biotinylated oSP2053 was increased to 30 total cycles and the exponential PCR with oSP1594 and indexed P7 primers was increased to 18 total cycles. The indices on the P7 primers were increased from 8 bases to 10 bases.

tag: cell line


title: LesionWM, Control, 43727_P8D7, rep6


title: blood, CAF10b, immu1, rep 1 CGB104.2019.06.25


title: Replicate 11, dialout library


title: MO_MCC_069, skin  - gd VDJ

value: gd VDJ


title: blood, CAF10b, immu2, rep 1 CGB097.2019.07.23


title: blood, CAF09hi, immu1, rep 1 CGC010.2019.06.25


title: LesionWM, Control, 43727_P8D6, rep6

value: male


title: Replicate 10, dialout library


title: blood, CAF10b, immu1, rep 1 CGB097.2019.06.25


title: MO_MCC_069, skin  - ADT


title: blood, CAF10b, immu2, rep 1 CGB093.2019.07.23


title: Replicate 9, dialout library


title: blood, CAF10b, immu1, rep 1 CGB093.2019.06.25


title: LesionWM, Control, 43727_P8D5, rep6


title: WT2


title: blood, CAF10b, baseline, rep 1 CGB097.2019.06.24


title: MO_MCC_068LN_abVDJ,skin

value: ab VDJ


title: LesionWM, Control, 43726_P7B9, rep5

value: 12 months


title: blood, CAF10b, baseline, rep 1 CGB093.2019.06.24


title: MO_MCC_068LN_ADT,skin

value: ADT


title: Replicate 8, dialout library


title: LesionWM, Control, 43725_P8D4, rep4


title: Replicate 7, dialout library


title: LesionWM, Control, 43726_P7B4, rep5


title: MO_MCC_069, skin  - ab VDJ


title: MO_MCC_068LN_gdVDJ,skin


title: blood, CAF10b, immu1, rep 1 CGB091.2019.06.25

value: blood


title: Replicate 6, dialout library


title: LesionWM, Control, 43726_P7B3, rep5


title: LesionWM, Control, 43726_P7B2, rep5


title: blood, CAF10b, immu2, rep 1 CGB091.2019.07.23


title: Replicate 5, dialout library


title: MO_MCC_068LN_RNA,skin

value: RNA


title: Replicate 3, dialout library


title: Replicate 4, dialout library


title: LesionWM, Control, 43725_P8D3, rep4


title: MO_MCC_069, skin  - RNA


title: LesionWM, Control, 43725_P8D2, rep4


title: MO_MCC_068skin_gdVDJ,skin


title: Replicate 2, dialout library


title: blood, CAF09hi, immu2, rep 1 CGB088.2019.07.23


title: Replicate 1, dialout library


title: blood, CAF09hi, immu1, rep 1 CGB088.2019.06.25


title: LesionWM, Control, 43712_P8D10, rep3


title: MMO_MCC_068skin_abVDJ,skin


title: MMO_MCC_068skin_ADT,skin


title: LesionWM, Control, 43725_P7D1, rep4


title: blood, CAF09hi, baseline, rep 1 CGB088.2019.06.24


title: LesionWM, Control, 43712_P7D4, rep3


title: CLIP-Input-1

city: Hangzhou

first: Yingjie

last: Wang

state: Zhejiang

address: Research Center C701,School of Medicine,Zhejiang University,866 Yuhangtang Road

department: Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine

institute: Zhejiang University

description: processed data file: OCT4_IP_1_peak_info.txt

data_processing:
Library strategy: CLIP-seq
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC; end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. While several mapped reads have the same start position and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of OCT4 on genome were identified using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_peak_info.txt: Tab-delimited text files include peak information for each group.

source_name: H1 cells

growth_protocol: H1 cells were cultured in mTeSR1 feeder free medium, 5% CO2, 37℃.

extract_protocol:
Briefly, cells were washed with ice-cold PBS for 3 times and UV cross-linking was performed with UV irradiation type C (254 nm) at 400 mJ/cm2. Cross-linked cells were scraped off the plates and collected by centrifugation at 1000 x g for 5 min. Cell lysis was performed in cold lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 1% RNase inhibitor (Takara) and 2% protease inhibitor cocktail (Roche) for 30 min. Cell lysates were cleared by centrifugation at 10,000 rpm for 10 min at 4℃ and the supernatants were used for immunoprecipitation. For DNA digestion, RQ1 (Promega) was added to the lysate that was incubated at 37℃ for 3 min. For immunoprecipitation, 600 μl lysate was incubated with 15 μl anti-FLAG M2 beads overnight at 4 ℃. After applying to magnet and removing the supernatants, the beads were sequentially washed with wash buffer (1× PBS, 1% SDS, 0.5% NP-40 and 5% sodium deoxycholate), high-salt wash buffer (5× PBS, 1% SDS, 0.5% NP-40 and 5% sodium deoxycholate), and PNK buffer (50 mM Tris pH=7.4, 10 mM MgCl2 and 0.5% NP-40) for two times, respectively. The on-bead digestion was performed by adding MNase (Thermo), followed by incubation at 37℃ for 10 min. After washing with PNK buffer as described above, dephosphorylation and phosphorylation was performed with calf intestinal alkaline phosphatase (CIP, NEB) and polynucleotide kinase (PNK, NEB), respectively. The immunoprecipitated protein-RNA complexes were eluted from the beads by heat denaturing and resolved on a Novex 4-12% Bis-Tris precast polyacrylamide gel (Invitrogen). The protein-RNA complexes were cut from the gel and RNA was extracted with Trizol after digesting the proteins.
The cDNA libraries were prepared using the KAPA Stranded RNA-Seq Library Preparation Kit (Kapa biosystems). The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing by ABLife, Inc. (Wuhan, China).

tag: genotype/variation

value: TAP tag knocked in to endogenous POU5F1 locus

tag: antibody


title: blood, CAF10b, baseline, rep 1 CGB091.2019.06.24


title: LesionWM, Control, 43712_P7D3, rep3


title: MO_MCC_066, skin - ab VDJ


title: blood, CAF09hi, immu1, rep 1 CGB065.2019.06.25


title: CLIP-OCT4-1

value: anti-FLAG M2


title: MMO_MCC_068skin_RNA,skin


title: MO_MCC_061, skin  - ab VDJ


title: CLIP-Input-2

description: processed data file: OCT4_IP_2_peak_info.txt


title: LesionWM, Control, 43711_P7C4, rep2


title: ARID1-GFP_IP_Rep2

first: Lei

address: Xinjiangwancheng

institute: Fudan University

data_processing:
Following a FastQC (version 0.12.0) quality control, adapter trimming was performed using TrimGalore (version 0.4.1).
Reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 (version 2.1.0), and subsequently PCR duplicates were removed using sambamba (version 0.6.6).
Deeptools (version 3.1.2) was used to examine correlations between the ChIP samples and generate Genome browser tracks.
Narrow peaks were called with MACS2 (version 2.1.0) using an FDR cutoff of 0.05 or P value cutoff of 0.00001.
Assembly: TAIR10
Supplementary files format and content: bigWig

organism: Arabidopsis thaliana

source_name: mature pollen

extract_protocol:
~150 µL of mature pollens were collected and resuspended in ice-cold pollen nuclei buffer (1.3 mM H3BO3, 3.6 mM CaCl2·2H2O, 0.74 mM KH2PO4, 438 mM Sucrose, 7 mM MOPS, 0.83 mM MgSO4·7H2O, adjust pH to 6.0), and then transferred to a 2 ml tube containing 2 mm BashingBead, vortex at the 49 Hz for 3 min with homogenizer. Debris was removed by filtering the suspension through a 10 µm nylon mesh. Nuclei were precipitated by centrifugation and resuspended in M1 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM 2-mercaptoethanol, and protease inhibitor) containing 1% formaldehyde and fixed with 20 min, the cross-linking reaction was stopped by the addition of 125 mM glycine. Nuclei were precipitated by centrifugation and washed three times with M2 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 1 M hexylene glycol, 10 mM MgCl2, 0.5% Triton X-100, 10 mM 2-mercaptoethanol, and protease inhibitor), and then further washed once with M3 buffer (10 mM sodium phosphate pH 7.0, 100 mM NaCl, 10 mM 2-mercaptoethanol, and protease inhibitor). Nuclei pellets were rinsed and resuspended in sonication buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS, and protease inhibitor), and then sonicated with a sonicator (QSonica, Q800R3) for 30 min (20 s on/40 s off). After chromatin shearing, the debris was removed by centrifugation and the solutions containing chromatin fragments were diluted with three times the volume of ChIP dilution buffer (16.7 mM Tris-HCl pH 8.0, 167 mM NaCl, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS, and protease inhibitor). For H3K9me2 ChIP, after dilution, protein G magnetic beads (Thermo Fisher Scientific) were added to sheared chromatin and incubated at 4˚C for 1 hour. Pre-cleared samples were collected and incubated with anti-H3K9me2 antibodies at 4˚C overnight with rotation. After incubation, samples were mixed with 30 µL of protein G magnetic beads, incubated at 4˚C for 3 hours with rotation. For SUVH6 ChIP, after dilution, the pre-cleared samples were collected and incubated with GFP-trap beads at 4˚C overnight with rotation. The beads then washed twice with low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), twice with high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, and 0.1% SDS), once with LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.25 M LiCl, 1% NP-40, and 0.1% deoxycholic acid), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). Immunoprecipitated DNA was incubated at 65 °C using 150 μL of elution buffer (1% SDS, 10 mM EDTA, 0.1 M NaHCO3) twice with shaking rigorously. After elution, the DNA-protein complex was reverse-crosslinked using 12 μL 5 M NaCl at 65 °C for 6 hours. 1 μL of Proteinase K, 10 μL of 0.5 M EDTA, 20 μL of 1 M Tris pH 6.5, 10 µg of RNaseA were added to digest the proteins and RNA. The DNA was then purified using phenol: chloroform and precipitated with sodium acetate, Glycogen and ethanol overnight at -20 °C. The precipitated DNA was collected and processed for the library construction.
ChIP-Seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V4 (Vazyme, ND610) following the manufacturer’s instructions. CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) following the manufacturer’s instructions. The libraries were sequenced with an Illumina NovaSeq 6000 or Illumina Hiseq 3000 to generate pair-end 150 bp reads. Samples were prepared from three or two independent biological replicates.

value: mature pollen


title: CLIP-OCT4-2


title: MO_MCC_066, skin  - RNA


title: MO_MCC_061, skin  - RNA


title: LesionWM, Control, 43712_P7D2, rep3


title: blood, CAF09hi, immu2, rep 1 CGB065.2019.07.23


title: blood, CAF09hi, immu2, rep 1 CGA054.2019.07.23


title: LesionWM, Control, 43711_P7C3, rep2


title: LesionWM, Control, 43711_P7C2, rep2


title: blood, CAF09hi, immu1, rep 1 CGA054.2019.06.25


title: ARID1-GFP_IP_Rep1


title: MO_MCC_059, lymph node - gd VDJ

source_name: lymph node

value: lymph node


title: MO_MCC_059, lymph node - ab VDJ


title: T1,tumor-PTEN

city: shanghai

first: jiaming

last: shen

address: SHANGHAI

institute: shanghai jiaotong university

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V2.1.1 (https://support. 10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
Place a sterile RNase-free culture dish containing an appropriate amount of calciumfree and magnesium-free 1 × PBS on ice, the tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with 1 × PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers. Tissus were dissociated into single cells in dissociation solution in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum, then pipetting 5-10 times with a Pasteur pipette.The resulting cell suspension was filtered by passing through 70-30um stacked cell strainer and centrifuged at 300g for 5 min at 4 °C. The cell pellet was resuspended in 100ul 1× PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×） and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300g for 5 min at room temperature.The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads(MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS(0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 8000 single cell according to the manufacturer’ s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) by Shanghai Personal Biotechnology (Shanghai, China)

value: tumor


title: blood, CAF10b, immu1, rep 1 CFL098.2019.06.25


title: blood, CAF09hi, baseline, rep 1 CGB065.2019.06.24


title: LesionWM, Control, 43711_P7C1, rep2

value: LesionWM, Brain

value: Saline


title: T2,tumor-PTEN

description: 10x genomics


title: LesionWM, Control, 43710_P7B8, rep1


title: LesionWM, Control, 43710_P7B7, rep1


title: MO_MCC_059, lymph node - ADT


title: MO_MCC_057, lymph node - gd VDJ


title: MO_MCC_059, lymph node - RNA


title: C3,tumor-PBS

description: 10x genomics


title: blood, CAF09hi, immu2, rep 1 CFL069.2019.07.23


title: blood, CAF09hi, baseline, rep 1 CGA054.2019.06.24


title: LesionWM, Control, 43710_P7B6, rep1


title: T3,tumor-PTEN

description: 10x genomics


title: C2,tumor-PBS

description: 10x genomics


title: LesionWM, BCG, 43724_P7F8, rep6

value: BCG


title: blood, CAF10b, baseline, rep 1 CFL098.2019.06.24


title: LesionWM, Control, 43710_P7B5, rep1


title: MO_MCC_057, lymph node - ab VDJ


title: blood, CAF09hi, immu1, rep 1 CFL069.2019.06.25


title: blood, CAF10b, immu2, rep 1 CFL098.2019.07.23


title: C1,tumor-PBS

description: 10x genomics


title: MO_MCC_057, lymph node - ADT


title: KO_axon_4

city: Wuerzburg

first: Michael

last: Briese

state: Bavaria

address: Versbacherstr. 5

department: Institute of Clinical Neurobiology

institute: University Hospital Wuerzburg

data_processing:
Illumina reads were quality- and adapter-trimmed via Cutadaptversion 2.5 using a cutoff Phred score of 20 in NextSeq mode, and reads without any remaining bases were discarded (command line parameters: --nextseq-trim=20 -m 1 -a CTGTCTCTTATACACATCT).
Processed reads were mapped to the mouse Mus musculus GRCm39 reference genome (RefSeq GCF_000001635.27_GRCm39) with splice junction-sensitive read mapper STAR version 2.7.2b using default parameters.
Read counts on exon level summarized for each gene were generated using featureCounts v1.6.4 from the Subread package. Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
The read abundance estimation and their differential expression were analyzed between sample libraries using DESeq2 version 1.24.0. Read counts were normalized by DESeq2 and fold-change shrinkage was applied by setting the parameter “betaPrior=TRUE”.
Assembly: mm39
Supplementary files format and content: Character (TAB) separated value file containing raw mRNA abundance measurements

source_name: spinal cord

growth_protocol: Lumbar spinal cords were isolated from E13 mouse embryos, and motoneurons were enriched by panning using a p75NTR antibody (clone MLR2, Biosensis). Motoneurons were plated in the central (somatodendritic) compartment of microfluidic chambers (Xona Microfluidics, IND150) pre-coated with 0.1% poly-L-lysine hydrobromide (Sigma-Alrich) and laminin-111 (Thermo Fisher Scientific) and maintained at 37°C, 5% CO2 in neurobasal medium (Gibco) supplemented with 2% B27 (Gibco), 2% heat-inactivated horse serum (Linaris), 500 µM GlutaMAX (Gibco). CNTF (5 ng/ml) was applied to both the somatodendritic and the axonal compartment. Axon growth was stimulated by adding 20 ng/ml BDNF only to the axonal compartment. Culture medium was exchanged on day 1 and then every second day.

extract_protocol:
RNA was purified from the somatodendritic and axonal compartment using the PicoPure RNA Isolation Kit (Thermo Fisher Scientific, KIT0204) with 10 μl elution volume.
cDNA libraries suitable for sequencing were prepared with SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara) according to the manufacturer’s instructions (1/4 volume for the somatodendritic samples and full volume for the axon samples).

value: spinal cord

value: primary motoneurons

value: hnRNP R KO

tag: compartment

value: axon


title: KO_axon_3


title: blood, CAF09hi, baseline, rep 1 CFL069.2019.06.24


title: LesionWM, BCG, 43724_P7F7, rep6

value: male


title: MO_MCC_057, lymph node - RNA

value: Merkel Cell Carcinoma (MCC) cell


title: LesionWM, BCG, 43724_P7F6, rep6

value: 12 months


title: KO_axon_2


title: MO_MCC_011, skin - ab VDJ

value: ab VDJ

value: skin


title: scRNA-Seq of the lung estrogen group

city: Nan Jing

first: Fang

last: Wen

address: Xianlin street

institute: Nanjing University

description: 10x Genomics

data_processing:
Cell barcode and UMI extraction
alignment
barcode correction
UMI filtering and correction
UMI count and call cells
Assembly: macFas6
Supplementary files format and content: barcodes.tsv
Supplementary files format and content: features.tsv
Supplementary files format and content: matrix.mtx

source_name: Lung

extract_protocol:
A total of 10 scRNA-seq data and 10 paired scATAC-seq data for different organs and groups were available
RNA: 3' transcriptome sequencing, cDNA fragmentation, end filling, adding A, connection connector, Index PCR; ATAC: Prepare Sample Index PCR Mix mixture, add SI PCR mix, add SI Index N SA, mix well, add SPRIselect, remove supernatant, add ethanol, remove ethanol, centrifuge.

value: Lung

value: female

value: All cells

value: Estrogen


title: KO_axon_1


title: MO_MCC_011, skin - RNA

value: RNA


title: scRNA-Seq of the uterus estrogen group

description: 10x Genomics

source_name: Uterus

value: Uterus


title: LesionWM, BCG, 43724_P7F5, rep6

value: LesionWM, Brain


title: LesionWM, BCG, 43723_P7F4, rep5

value: BCG


title: scRNA-Seq of the liver estrogen group

description: 10x Genomics

source_name: Liver

value: Liver


title: WT_axon_4

value: spinal cord

value: primary motoneurons

value: WT


title: scRNA-Seq of the colon estrogen group

description: 10x Genomics

source_name: Colon

value: Colon


title: HPO66_PC

city: Créteil

first: Céline

last: Colnot

address: 8 rue du Général Sarrail

country: France

institute: INSERM U955

data_processing:
FASTQ files were mapped to the ENSEMBL Human (GRCh38/hg38) reference using HISAT2 and counted by featureCounts from the Subread R package.
Assembly: ENSEMBL Human (GRCh38/hg38)

source_name: periosteal SSPCs

extract_protocol:
Periosteum collected at the pseudarthrosis site or the iliac crest was divided in several pieces and placed in a culture dish for explant culture with drops of culture medium composed of MEMα, supplemented with 20% of FBS, 1% of Penicillin-Streptomycin and 10 ng/ml bFGF. Drops of medium were replaced every day until the tissue attached to the culture dish. Periosteal cells progressively migrated in the dish. After one to two weeks, periosteum explants were removed and periosteal cells were trypsinised for RNA extraction.
RNAs were extracted from primary periosteal cells from IC and PA site of patients 3 and 7 using the RNeasy Kit (Qiagen) use a DNA removal step accordingly to manufacturer’s recommendation. RNA qualities were assessed by capillary electrophoresis using High Sensitivity RNA reagents with the Fragment Analyzer (Agilent Technologies) and the RNA concentrations were measured by using spectrophometry using Xpose (Trinean) and Fragment Analyzer capillary electrophoresis. RNAseq libraries were prepared from 1 µg of total RNA using the Universal Plus mRNA-Seq kit (Nugen) as recommended by the manufacturer.

value: periosteal SSPCs

value: NF1 WT


title: WT_axon_3

value: axon


title: WT_axon_2


title: LesionWM, BCG, 43723_P7F3, rep5

value: male

value: 12 months


title: scRNA-Seq of the breast estrogen group

description: 10x Genomics

source_name: Breast

value: Breast

value: female


title: scATAC-Seq of the uterus estrogen group

description: 10x Genomics

library_source: genomic single cell

data_processing:
Cell barcode and UMI extraction
alignment
barcode correction
UMI filtering and correction
UMI count and call cells
Assembly: macFas6
Supplementary files format and content: barcodes.tsv
Supplementary files format and content: matrix.mtx
Supplementary files format and content: peaks.bed

value: All cells

value: Estrogen


title: WT_axon_1


title: HPO57_PC


title: HPO66_PP

value: NF1 mutated


title: KO_soma_4

value: hnRNP R KO

value: somatodendritic


title: LesionWM, BCG, 43723_P7D10, rep5

value: LesionWM, Brain

value: BCG


title: HPO57_PP


title: scATAC-Seq of the colon estrogen group

description: 10x Genomics


title: LesionWM, BCG, 43722_P7C9, rep4


title: P13_iliaccrest_periosteum

data_processing:
Fastq files were processed with the CellRanger pipeline with the default’s parameters
Reads were align against the HG38 2020-A reference genome
Filtered features barcodes matrices were used to perform data analysis
Assembly: HG38 2020-A

source_name: Periosteum

extract_protocol:
Nuclei extraction was performed on snap-frozen human periosteum samples from PA site and IC of patient P13 and from PA site of patient P5. RNA integrity was checked beforehand on identical tissue samples (RIN > 6.5). Periosteum samples were briefly defrosted in nuclei extraction buffer before mincing and nuclei extraction. Collected tissues were minced and placed 5 min in ice-cold Nuclei Buffer (NUC101, Merck) before mechanical nuclei extraction using a glass douncer. Extraction was performed by 20 strokes of pestle A followed by 10-20 of pestle B. Nuclei suspension was filtered, centrifuged and resuspensed in RNAse-free PBS with 2% Bovine Serum Albumin and 0.2 U/µL RNAse inhibitor. A second step of centrifugation was performed to reduce contamination by cytoplasmic RNAs. Sytox™ AADvanced™ was added (1/200) to label nuclei and Sytox-AAD+ nuclei were sorted using Sony SH800.
The snRNA-seq libraries were generated using Chromium Single Cell Next GEM 3′ Library & Gel Bead Kit v.3.1 (10x Genomics) according to the manufacturer’s protocol. Briefly, 10 000 to 20 000 nuclei were loaded in the 10x Chromium Controller to generate single-nuclei gel- beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq (Illumina) with 28 cycles of read 1, 8 cycles of i7 index and 91 cycles of read 2. Sequencing data were processed using the Cell Ranger Count pipeline and reads were mapped on the HG38 2020-A reference human genome, with intronic and exonic sequences.

value: Periosteum

value: Control periosteum


title: scATAC-Seq of the heart estrogen group

description: 10x Genomics

source_name: Heart

value: Heart


title: KO_soma_3

value: spinal cord

value: primary motoneurons


title: LesionWM, BCG, 43722_P7C6, rep4


title: P13_pseudarthrosis_periosteum

value: Affected periosteum


title: KO_soma_2


title: scATAC-Seq of the liver estrogen group

description: 10x Genomics

value: Liver


title: scATAC-Seq of the lung estrogen group

description: 10x Genomics

value: Lung


title: P5_pseudarthrosis_periosteum


title: LesionWM, BCG, 43722_P7C5, rep4

value: male

value: 12 months


title: LesionWM, BCG, 43708_P7D8, rep3


title: WT_soma_4

value: WT


title: A549 cells transiently transfected with siRNA APE1, Vescicular RNA, replicate 4

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

country: Italy

institute: ICGEB

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, Vescicular RNA, replicate 4
EV-siAPE_rep4

data_processing:
Basecalls performed using CASAVA (Illumina Inc.)
We used sRNAtoolbox, a collection of small RNA analysis tools, to generate the features’ counts.
The generated feature counts were consequently analysed using R’s package DESeq2 (Love,2014).  An adjusted p-value cut off of 0.05 was decided as threshold for detection of DEGs.
Assembly: human genome version GRCh38 and with reference annotation.
Supplementary files format and content: tab-delimited text files include COUNTS values for each Sample

source_name: lung

growth_protocol: A549 hepatocarcinoma cells were grown in RPMI 1640, supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100μg/ml streptomycin (Euroclone)

extract_protocol:
Cellular and exosomal miRNAs extraction was executed, using respectively the miRNeasy Mini Kit (QIAGEN, Hilden, Germany), and the Total Exosome RNA & Protein Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
Library preparation was performed using  QIAseq miRNA Library Kit (Qiagen) following the manufacturer's instructions.
RNA-Seq on a Illumina HiSeq NovaSeq 6000 instrument using a 75-bp, single-end sequencing configuration

treatment_protocol: A549 cells were seeded in the number of  1.0*10^6 in 10 cm dish. One day later, the transfection was performed using 17 pmol of custom hAPE1 siRNA or with non-targeting siRNA pool (siSCR) as a control, (GE Healthcare Dharmacon, Colorado, USA). The transfection was carried out with the DharmaFECT transfection reagent (Thermo Fisher Scientific, Massachusetts, United States), according to the manufacturer’s instructions. Six hr after transfections, fresh medium was added to the complexes for reducing cytotoxicity. The day after transfection, cells were washed twice with PBS, medium supplemented with 10% FBS exosome-depleted (Thermo Fisher Scientific), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone) was added and after 72 hr from transfection cells and media were collected.

value: lung


title: LesionWM, BCG, 43708_P7D7, rep3


title: A549 cells transiently transfected with siRNA APE1, Vescicular RNA, replicate 3

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, Vescicular RNA, replicate 3
EV-siAPE_rep3


title: LesionWM, BCG, 43723_P7F2, rep5


title: Col-0 hypoxia/mock rep3 [10Col-0HM-3]

city: Maynooth

first: Emmanuelle

last: Graciet

state: Kildare

address: Biology Department

department: Biology

country: Ireland

institute: Maynooth University

data_processing:
Data processing was carried out by BGI using the filtering software SOAPnuke (including removal of reads containing the adaptor; removal of reads whose N content is greater than 5%; and removal of low-quality reads).
The Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT) software was then used for mapping clean reads to the reference genome.
Differential gene expression was determined using DESeq2.
Assembly: Reference Genome Version: GCF_000001735.4_TAIR10.1
Supplementary files format and content: Tab-delimited file including gene counts for each sample

source_name: whole seedlings

growth_protocol: Arabidopsis seedlings were sown and grown on 0.5xMS agar with 0.5% (w/v) sucrose plates in continuous light at 20°C.

extract_protocol:
Total RNA was extracted using Spectrum Plant Total RNA extraction kit (Merck)
Libraries were prepared by BGI Genomics (Hong Kong)

treatment_protocol: Five 9-day old seedlings per genotype per treatment were transferred to 35 mm x 10 mm dishes, each containing 4 mL of 0.5xMS liquid medium and placed on a shaker at 120 rpm overnight in continuous light conditions, 20°C. On day 10, seedlings were treated simultaneously with 100 nM flg22, or equivalent volume of water (mock), and hypoxia in anaerojars or normoxia at ambient oxygen levels. After 1 hr, the seedlings were harvested in liquid nitrogen and stored at -80°C for total RNA extraction.

value: whole seedlings

tag: accession

value: wild type

value: hypoxia/mock


title: Col-0 normoxia/flg22 rep3 [11Col-0NF-3]


title: Col-0 normoxia/mock rep3 [12Col-0NM-3]

value: normoxia/mock


title: LesionWM, BCG, 43708_P7D6, rep3

source_name: LesionWM, Brain

value: LesionWM, Brain

value: BCG


title: Col-0 normoxia/mock rep2 [8Col-0NM-2]


title: LesionWM, BCG, 43707_P7E7, rep2


title: Col-0 normoxia/flg22 rep2 [7Col-0NF-2]


title: LesionWM, BCG, 43722_P7C7, rep4


title: WT_soma_2

value: somatodendritic


title: Col-0 hypoxia/flg22 rep3 [9Col-0HF-3]


title: A549 cells transiently transfected with siRNA APE1, Vescicular RNA, replicate 1

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, Vescicular RNA, replicate 1
EV-siAPE_rep1


title: LesionWM, BCG, 43708_P7D5, rep3


title: LesionWM, BCG, 43707_P7E6, rep2


title: LesionWM, BCG, 43707_P7E8, rep2


title: A549 cells transiently transfected with scramble control siRNA, Vescicular RNA, replicate 2

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, Vescicular RNA, replicate 2
EV-SCR_rep2

value: control


title: A549 cells transiently transfected with scramble control siRNA, Vescicular RNA, replicate 3

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, Vescicular RNA, replicate 3
EV-SCR_rep3


title: WT_soma_3

value: spinal cord


title: A549 cells transiently transfected with siRNA APE1, Vescicular RNA, replicate 2

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, Vescicular RNA, replicate 2
EV-siAPE_rep2


title: Col-0 hypoxia/mock rep2 [6Col-0HM-2]


title: KO_soma_1

value: primary motoneurons

value: hnRNP R KO


title: Col-0 hypoxia/flg22 rep2 [5Col-0HF-2]


title: WT_soma_1


title: LesionWM, BCG, 43707_P7E5, rep2


title: A549 cells transiently transfected with siRNA APE1, replicate 4

description:
Total RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, replicate 4
CE-siAPE_rep4


title: LesionWM, BCG, 43706_P7E4, rep1


title: A549 cells transiently transfected with scramble control siRNA, Vescicular RNA, replicate 1

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, Vescicular RNA, replicate 1
EV-SCR_rep1


title: A549 cells transiently transfected with scramble control siRNA, Vescicular RNA, replicate 4

description:
Vesicular RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, Vescicular RNA, replicate 4
EV-SCR_rep4


title: Col-0 normoxia/mock rep1 [4Col-0NM-1]


title: Col-0 hypoxia/mock rep1 [2Col-0HM-1]


title: Col-0 normoxia/flg22 rep1 [3Col-0NF-1]


title: A549 cells transiently transfected with siRNA APE1, replicate 1

description:
Total RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, replicate 1
CE-siAPE_rep1


title: LesionWM, BCG, 43706_P7E3, rep1


title: A549 cells transiently transfected with siRNA APE1, replicate 3

description:
Total RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, replicate 3
CE-siAPE_rep3


title: A549 cells transiently transfected with siRNA APE1, replicate 2

description:
Total RNA
A549 cells transiently transfected with 17 pmol siRNA APE1, replicate 2
CE-siAPE_rep2


title: LesionWM, BCG, 43706_P7E2, rep1


title: 10-day old ate1-2 ate2-1 seedlings flg22-treated (1 hour)_rep3

source_name: Whole seedlings

treatment_protocol: Fifty 9-day old seedlings per genotype per treatment were transferred to 2 wells of a 6-well plate, each containing 6 mL of 0.5xMS with 0.5% sucrose liquid medium and returned to the growth room in continuous light with gentle agitation at 120 rpm. 24 hrs after transfer, 1 µM flg22 or an equivalent volume of water (mock treatment) was added to each well for 1 hr, after which seedlings were collected and frozen in liquid nitrogen for total RNA extraction

value: Whole seedlings

tag: ecotype

value: ate1-2 ate2-1


title: LesionWM, BCG, 43706_P7E1, rep1

value: male


title: A549 cells transiently transfected with scramble control siRNA, replicate 4

description:
Total RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, replicate 4
CE-SCR_rep4


title: Col-0 hypoxia/flg22 rep1 [1Col-0HF-1]

tag: genotype


title: A549 cells transiently transfected with scramble control siRNA, replicate 3

description:
Total RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, replicate 3
CE-SCR_rep3


title: 10-day old ate1-2 ate2-1 seedlings mock-treated (1 hour)_rep3

value: mock


title: A549 cells transiently transfected with scramble control siRNA, replicate 2

description:
Total RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, replicate 2
CE-SCR_rep2


title: Screen 2 HSV-1-GFP infected and FACS of GFP High [Screen_2_High_libraryB]

city: Aarhus

first: Søren

middle: Riis

last: Paludan

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

institute: Aarhus University

description:
Screen_2_mapped_readcounts_libraryB.txt
Screen_2_HSV-1_GFP_High_Geckov2_libraryB
Screen 2 HSV-1-GFP infected and FACS of GFP High compared to an unsorted control(USC)

data_processing:
*library strategy: CRISPR screen
Raw sequencing reads were processed to remove known adapter sequences located 5' and 3’ of the 20 bp sgRNA sequence using cutadapt 3.7. cutadapt -g TGTGGAAAGGACGAAACACCG...GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGTCCGTTATCAA -e 0.1 -m 17 -M 20
Using the -count command of MAGeCK v0.5.9.4, trimmed reads were mapped to unique sgRNA sequences found in the references library of Human CRISPR Knockout Pooled Library (Gecko v2)
Assembly: The references library of Human CRISPR Knockout Pooled Library (Gecko v2), availiable from addgene PMID:25075903. Was used to map unique 20bp long spacer sequences to their specific sgRNAs and the respective targeted gene
Supplementary files format and content: Tab delimited text file with four columns each; "sgRNA" "Gene" and two sample specific columns with sgRNA readcounts corresponding to each sgRNA

source_name: Brain

growth_protocol: SK-N-SH cells were cultured in DMEM (Sigma Aldrich) and RPMI-1640 (Sigma Aldrich) w/L-glutamine supplemented with 10% heat-inactivated FBS [Life Technologies], 1% penicillin/streptomycin (Life Technologies).

extract_protocol:
QIAamp DNA Blood Mini Kit_ID:51104
PCR products for trageted sequencing of the sgRNA cassette was amplified as described by Sanjana  et al. 2014 (Improved vectors and genome-wide libraries for CRISPR screening) PMID:25075903

treatment_protocol: HSV-1-K26GFP at an MOI of 0.25, FACS after 17 h

value: Brain

value: SK-N-SH

tag: cell type

value: Neuroblastoma

value: female

value: FACS of eGFP High


title: 10-day old Col-0 (wild type) seedlings flg22-treated (1 hour)_rep3

tag: tissue

value: wildtype


title: Screen 1 HSV-1-GFP infected and unsorted control (USC) [Screen_1_USC_libraryA]

description:
Screen_1_mapped_readcounts_libraryA.txt
Screen_1_HSV-1_GFP_High_Geckov2_libraryA
Screen 1 HSV-1-GFP infected and FACS of GFP High compared to an unsorted control(USC)


title: A549 cells transiently transfected with scramble control siRNA, replicate 1

description:
Total RNA
A549 cells transiently transfected with 17 pmol scramble control siRNA, replicate 1
CE-SCR_rep1

value: lung


title: 10-day old Col-0 (wild type) seedlings mock-treated (1 hour)_rep3


title: Screen 2 HSV-1-GFP infected and unsorted control (USC) [Screen_2_USC_libraryB]


title: Screen 1 HSV-1-GFP infected and FACS of GFP High [Screen_1_High_libraryA]


title: 10-day old ate1-2 ate2-1 seedlings flg22-treated (1 hour)_rep2


title: 10-day old Col-0 (wild type) seedlings flg22-treated (1 hour)_rep2


title: Control, replicant 3 [miRNA]

city: Harbin

first: Lijun

last: Hao

address: 23 Youzheng Street

institute: the First Affiliated Hospital of Harbin Medical University

description: Sample A3

data_processing:
Quality control of the raw sequencing reads is performed using FastQC (version 1.0.0) to ensure data integrity. Low-quality bases and adapter sequences are then removed from the reads using trimming tools Trimmomatic (version 0.40). The high-quality reads are aligned to transcriptome with aligners STAR (version 2.7.6a). The aligned reads are stored in BAM files, which are then sorted, indexed, and processed to mark duplicate reads and generate alignment statistics. Gene and transcript expression levels are quantified from the aligned reads using tools HTSeq (version 2.0.3). The expression data are normalized to account for technical variations, and differential expression analysis is conducted using DESeq2 (version 1.30.1) to identify genes with significant expression changes between experimental conditions.
Assembly: OryCun3.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Oryctolagus cuniculus

source_name: Hypertrophic scars

extract_protocol:
Briefly, total RNA was extracted from samples with an achieved yield of 1 µg per sample. Integrity and purity were confirmed using agarose gel electrophoresis (28S:18S ≥ 1.5) and Nanodrop spectrophotometry (OD260/280 ratio between 1.8 and 2.2), respectively. RNA concentration was quantified using a Qubit 4 Fluorometer (Thermo Fisher Scientific, Inc.), with minimum readings of 500 ng/µl.
Adaptors were added to both ends of small RNAs, and cDNA was synthesized through reverse transcription, followed by purificatiox n using QIAseq  miRNA NGS Beads (cat. no., 333923; Qiagen).

value: Hypertrophic scars

tag: breed

value: New Zealand White

value: Treated with saline for 21 days


title: ADSC-Exos, replicant 1 [miRNA]

description: Sample B1

value: Treated with ADSCs-Exos (100µg/2ml) for 21 days


title: Control, replicant 2 [miRNA]

description: Sample A2


title: ADSC-Exos, replicant 3 [miRNA]

description: Sample B3


title: ADSC-Exos, replicant 2 [miRNA]

description: Sample B2


title: HAB rep2

city: 北京

first: yixue

last: Luo

state: 北京市

address: Biomanufacturing and Rapid Forming Technology Key Laboratory of Beijing, Department of Mechanical Engineering, Tsinghua University, Beijing 100084, China

institute: 清华大学

data_processing:
Sequencing was performed with an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Reads were filtered and mapped to the reference genome sequence with Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Homo_sapiens_Ensembl_94
Supplementary files format and content: The fragments per kilobase of exon per million fragments mapped (FPKM) method was used to calculated gene expression levels.

source_name: liver\Human Umbilical Vein

growth_protocol: HepaRG cells were cultured in growth medium, which was composed of DMEM  supplemented with 10% FBS , 1% GlutaMAX™ supplement, 1% MEM NEAA solution , 0.05% insulin, and 5×10-5 M hydrocortisone sodium succinate .  HUVECs were  cultured in DMEM supplemented with 10% (v/v) FBS, 0.1% insulin , and 5ng/ml VEGF . HepaRG cells and HUVECs were incubated in humidified air containing 5% CO2 at 37 °C.

extract_protocol:
The samples for RNA-seq were collected in TriZol. 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Organoid:   HepaRG cells and HUVECs were co-cultured in HepaRG growth medium with PMPs to form organoids.  3D bio-printed and Hepatobiliary differentiation: The bioprinted constructs were cultured with differentiation media ( HepaRG growth medium supplemented with 0.5% DMSO) for 14 days.

value: liver\Human Umbilical Vein

value: hepaRG\HUVEC

value: hepatoblasts\Endothelial Cells

value: WT


title: Control, replicant 1 [miRNA]

description: Sample A1


title: HAB rep1

value: 3D bio-printed and Hepatobiliary differentiation


title: MiaPaCa-2_rep3

type: RNA

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: HumanHT v4 Expression BeadChip Kit

scan_protocol: iScan system

data_processing: Data was analyzed using Partek Genomics Suite version 6.12.1213

label: biotin

source_name: MiaPaCa-2 pancreatic cells

label_protocol: Ambion Illulmina TotalPrep-96 RNA Amplification Kit

growth_protocol: HEI-286 and MiaPaCa-2 were grown in 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium (DMEM, Cellgro, Herndon, VA) containing 10% fetal bovine serum (Gemini, Woodland, CA).

extract_protocol: RNA was extracted from cells by using RNeasy mini kit (QIAGEN, cat #74104) as per the manufacturer’s instructions.

value: pancreatic cells


title: 10-day old ate1-2 ate2-1 seedlings mock-treated (1 hour)_rep2

value: Whole seedlings

value: ate1-2 ate2-1

value: mock


title: ADSC-Exos, replicant 3

description:
Sample B3
LncRNA_cirRNA_HS_Rabbit.xls

value: female


title: 10-day old Col-0 (wild type) seedlings mock-treated (1 hour)_rep2


title: HOBB rep3

value: organoid


title: ADSC-Exos, replicant 2

description:
Sample B2
LncRNA_cirRNA_HS_Rabbit.xls


title: HAB rep3


title: MiaPaCa-2_rep4


title: rifampicin 100uM 24h, rep1

city: Setagaya-ku

first: Hideya

last: Kawaji

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Research Center for Genome & Medical Sciences

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

data_processing:
Obtained reads were aligned with the reference human genome GRCh38 by using STAR (v2.7.5a), taking splice junctions of Gencode transcripts (v37) to improve the alignment accuracy. The first position of each uniquely mapped read was counted as the transcription initiation with CREate (https://github.com/hkawaji/CREate), bedtools (v2.29.2), and the utility programs of the UCSC Genome Browser Database (v425).
Assembly: GRCh38 (hg38)
Supplementary files format and content: The observed counts of transcription starting sites (CAGE tag starting site, CTSS) are included in BED format.

source_name: ShP51 (HepG2 derived)

growth_protocol: ShP51 cell lines were cultured in Dulbecco’s modified Eagle’s medium (high glucose) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, Waltham, MA, USA), 1× MEM Non-Essential Amino Acids Solution (Thermo Fisher Scientific), 100 U/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific). Cells were maintained in a humidified incubator, which provided an atmosphere of 5% CO2 and 95% air at a constant temperature of 37°C.

extract_protocol:
Total RNA was isolated using a miRNeasy Mini Kit (Qiagen, Venlo, Netherlands).
CAGE libraries were prepared using a CAGE Library preparation kit (DNAform, Kanagawa, Japan). Briefly, cDNA was synthesized from total RNA using random primers. The ribose diols in the 5′ cap structures of RNA were oxidized and then biotinylated. The biotinylated RNA/cDNAs were selected by streptavidin beads (a process known as cap-trapping). RNA was digested with RNaseONE/H, adaptors were ligated to both ends of cDNA, and CAGE libraries of double-stranded cDNA were constructed.

treatment_protocol: Cells were treated with dimethyl sulfoxide (DMSO), or with 10µM or 100µM rifampicin dissolved in DMSO (Sigma-Aldrich, Burlington, MA, USA) for 24 h.

value: ShP51 (HepG2 derived)

value: hepatocellular carcinoma

value: rifampicin 100uM


title: rifampicin 10uM 24h, rep3

value: rifampicin 10uM


title: rifampicin 100uM 24h, rep2


title: HEI_rep2

source_name: HEI-286 human Schwann cells

value: Schwann cells


title: rifampicin 10uM 24h, rep2


title: HEI_rep4


title: 10-day old ate1-2 ate2-1 seedlings flg22-treated (1 hour)_rep1


title: HOBB rep2


title: ADSC-Exos, replicant 1

description:
Sample B1
LncRNA_mRNA_HS_Rabbit.xls

value: Hypertrophic scars

value: New Zealand White

value: Treated with ADSCs-Exos (100µg/2ml) for 21 days


title: HOBB rep1

value: liver\Human Umbilical Vein

value: hepaRG\HUVEC

value: hepatoblasts\Endothelial Cells


title: 10-day old ate1-2 ate2-1 seedlings mock-treated (1 hour)_rep1


title: rifampicin 10uM 24h, rep1


title: MiaPaCa-2_rep1

value: pancreatic cells


title: HEI_rep3


title: HEI_rep1


title: 10-day old Col-0 (wild type) seedlings mock-treated (1 hour)_rep1

value: Whole seedlings

value: wildtype


title: MiaPaCa-2_rep2


title: 2D rep3

value: WT

value: planar cell culture


title: DMSO 24h, rep3

value: DMSO


title: Control, replicant 1

description:
Sample A1
LncRNA_lncRNA_HS_Rabbit.xls

value: female

value: Treated with saline for 21 days


title: 2D rep2


title: DMSO 24h, rep1

value: ShP51 (HepG2 derived)

value: hepatocellular carcinoma


title: Control, replicant 3

description:
Sample A3
LncRNA_mRNA_HS_Rabbit.xls


title: 10-day old Col-0 (wild type) seedlings flg22-treated (1 hour)_rep1


title: Control, replicant 2

description:
Sample A2
LncRNA_lncRNA_HS_Rabbit.xls


title: DMSO 24h, rep2


title: ebp1_SEC#2

status: Public on Jul 23 2024

city: Daegu

first: Ju

last: Yun

address: 333, Techno jungang-daero

department: New Biology

country: South Korea

institute: DGIST

data_processing:
Illumina HiSeq generated raw images using HiSeq Control Software v2.2 for the system control and base calling using Real Time Analysis v1.18-integrated primary analysis software.
The BCL (base calls) binary files were converted into FASTQ format using Illumina package bcl2fastq (v1.8.4).
Quality control and preprocessing of metagenomic data were performed using FastQC (v0.11.2; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapters and low quality sequences were filtered out with Trimmomatic v0.32.3 (Bolger et al., 2014), and alignment was performed using the Arabidopsis TAIR10 genome (ENSEMBL annotation) and TopHat 2.0.9 (Trapnell et al., 2009). PCR duplication was removed using Picard (v1.119; http://broadinstitute.github.io/picard/), and only uniquely mapped reads were counted using HTSeq v0.6.1 (Anders et al., 2015).
A differential gene expression analysis was performed using DESeq2 (Love et al., 2014). P-values were adjusted via the Benjamini–Hochberg method (Benjamini and Hochberg, 1995), and differentially expressed genes with false discovery rates (FDR) < 0.05 were considered significant.
Assembly: Arabidopsis_thaliana.TAIR10
Supplementary files format and content: tab-delimited text file including read counts processed by HTSeq-count.

source_name: abscission zone of separated floral organs

growth_protocol: Arabidopsis plants were grown in soil in growth chambers at 22°C ± 2°C. The photoperiod was 16-h light/8-h dark (110 μmol m−2 s−1).

extract_protocol:
Total RNA from the protoplasts was extracted using the RNeasy™ Micro Kit (QIAGEN) according to the manufacturer’s instructions. RNA was eluted in 14-μl water, and RNA quality was monitored using a Bioanalyzer Pico chip (Agilent Technologies).
cDNA was generated using SMART-Seq V4 Ultra Low Input RNA Kit (Clontech) with 18 amplification cycles, and RNA-seq libraries were generated using the TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s manual. The libraries were qualitatively and quantitatively verified and then loaded onto a flow cell for cluster generation using cBot and TruSeq PE Cluster Kit v3 (Illumina).

tag: ecotype background

value: SECs (Secession cells)


title: ebp1_SEC#1

value: abscission zone of separated floral organs


title: ebp1_REC#2

source_name: abscission zone of receptacle

value: abscission zone of receptacle

value: RECs (Residuum cells)


title: Plate7_I15

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

data_processing:
The libraries were sequenced (single-end, 50 bp in length) using HiSeq 2500 v.2 (Illumina, San Diego, CA).
This pipeline includes the use of STAR aligner (Dobin et al., 2013) and parameters used herein included a maximum number of mismatches of 3 and insertion and deletion open and extension penalties of 0.
the following steps were undertaken to filter out low-count genes and samples across the entire dataset: 1) Genes with fewer than 10 mean counts across all samples (n = 4558) were excluded, 2) Samples with an average expression across all genes lower than 15 were also removed. Principal component analysis (PCA) was conducted on vehicle controls from all samples across 16 plates to assess potential plate effects. Outliers in vehicle control samples were identified and excluded using a mean correlation threshold of <0.85, ensuring the reliability of the subsequent transcriptomic dose-response and differential expression analyses.
Assembly: Whole transcriptome assay
Supplementary files format and content: with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: meta data of the QC samples

source_name: iPSC-Cardiomyocytes

extract_protocol:
The media and chemicals from the 384-well plates was fully aspirated and replaced with 10 μL/well of 2X lysis buffer. The plates were then shaken using an orbital plate shaker for 10 minutes. The plates were then checked to ensure that the cells were lysed, and if not placed back on the plate shaker for an additional five minutes. Once the cells were lysed, adhesive seals were placed on the plates and the lysates were frozen in the 384-well plates and stored at −80 °C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (Grimm et al., 2016; House et al., 2022).
TempO-seq libraries were prepared using the human whole transcriptome panel consisting of 22,537 protein-coding transcripts.

value: iPSC-Cardiomyocytes


title: Plate7_I17


title: Plate7_I08


title: Plate7_I13

value: Triphenyl phosphate_10_uM


title: Plate7_I07


title: Plate7_I11


title: Plate7_I10


title: Plate7_I16


title: Plate7_I19


title: 2D rep1

value: liver\Human Umbilical Vein

value: hepaRG\HUVEC

value: hepatoblasts\Endothelial Cells


title: Plate7_I20


title: Plate7_I21


title: Plate7_I23


title: Plate7_I22


title: Plate7_J02


title: Plate7_I09


title: Plate7_J09


title: Plate7_J04


title: Plate7_J06


title: Plate7_J07


title: Plate7_J05

value: Adipic acid_1_uM


title: Plate7_J03


title: Plate7_J12


title: Plate7_J10


title: ebp1_REC#1


title: Plate7_J08


title: Plate7_J11


title: Plate7_I12


title: Plate7_I14


title: Plate7_I18

value: Chlorpromazine hydrochloride_10_uM


title: Plate7_J15


title: Plate7_J14


title: Plate7_H03


title: Plate7_J17


title: Plate7_J19


title: Plate7_J18

value: Chlorpromazine hydrochloride_1_uM


title: Plate7_H04


title: Plate7_J16


title: Plate7_H06


title: Plate7_H08


title: Plate7_H07


title: Plate7_H13

value: Triphenyl phosphate_0.2_uM


title: Plate7_H05

value: Adipic acid_0.2_uM


title: Plate7_H10


title: Plate7_H11


title: Plate7_H09


title: Plate7_H12


title: Plate7_H16


title: Plate7_H14


title: Plate7_H17


title: Plate7_J13

value: Triphenyl phosphate_1_uM


title: Plate7_I02


title: Plate7_H21


title: Plate7_H22


title: Plate7_H19


title: Plate7_H20


title: Plate7_H23


title: Plate7_I03


title: Plate7_I05

value: Adipic acid_10_uM


title: Plate7_G09


title: Plate7_G10


title: Plate7_I06


title: Plate7_G08


title: Plate7_G12


title: Plate7_G11


title: Plate7_G14


title: Plate7_H15


title: Plate7_G15


title: Plate7_G16


title: Plate7_G19


title: Plate7_H18

value: Chlorpromazine hydrochloride_0.2_uM


title: Plate7_G22


title: Plate7_G23


title: Plate7_G17


title: Plate7_G21


title: Plate7_G20


title: Plate7_G18


title: Plate7_H02


title: Plate7_F12


title: Plate7_I04


title: Plate7_F13


title: Plate7_G13


title: Plate7_F22


title: Plate7_F21


title: Plate7_G02


title: Plate7_F16


title: Plate7_G03


title: Plate7_F17


title: Plate7_F23


title: Plate7_G04


title: Plate7_F15


title: Plate7_F19


title: Plate7_F18


title: Plate7_G05


title: Plate7_G06


title: Plate7_E21


title: Plate7_E18


title: Plate7_E17


title: Plate7_E23


title: Plate7_E22


title: Plate7_F02


title: Plate7_E20


title: Plate7_F04


title: Plate7_F03


title: Plate7_F14


title: Plate7_F05


title: Plate7_F20


title: Plate7_F06


title: Plate7_F07


title: Plate7_E19


title: Plate7_G07


title: Plate7_F08


title: Plate7_F10


title: Plate7_F11


title: Plate7_E09


title: Plate7_E06


title: Plate7_E08


title: Plate7_E10


title: Plate7_E05


title: Plate7_E04


title: Plate7_E11


title: Plate7_D05


title: Plate7_D07


title: Plate7_E03


title: Plate7_E13


title: Plate7_E12


title: Plate7_E14


title: Plate7_D10


title: Plate7_D09


title: Plate7_D08


title: Plate7_E15


title: Plate7_D12


title: Plate7_E16


title: Plate7_D11


title: Plate7_D13


title: Plate7_D15


title: Plate7_D14


title: Plate7_E07


title: Plate7_F09


title: Plate7_D17


title: Plate7_D16


title: Plate7_D20


title: Plate7_C12


title: Plate7_D23


title: Plate7_C11


title: Plate7_D06


title: Plate7_D21


title: Plate7_D22


title: Plate7_E02


title: Plate7_C10


title: Plate7_C16


title: Plate7_C18


title: Plate7_C23


title: Plate7_C13


title: Plate7_C19


title: Plate7_C15


title: Plate7_C20


title: Plate7_C21


title: Plate7_C17


title: Plate7_C22


title: Plate7_D03


title: Plate7_D02


title: Plate7_B14


title: Plate7_D04


title: Plate7_D18


title: Plate7_B16


title: Plate7_D19


title: Plate7_B18


title: Plate7_B17


title: Plate7_B15


title: Plate7_B19


title: Plate7_B20


title: Plate7_B22


title: Plate7_C14


title: Plate7_C03


title: Plate7_B23


title: Plate7_C07


title: Plate7_C06


title: Plate7_B02


title: Plate7_B21


title: Plate7_C02


title: Plate7_C08


title: Plate7_C04


title: Plate7_C09


title: Plate7_B10


title: Plate7_B09


title: Plate7_B06


title: Plate7_C05


title: Plate7_B07


title: Plate7_B08


title: Plate7_B11


title: Plate7_B12


title: Plate6_N10

value: Diltiazem hydrochloride_0.2_uM


title: Plate7_B13


title: Plate6_N11


title: Plate6_N08


title: Plate6_N09


title: Plate6_N12


title: Plate6_N13


title: Plate7_B03


title: Plate7_B05


title: Plate6_M13


title: Plate6_N20


title: Plate6_N17


title: Plate6_N19


title: Plate6_M12


title: Plate6_N15

value: Diethyl phthalate_0.2_uM


title: Plate6_N21


title: Plate6_N18


title: Plate7_B04


title: Plate6_M09

value: Diltiazem hydrochloride_1_uM


title: Plate6_N14


title: Plate6_M11


title: Plate6_N16


title: Plate6_M16

value: Diethyl phthalate_1_uM


title: Plate6_M15

value: iPSC-Cardiomyocytes


title: Plate6_M14


title: Plate6_M23


title: Plate6_M17


title: Plate6_M19


title: Plate6_M21


title: Plate6_M18


title: Plate6_M22


title: Plate6_N02


title: Plate6_N03


title: Plate6_M20


title: Plate6_M10


title: Plate6_N22


title: Plate6_N23


title: Plate6_N06


title: Plate6_N05


title: Plate6_L11


title: Plate6_L14

value: Diethyl phthalate_10_uM


title: Plate6_L16


title: Plate6_L12


title: Plate6_L18


title: Plate6_L20


title: Plate6_L13


title: Plate6_N04


title: Plate6_M03


title: Plate6_L15


title: Plate6_L22


title: Plate6_M04


title: Plate6_L23


title: Plate6_K12


title: Plate6_M08


title: Plate6_M02


title: Plate6_L17


title: Plate6_L21


title: Plate6_K14


title: Plate6_M07


title: Plate6_K13


title: Plate6_K15


title: Plate6_M06


title: Plate6_K17


title: Plate6_M05


title: Plate6_N07


title: Plate6_K16


title: Plate6_L19


title: Plate6_K18


title: Plate6_K20


title: Plate6_K19


title: Plate6_K22

value: Oxytetracycline hydrochloride_0.2_uM


title: Plate6_K23


title: Plate6_K21


title: Plate6_L03


title: Plate6_L07


title: Plate6_L05


title: Plate6_L02


title: Plate6_L04


title: Plate6_L06


title: Plate6_L08

value: Diltiazem hydrochloride_10_uM


title: Plate6_L09


title: Plate6_J19

value: Potassium perfluorobutanesulfonate_1_uM


title: Plate6_J18


title: Plate6_J23


title: Plate6_J16


title: Plate6_J22

value: Oxytetracycline hydrochloride_1_uM


title: Plate6_K03


title: Plate6_L10


title: Plate6_J15


title: Plate6_K05


title: Plate6_K07


title: Plate6_J20


title: Plate6_K02


title: Plate6_K08


title: Plate6_K04


title: Plate6_J21


title: Plate6_K10


title: Plate6_J17


title: Plate6_K06


title: Plate6_K11


title: Plate6_I22

value: Oxytetracycline hydrochloride_10_uM


title: Plate6_K09


title: Plate6_I23


title: Plate6_I20


title: Plate6_J04


title: Plate6_I19


title: Plate6_J05


title: Plate6_J02


title: Plate6_J09


title: Plate6_I21


title: Plate6_J03


title: Plate6_J12


title: Plate6_J06


title: Plate6_J08


title: Plate6_J13


title: Plate6_J10


title: Plate6_J14


title: Plate6_H23


title: Plate6_I02


title: Plate6_H22


title: Plate6_I05


title: Plate6_I03


title: Plate6_I06


title: Plate6_I07


title: Plate6_I09


title: Plate6_I08


title: Plate6_J07


title: Plate6_I10


title: Plate6_J11


title: Plate6_I11


title: Plate6_I14


title: Plate6_I13


title: Plate6_I12


title: Plate6_I16


title: Plate6_I18


title: Plate6_H07


title: Plate6_I15


title: Plate6_H08


title: Plate6_I17


title: Plate6_I04


title: Plate6_H09


title: Plate6_H05


title: Plate6_H11


title: Plate6_H14


title: Plate6_H15


title: Plate6_H10


title: Plate6_H12


title: Plate6_H17


title: Plate6_H18


title: Plate6_H16


title: Plate6_H19


title: Plate6_H21


title: Plate6_F22


title: Plate6_F23


title: Plate6_G02


title: Plate6_H20


title: Plate6_G03


title: Plate6_H13


title: Plate6_G05


title: Plate6_G06


title: Plate6_H06


title: Plate6_G08


title: Plate6_G13


title: Plate6_G07


title: Plate6_G11


title: Plate6_G17


title: Plate6_G14


title: Plate6_G15


title: Plate6_G16


title: Plate6_G19


title: Plate6_G12


title: Plate6_G20


title: Plate6_G21


title: Plate6_H02


title: Plate6_G18


title: Plate6_G22


title: Plate6_G23


title: Plate6_G04


title: Plate6_D09


title: Plate6_H03


title: Plate6_D11


title: Plate6_H04


title: Plate6_D08


title: Plate6_D12


title: Plate6_D10


title: Plate6_G10


title: Plate6_D15


title: Plate6_D16


title: Plate6_G09


title: Plate6_D13


title: Plate6_D14


title: Plate6_D19


title: Plate6_D22


title: Plate6_D21


title: Plate6_D20


title: Plate6_E05


title: Plate6_E02


title: Plate6_E04


title: Plate6_E03


title: Plate6_E06


title: Plate6_E08


title: Plate6_E07


title: Plate6_E10


title: Plate6_E11


title: Plate6_E15


title: Plate6_E13


title: Plate6_E20


title: Plate6_E14


title: Plate6_E12


title: Plate6_E16


title: Plate6_D17


title: Plate6_E17


title: Plate6_E22


title: Plate6_D23


title: Plate6_E19


title: Plate6_F02


title: Plate6_E23


title: Plate6_F03


title: Plate6_E21


title: Plate6_D18


title: Plate6_F09


title: Plate6_F08


title: Plate6_E09


title: Plate6_F04


title: Plate6_F10


title: Plate6_F12


title: Plate6_F07


title: Plate6_F11


title: Plate6_F13


title: Plate6_E18


title: Plate6_F19


title: Plate6_F16


title: Plate6_F21


title: Plate6_F20


title: Plate6_F05


title: Plate6_B04


title: Plate6_F15


title: Plate6_F14


title: Plate6_F17


title: Plate6_B02


title: Plate6_F06


title: Plate6_B03


title: Plate6_B10


title: Plate6_F18


title: Plate6_B05


title: Plate6_B06


title: Plate6_B13


title: Plate6_B14


title: Plate6_B08


title: Plate6_B15


title: Plate6_B09


title: Plate6_B17


title: Plate6_B12


title: Plate6_B11


title: Plate6_B20


title: Plate6_B07


title: Plate6_B19


title: Plate6_B22


title: Plate6_B18


title: Plate6_B21


title: Plate6_B23


title: Plate6_C03


title: Plate6_C04


title: Plate6_C05


title: Plate6_C02


title: Plate6_C08


title: Plate6_C09


title: Plate6_C06


title: Plate6_B16


title: Plate6_C12


title: Plate6_C10


title: Plate6_C11


title: Plate6_C13


title: Plate6_C16


title: Plate6_C15


title: Plate6_C14


title: Plate6_C19


title: Plate6_C18


title: Plate6_C17


title: Plate6_C22


title: Plate6_C21


title: Plate6_C23


title: Plate6_D05


title: Plate6_D02


title: Plate6_D03


title: Plate5_N22

value: Diisopropyl methylphosphonate_0.2_uM


title: Plate6_C07


title: Plate5_N04


title: Plate6_D06


title: Plate6_D07


title: Plate5_N05


title: Plate5_N23


title: Plate5_N06


title: Plate5_N08


title: Plate5_N09


title: Plate5_N10


title: Plate5_N11

value: Bis(2-ethylhexyl) nonanedioate_0.2_uM


title: Plate5_N12


title: Plate6_C20


title: Plate5_N13


title: Plate5_N14


title: Plate5_N15


title: Plate5_N17


title: Plate5_N18


title: Plate5_N20


title: Plate5_N16


title: Plate5_N19


title: Plate6_D04


title: Plate5_M08


title: Plate5_M07


title: Plate5_N21


title: Plate5_M10


title: Plate5_M12

value: Bis(2-ethylhexyl) nonanedioate_1_uM


title: Plate5_N07


title: Plate5_M17


title: Plate5_M16


title: Plate5_M15


title: Plate5_M13


title: Plate5_M14


title: Plate5_M18


title: Plate5_M19


title: Plate5_M20

value: Diisopropyl methylphosphonate_1_uM


title: Plate5_M22


title: Plate5_N02


title: Plate5_M23


title: Plate5_L12

value: Bis(2-ethylhexyl) nonanedioate_10_uM


title: Plate5_N03


title: Plate5_M21


title: Plate5_L17


title: Plate5_L11


title: Plate5_L15


title: Plate5_L14


title: Plate5_L20

value: Diisopropyl methylphosphonate_10_uM


title: Plate5_L16


title: Plate5_M11


title: Plate5_L18


title: Plate5_L21


title: Plate5_L19


title: Plate5_M09


title: Plate5_L23


title: Plate5_M04


title: Plate5_M05


title: Plate5_K14


title: Plate5_K18


title: Plate5_L13


title: Plate5_K19


title: Plate5_L22


title: Plate5_L05


title: Plate5_L04


title: Plate5_L07


title: Plate5_L06


title: Plate5_L08


title: Plate5_M03


title: Plate5_M02


title: Plate5_J21


title: Plate5_L10


title: Plate5_K15


title: Plate5_K16


title: Plate5_K17


title: Plate5_K20


title: Plate5_K21


title: Plate5_K04


title: Plate5_K06


title: Plate5_K23


title: Plate5_J22


title: Plate5_L02


title: Plate5_L03


title: Plate5_K10


title: Plate5_K08


title: Plate5_K09


title: Plate5_K12

value: L-Tartaric acid_0.2_uM


title: Plate5_K13


title: Plate5_L09


title: Plate5_J03

value: Ammonium perfluorooctanoate_1_uM


title: Plate5_J06


title: Plate5_J20


title: Plate5_J07


title: Plate5_J05


title: Plate5_J23


title: Plate5_M06


title: Plate5_K02


title: Plate5_J08


title: Plate5_K03

value: Ammonium perfluorooctanoate_0.2_uM


title: Plate5_J09


title: Plate5_K22


title: Plate5_J19

value: Dipropyl 2,5-pyridinedicarboxylate_1_uM


title: Plate5_J10

value: iPSC-Cardiomyocytes


title: Plate5_K05


title: Plate5_K07


title: Plate5_K11


title: Plate5_J02


title: Plate5_J04


title: Plate5_J16


title: Plate5_I11


title: Plate5_J11


title: Plate5_J12

value: L-Tartaric acid_1_uM


title: Plate5_J14


title: Plate5_I16


title: Plate5_J15


title: Plate5_J18


title: Plate5_I09


title: Plate5_I18


title: Plate5_I19


title: Plate5_I20


title: Plate5_J13


title: Plate5_I10


title: Plate5_I13


title: Plate5_H09


title: Plate5_H11


title: Plate5_H10


title: Plate5_I12

value: L-Tartaric acid_10_uM


title: Plate5_I17


title: Plate5_I14


title: Plate5_I22


title: Plate5_J17


title: Plate5_I21


title: Plate5_H13


title: Plate5_I23


title: Plate5_H12


title: Plate5_I15


title: Plate5_H15


title: Plate5_H14


title: Plate5_H16


title: Plate5_H17


title: Plate5_H19


title: Plate5_H21


title: Plate5_H18


title: Plate5_H20


title: Plate5_H22


title: Plate5_I04


title: Plate5_I02


title: Plate5_I03

value: Ammonium perfluorooctanoate_10_uM


title: Plate5_I05


title: Plate5_I06


title: Plate5_I07


title: Plate5_E22


title: Plate5_E20


title: Plate5_E21


title: Plate5_F03


title: Plate5_F04


title: Plate5_F02


title: Plate5_F06


title: Plate5_E23


title: Plate5_F10


title: Plate5_F11


title: Plate5_F07


title: Plate5_F12


title: Plate5_F13


title: Plate5_F08


title: Plate5_F09


title: Plate5_F15


title: Plate5_H23


title: Plate5_F18


title: Plate5_F17


title: Plate5_F16


title: Plate5_F14


title: Plate5_F19


title: Plate5_F22


title: Plate5_I08


title: Plate5_F21


title: Plate5_G04


title: Plate5_F20


title: Plate5_F05


title: Plate5_G02


title: Plate5_G03


title: Plate5_G11


title: Plate5_G07


title: Plate5_F23


title: Plate5_G06


title: Plate5_G05


title: Plate5_G10


title: Plate5_G09


title: Plate5_G17


title: Plate5_G16


title: Plate5_G15


title: Plate5_G14


title: Plate5_G12


title: Plate5_G18


title: Plate5_G19


title: Plate5_G21


title: Plate5_G22


title: Plate5_G20


title: Plate5_H03


title: Plate5_H02


title: Plate5_H04


title: Plate5_G23


title: Plate5_G08


title: Plate5_H06


title: Plate5_H05


title: Plate5_H08


title: Plate5_G13


title: Plate16_M20


title: Plate16_M17


title: Plate16_M15


title: Plate16_M19


title: Plate16_M16


title: Plate16_M18


title: Plate16_M21


title: Plate16_M22


title: Plate16_M23


title: Plate16_N03

value: Citalopram hydrobromide_0.2_uM


title: Plate16_N06

value: Moxifloxacin hydrochloride_0.2_uM


title: Plate16_N08


title: Plate16_N05


title: Plate16_N09


title: Plate16_N07


title: Plate16_N11


title: Plate16_N12


title: Plate5_H07


title: Plate16_N16


title: Plate16_N20


title: Plate16_N19


title: Plate16_N17


title: Plate16_N14


title: Plate16_N15


title: Plate16_N04


title: Plate16_N02


title: Plate16_N23


title: Plate16_N21


title: Plate16_H14


title: Plate16_H18


title: Plate16_N10


title: Plate16_N22


title: Plate16_H21


title: Plate16_H19


title: Plate16_H16


title: Plate16_H15


title: Plate16_H20


title: Plate16_H17


title: Plate16_I03


title: Plate16_N13


title: Plate16_I04

value: D,1 Sotalol_10_uM


title: Plate16_H23


title: Plate16_I02


title: Plate16_I06


title: Plate16_N18


title: Plate16_I05


title: Plate16_I07


title: Plate16_I12


title: Plate16_I14


title: Plate16_I10


title: Plate16_I13


title: Plate16_I11


title: Plate16_I15


title: Plate16_H22


title: Plate16_I16


title: Plate16_I19


title: Plate16_I20


title: Plate16_I17


title: Plate16_I18


title: Plate16_I23


title: Plate16_J02


title: Plate16_J03


title: Plate16_J05


title: Plate16_J04

value: D,1 Sotalol_1_uM


title: Plate16_J09


title: Plate16_I22


title: Plate16_J08


title: Plate16_J06


title: Plate16_J12


title: Plate16_J07


title: Plate16_J11


title: Plate16_J10


title: Plate16_I08


title: Plate16_J14


title: Plate16_I09


title: Plate16_J17


title: Plate16_J16


title: Plate16_J18


title: Plate16_J15


title: Plate16_J19


title: Plate16_I21


title: Plate16_J21


title: Plate16_J22


title: Plate16_J20


title: Plate16_J23


title: Plate16_K03


title: Plate16_K02


title: Plate16_K06


title: Plate16_K05


title: Plate16_K04

value: D,1 Sotalol_0.2_uM


title: Plate16_K07


title: Plate16_K10


title: Plate16_K08


title: Plate16_K09


title: Plate16_J13


title: Plate16_K14


title: Plate16_K16


title: Plate16_K15


title: Plate16_K13


title: Plate16_K11


title: Plate16_K19


title: Plate16_K18


title: Plate16_K12


title: Plate16_K21


title: Plate16_L03

value: Citalopram hydrobromide_10_uM


title: Plate16_L02


title: Plate16_K22


title: Plate16_K17


title: Plate16_L05

value: Moxifloxacin hydrochloride_10_uM


title: Plate16_K20


title: Plate16_K23


title: Plate16_L04


title: Plate16_L06


title: Plate16_L07


title: Plate16_L10


title: Plate16_L08


title: Plate16_L12


title: Plate16_L09


title: Plate16_L18


title: Plate16_L15


title: Plate16_L11


title: Plate16_L19


title: Plate16_L13


title: Plate16_L14


title: Plate16_L23


title: Plate16_L16


title: Plate16_M06

value: Moxifloxacin hydrochloride_1_uM


title: Plate16_L20


title: Plate16_M03

value: Citalopram hydrobromide_1_uM


title: Plate16_M04


title: Plate16_L21


title: Plate16_M02


title: Plate16_M09


title: Plate16_M07


title: Plate16_M05


title: Plate16_M08


title: Plate16_M10


title: Plate16_M12


title: Plate16_C14


title: Plate16_M11


title: Plate16_C16


title: Plate16_C17


title: Plate16_L22


title: Plate16_M13


title: Plate16_C13


title: Plate16_L17


title: Plate16_C21


title: Plate16_C20


title: Plate16_C15


title: Plate16_C19


title: Plate16_C18


title: Plate16_D02


title: Plate16_C22


title: Plate16_M14


title: Plate16_D04


title: Plate16_D07


title: Plate16_D08


title: Plate16_D10


title: Plate16_D05


title: Plate16_D09


title: Plate16_D06


title: Plate16_D12


title: Plate16_D14


title: Plate16_D13


title: Plate16_D16


title: Plate16_D15


title: Plate16_D17


title: Plate16_D18


title: Plate16_D19


title: Plate16_D21


title: Plate16_D20


title: Plate16_D22


title: Plate16_C23


title: Plate16_D23


title: Plate16_D03


title: Plate16_E07


title: Plate16_E02


title: Plate16_E06


title: Plate16_D11


title: Plate16_E09


title: Plate16_E08


title: Plate16_E03


title: Plate16_E10


title: Plate16_E15


title: Plate16_E16


title: Plate16_E11


title: Plate16_E12


title: Plate16_E18


title: Plate16_E19


title: Plate16_E22


title: Plate16_E20


title: Plate16_E14


title: Plate16_F03


title: Plate16_E17


title: Plate16_F06


title: Plate16_F04


title: Plate16_E04


title: Plate16_E05


title: Plate16_F07


title: Plate16_F02


title: Plate16_F05


title: Plate16_F10


title: Plate16_F11


title: Plate16_F14


title: Plate16_F08


title: Plate16_F13


title: Plate16_F12


title: Plate16_E13


title: Plate16_E21


title: Plate16_F17


title: Plate16_F19


title: Plate16_F18


title: Plate16_E23


title: Plate16_F22


title: Plate16_F20


title: Plate16_F21


title: Plate16_G02


title: Plate16_F23


title: Plate16_F09


title: Plate16_G06


title: Plate16_G03


title: Plate16_F15


title: Plate16_G04


title: Plate16_G08


title: Plate16_G05


title: Plate16_F16


title: Plate16_G14


title: Plate16_G10


title: Plate16_G15


title: Plate16_G13


title: Plate16_G16


title: Plate16_G09


title: Plate16_G11


title: Plate16_G07


title: Plate16_G12


title: Plate16_G17


title: Plate16_G18


title: Plate16_G19


title: Plate16_G20


title: Plate16_G23


title: Plate16_G21


title: Plate16_H02


title: Plate16_H04


title: Plate16_H06


title: Plate16_H07


title: Plate16_H05


title: Plate16_H03


title: Plate16_H09


title: Plate16_H08


title: Plate16_B02


title: Plate16_H10


title: Plate16_H12


title: Plate16_H11


title: Plate16_H13


title: Plate16_B03


title: Plate16_B05


title: Plate16_B04


title: Plate16_B06


title: Plate16_B08


title: Plate16_B09


title: Plate16_B07


title: Plate16_B10


title: Plate16_B11


title: Plate16_B12


title: Plate16_G22


title: Plate16_B13


title: Plate16_B14


title: Plate16_B18


title: Plate16_B15


title: Plate16_B21


title: Plate16_C02


title: Plate16_B16


title: Plate16_B17


title: Plate16_B22


title: Plate16_C03


title: Plate16_C04


title: Plate16_B19


title: Plate16_B20


title: Plate16_C07


title: Plate16_C09


title: Plate16_B23


title: Plate16_C11


title: Plate16_C12


title: Plate15_J18


title: Plate15_J16


title: Plate15_J19


title: Plate16_C08


title: Plate16_C10


title: Plate15_J17


title: Plate15_J20


title: Plate15_J21

value: Dimethyl phthalate_1_uM


title: Plate15_J15


title: Plate16_C05


title: Plate15_J23


title: Plate15_K05


title: Plate15_K07

value: Monomethyl phthalate_0.2_uM


title: Plate16_C06


title: Plate15_K08


title: Plate15_K09


title: Plate15_J22


title: Plate15_K03


title: Plate15_K14


title: Plate15_K02


title: Plate15_K12


title: Plate15_K10


title: Plate15_K04


title: Plate15_K17


title: Plate15_K06

value: 4-Aminobenzoic acid_0.2_uM


title: Plate15_K11


title: Plate15_K15


title: Plate15_K13


title: Plate15_K18


title: Plate15_K22


title: Plate15_K16


title: Plate15_K19


title: Plate15_L05


title: Plate15_L06


title: Plate15_K20


title: Plate15_L03


title: Plate15_L07


title: Plate15_L02


title: Plate15_L04


title: Plate15_L11


title: Plate15_L10


title: Plate15_L09


title: Plate15_L12


title: Plate15_L15


title: Plate15_L17


title: Plate15_L16


title: Plate15_L20


title: Plate15_K23


title: Plate15_L18


title: Plate15_K21

value: Dimethyl phthalate_0.2_uM


title: Plate15_L19

value: iPSC-Cardiomyocytes


title: Plate15_L13


title: Plate15_L23


title: Plate15_M03


title: Plate15_M02


title: Plate15_M05


title: Plate15_L22


title: Plate15_M04


title: Plate15_L08


title: Plate15_M08


title: Plate15_M07


title: Plate15_L14


title: Plate15_M09


title: Plate15_M11


title: Plate15_L21


title: Plate15_M10


title: Plate15_M14


title: Plate15_M15


title: Plate15_M12


title: Plate15_M16


title: Plate15_M06


title: Plate15_M18


title: Plate15_M17


title: Plate15_M21


title: Plate15_M19


title: Plate15_M22


title: Plate15_M20


title: Plate15_M23


title: Plate15_N04


title: Plate15_N02


title: Plate15_N03


title: Plate15_N05


title: Plate15_N06


title: Plate15_N09


title: Plate15_N10


title: Plate15_N11


title: Plate15_M13


title: Plate15_N12


title: Plate15_N13


title: Plate15_N14


title: Plate15_N16


title: Plate15_N15


title: Plate15_N17


title: Plate15_N22


title: Plate15_N23


title: Plate15_N18


title: Plate15_N07


title: Plate15_N20


title: Plate15_F15


title: Plate15_F18


title: Plate15_N21


title: Plate15_F20


title: Plate15_F22


title: Plate15_F21

value: Dimethyl phthalate_10_uM


title: Plate15_N08


title: Plate15_G03


title: Plate15_G05


title: Plate15_F17


title: Plate15_F14


title: Plate15_F19


title: Plate15_F23


title: Plate15_N19


title: Plate15_G06

value: 4-Aminobenzoic acid_1_uM


title: Plate15_G09


title: Plate15_G07

value: Monomethyl phthalate_1_uM


title: Plate15_G10


title: Plate15_G08


title: Plate15_G12


title: Plate15_F16


title: Plate15_G04


title: Plate15_G19


title: Plate15_G18


title: Plate15_G16


title: Plate15_F13


title: Plate15_G15


title: Plate15_G13


title: Plate15_G23


title: Plate15_G22


title: Plate15_H04


title: Plate15_H06


title: Plate15_G14


title: Plate15_G11


title: Plate15_G17


title: Plate15_H07


title: Plate15_G02


title: Plate15_H11


title: Plate15_G20


title: Plate15_H15


title: Plate15_H12


title: Plate15_H16


title: Plate15_H02


title: Plate15_H03


title: Plate15_G21


title: Plate15_H14


title: Plate15_H17


title: Plate15_H22


title: Plate15_H05


title: Plate15_H08


title: Plate15_H13


title: Plate15_H21


title: Plate15_I04


title: Plate15_I07

value: Monomethyl phthalate_10_uM


title: Plate15_H09


title: Plate15_H10


title: Plate15_I08


title: Plate15_H18


title: Plate15_H19


title: Plate15_H23


title: Plate15_H20


title: Plate15_I11


title: Plate15_I13


title: Plate15_I02


title: Plate15_I03


title: Plate15_I16


title: Plate15_I17


title: Plate15_I05


title: Plate15_I19


title: Plate15_I06

value: 4-Aminobenzoic acid_10_uM


title: Plate15_I09


title: Plate15_I12


title: Plate15_J06


title: Plate15_I18


title: Plate15_I14


title: Plate15_I10


title: Plate15_J05


title: Plate15_J03


title: Plate15_I20


title: Plate15_I15


title: Plate15_I22


title: Plate15_J09


title: Plate15_J04


title: Plate15_J12


title: Plate15_J13


title: Plate15_J07


title: Plate15_J08


title: Plate15_I23


title: Plate15_J11


title: Plate15_J10


title: Plate15_J14


title: Plate15_B08


title: Plate15_B07


title: Plate15_B05


title: Plate15_B10


title: Plate15_B06


title: Plate15_B11


title: Plate15_B09


title: Plate15_I21


title: Plate15_J02


title: Plate15_B13


title: Plate15_B16


title: Plate15_B14


title: Plate15_B17


title: Plate15_B15


title: Plate15_B19


title: Plate15_B20


title: Plate15_B22


title: Plate15_C06


title: Plate15_C03


title: Plate15_C02


title: Plate15_B21


title: Plate15_C08


title: Plate15_C11


title: Plate15_C09


title: Plate15_C04


title: Plate15_C17


title: Plate15_C16


title: Plate15_C07


title: Plate15_C12


title: Plate15_C19


title: Plate15_C05


title: Plate15_C15


title: Plate15_C10


title: Plate15_B12


title: Plate15_B18


title: Plate15_C13


title: Plate15_C14


title: Plate15_C18


title: Plate15_B23


title: Plate15_C22


title: Plate15_C23


title: Plate15_D02


title: Plate15_D04


title: Plate15_D03


title: Plate15_D09


title: Plate15_D08


title: Plate15_C21


title: Plate15_D07


title: Plate15_D06


title: Plate15_D05


title: Plate15_D12


title: Plate15_D13


title: Plate15_D21


title: Plate15_D15


title: Plate15_D18


title: Plate15_E02


title: Plate15_D19


title: Plate15_D14


title: Plate15_E03


title: Plate15_D17


title: Plate15_C20


title: Plate15_D23


title: Plate15_D22


title: Plate15_E04


title: Plate15_D10


title: Plate15_D11


title: Plate15_E05


title: Plate15_D16


title: Plate15_E10


title: Plate15_E12


title: Plate15_E07


title: Plate15_E06


title: Plate15_E08


title: Plate15_E13


title: Plate15_D20


title: Plate15_E15


title: Plate15_E14


title: Plate15_E16


title: Plate15_E17


title: Plate15_E20


title: Plate15_E18


title: Plate15_E19


title: Plate15_E22


title: Plate15_F02


title: Plate15_E21


title: Plate15_E23


title: Plate15_F04


title: Plate15_E09


title: Plate15_F08


title: Plate15_F03


title: Plate15_F06


title: Plate15_F07


title: Plate15_F11


title: Plate15_F09


title: Plate15_E11


title: Plate15_B04


title: Plate15_F12


title: Plate15_B03


title: Plate15_B02


title: Plate14_M12


title: Plate14_M13


title: Plate14_M11


title: Plate14_M14

value: 2,2'-Bisphenol F_1_uM


title: Plate15_F05


title: Plate14_M15


title: Plate14_M16


title: Plate14_M18

value: Methyl dodecanoate_1_uM


title: Plate14_M17


title: Plate14_M20


title: Plate14_M22


title: Plate14_N04


title: Plate14_M21


title: Plate14_N03


title: Plate14_M23


title: Plate14_M19


title: Plate14_N02


title: Plate14_N06

value: Pirinixic acid_0.2_uM


title: Plate14_N11


title: Plate14_N10


title: Plate14_N12


title: Plate14_N08


title: Plate14_N05


title: Plate14_N16

value: 2,2'-Bisphenol F_0.2_uM


title: Plate14_N09


title: Plate14_N13


title: Plate14_N15


title: Plate14_N20


title: Plate14_N14


title: Plate14_N07


title: Plate14_N23


title: Plate14_N21


title: Plate14_K21


title: Plate14_K22

value: Benzyl butyl phthalate_0.2_uM


title: Plate15_F10


title: Plate14_K23


title: Plate14_L02


title: Plate14_L03


title: Plate14_L04


title: Plate14_L06

value: Pirinixic acid_10_uM