title: Nifedipine, Con2, Screening plate 2, Well G7 [S4881Nr7_G7]

value: Nifedipine, Con2


title: Nifedipine, Con1, Screening plate 2, Well G8 [S4881Nr7_G8]

status: Public on Oct 10 2023

type: SRA

city: Göttingen

first: Christopher

last: Bruhn

address: Marie-Curie-Str. 7

country: Germany

institute: Evotec International GmbH

library_source: transcriptomic

data_processing:
Transcriptomic profiling was performed in batches of 382 samples. Each batch contained 22 negative-control (i.e. DMSO-treated) samples, and 15 blocks of compound-treated samples. Every block included 8 compound concentrations, each in triplicate.
Reads were mapped to the human genome (genome-build GRCh38.p13 – accession GCA_000001405.28) using STAR (version 2.7.9a).
Multi-mapped reads, reads with mapping to inter-genic regions (with respect to Ensembl gene annotation information version 104) and reads with ambiguous mapping location (i.e. location associated with more than one gene) were discarded, and UMI-based deduplication was performed.
Sequencing files were demultiplexed and barcodes were stripped.
Assembly: GRCh38.p13 – accession GCA_000001405.28
Supplementary files format and content: processed_data_counts.txt: RNA unique moecular identifier (UMI) counts per gene. The column EnsemblID provides the unique gene identifier. One column is included per sample with column names matching the column "description" in the table "SAMPLES".

molecule: polyA RNA

organism: Homo sapiens

source_name: hiPSC-CM

growth_protocol: human iPSC-derived cardiomyocytes (hiPSC-CMs) were seeded in 384-well plates (Corning® Cat. No.: 3764) pre-coated with a 0.1 µg/mL fibronectin solution (Sigma Cat. No. F1141) in phosphate buffered saline (PBS) containing Mg2+ and Ca2+. Fibronectin pre-coated plates were incubated at 37°C for 3 h (5% CO2, 95% humidity), after which the coating was carefully removed using an automated liquid handling robot (Bravo Agilent). Subsequently, hiPSC-CMs were seeded at 10,000 cells/well and cultured for 10 days in CD-4 media. Media was initially refreshed 24 h post-seeding and then, every 48 h thereafter while the cells were in culture.

extract_protocol:
High-throughput transcriptomics was performed using Evotec’s (semi)-automated ScreenSeqTM platform. Cell lysis was performed in a 384-well plate format followed by well-specific labeling of samples.
Plate RNASeq of polyA RNA (ScreenSeqTM); Purified mRNAs were labeled with a unique molecular identifier (UMI). After pooled cDNA synthesis, adapters containing Illumina’s unique dual indexes were attached for final library preparation and sequenced on a NovaSeq 6000 system.

treatment_protocol: All compounds were dissolved in 100% dimethylsulfoxide (DMSO) (stock solutions). The stock solutions were further diluted in CD-4 media and cells were dosed in triplicate at an eight-point dose response range using a half-log dilution series to achieve a final DMSO concentration of 0.5% (v/v). Vehicle controls were dosed with 0.5% (v/v) DMSO, while positive controls were dosed with sunitinib, a functional and structural cardiotoxicant.

tag: cell line

value: hiPSC-CM

tag: genotype

value: WT

tag: treatment

value: Nifedipine, Con1

tag: time


title: Nifedipine, Con2, Screening plate 2, Well H7 [S4881Nr7_H7]


title: Nifedipine, Con2, Screening plate 2, Well I7 [S4881Nr7_I7]


title: Nifedipine, Con3, Screening plate 2, Well G6 [S4881Nr7_G6]

value: Nifedipine, Con3


title: Propranolol, Con2, Screening plate 2, Well G15 [S4881Nr7_G15]

value: Propranolol, Con2


title: Nifedipine, Con3, Screening plate 2, Well H6 [S4881Nr7_H6]


title: Nifedipine, Con4, Screening plate 2, Well H5 [S4881Nr7_H5]

value: Nifedipine, Con4


title: Nifedipine, Con6, Screening plate 2, Well I3 [S4881Nr7_I3]

value: Nifedipine, Con6


title: Nifedipine, Con4, Screening plate 2, Well G5 [S4881Nr7_G5]


title: Nifedipine, Con5, Screening plate 2, Well I4 [S4881Nr7_I4]

value: Nifedipine, Con5


title: Nifedipine, Con4, Screening plate 2, Well I5 [S4881Nr7_I5]


title: Nifedipine, Con8, Screening plate 2, Well I1 [S4881Nr7_I1]

value: Nifedipine, Con8


title: Nifedipine, Con7, Screening plate 2, Well H2 [S4881Nr7_H2]

value: Nifedipine, Con7


title: Nifedipine, Con7, Screening plate 2, Well I2 [S4881Nr7_I2]


title: Nifedipine, Con6, Screening plate 2, Well G3 [S4881Nr7_G3]


title: Nifedipine, Con6, Screening plate 2, Well H3 [S4881Nr7_H3]


title: Nifedipine, Con7, Screening plate 2, Well G2 [S4881Nr7_G2]


title: Lidocaine, Con1, Screening plate 2, Well F24 [S4881Nr7_F24]

value: Lidocaine, Con1


title: Nifedipine, Con8, Screening plate 2, Well H1 [S4881Nr7_H1]


title: Nifedipine, Con8, Screening plate 2, Well G1 [S4881Nr7_G1]


title: Lidocaine, Con2, Screening plate 2, Well E23 [S4881Nr7_E23]

value: Lidocaine, Con2


title: Lidocaine, Con2, Screening plate 2, Well D23 [S4881Nr7_D23]


title: Lidocaine, Con2, Screening plate 2, Well F23 [S4881Nr7_F23]


title: Lidocaine, Con3, Screening plate 2, Well F22 [S4881Nr7_F22]

value: Lidocaine, Con3


title: Nifedipine, Con3, Screening plate 2, Well I6 [S4881Nr7_I6]


title: Lidocaine, Con4, Screening plate 2, Well F21 [S4881Nr7_F21]

value: Lidocaine, Con4


title: Lidocaine, Con3, Screening plate 2, Well E22 [S4881Nr7_E22]


title: Nifedipine, Con5, Screening plate 2, Well H4 [S4881Nr7_H4]


title: Lidocaine, Con4, Screening plate 2, Well E21 [S4881Nr7_E21]


title: Lidocaine, Con5, Screening plate 2, Well D20 [S4881Nr7_D20]

value: Lidocaine, Con5


title: Lidocaine, Con5, Screening plate 2, Well F20 [S4881Nr7_F20]


title: Lidocaine, Con5, Screening plate 2, Well E20 [S4881Nr7_E20]


title: Lidocaine, Con4, Screening plate 2, Well D21 [S4881Nr7_D21]


title: Nifedipine, Con5, Screening plate 2, Well G4 [S4881Nr7_G4]


title: Lidocaine, Con6, Screening plate 2, Well E19 [S4881Nr7_E19]

value: Lidocaine, Con6


title: Lidocaine, Con6, Screening plate 2, Well F19 [S4881Nr7_F19]


title: Lidocaine, Con6, Screening plate 2, Well D19 [S4881Nr7_D19]


title: Lidocaine, Con1, Screening plate 2, Well E24 [S4881Nr7_E24]


title: Lidocaine, Con7, Screening plate 2, Well F18 [S4881Nr7_F18]

value: Lidocaine, Con7


title: Lidocaine, Con7, Screening plate 2, Well D18 [S4881Nr7_D18]

value: hiPSC-CM


title: Lidocaine, Con8, Screening plate 2, Well F17 [S4881Nr7_F17]

value: WT

value: Lidocaine, Con8


title: Lidocaine, Con7, Screening plate 2, Well E18 [S4881Nr7_E18]


title: Lidocaine, Con8, Screening plate 2, Well D17 [S4881Nr7_D17]


title: Lidocaine, Con1, Screening plate 2, Well D24 [S4881Nr7_D24]


title: Levosimendan, Con1, Screening plate 2, Well E16 [S4881Nr7_E16]

value: Levosimendan, Con1


title: Levosimendan, Con1, Screening plate 2, Well D16 [S4881Nr7_D16]


title: Levosimendan, Con2, Screening plate 2, Well F15 [S4881Nr7_F15]

value: Levosimendan, Con2


title: Lidocaine, Con3, Screening plate 2, Well D22 [S4881Nr7_D22]


title: Levosimendan, Con2, Screening plate 2, Well E15 [S4881Nr7_E15]


title: Levosimendan, Con3, Screening plate 2, Well F14 [S4881Nr7_F14]

value: Levosimendan, Con3


title: Levosimendan, Con3, Screening plate 2, Well E14 [S4881Nr7_E14]


title: Levosimendan, Con2, Screening plate 2, Well D15 [S4881Nr7_D15]


title: Levosimendan, Con4, Screening plate 2, Well E13 [S4881Nr7_E13]

value: Levosimendan, Con4


title: Levosimendan, Con5, Screening plate 2, Well F12 [S4881Nr7_F12]

value: Levosimendan, Con5


title: Levosimendan, Con3, Screening plate 2, Well D14 [S4881Nr7_D14]


title: Levosimendan, Con5, Screening plate 2, Well D12 [S4881Nr7_D12]


title: Levosimendan, Con5, Screening plate 2, Well E12 [S4881Nr7_E12]


title: Levosimendan, Con6, Screening plate 2, Well E11 [S4881Nr7_E11]

value: Levosimendan, Con6


title: Levosimendan, Con4, Screening plate 2, Well F13 [S4881Nr7_F13]


title: Levosimendan, Con7, Screening plate 2, Well F10 [S4881Nr7_F10]

value: Levosimendan, Con7


title: Levosimendan, Con7, Screening plate 2, Well E10 [S4881Nr7_E10]


title: Levosimendan, Con4, Screening plate 2, Well D13 [S4881Nr7_D13]


title: Levosimendan, Con6, Screening plate 2, Well D11 [S4881Nr7_D11]


title: Lidocaine, Con8, Screening plate 2, Well E17 [S4881Nr7_E17]


title: Levosimendan, Con8, Screening plate 2, Well F9 [S4881Nr7_F9]

value: Levosimendan, Con8


title: Levosimendan, Con7, Screening plate 2, Well D10 [S4881Nr7_D10]


title: Epinephrine, Con1, Screening plate 2, Well F8 [S4881Nr7_F8]

value: Epinephrine, Con1


title: Levosimendan, Con8, Screening plate 2, Well D9 [S4881Nr7_D9]


title: Levosimendan, Con1, Screening plate 2, Well F16 [S4881Nr7_F16]


title: Epinephrine, Con1, Screening plate 2, Well E8 [S4881Nr7_E8]


title: Epinephrine, Con1, Screening plate 2, Well D8 [S4881Nr7_D8]


title: Epinephrine, Con2, Screening plate 2, Well F7 [S4881Nr7_F7]

value: Epinephrine, Con2


title: Levosimendan, Con8, Screening plate 2, Well E9 [S4881Nr7_E9]


title: Epinephrine, Con2, Screening plate 2, Well E7 [S4881Nr7_E7]


title: Epinephrine, Con3, Screening plate 2, Well F6 [S4881Nr7_F6]

value: Epinephrine, Con3


title: Epinephrine, Con2, Screening plate 2, Well D7 [S4881Nr7_D7]


title: Epinephrine, Con4, Screening plate 2, Well F5 [S4881Nr7_F5]

value: Epinephrine, Con4


title: Epinephrine, Con3, Screening plate 2, Well E6 [S4881Nr7_E6]


title: Epinephrine, Con4, Screening plate 2, Well E5 [S4881Nr7_E5]


title: Epinephrine, Con3, Screening plate 2, Well D6 [S4881Nr7_D6]


title: Epinephrine, Con4, Screening plate 2, Well D5 [S4881Nr7_D5]


title: Epinephrine, Con5, Screening plate 2, Well F4 [S4881Nr7_F4]

value: Epinephrine, Con5


title: Levosimendan, Con6, Screening plate 2, Well F11 [S4881Nr7_F11]


title: Epinephrine, Con5, Screening plate 2, Well E4 [S4881Nr7_E4]


title: Epinephrine, Con6, Screening plate 2, Well F3 [S4881Nr7_F3]

value: Epinephrine, Con6


title: Epinephrine, Con5, Screening plate 2, Well D4 [S4881Nr7_D4]

value: hiPSC-CM


title: Epinephrine, Con7, Screening plate 2, Well F2 [S4881Nr7_F2]

value: WT

value: Epinephrine, Con7


title: Epinephrine, Con6, Screening plate 2, Well E3 [S4881Nr7_E3]


title: Epinephrine, Con6, Screening plate 2, Well D3 [S4881Nr7_D3]


title: Epinephrine, Con7, Screening plate 2, Well D2 [S4881Nr7_D2]


title: Epinephrine, Con8, Screening plate 2, Well F1 [S4881Nr7_F1]

value: Epinephrine, Con8


title: Epinephrine, Con8, Screening plate 2, Well E1 [S4881Nr7_E1]


title: DMSO, Con0, Screening plate 2, Well P9 [S4881Nr7_P9]

value: DMSO, Con0


title: Epinephrine, Con8, Screening plate 2, Well D1 [S4881Nr7_D1]


title: DMSO, Con0, Screening plate 2, Well P8 [S4881Nr7_P8]


title: DMSO, Con0, Screening plate 2, Well P7 [S4881Nr7_P7]


title: DMSO, Con0, Screening plate 2, Well P5 [S4881Nr7_P5]


title: DMSO, Con0, Screening plate 2, Well P6 [S4881Nr7_P6]


title: DMSO, Con0, Screening plate 2, Well P4 [S4881Nr7_P4]


title: DMSO, Con0, Screening plate 2, Well P3 [S4881Nr7_P3]


title: DMSO, Con0, Screening plate 2, Well P23 [S4881Nr7_P23]


title: DMSO, Con0, Screening plate 2, Well P22 [S4881Nr7_P22]


title: DMSO, Con0, Screening plate 2, Well P2 [S4881Nr7_P2]


title: DMSO, Con0, Screening plate 2, Well P20 [S4881Nr7_P20]


title: DMSO, Con0, Screening plate 2, Well P21 [S4881Nr7_P21]


title: DMSO, Con0, Screening plate 2, Well P19 [S4881Nr7_P19]


title: DMSO, Con0, Screening plate 2, Well P18 [S4881Nr7_P18]


title: DMSO, Con0, Screening plate 2, Well P17 [S4881Nr7_P17]


title: DMSO, Con0, Screening plate 2, Well P15 [S4881Nr7_P15]


title: Epinephrine, Con7, Screening plate 2, Well E2 [S4881Nr7_E2]


title: DMSO, Con0, Screening plate 2, Well P13 [S4881Nr7_P13]


title: DMSO, Con0, Screening plate 2, Well P14 [S4881Nr7_P14]


title: DMSO, Con0, Screening plate 2, Well P12 [S4881Nr7_P12]


title: DMSO, Con0, Screening plate 2, Well P10 [S4881Nr7_P10]


title: DMSO, Con0, Screening plate 2, Well P11 [S4881Nr7_P11]


title: Dopamine, Con2, Screening plate 2, Well C23 [S4881Nr7_C23]

value: Dopamine, Con2


title: Dopamine, Con2, Screening plate 2, Well B23 [S4881Nr7_B23]


title: Dopamine, Con1, Screening plate 2, Well B24 [S4881Nr7_B24]

value: Dopamine, Con1


title: Dopamine, Con3, Screening plate 2, Well A22 [S4881Nr7_A22]

value: Dopamine, Con3


title: Dopamine, Con3, Screening plate 2, Well C22 [S4881Nr7_C22]


title: Dopamine, Con3, Screening plate 2, Well B22 [S4881Nr7_B22]


title: Dopamine, Con1, Screening plate 2, Well A24 [S4881Nr7_A24]


title: Dopamine, Con4, Screening plate 2, Well B21 [S4881Nr7_B21]

value: Dopamine, Con4


title: Dopamine, Con2, Screening plate 2, Well A23 [S4881Nr7_A23]


title: Dopamine, Con4, Screening plate 2, Well C21 [S4881Nr7_C21]


title: Dopamine, Con4, Screening plate 2, Well A21 [S4881Nr7_A21]


title: Dopamine, Con5, Screening plate 2, Well C20 [S4881Nr7_C20]

value: Dopamine, Con5


title: DMSO, Con0, Screening plate 2, Well P16 [S4881Nr7_P16]


title: Dopamine, Con5, Screening plate 2, Well A20 [S4881Nr7_A20]


title: Dopamine, Con6, Screening plate 2, Well A19 [S4881Nr7_A19]

value: Dopamine, Con6


title: Dopamine, Con6, Screening plate 2, Well C19 [S4881Nr7_C19]


title: Dopamine, Con6, Screening plate 2, Well B19 [S4881Nr7_B19]


title: Dopamine, Con5, Screening plate 2, Well B20 [S4881Nr7_B20]


title: Dopamine, Con7, Screening plate 2, Well A18 [S4881Nr7_A18]

value: Dopamine, Con7


title: Dopamine, Con7, Screening plate 2, Well B18 [S4881Nr7_B18]


title: Dopamine, Con8, Screening plate 2, Well C17 [S4881Nr7_C17]

value: Dopamine, Con8


title: Dopamine, Con8, Screening plate 2, Well B17 [S4881Nr7_B17]


title: Dopamine, Con8, Screening plate 2, Well A17 [S4881Nr7_A17]


title: Dopamine, Con1, Screening plate 2, Well C24 [S4881Nr7_C24]


title: Dobutamine, Con1, Screening plate 2, Well C16 [S4881Nr7_C16]

value: Dobutamine, Con1


title: Dobutamine, Con2, Screening plate 2, Well B15 [S4881Nr7_B15]

value: Dobutamine, Con2


title: Dobutamine, Con2, Screening plate 2, Well C15 [S4881Nr7_C15]


title: Dobutamine, Con1, Screening plate 2, Well A16 [S4881Nr7_A16]


title: Dobutamine, Con1, Screening plate 2, Well B16 [S4881Nr7_B16]


title: Dobutamine, Con3, Screening plate 2, Well C14 [S4881Nr7_C14]

value: Dobutamine, Con3


title: Dobutamine, Con3, Screening plate 2, Well B14 [S4881Nr7_B14]


title: Dobutamine, Con3, Screening plate 2, Well A14 [S4881Nr7_A14]


title: Dobutamine, Con5, Screening plate 2, Well C12 [S4881Nr7_C12]

value: Dobutamine, Con5


title: Dobutamine, Con4, Screening plate 2, Well B13 [S4881Nr7_B13]

value: hiPSC-CM

value: Dobutamine, Con4


title: Dobutamine, Con4, Screening plate 2, Well A13 [S4881Nr7_A13]

value: WT


title: Dobutamine, Con5, Screening plate 2, Well B12 [S4881Nr7_B12]


title: Dobutamine, Con4, Screening plate 2, Well C13 [S4881Nr7_C13]


title: Dobutamine, Con6, Screening plate 2, Well C11 [S4881Nr7_C11]

value: Dobutamine, Con6


title: Dobutamine, Con5, Screening plate 2, Well A12 [S4881Nr7_A12]


title: Dopamine, Con7, Screening plate 2, Well C18 [S4881Nr7_C18]


title: Dobutamine, Con6, Screening plate 2, Well B11 [S4881Nr7_B11]


title: Dobutamine, Con7, Screening plate 2, Well A10 [S4881Nr7_A10]

value: Dobutamine, Con7


title: Dobutamine, Con7, Screening plate 2, Well B10 [S4881Nr7_B10]


title: Dobutamine, Con7, Screening plate 2, Well C10 [S4881Nr7_C10]


title: Dobutamine, Con8, Screening plate 2, Well C9 [S4881Nr7_C9]

value: Dobutamine, Con8


title: Dobutamine, Con8, Screening plate 2, Well B9 [S4881Nr7_B9]


title: Dobutamine, Con8, Screening plate 2, Well A9 [S4881Nr7_A9]


title: Dobutamine, Con6, Screening plate 2, Well A11 [S4881Nr7_A11]


title: Clozapine, Con1, Screening plate 2, Well C8 [S4881Nr7_C8]

value: Clozapine, Con1


title: Clozapine, Con1, Screening plate 2, Well B8 [S4881Nr7_B8]


title: Clozapine, Con2, Screening plate 2, Well A7 [S4881Nr7_A7]

value: Clozapine, Con2


title: Clozapine, Con2, Screening plate 2, Well C7 [S4881Nr7_C7]


title: Clozapine, Con2, Screening plate 2, Well B7 [S4881Nr7_B7]


title: Clozapine, Con3, Screening plate 2, Well C6 [S4881Nr7_C6]

value: Clozapine, Con3


title: Clozapine, Con3, Screening plate 2, Well A6 [S4881Nr7_A6]


title: Clozapine, Con1, Screening plate 2, Well A8 [S4881Nr7_A8]


title: Clozapine, Con3, Screening plate 2, Well B6 [S4881Nr7_B6]


title: Clozapine, Con4, Screening plate 2, Well C5 [S4881Nr7_C5]

value: Clozapine, Con4


title: Clozapine, Con5, Screening plate 2, Well C4 [S4881Nr7_C4]

value: Clozapine, Con5


title: Clozapine, Con4, Screening plate 2, Well B5 [S4881Nr7_B5]


title: Dobutamine, Con2, Screening plate 2, Well A15 [S4881Nr7_A15]


title: Clozapine, Con5, Screening plate 2, Well B4 [S4881Nr7_B4]


title: Clozapine, Con5, Screening plate 2, Well A4 [S4881Nr7_A4]


title: Clozapine, Con4, Screening plate 2, Well A5 [S4881Nr7_A5]


title: Clozapine, Con6, Screening plate 2, Well C3 [S4881Nr7_C3]

value: Clozapine, Con6


title: Clozapine, Con6, Screening plate 2, Well B3 [S4881Nr7_B3]


title: Clozapine, Con7, Screening plate 2, Well C2 [S4881Nr7_C2]

value: Clozapine, Con7


title: Clozapine, Con6, Screening plate 2, Well A3 [S4881Nr7_A3]


title: Clozapine, Con7, Screening plate 2, Well B2 [S4881Nr7_B2]


title: Clozapine, Con8, Screening plate 2, Well C1 [S4881Nr7_C1]

value: Clozapine, Con8


title: Clozapine, Con8, Screening plate 2, Well B1 [S4881Nr7_B1]


title: NoTreatment, NoTreatment, Screening plate 1, Well P24 [S4881Nr6_P24]

value: NoTreatment, NoTreatment


title: Clozapine, Con7, Screening plate 2, Well A2 [S4881Nr7_A2]


title: Clozapine, Con8, Screening plate 2, Well A1 [S4881Nr7_A1]


title: Sunitinib, Con1, Screening plate 1, Well M24 [S4881Nr6_M24]

value: Sunitinib, Con1


title: Sunitinib, Con1, Screening plate 1, Well N24 [S4881Nr6_N24]


title: Sunitinib, Con2, Screening plate 1, Well O23 [S4881Nr6_O23]

value: Sunitinib, Con2


title: Sunitinib, Con3, Screening plate 1, Well O22 [S4881Nr6_O22]

value: hiPSC-CM

value: Sunitinib, Con3


title: Sunitinib, Con2, Screening plate 1, Well M23 [S4881Nr6_M23]

value: WT


title: Sunitinib, Con2, Screening plate 1, Well N23 [S4881Nr6_N23]


title: Sunitinib, Con4, Screening plate 1, Well N21 [S4881Nr6_N21]

value: Sunitinib, Con4


title: Sunitinib, Con3, Screening plate 1, Well M22 [S4881Nr6_M22]


title: Sunitinib, Con4, Screening plate 1, Well O21 [S4881Nr6_O21]


title: Sunitinib, Con3, Screening plate 1, Well N22 [S4881Nr6_N22]


title: Sunitinib, Con4, Screening plate 1, Well M21 [S4881Nr6_M21]


title: Sunitinib, Con5, Screening plate 1, Well N20 [S4881Nr6_N20]

value: Sunitinib, Con5


title: Sunitinib, Con5, Screening plate 1, Well M20 [S4881Nr6_M20]


title: Sunitinib, Con6, Screening plate 1, Well N19 [S4881Nr6_N19]

value: Sunitinib, Con6


title: Sunitinib, Con7, Screening plate 1, Well O18 [S4881Nr6_O18]

value: Sunitinib, Con7


title: Sunitinib, Con6, Screening plate 1, Well M19 [S4881Nr6_M19]


title: Sunitinib, Con7, Screening plate 1, Well N18 [S4881Nr6_N18]


title: Sunitinib, Con7, Screening plate 1, Well M18 [S4881Nr6_M18]


title: Sunitinib, Con1, Screening plate 1, Well O24 [S4881Nr6_O24]


title: Sunitinib, Con6, Screening plate 1, Well O19 [S4881Nr6_O19]


title: NoTreatment, NoTreatment, Screening plate 1, Well P1 [S4881Nr6_P1]


title: Sunitinib, Con8, Screening plate 1, Well N17 [S4881Nr6_N17]

value: Sunitinib, Con8


title: Sunitinib, Con8, Screening plate 1, Well O17 [S4881Nr6_O17]


title: Digoxin, Con1, Screening plate 1, Well N16 [S4881Nr6_N16]

value: Digoxin, Con1


title: Digoxin, Con2, Screening plate 1, Well N15 [S4881Nr6_N15]

value: Digoxin, Con2


title: Digoxin, Con2, Screening plate 1, Well O15 [S4881Nr6_O15]


title: Digoxin, Con3, Screening plate 1, Well O14 [S4881Nr6_O14]

value: Digoxin, Con3


title: Digoxin, Con2, Screening plate 1, Well M15 [S4881Nr6_M15]


title: Digoxin, Con1, Screening plate 1, Well M16 [S4881Nr6_M16]


title: Digoxin, Con3, Screening plate 1, Well M14 [S4881Nr6_M14]


title: Digoxin, Con4, Screening plate 1, Well O13 [S4881Nr6_O13]

value: Digoxin, Con4


title: Digoxin, Con4, Screening plate 1, Well N13 [S4881Nr6_N13]


title: Sunitinib, Con5, Screening plate 1, Well O20 [S4881Nr6_O20]


title: Digoxin, Con4, Screening plate 1, Well M13 [S4881Nr6_M13]


title: Digoxin, Con5, Screening plate 1, Well N12 [S4881Nr6_N12]

value: Digoxin, Con5


title: Digoxin, Con5, Screening plate 1, Well O12 [S4881Nr6_O12]


title: Digoxin, Con5, Screening plate 1, Well M12 [S4881Nr6_M12]


title: Digoxin, Con6, Screening plate 1, Well O11 [S4881Nr6_O11]

value: Digoxin, Con6


title: Digoxin, Con6, Screening plate 1, Well M11 [S4881Nr6_M11]


title: Sunitinib, Con8, Screening plate 1, Well M17 [S4881Nr6_M17]


title: Digoxin, Con1, Screening plate 1, Well O16 [S4881Nr6_O16]


title: Cisapride, Con1, Screening plate 1, Well N8 [S4881Nr6_N8]

value: Cisapride, Con1


title: Cisapride, Con1, Screening plate 1, Well O8 [S4881Nr6_O8]


title: Digoxin, Con8, Screening plate 1, Well M9 [S4881Nr6_M9]

value: Digoxin, Con8


title: Digoxin, Con8, Screening plate 1, Well N9 [S4881Nr6_N9]


title: Digoxin, Con8, Screening plate 1, Well O9 [S4881Nr6_O9]


title: Cisapride, Con1, Screening plate 1, Well M8 [S4881Nr6_M8]


title: Digoxin, Con7, Screening plate 1, Well O10 [S4881Nr6_O10]

value: Digoxin, Con7


title: Digoxin, Con7, Screening plate 1, Well M10 [S4881Nr6_M10]

value: hiPSC-CM


title: Digoxin, Con3, Screening plate 1, Well N14 [S4881Nr6_N14]


title: Cisapride, Con2, Screening plate 1, Well O7 [S4881Nr6_O7]

value: Cisapride, Con2


title: Cisapride, Con3, Screening plate 1, Well N6 [S4881Nr6_N6]

value: WT

value: Cisapride, Con3


title: Cisapride, Con3, Screening plate 1, Well O6 [S4881Nr6_O6]


title: Cisapride, Con2, Screening plate 1, Well M7 [S4881Nr6_M7]


title: Cisapride, Con4, Screening plate 1, Well O5 [S4881Nr6_O5]

value: Cisapride, Con4


title: Cisapride, Con3, Screening plate 1, Well M6 [S4881Nr6_M6]


title: Cisapride, Con4, Screening plate 1, Well N5 [S4881Nr6_N5]


title: Cisapride, Con5, Screening plate 1, Well O4 [S4881Nr6_O4]

value: Cisapride, Con5


title: Cisapride, Con5, Screening plate 1, Well N4 [S4881Nr6_N4]


title: Cisapride, Con6, Screening plate 1, Well O3 [S4881Nr6_O3]

value: Cisapride, Con6


title: Cisapride, Con6, Screening plate 1, Well N3 [S4881Nr6_N3]


title: Cisapride, Con6, Screening plate 1, Well M3 [S4881Nr6_M3]


title: Cisapride, Con4, Screening plate 1, Well M5 [S4881Nr6_M5]


title: Cisapride, Con7, Screening plate 1, Well O2 [S4881Nr6_O2]

value: Cisapride, Con7


title: Digoxin, Con6, Screening plate 1, Well N11 [S4881Nr6_N11]


title: Cisapride, Con7, Screening plate 1, Well N2 [S4881Nr6_N2]


title: Cisapride, Con7, Screening plate 1, Well M2 [S4881Nr6_M2]


title: Cisapride, Con8, Screening plate 1, Well O1 [S4881Nr6_O1]

value: Cisapride, Con8


title: Digoxin, Con7, Screening plate 1, Well N10 [S4881Nr6_N10]


title: Cisapride, Con8, Screening plate 1, Well N1 [S4881Nr6_N1]


title: Cisapride, Con2, Screening plate 1, Well N7 [S4881Nr6_N7]


title: Bepridil, Con2, Screening plate 1, Well L23 [S4881Nr6_L23]

value: Bepridil, Con2


title: Cisapride, Con8, Screening plate 1, Well M1 [S4881Nr6_M1]


title: Bepridil, Con2, Screening plate 1, Well K23 [S4881Nr6_K23]


title: Bepridil, Con1, Screening plate 1, Well L24 [S4881Nr6_L24]

value: Bepridil, Con1


title: Bepridil, Con1, Screening plate 1, Well K24 [S4881Nr6_K24]


title: Bepridil, Con2, Screening plate 1, Well J23 [S4881Nr6_J23]


title: Bepridil, Con3, Screening plate 1, Well J22 [S4881Nr6_J22]

value: Bepridil, Con3


title: Bepridil, Con4, Screening plate 1, Well J21 [S4881Nr6_J21]

value: Bepridil, Con4


title: Bepridil, Con5, Screening plate 1, Well L20 [S4881Nr6_L20]

value: Bepridil, Con5


title: Bepridil, Con3, Screening plate 1, Well L22 [S4881Nr6_L22]


title: Bepridil, Con5, Screening plate 1, Well J20 [S4881Nr6_J20]


title: Bepridil, Con5, Screening plate 1, Well K20 [S4881Nr6_K20]


title: Bepridil, Con6, Screening plate 1, Well L19 [S4881Nr6_L19]

value: Bepridil, Con6


title: Bepridil, Con6, Screening plate 1, Well J19 [S4881Nr6_J19]


title: Bepridil, Con7, Screening plate 1, Well L18 [S4881Nr6_L18]

value: Bepridil, Con7


title: Bepridil, Con7, Screening plate 1, Well J18 [S4881Nr6_J18]


title: Bepridil, Con4, Screening plate 1, Well L21 [S4881Nr6_L21]


title: Bepridil, Con8, Screening plate 1, Well L17 [S4881Nr6_L17]

value: Bepridil, Con8


title: Cisapride, Con5, Screening plate 1, Well M4 [S4881Nr6_M4]

value: hiPSC-CM


title: Bepridil, Con7, Screening plate 1, Well K18 [S4881Nr6_K18]


title: Bepridil, Con8, Screening plate 1, Well K17 [S4881Nr6_K17]


title: Bepridil, Con1, Screening plate 1, Well J24 [S4881Nr6_J24]


title: Bepridil, Con8, Screening plate 1, Well J17 [S4881Nr6_J17]


title: Atenolol, Con1, Screening plate 1, Well L16 [S4881Nr6_L16]

value: Atenolol, Con1


title: Atenolol, Con1, Screening plate 1, Well K16 [S4881Nr6_K16]

value: WT


title: Bepridil, Con3, Screening plate 1, Well K22 [S4881Nr6_K22]


title: Bepridil, Con4, Screening plate 1, Well K21 [S4881Nr6_K21]


title: Atenolol, Con1, Screening plate 1, Well J16 [S4881Nr6_J16]


title: Atenolol, Con2, Screening plate 1, Well L15 [S4881Nr6_L15]

value: Atenolol, Con2


title: Atenolol, Con3, Screening plate 1, Well L14 [S4881Nr6_L14]

value: Atenolol, Con3


title: Atenolol, Con2, Screening plate 1, Well K15 [S4881Nr6_K15]


title: Atenolol, Con2, Screening plate 1, Well J15 [S4881Nr6_J15]


title: Atenolol, Con4, Screening plate 1, Well L13 [S4881Nr6_L13]

value: Atenolol, Con4


title: Atenolol, Con3, Screening plate 1, Well J14 [S4881Nr6_J14]


title: Atenolol, Con3, Screening plate 1, Well K14 [S4881Nr6_K14]


title: Bepridil, Con6, Screening plate 1, Well K19 [S4881Nr6_K19]


title: Atenolol, Con4, Screening plate 1, Well J13 [S4881Nr6_J13]


title: Atenolol, Con4, Screening plate 1, Well K13 [S4881Nr6_K13]


title: Atenolol, Con8, Screening plate 1, Well L9 [S4881Nr6_L9]

value: Atenolol, Con8


title: Atenolol, Con7, Screening plate 1, Well J10 [S4881Nr6_J10]

value: Atenolol, Con7


title: Atenolol, Con8, Screening plate 1, Well K9 [S4881Nr6_K9]


title: Atenolol, Con5, Screening plate 1, Well L12 [S4881Nr6_L12]

value: Atenolol, Con5


title: Atenolol, Con6, Screening plate 1, Well L11 [S4881Nr6_L11]

value: Atenolol, Con6


title: Atenolol, Con5, Screening plate 1, Well K12 [S4881Nr6_K12]


title: Atenolol, Con6, Screening plate 1, Well K11 [S4881Nr6_K11]


title: Atenolol, Con7, Screening plate 1, Well L10 [S4881Nr6_L10]


title: Atenolol, Con7, Screening plate 1, Well K10 [S4881Nr6_K10]


title: Atenolol, Con8, Screening plate 1, Well J9 [S4881Nr6_J9]


title: Amitriptyline, Con1, Screening plate 1, Well J8 [S4881Nr6_J8]

value: Amitriptyline, Con1


title: Amitriptyline, Con1, Screening plate 1, Well L8 [S4881Nr6_L8]


title: Amitriptyline, Con1, Screening plate 1, Well K8 [S4881Nr6_K8]


title: Amitriptyline, Con4, Screening plate 1, Well K5 [S4881Nr6_K5]

value: Amitriptyline, Con4


title: Amitriptyline, Con4, Screening plate 1, Well L5 [S4881Nr6_L5]


title: Amitriptyline, Con3, Screening plate 1, Well K6 [S4881Nr6_K6]

value: Amitriptyline, Con3


title: Amitriptyline, Con2, Screening plate 1, Well L7 [S4881Nr6_L7]

value: Amitriptyline, Con2


title: Amitriptyline, Con5, Screening plate 1, Well J4 [S4881Nr6_J4]

value: Amitriptyline, Con5


title: Amitriptyline, Con5, Screening plate 1, Well K4 [S4881Nr6_K4]


title: Atenolol, Con5, Screening plate 1, Well J12 [S4881Nr6_J12]


title: Amitriptyline, Con3, Screening plate 1, Well J6 [S4881Nr6_J6]


title: Amitriptyline, Con4, Screening plate 1, Well J5 [S4881Nr6_J5]


title: Amitriptyline, Con2, Screening plate 1, Well K7 [S4881Nr6_K7]


title: Amitriptyline, Con2, Screening plate 1, Well J7 [S4881Nr6_J7]


title: Amitriptyline, Con3, Screening plate 1, Well L6 [S4881Nr6_L6]


title: Amitriptyline, Con6, Screening plate 1, Well K3 [S4881Nr6_K3]

value: Amitriptyline, Con6


title: Amitriptyline, Con6, Screening plate 1, Well J3 [S4881Nr6_J3]


title: Amitriptyline, Con5, Screening plate 1, Well L4 [S4881Nr6_L4]


title: Amitriptyline, Con6, Screening plate 1, Well L3 [S4881Nr6_L3]


title: Atenolol, Con6, Screening plate 1, Well J11 [S4881Nr6_J11]


title: Amitriptyline, Con7, Screening plate 1, Well K2 [S4881Nr6_K2]

value: Amitriptyline, Con7


title: Amitriptyline, Con7, Screening plate 1, Well L2 [S4881Nr6_L2]

value: hiPSC-CM


title: Amitriptyline, Con7, Screening plate 1, Well J2 [S4881Nr6_J2]


title: Amitriptyline, Con8, Screening plate 1, Well L1 [S4881Nr6_L1]

value: Amitriptyline, Con8


title: Amitriptyline, Con8, Screening plate 1, Well K1 [S4881Nr6_K1]

value: WT


title: Amitriptyline, Con8, Screening plate 1, Well J1 [S4881Nr6_J1]


title: Diltiazem, Con1, Screening plate 1, Well I24 [S4881Nr6_I24]

value: Diltiazem, Con1


title: Diltiazem, Con2, Screening plate 1, Well I23 [S4881Nr6_I23]

value: Diltiazem, Con2


title: Diltiazem, Con1, Screening plate 1, Well H24 [S4881Nr6_H24]


title: Diltiazem, Con2, Screening plate 1, Well H23 [S4881Nr6_H23]


title: Diltiazem, Con3, Screening plate 1, Well I22 [S4881Nr6_I22]

value: Diltiazem, Con3


title: Diltiazem, Con3, Screening plate 1, Well G22 [S4881Nr6_G22]


title: Diltiazem, Con4, Screening plate 1, Well I21 [S4881Nr6_I21]

value: Diltiazem, Con4


title: Diltiazem, Con4, Screening plate 1, Well H21 [S4881Nr6_H21]


title: Diltiazem, Con4, Screening plate 1, Well G21 [S4881Nr6_G21]


title: Diltiazem, Con5, Screening plate 1, Well G20 [S4881Nr6_G20]

value: Diltiazem, Con5


title: Diltiazem, Con5, Screening plate 1, Well H20 [S4881Nr6_H20]


title: Diltiazem, Con6, Screening plate 1, Well I19 [S4881Nr6_I19]

value: Diltiazem, Con6


title: Diltiazem, Con7, Screening plate 1, Well I18 [S4881Nr6_I18]

value: Diltiazem, Con7


title: Diltiazem, Con6, Screening plate 1, Well G19 [S4881Nr6_G19]


title: Diltiazem, Con6, Screening plate 1, Well H19 [S4881Nr6_H19]


title: Diltiazem, Con8, Screening plate 1, Well I17 [S4881Nr6_I17]

value: Diltiazem, Con8


title: Sildenafil, Con1, Screening plate 1, Well H16 [S4881Nr6_H16]

value: Sildenafil, Con1


title: Sildenafil, Con1, Screening plate 1, Well G16 [S4881Nr6_G16]


title: Sildenafil, Con1, Screening plate 1, Well I16 [S4881Nr6_I16]


title: Diltiazem, Con8, Screening plate 1, Well G17 [S4881Nr6_G17]


title: Sildenafil, Con2, Screening plate 1, Well H15 [S4881Nr6_H15]

value: Sildenafil, Con2


title: Diltiazem, Con8, Screening plate 1, Well H17 [S4881Nr6_H17]


title: Sildenafil, Con3, Screening plate 1, Well H14 [S4881Nr6_H14]

value: Sildenafil, Con3


title: Diltiazem, Con1, Screening plate 1, Well G24 [S4881Nr6_G24]


title: Diltiazem, Con5, Screening plate 1, Well I20 [S4881Nr6_I20]


title: Diltiazem, Con2, Screening plate 1, Well G23 [S4881Nr6_G23]


title: Sildenafil, Con3, Screening plate 1, Well I14 [S4881Nr6_I14]


title: Sildenafil, Con2, Screening plate 1, Well G15 [S4881Nr6_G15]


title: Sildenafil, Con2, Screening plate 1, Well I15 [S4881Nr6_I15]


title: Sildenafil, Con6, Screening plate 1, Well I11 [S4881Nr6_I11]

value: Sildenafil, Con6


title: Diltiazem, Con3, Screening plate 1, Well H22 [S4881Nr6_H22]


title: Sildenafil, Con6, Screening plate 1, Well H11 [S4881Nr6_H11]


title: Sildenafil, Con3, Screening plate 1, Well G14 [S4881Nr6_G14]


title: Sildenafil, Con4, Screening plate 1, Well I13 [S4881Nr6_I13]

value: Sildenafil, Con4


title: Sildenafil, Con7, Screening plate 1, Well H10 [S4881Nr6_H10]

value: Sildenafil, Con7


title: Sildenafil, Con7, Screening plate 1, Well G10 [S4881Nr6_G10]

value: hiPSC-CM


title: Sildenafil, Con8, Screening plate 1, Well H9 [S4881Nr6_H9]

value: Sildenafil, Con8


title: Sildenafil, Con4, Screening plate 1, Well H13 [S4881Nr6_H13]

value: WT


title: Sildenafil, Con5, Screening plate 1, Well I12 [S4881Nr6_I12]

value: Sildenafil, Con5


title: Sildenafil, Con5, Screening plate 1, Well H12 [S4881Nr6_H12]


title: Diltiazem, Con7, Screening plate 1, Well H18 [S4881Nr6_H18]


title: Sildenafil, Con5, Screening plate 1, Well G12 [S4881Nr6_G12]


title: Diltiazem, Con7, Screening plate 1, Well G18 [S4881Nr6_G18]


title: Sildenafil, Con7, Screening plate 1, Well I10 [S4881Nr6_I10]


title: Sildenafil, Con6, Screening plate 1, Well G11 [S4881Nr6_G11]


title: Furosemide, Con1, Screening plate 1, Well H8 [S4881Nr6_H8]

value: Furosemide, Con1


title: Sildenafil, Con8, Screening plate 1, Well G9 [S4881Nr6_G9]


title: Furosemide, Con3, Screening plate 1, Well I6 [S4881Nr6_I6]

value: Furosemide, Con3


title: Furosemide, Con5, Screening plate 1, Well I4 [S4881Nr6_I4]

value: Furosemide, Con5


title: Furosemide, Con5, Screening plate 1, Well G4 [S4881Nr6_G4]


title: Furosemide, Con4, Screening plate 1, Well G5 [S4881Nr6_G5]

value: Furosemide, Con4


title: Sildenafil, Con8, Screening plate 1, Well I9 [S4881Nr6_I9]


title: Furosemide, Con1, Screening plate 1, Well I8 [S4881Nr6_I8]


title: Furosemide, Con6, Screening plate 1, Well I3 [S4881Nr6_I3]

value: Furosemide, Con6


title: Sildenafil, Con4, Screening plate 1, Well G13 [S4881Nr6_G13]


title: Furosemide, Con3, Screening plate 1, Well H6 [S4881Nr6_H6]


title: Furosemide, Con6, Screening plate 1, Well G3 [S4881Nr6_G3]


title: Furosemide, Con4, Screening plate 1, Well I5 [S4881Nr6_I5]


title: Furosemide, Con2, Screening plate 1, Well I7 [S4881Nr6_I7]

value: Furosemide, Con2


title: Furosemide, Con1, Screening plate 1, Well G8 [S4881Nr6_G8]


title: Furosemide, Con2, Screening plate 1, Well G7 [S4881Nr6_G7]


title: Furosemide, Con3, Screening plate 1, Well G6 [S4881Nr6_G6]


title: Furosemide, Con7, Screening plate 1, Well I2 [S4881Nr6_I2]

value: Furosemide, Con7


title: Furosemide, Con8, Screening plate 1, Well I1 [S4881Nr6_I1]

value: Furosemide, Con8


title: Furosemide, Con8, Screening plate 1, Well H1 [S4881Nr6_H1]


title: Furosemide, Con8, Screening plate 1, Well G1 [S4881Nr6_G1]


title: Enalapril, Con1, Screening plate 1, Well F24 [S4881Nr6_F24]

value: Enalapril, Con1


title: Furosemide, Con4, Screening plate 1, Well H5 [S4881Nr6_H5]


title: Furosemide, Con5, Screening plate 1, Well H4 [S4881Nr6_H4]


title: Furosemide, Con6, Screening plate 1, Well H3 [S4881Nr6_H3]


title: Furosemide, Con7, Screening plate 1, Well H2 [S4881Nr6_H2]


title: Enalapril, Con2, Screening plate 1, Well F23 [S4881Nr6_F23]

value: Enalapril, Con2


title: Furosemide, Con2, Screening plate 1, Well H7 [S4881Nr6_H7]


title: Furosemide, Con7, Screening plate 1, Well G2 [S4881Nr6_G2]


title: Enalapril, Con4, Screening plate 1, Well E21 [S4881Nr6_E21]

value: Enalapril, Con4


title: Enalapril, Con4, Screening plate 1, Well D21 [S4881Nr6_D21]


title: Enalapril, Con5, Screening plate 1, Well F20 [S4881Nr6_F20]

value: Enalapril, Con5


title: Enalapril, Con5, Screening plate 1, Well E20 [S4881Nr6_E20]


title: Enalapril, Con6, Screening plate 1, Well F19 [S4881Nr6_F19]

value: Enalapril, Con6


title: Enalapril, Con7, Screening plate 1, Well E18 [S4881Nr6_E18]

value: hiPSC-CM

value: Enalapril, Con7


title: Enalapril, Con7, Screening plate 1, Well D18 [S4881Nr6_D18]

value: WT


title: Enalapril, Con1, Screening plate 1, Well E24 [S4881Nr6_E24]


title: Enalapril, Con1, Screening plate 1, Well D24 [S4881Nr6_D24]


title: Enalapril, Con8, Screening plate 1, Well F17 [S4881Nr6_F17]

value: Enalapril, Con8


title: Enalapril, Con8, Screening plate 1, Well D17 [S4881Nr6_D17]


title: Enalapril, Con8, Screening plate 1, Well E17 [S4881Nr6_E17]


title: Buspirone, Con1, Screening plate 1, Well D16 [S4881Nr6_D16]

value: Buspirone, Con1


title: Buspirone, Con2, Screening plate 1, Well E15 [S4881Nr6_E15]

value: Buspirone, Con2


title: Buspirone, Con3, Screening plate 1, Well E14 [S4881Nr6_E14]

value: Buspirone, Con3


title: Buspirone, Con4, Screening plate 1, Well F13 [S4881Nr6_F13]

value: Buspirone, Con4


title: Enalapril, Con2, Screening plate 1, Well E23 [S4881Nr6_E23]


title: Buspirone, Con4, Screening plate 1, Well D13 [S4881Nr6_D13]


title: Buspirone, Con4, Screening plate 1, Well E13 [S4881Nr6_E13]


title: Enalapril, Con2, Screening plate 1, Well D23 [S4881Nr6_D23]


title: Enalapril, Con3, Screening plate 1, Well F22 [S4881Nr6_F22]

value: Enalapril, Con3


title: Enalapril, Con3, Screening plate 1, Well E22 [S4881Nr6_E22]


title: Buspirone, Con5, Screening plate 1, Well D12 [S4881Nr6_D12]

value: Buspirone, Con5


title: Buspirone, Con6, Screening plate 1, Well E11 [S4881Nr6_E11]

value: Buspirone, Con6


title: Buspirone, Con5, Screening plate 1, Well E12 [S4881Nr6_E12]


title: Buspirone, Con6, Screening plate 1, Well F11 [S4881Nr6_F11]


title: Buspirone, Con6, Screening plate 1, Well D11 [S4881Nr6_D11]


title: Enalapril, Con3, Screening plate 1, Well D22 [S4881Nr6_D22]


title: Buspirone, Con7, Screening plate 1, Well F10 [S4881Nr6_F10]

value: Buspirone, Con7


title: Enalapril, Con4, Screening plate 1, Well F21 [S4881Nr6_F21]


title: Buspirone, Con7, Screening plate 1, Well E10 [S4881Nr6_E10]


title: Enalapril, Con5, Screening plate 1, Well D20 [S4881Nr6_D20]


title: Enalapril, Con6, Screening plate 1, Well E19 [S4881Nr6_E19]


title: Enalapril, Con7, Screening plate 1, Well F18 [S4881Nr6_F18]


title: Buspirone, Con1, Screening plate 1, Well F16 [S4881Nr6_F16]


title: Buspirone, Con2, Screening plate 1, Well D15 [S4881Nr6_D15]


title: Buspirone, Con1, Screening plate 1, Well E16 [S4881Nr6_E16]


title: Buspirone, Con2, Screening plate 1, Well F15 [S4881Nr6_F15]


title: Amoxicillin, Con1, Screening plate 1, Well D8 [S4881Nr6_D8]

value: Amoxicillin, Con1


title: Amoxicillin, Con2, Screening plate 1, Well F7 [S4881Nr6_F7]

value: Amoxicillin, Con2


title: Enalapril, Con6, Screening plate 1, Well D19 [S4881Nr6_D19]


title: Amoxicillin, Con2, Screening plate 1, Well E7 [S4881Nr6_E7]


title: Buspirone, Con3, Screening plate 1, Well D14 [S4881Nr6_D14]


title: Buspirone, Con3, Screening plate 1, Well F14 [S4881Nr6_F14]


title: Buspirone, Con5, Screening plate 1, Well F12 [S4881Nr6_F12]


title: Amoxicillin, Con4, Screening plate 1, Well F5 [S4881Nr6_F5]

value: Amoxicillin, Con4


title: Amoxicillin, Con3, Screening plate 1, Well D6 [S4881Nr6_D6]

value: Amoxicillin, Con3


title: Buspirone, Con7, Screening plate 1, Well D10 [S4881Nr6_D10]


title: Amoxicillin, Con4, Screening plate 1, Well E5 [S4881Nr6_E5]


title: Buspirone, Con8, Screening plate 1, Well F9 [S4881Nr6_F9]

value: Buspirone, Con8


title: Buspirone, Con8, Screening plate 1, Well D9 [S4881Nr6_D9]

value: hiPSC-CM


title: Buspirone, Con8, Screening plate 1, Well E9 [S4881Nr6_E9]


title: Amoxicillin, Con1, Screening plate 1, Well F8 [S4881Nr6_F8]


title: Amoxicillin, Con5, Screening plate 1, Well D4 [S4881Nr6_D4]

value: Amoxicillin, Con5


title: Amoxicillin, Con4, Screening plate 1, Well D5 [S4881Nr6_D5]

value: WT


title: Amoxicillin, Con1, Screening plate 1, Well E8 [S4881Nr6_E8]


title: Amoxicillin, Con6, Screening plate 1, Well E3 [S4881Nr6_E3]

value: Amoxicillin, Con6


title: Amoxicillin, Con6, Screening plate 1, Well D3 [S4881Nr6_D3]


title: Amoxicillin, Con7, Screening plate 1, Well F2 [S4881Nr6_F2]

value: Amoxicillin, Con7


title: Amoxicillin, Con3, Screening plate 1, Well F6 [S4881Nr6_F6]


title: Amoxicillin, Con7, Screening plate 1, Well E2 [S4881Nr6_E2]


title: Amoxicillin, Con2, Screening plate 1, Well D7 [S4881Nr6_D7]


title: Amoxicillin, Con8, Screening plate 1, Well E1 [S4881Nr6_E1]

value: Amoxicillin, Con8


title: Amoxicillin, Con5, Screening plate 1, Well F4 [S4881Nr6_F4]


title: Amoxicillin, Con3, Screening plate 1, Well E6 [S4881Nr6_E6]


title: DMSO, Con0, Screening plate 1, Well P6 [S4881Nr6_P6]

value: DMSO, Con0


title: Amoxicillin, Con6, Screening plate 1, Well F3 [S4881Nr6_F3]


title: Amoxicillin, Con8, Screening plate 1, Well F1 [S4881Nr6_F1]


title: Amoxicillin, Con5, Screening plate 1, Well E4 [S4881Nr6_E4]


title: DMSO, Con0, Screening plate 1, Well P9 [S4881Nr6_P9]


title: DMSO, Con0, Screening plate 1, Well P8 [S4881Nr6_P8]


title: Amoxicillin, Con8, Screening plate 1, Well D1 [S4881Nr6_D1]


title: DMSO, Con0, Screening plate 1, Well P3 [S4881Nr6_P3]


title: DMSO, Con0, Screening plate 1, Well P22 [S4881Nr6_P22]


title: DMSO, Con0, Screening plate 1, Well P20 [S4881Nr6_P20]


title: DMSO, Con0, Screening plate 1, Well P5 [S4881Nr6_P5]


title: DMSO, Con0, Screening plate 1, Well P19 [S4881Nr6_P19]


title: DMSO, Con0, Screening plate 1, Well P18 [S4881Nr6_P18]


title: DMSO, Con0, Screening plate 1, Well P4 [S4881Nr6_P4]


title: DMSO, Con0, Screening plate 1, Well P14 [S4881Nr6_P14]


title: DMSO, Con0, Screening plate 1, Well P16 [S4881Nr6_P16]


title: DMSO, Con0, Screening plate 1, Well P13 [S4881Nr6_P13]


title: DMSO, Con0, Screening plate 1, Well P21 [S4881Nr6_P21]


title: DMSO, Con0, Screening plate 1, Well P15 [S4881Nr6_P15]


title: DMSO, Con0, Screening plate 1, Well P2 [S4881Nr6_P2]


title: DMSO, Con0, Screening plate 1, Well P23 [S4881Nr6_P23]


title: DMSO, Con0, Screening plate 1, Well P17 [S4881Nr6_P17]


title: Amoxicillin, Con7, Screening plate 1, Well D2 [S4881Nr6_D2]


title: Acyclovir, Con2, Screening plate 1, Well B23 [S4881Nr6_B23]

value: Acyclovir, Con2


title: DMSO, Con0, Screening plate 1, Well P12 [S4881Nr6_P12]


title: DMSO, Con0, Screening plate 1, Well P11 [S4881Nr6_P11]


title: Acyclovir, Con2, Screening plate 1, Well A23 [S4881Nr6_A23]


title: Acyclovir, Con3, Screening plate 1, Well B22 [S4881Nr6_B22]

value: Acyclovir, Con3


title: Acyclovir, Con3, Screening plate 1, Well C22 [S4881Nr6_C22]


title: Acyclovir, Con2, Screening plate 1, Well C23 [S4881Nr6_C23]


title: DMSO, Con0, Screening plate 1, Well P7 [S4881Nr6_P7]


title: Acyclovir, Con1, Screening plate 1, Well C24 [S4881Nr6_C24]

value: Acyclovir, Con1


title: DMSO, Con0, Screening plate 1, Well P10 [S4881Nr6_P10]


title: Acyclovir, Con4, Screening plate 1, Well C21 [S4881Nr6_C21]

value: Acyclovir, Con4


title: Acyclovir, Con5, Screening plate 1, Well A20 [S4881Nr6_A20]

value: Acyclovir, Con5


title: Acyclovir, Con5, Screening plate 1, Well B20 [S4881Nr6_B20]


title: Acyclovir, Con3, Screening plate 1, Well A22 [S4881Nr6_A22]


title: Acyclovir, Con6, Screening plate 1, Well C19 [S4881Nr6_C19]

value: Acyclovir, Con6


title: Acyclovir, Con6, Screening plate 1, Well B19 [S4881Nr6_B19]


title: Acyclovir, Con7, Screening plate 1, Well C18 [S4881Nr6_C18]

value: Acyclovir, Con7


title: Acyclovir, Con6, Screening plate 1, Well A19 [S4881Nr6_A19]


title: Acyclovir, Con7, Screening plate 1, Well B18 [S4881Nr6_B18]


title: Acyclovir, Con1, Screening plate 1, Well A24 [S4881Nr6_A24]


title: Acyclovir, Con7, Screening plate 1, Well A18 [S4881Nr6_A18]


title: Acyclovir, Con1, Screening plate 1, Well B24 [S4881Nr6_B24]


title: Acyclovir, Con8, Screening plate 1, Well C17 [S4881Nr6_C17]

value: Acyclovir, Con8


title: Acyclovir, Con8, Screening plate 1, Well A17 [S4881Nr6_A17]


title: Acetylsalicylic_acid, Con1, Screening plate 1, Well C16 [S4881Nr6_C16]

value: Acetylsalicylic_acid, Con1


title: Acyclovir, Con4, Screening plate 1, Well B21 [S4881Nr6_B21]


title: Acyclovir, Con4, Screening plate 1, Well A21 [S4881Nr6_A21]


title: Acetylsalicylic_acid, Con1, Screening plate 1, Well A16 [S4881Nr6_A16]


title: Acyclovir, Con5, Screening plate 1, Well C20 [S4881Nr6_C20]


title: Acetylsalicylic_acid, Con2, Screening plate 1, Well A15 [S4881Nr6_A15]

value: Acetylsalicylic_acid, Con2


title: Acetylsalicylic_acid, Con3, Screening plate 1, Well B14 [S4881Nr6_B14]

value: hiPSC-CM

value: Acetylsalicylic_acid, Con3


title: Acetylsalicylic_acid, Con3, Screening plate 1, Well A14 [S4881Nr6_A14]

value: WT


title: Acetylsalicylic_acid, Con2, Screening plate 1, Well B15 [S4881Nr6_B15]


title: Acetylsalicylic_acid, Con3, Screening plate 1, Well C14 [S4881Nr6_C14]


title: Acetylsalicylic_acid, Con4, Screening plate 1, Well C13 [S4881Nr6_C13]

value: Acetylsalicylic_acid, Con4


title: Acetylsalicylic_acid, Con4, Screening plate 1, Well B13 [S4881Nr6_B13]


title: Acetylsalicylic_acid, Con4, Screening plate 1, Well A13 [S4881Nr6_A13]


title: Acetylsalicylic_acid, Con5, Screening plate 1, Well B12 [S4881Nr6_B12]

value: Acetylsalicylic_acid, Con5


title: Acyclovir, Con8, Screening plate 1, Well B17 [S4881Nr6_B17]


title: Acetylsalicylic_acid, Con5, Screening plate 1, Well C12 [S4881Nr6_C12]


title: Acetylsalicylic_acid, Con7, Screening plate 1, Well B10 [S4881Nr6_B10]

value: Acetylsalicylic_acid, Con7


title: Acetylsalicylic_acid, Con8, Screening plate 1, Well C9 [S4881Nr6_C9]

value: Acetylsalicylic_acid, Con8


title: Acetylsalicylic_acid, Con8, Screening plate 1, Well A9 [S4881Nr6_A9]


title: Acetylsalicylic_acid, Con6, Screening plate 1, Well B11 [S4881Nr6_B11]

value: Acetylsalicylic_acid, Con6


title: Acetylsalicylic_acid, Con5, Screening plate 1, Well A12 [S4881Nr6_A12]


title: Acetylsalicylic_acid, Con6, Screening plate 1, Well C11 [S4881Nr6_C11]


title: Acetylsalicylic_acid, Con7, Screening plate 1, Well A10 [S4881Nr6_A10]


title: Acetaminophen, Con1, Screening plate 1, Well C8 [S4881Nr6_C8]

value: Acetaminophen, Con1


title: Acetylsalicylic_acid, Con8, Screening plate 1, Well B9 [S4881Nr6_B9]


title: Acetylsalicylic_acid, Con6, Screening plate 1, Well A11 [S4881Nr6_A11]


title: Acetaminophen, Con1, Screening plate 1, Well B8 [S4881Nr6_B8]


title: Acetaminophen, Con2, Screening plate 1, Well B7 [S4881Nr6_B7]

value: Acetaminophen, Con2


title: Acetylsalicylic_acid, Con2, Screening plate 1, Well C15 [S4881Nr6_C15]


title: Acetaminophen, Con1, Screening plate 1, Well A8 [S4881Nr6_A8]


title: Acetaminophen, Con2, Screening plate 1, Well C7 [S4881Nr6_C7]


title: Acetaminophen, Con2, Screening plate 1, Well A7 [S4881Nr6_A7]


title: Acetaminophen, Con3, Screening plate 1, Well C6 [S4881Nr6_C6]

value: Acetaminophen, Con3


title: Acetaminophen, Con4, Screening plate 1, Well C5 [S4881Nr6_C5]

value: Acetaminophen, Con4


title: Acetaminophen, Con4, Screening plate 1, Well A5 [S4881Nr6_A5]


title: Acetaminophen, Con3, Screening plate 1, Well A6 [S4881Nr6_A6]


title: Acetaminophen, Con5, Screening plate 1, Well B4 [S4881Nr6_B4]

value: Acetaminophen, Con5


title: Acetaminophen, Con4, Screening plate 1, Well B5 [S4881Nr6_B5]


title: Acetaminophen, Con5, Screening plate 1, Well C4 [S4881Nr6_C4]


title: Acetaminophen, Con3, Screening plate 1, Well B6 [S4881Nr6_B6]


title: Acetaminophen, Con5, Screening plate 1, Well A4 [S4881Nr6_A4]


title: Acetaminophen, Con6, Screening plate 1, Well C3 [S4881Nr6_C3]

value: Acetaminophen, Con6


title: Acetaminophen, Con6, Screening plate 1, Well B3 [S4881Nr6_B3]


title: Acetaminophen, Con7, Screening plate 1, Well B2 [S4881Nr6_B2]

value: Acetaminophen, Con7


title: Acetaminophen, Con7, Screening plate 1, Well C2 [S4881Nr6_C2]


title: Acetaminophen, Con7, Screening plate 1, Well A2 [S4881Nr6_A2]


title: Acetaminophen, Con8, Screening plate 1, Well C1 [S4881Nr6_C1]

value: Acetaminophen, Con8


title: Acetylsalicylic_acid, Con7, Screening plate 1, Well C10 [S4881Nr6_C10]


title: Sunitinib, Con1, Optimization plate 5, Well O24 [S4881Nr5_O24]

value: Sunitinib, Con1


title: Acetaminophen, Con8, Screening plate 1, Well A1 [S4881Nr6_A1]

value: hiPSC-CM


title: Sunitinib, Con1, Optimization plate 5, Well M24 [S4881Nr5_M24]


title: Sunitinib, Con3, Optimization plate 5, Well O22 [S4881Nr5_O22]

value: Sunitinib, Con3


title: Acetylsalicylic_acid, Con1, Screening plate 1, Well B16 [S4881Nr6_B16]

value: WT

value: Acetylsalicylic_acid, Con1


title: NoTreatment, NoTreatment, Optimization plate 5, Well P24 [S4881Nr5_P24]

value: NoTreatment, NoTreatment


title: Sunitinib, Con1, Optimization plate 5, Well N24 [S4881Nr5_N24]


title: NoTreatment, NoTreatment, Optimization plate 5, Well P1 [S4881Nr5_P1]


title: Sunitinib, Con2, Optimization plate 5, Well N23 [S4881Nr5_N23]

value: Sunitinib, Con2


title: Sunitinib, Con2, Optimization plate 5, Well O23 [S4881Nr5_O23]


title: Sunitinib, Con4, Optimization plate 5, Well O21 [S4881Nr5_O21]

value: Sunitinib, Con4


title: Sunitinib, Con3, Optimization plate 5, Well M22 [S4881Nr5_M22]


title: Sunitinib, Con4, Optimization plate 5, Well N21 [S4881Nr5_N21]


title: Sunitinib, Con5, Optimization plate 5, Well M20 [S4881Nr5_M20]

value: Sunitinib, Con5


title: Sunitinib, Con6, Optimization plate 5, Well O19 [S4881Nr5_O19]

value: Sunitinib, Con6


title: Sunitinib, Con5, Optimization plate 5, Well N20 [S4881Nr5_N20]


title: Sunitinib, Con6, Optimization plate 5, Well N19 [S4881Nr5_N19]


title: Sunitinib, Con4, Optimization plate 5, Well M21 [S4881Nr5_M21]


title: Sunitinib, Con7, Optimization plate 5, Well N18 [S4881Nr5_N18]

value: Sunitinib, Con7


title: Sunitinib, Con8, Optimization plate 5, Well O17 [S4881Nr5_O17]

value: Sunitinib, Con8


title: Sunitinib, Con7, Optimization plate 5, Well O18 [S4881Nr5_O18]


title: Sunitinib, Con8, Optimization plate 5, Well N17 [S4881Nr5_N17]


title: Sunitinib, Con7, Optimization plate 5, Well M18 [S4881Nr5_M18]


title: Sunitinib, Con8, Optimization plate 5, Well M17 [S4881Nr5_M17]


title: Acetaminophen, Con8, Screening plate 1, Well B1 [S4881Nr6_B1]


title: Sunitinib, Con2, Optimization plate 5, Well M23 [S4881Nr5_M23]


title: Sunitinib, Con3, Optimization plate 5, Well N22 [S4881Nr5_N22]


title: Imatinib, Con1, Optimization plate 5, Well N16 [S4881Nr5_N16]

value: Imatinib, Con1


title: Imatinib, Con2, Optimization plate 5, Well M15 [S4881Nr5_M15]

value: Imatinib, Con2


title: Imatinib, Con2, Optimization plate 5, Well O15 [S4881Nr5_O15]


title: Imatinib, Con2, Optimization plate 5, Well N15 [S4881Nr5_N15]


title: Sunitinib, Con6, Optimization plate 5, Well M19 [S4881Nr5_M19]


title: Imatinib, Con1, Optimization plate 5, Well M16 [S4881Nr5_M16]


title: Imatinib, Con1, Optimization plate 5, Well O16 [S4881Nr5_O16]


title: Plate 1 Cell P1_C2

city: Baltimore

first: Rong

last: Li

state: MD

address: 855 N. Wolfe St., Suite 440.

department: Cell Biology

country: USA

institute: Johns Hopkins School of Medicine

data_processing:
Paired reads were then aligned with STAR and gene expression was quantified with HTSeq to generate a count matrix using Partek Flow software
Assembly: GRCh38
Supplementary files format and content: Tab-seperated value file, gene count matrix

source_name: colonoid

growth_protocol: Colonoids were dissociated to single cells then plated in 25 µl of Matrigel at a density of 600 cells/µl Matrigel and 500 µl proliferation media (50% Wnt-3a conditioned media, 15% R-spondin-1 conditioned media, 10% Noggin conditioned media, EGF, B27 supplement, A-83-01, SB202190, and primocin)

extract_protocol:
Organoids were then dissociated to single cells by adding 1 ml 1x TrypLE Express directly to each well. Organoids were incubated at 37˚C for 20 minutes with trituration every 5 minutes until a single cell suspension was generated. Cells were stained with ethidium homodimer to exclude dead cells. Single cells were then sorted directly into 96 well PCR plates containing 5 µl NEBNext cell lysis buffer with murine RNase inhibitor and flash frozen on dry ice
Libraries were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit manufacturer’s protocol

treatment_protocol: 0.5 µM reversine or 0.05% DMSO was added for 24 hours on day 4 after passaging. Reversine and DMSO were then washed out and colonoids were grown in proliferation media for 24 hours

value: colonoid

value: DMSO


title: Plate 1 Cell P1_B11


title: Plate 1 Cell P1_C12


title: Plate 1 Cell P1_C8


title: Plate 1 Cell P1_B7


title: Plate 1 Cell P1_C1


title: Plate 1 Cell P1_C10


title: Plate 1 Cell P1_C7


title: Plate 1 Cell P1_C11


title: Plate 1 Cell P1_B10


title: Plate 1 Cell P1_C4


title: Plate 1 Cell P1_C6


title: Plate 1 Cell P1_C9


title: Plate 1 Cell P1_C3


title: Plate 1 Cell P1_B8


title: Plate 1 Cell P1_D1


title: Plate 1 Cell P1_B6


title: Plate 1 Cell P1_B12


title: Plate 1 Cell P1_B5


title: Plate 1 Cell P1_B9


title: Plate 1 Cell P1_B4


title: Plate 1 Cell P1_B3


title: Plate 1 Cell P1_C5


title: Plate 1 Cell P1_A12


title: Plate 1 Cell P1_B2


title: Plate 1 Cell P1_B1


title: Acetaminophen, Con6, Screening plate 1, Well A3 [S4881Nr6_A3]

value: Acetaminophen, Con6


title: Plate 1 Cell P1_A10


title: Plate 1 Cell P1_A5


title: Plate 1 Cell P1_A4


title: Plate 1 Cell P1_A6


title: Plate 1 Cell P1_A2


title: Plate 1 Cell P1_A1


title: Plate 1 Cell P1_A3


title: patient8_NN

city: New York

first: Mohamed

last: Omar

state: New York

address: 413 East 69th Street

department: Department of Pathology and Laboratory Medicine

institute: Weill Cornell Medicine

library_source: transcriptomic single cell

data_processing:
Expression matrices were generated from raw Illumina sequencing output using CellRanger. Bcl files were demultiplexed by bcl2fastq, then reads were aligned to GRCh38 using STAR. The expression matrices from the nine human samples were concatenated into a single count matrix.
Assembly: hg38
Supplementary files format and content: anndata (annotated data matrix) object saved in h5ad-file format. The file contains the preprocessed, normalized and annotated count data of the stromal cells derived from the human data.

molecule: total RNA

source_name: Prostate

extract_protocol:
Human prostate tissues were first digested in aDMEM/F12/Collagenase II (1.5mg/ml)/Hyaluronidase VIII (1000 u/ml; Thermo Fisher Scientific) plus 10  μM Y-27632 (Tocris) for 1 hour at 37°C with 1500 rpm mixing, continuously agitated. Subsequently, after centrifuging at 150 g for 5 min at 4°C, digested cells were suspended in 1 ml TrypLE with 10 µM Y-27632 and digested for 15 min at 37°C and neutralized in aDMEM/F12/FBS (0.05%). Dissociated cells were subsequently passed through 70 μm and 40 μm cell strainers (BD Biosciences, San Jose, CA) to get single cells. Samples were resuspended in 1x PBS and sorted for DAPI to enrich living cells.
Barcoded cDNA libraries were created from single-cell suspensions using the Chromium Single Cell 3’ Library and Gel Bead Kit, and Chip Kit from 10x Genomics70, according to manufacturer recommendations. 8,000-16,000 cells were targeted for 3’ RNA library preparation, multiplexed in an Illumina NovaSeq 6000, and sequenced at an average depth of 25,000 reads per cell.

tag: tissue

value: Prostate


title: patient8_T


title: patient7_T


title: patient7_NN


title: patient7_FN


title: Plate 1 Cell P1_A9


title: patient9_N


title: Plate 1 Cell P1_A8


title: H1048 cells,DMSO,48h,rep 3

city: shanghai

first: yongle

last: xu

state: shanghai

address: shanghaijiaotong university

country: China

institute: shanghaijiaotong university

data_processing:
STAR
Trimmomatic software were used to remove adapter and low quality reads.(Parameter-quality limit:0.05)
STAR is used to align clean reads to reference genome.
Read counts for individual transcripts of each sample were produced with HTSeq-count.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample.
Supplementary files format and content: Tab-delimited text files includes PRKM values for each sample to standardize.

source_name: cell line

growth_protocol: H1048 cells were maintained in 1640 medium supplemented with 10% fetal bovine serum(FBS) and 100 U/mL penicillin/streptomycin  at 37°C, 5% CO2, and appropriate humidity.

extract_protocol:
Total RNA from ISP-I (10μM) or DMSO (control) treated SCLC H1048 cells was extracted using TRIzol reagent (Thermo Fisher Scientific, Cat No. 15596018).
The NEBNext UltraTM RNA Library Prep Kit (NEB #E7490) and beads (AMPure XP system) were applied to prepare the sequencing library. Then the library was sequenced using the Novaseq 6000 platform with PE150 sequencing.

treatment_protocol: H1048 cells were treated with ISP-I(10uM) or DMSO(no more than 0.02%，sigma)  for 48h.

value: cell line

tag: cell type

value: small cell lung cancer

value: wt


title: H1048 cells,DMSO,48h,rep 1


title: patient7_CZ


title: H1048 cells,ISP-I,48h,rep 1

value: ISP-I


title: patient8_CZ


title: patient8_FN


title: patient9_T


title: H1048 cells,DMSO,48h,rep 2


title: Plate 1 Cell P1_A11


title: Sunitinib, Con5, Optimization plate 5, Well O20 [S4881Nr5_O20]

value: hiPSC-CM

value: WT


title: patient6_T1


title: patient6_T2


title: H1048 cells,ISP-I,48h,rep 3


title: H1048 cells,ISP-I,48h,rep 2


title: patient6_N


title: Plate 1 Cell P1_A7


title: patient5_T


title: patient5_N


title: patient4_N


title: patient4_T


title: patient3_T


title: patient3_FN


title: patient3_NN


title: patient1_HCZ


title: patient1_HNN


title: patient1_HST


title: patient3_CZ


title: patient1_HFN


title: AG10047_MSN_1

city: Saint Louis

first: Youngmi

last: Oh

state: MO

address: 660 S. Euclid Avenue

department: Development department

institute: Washington University in St. Louis

data_processing:
The raw data obtained was aligned, quantified and analyzed by usingPartek Flow® Software Analysis Pipeline.
Trim bases (from 3’ end with minimum quality score (Phred) of 20)
RNA-seq reads were mapped to the human reference genome (GRCh38) using STAR STAR version 2.7.3a.
Differential gene expression (GSA) analysis was done using CPM normalization
Assembly: hg38

source_name: Dermal fibroblasts

growth_protocol: Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).

extract_protocol:
At 4 weeks, total RNA from reprogramming cells was extracted using the RNeasy Micro Kit (Qiagen).
Samples were prepared according to the library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.

tag: subject

value: Individual II

tag: age group

value: Young

value: Coriell AG10047

tag: overexpression 1

tag: overexpression 2

value: CTIP2, DLX1, DLX2, MYT1L


title: AG14251_MSN_1

value: Individual III

value: Old

value: Coriell AG14251


title: patient2_FN


title: AG14251_MSN_2


title: AG16030_MSN_1

value: Individual I

value: Coriell AG16030


title: AG14048_MSN_2

value: Coriell AG14048


title: AG14048_MSN_1


title: AG10047_MSN_2


title: AG16030_MSN_2


title: AG4456_MSN_2

value: Coriell AG4456


title: patient2_NN

value: Prostate


title: AG10049_MSN_2

value: Coriell AG10049


title: AG4456_FB_1


title: patient1_HT


title: patient2_T


title: AG4456_FB_2


title: AG14251_FB_1


title: AG10049_MSN_1


title: AG4456_MSN_1


title: AG14048_FB_2


title: AG14251_FB_2


title: AG10047_FB_2


title: AG14048_FB_1


title: AG16030_FB_2


title: AG16030_FB_1


title: AG10049_FB_1


title: AG10049_FB_2


title: A2058 cell IP, control, H3ac, rep1

city: 陕西省

first: hao

last: wang

address: 长乐西路

institute: xijing hospital

library_source: genomic

data_processing:
Raw sequencing data was first filtered by fastp (version 0.23.4), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The clean reads were used for protein binding site analysis. They were mapped to the reference genome of GRCh38 using STAR software (version 2.5.3a) with default parameters.
The Epic2 software was used for peak calling. The bedtools（Version 2.25.0）was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by csaw(version 1.30.1).
The Homer（version 4.10）was used for motifs analysis.
Assembly: GRCh38
Supplementary files format and content: Bigwig

molecule: genomic DNA

source_name: melanoma

extract_protocol:
The cell was fixed in 1% formaldehyde for 10 min at room temperature. After quenching cell was treated with cell lysis buffer and nucleus was collected by centrifuging at 2000g for 5min. Then, nucleus was treated with nucleus lysis buffer and sonicated to fragment chromatin DNA.
The high-throughput DNA sequencing libraries were prepared by using VAHTS Universal DNA Library Prep Kit for Illumina V3（Catalog NO. ND607, Vazyme）. The library products corresponding to 200-500 bp were enriched and quantified.

value: melanoma

value: melanoma cell line


title: A2058 cell IP, treatment, H3ac, rep2


title: A2058 cell Input, treatment, H3ac, rep1


title: AG10047_FB_1


title: A2058 cell IP, treatment, H3ac, rep1


title: A2058 cell Input, treatment, H3ac, rep2


title: A2058 cell Input, control, H3ac, rep2


title: A2058 cell IP, control, H3ac, rep2


title: sgCDK6left-2607283_JWH018

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore.
Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM".
Read duplication was marked with MarkDuplicates from GATK (v4.1.2.0).
RSEM was used to quantify read counts per gene.
Assembly: hg19 (GRCh37.p13)
Supplementary files format and content: gene-based raw counts in tab delimiter text file tsv
Supplementary files format and content: gene-based TPM in tab delimiter text file tsv

source_name: SEM

growth_protocol: The SEM  cells were maintained in RPMI-1640 medium (Lonza) containing 10 % fetal bovine serum (FBS) (Hyclone), 2 mM glutamine (Sigma) and 1% penicillin/streptomycin (Thermo Fisher Scientific). All cells were maintained at 37 °C in a 5 % CO2 atmosphere and 95 % humidity. Cells were tested negative for mycoplasma infection. Cell identity of SEM was confirmed by short tandem repeat (STR) analysis.

extract_protocol:
RNA was purified by Trizol protocol and sonicated for library construction.
Two millions of cells targeted with sgRNAs were collected for RNA extration following the standard protocol. The RNA-seq library was constructed  for deep sequencing using a Novaseq system (illumina) for single-end 100-bp reads.

treatment_protocol: SEM cells  were infected with lenti-dCas9-KRAB and selected for blasticidine (100ug/ml for 7 days) for stable cell lines. The lenti-sgRNA-CFP-puro carrying different sgRNAs were infected into the stable cell line to generate each targeted cell lines by puromycin selection (1ug/ml for 3 days).

value: SEM


title: sgCDK6left-2607281_JWH016


title: A2058 cell Input, control, H3ac, rep1


title: sgCDK6left-2607280_JWH015


title: lenti_puro_CFP-2607266_JWH001

value: Lenti


title: lenti_puro_CFP-2607267_JWH002


title: WT2

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description: whole genome sequences

data_processing:
library strategy: whole genome sequencing
We aligned the reads to the GRCh38 genome assembly using BWA-MEM v0.7.17-r1194 with the -M option (Li & Durbin 2009).
After removing duplicate reads and filtering for properly paired reads with mapping quality ≥30 with samtools v1.9 (Li et al., 2009), we retained remaining uniquely aligned primary reads per library for downstream analyses.
We identified all somatic variants (including single nucleotide polymorphisms (SNVs) and indels) in 250bp flanking regions of the predicted cleavage sites that are present in only TCF7L2 KO lines but not in the WTs using GATK v4.0.5.1 Mutect2 (pair-wse comparisons) with the “--min-base-quality-score 30” option (Auwera and O’Connor, 2020).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include somatic variants in flanking regions of predicted cleavage sites and their allele frequencies.

source_name: MEL1 (INSGFP/W)

extract_protocol:
1x10^7 cells  were collected and gDNA was extracted according to the protocol of QIAGEN's DNeasy® Blood & Tissue Kit.
gDNA was used to created paired-end libraries using Illumina Truseq V3 kit according to manufacturers protocol.

value: MEL1 (INSGFP/W)

value: human embryonic stem cell

value: Wild type

value: beta-cell differentiation


title: KO1

description: whole genome sequences

value: TCF7L2 knockout


title: WT1

description: whole genome sequences


title: KO2

description: whole genome sequences


title: SEMdCas9-KRAB-Day14-Rep1-SFM016-2583717

data_processing:
We reviewed and confirmed the data quality by FASTQC.
sgRNA were counted by bbmap(v37.28, kmercountexact.sh) and matched to sgRNA list. Only R1 were used for counting.
Statical test were performed using MAGeCK(v0.5.9.4)
Supplementary files format and content: hg19
Supplementary files format and content: abundance measurements and Mageck results

extract_protocol:
A set of ~5700 sgRNA oligos that target 229 HOXA9 binding peaks were designed for array-based oligonucleotide synthesis (CustomArray). The unique binding of each sgRNA was verified by sequence blast against the whole human genome in the sgRNA pooled library. The synthesized oligo pool was amplified by PCR and cloned into the LentiGuide-Puro-IRES-CFP backbone by the in-fusion assembly (Clontech #638909). The Cas9-expressing MLL-r SEM cell line was infected by pooled sgRNA library at low M.O.I (~0.3). Infected cells were selected by blasticidin and puromycin. After cell recovery from selection, the pooled population was collected on day 0 and maintained in liquid culture for 7, 14, and 21 days. The sgRNA sequences were recovered by genomic PCR analysis and deep sequencing using Novaseq for paired-end 150 bp read length (Illumina). The primer sequences used for cloning and sequencing are listed in Supplementary file 1. The sgRNA sequences are described in Supplementary file 2. High-titer lentivirus stocks were generated in 293 T cells, as previously described (Vo et al., 2017).
CRISPR

tag: time point

value: Day 14


title: SEMdCas9-KRAB-Day7-Rep1-SFM013-2583714

value: Day 7


title: SEMdCas9-KRAB-Day7-Rep2-SFM014-2583715


title: SEMdCas9-KRAB-Day14-Rep2-SFM017-2583718


title: SEMdCas9-KRAB-Day14-Rep3-SFM018-2583719


title: SEMdCas9-KRAB-Day7-Rep3-SFM015-2583716


title: SEMdCas9-KRAB-Day0-Rep2-SFM011-2583712

value: Day 0


title: SEMdCas9-KRAB-Day0-Rep3-SFM012-2583713


title: SEMdCas9-KRAB-Day0-Rep1-SFM010-2583711


title: SEMCas9-Day14-Rep3-SFM009-2583710


title: SEMCas9-Day7-Rep3-SFM006-2583707


title: SEMCas9-Day0-Rep3-SFM003-2583704


title: MOLM13-Day7-Rep3-SFM024-2583725


title: SEMCas9-Day0-Rep1-SFM001-2583702


title: SEMCas9-Day0-Rep2-SFM002-2583703


title: SEMCas9-Day14-Rep2-SFM008-2583709


title: SEMCas9-Day14-Rep1-SFM007-2583708


title: MOLM13-Day14-Rep3-SFM027-2583728


title: MOLM13-Day7-Rep1-SFM022-2583723


title: MOLM13-Day14-Rep2-SFM026-2583727


title: MOLM13-Day0-Rep2-SFM020-2583721


title: MOLM13-Day0-Rep3-SFM021-2583722


title: INPUT-SEM-TRE3G-HoxAID-HA-zeo-plusDox-Rep3

data_processing:
Single-end reads of 50bp were mapped human genome hg19(GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with Picard(version 2.6.0-SNAPSHOT) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control and confirmed high quality (>50 million uniquely mapped reads each sample).
We extend reads to fragment size detected by SPP(v1.1) and generate bigwig files normalized to 15 million reads.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: The SEM cells were maintained in RPMI-1640 medium (Lonza) containing 10 % fetal bovine serum (FBS) (Hyclone), 2 mM glutamine (Sigma) and 1% penicillin/streptomycin (Thermo Fisher Scientific). All cells were maintained at 37 °C in a 5 % CO2 atmosphere and 95 % humidity. Cells were tested negative for mycoplasma infection. Cell identity of SEM was confirmed by short tandem repeat (STR) analysis.

extract_protocol:
About 20 million cells with or without doxcycycline treatment were fixed by formaldehyde treatment followed by sonication.
ChIP-seq was done by incubating fragmented genomic DNA with HA-beads and pull-down. Enriched DNA was then amplified for NGS sequencing for ChIP-seq analysis.

treatment_protocol: Doxycycline (1ug/ml) was added to liquid culture to induce the ectopic expresshion of HOXA9-HA for 24 hours.

tag: chip antibody

value: INPUT

value: Dox


title: INPUT-SEM-TRE3G-HoxAID-HA-zeo-plusDox-Rep2


title: INPUT-SEM-TRE3G-HoxAID-HA-zeo_PlusDox-Rep1


title: MOLM13-Day0-Rep1-SFM019-2583720


title: SEMCas9-Day7-Rep1-SFM004-2583705


title: SEMCas9-Day7-Rep2-SFM005-2583706


title: HOXA9-SEM-TRE3G-HoxAID-HA-zeo-plusDox-Rep1

value: Anti-HA


title: INPUT-SEM-TRE3G-HoxAID-HA-zeo-minuxDox-Rep2


title: INPUT-SEM-TRE3G-HoxAID-HA-zeo-minuxDox-Rep3


title: HOXA9-SEM-TRE3G-HoxAID-HA-zeo-plusDox-Rep2


title: INPUT-SEM-TRE3G-HoxAID-HA-zeo-minuxDox-Rep1


title: HOXA9-SEM-TRE3G-HoxAID-HA-zeo-plusDox-Rep3


title: HOXA9-SEM-TRE3G-HoxAID-HA-zeo-minuxDox-Rep1


title: HOXA9-SEM-TRE3G-HoxAID-HA-zeo-minuxDox-Rep2


title: MOLM13-Day7-Rep2-SFM023-2583724


title: sgRUNX1_20_SEM_KRAB-Rep1

data_processing:
For ATAC-seq, reads were trimmed for Nextera adapter by cutadapt (version 1.9, paired-end mode, default parameter with “ -m 6 -O 20 ”) and aligned to human genome hg19(GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter).
The duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated proper paired reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2). After removing mitochondrial DNA reads, the rest of reads were classified into four groups including nucleosome free, mono-, di-, and tri-nucleosome by fragment size. The bigwig files were generated using the center 80-bp of fragments and scaled to 20 million nucleosome free reads.
We observed reasonable nucleosome free peaks and pattern of mono-, di-, tri-nucleosome peaks surrounding nucleosome free peaks on IGV.
Given all samples exhibited more than 10 million nucleosome free fragments after merging replicates, we are confidence most strong nucleosome free regions won’t be missed.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Briefly, 10,000 of SEM cells were treated with transposition mix consisting of 22 μL nuclease-free water; 25 μL 2 × TD Buffer; 2.5 μL TDE1 transposase; and 0.5 μL of 1% digitonin (added immediately before removing the supernatant from cell pellets), followed by incubation at 37°C on an Eppendorf ThmorMixer at 300 rpm for 30 minutes.
DNA was purified with using the MinElute Reaction Cleanup Kit (Qiagen, 28204) and amplified for 5 cycles using the PCR mix composed of 10 μL transposed DNA, 2.2 μL nuclease-free water, 6.25 μL 10 μM barcoded Nextera primer-F, 6.25 μL 10 μM barcoded Nextera primer-R, 0.3 μL 100 × SYBR Green I (Invitrogen, S-7563), and 25 μL NEBNext® High-Fidelity 2 × PCR Master Mix (NEB, M0541). PCR products were subsequently re-amplified for another 6 PCR cycles, followed by purification using SPRIselect beads (Beckman Coulter, B23317). Paired-end sequencing (2 × 100 bp) was performed using the Illumina HISeq 4000 platform.

treatment_protocol: SEM cells were infected with lenti-dCas9-KRAB and selected for blasticidine (100ug/ml for 7 days) for stable cell lines. The lenti-sgRNA-CFP-puro carrying different sgRNAs were infected into the stable cell line to generate each targeted cell lines by puromycin selection (1ug/ml for 3 days).


title: sgRUNX1_18_SEM_KRAB-Rep2


title: sgRUNX1_18_SEM_KRAB-Rep1


title: sgFLT3_DE1_SEM_KRAB-Rep1


title: sgFLT3_DE1_SEM_KRAB-Rep2


title: sgDCAF11_2_SEM_KRAB-Rep1


title: sgDCAF11_2_SEM_KRAB-Rep2


title: sgCDK6left_8_SEM_KRAB-Rep2


title: MOLM13-Day14-Rep1-SFM025-2583726


title: sgRUNX1_20_SEM_KRAB-Rep2


title: sgDCAF11_20_SEM_KRAB-Rep2


title: sgDCAF11_20_SEM_KRAB-Rep1


title: sgCDK6left_54_SEM_KRAB-Rep1


title: Lenti_Puro_CFP_SEM_KRAB-Rep2


title: sgCDK6left_8_SEM_KRAB-Rep1


title: RNAseq, 12_B3-2_Hepatoblast1

city: Beijing

first: Ziyan

last: Rao

address: 38 Xueyuan Rd, Haidian District

institute: Peking University Health Science Center

data_processing:
RNA-seq raw reads were mapped to the human genome hg38 using HISAT2 (v.2.2.0) with default parameters. SAM/BAM file formats were transformed by samtools (v.1.6). Expression value (number of raw reads) for each gene was determined by the software HTSeq version v.2.0.2 under the parameters --stranded=no and --mode= intersection-nonempty.  Normalized (the TMM method) expression values were determined by edgeR version 3.38.4 ran with an R version 4.2.0.
The reads of samples were aligned to the GRCh38 human genome provided by 10x Genomics (refdata-gex-GRCh38-2020-A) and pre-processed using the Cell Ranger 10x Genomics software cellranger-7.0.1.
Assembly: hg38
Supplementary files format and content: For RNA-Seq data, tab-delimited text files contian raw count values for each gene of each sample. For scRNA-seq data, tab-separated values files and matrix files were generated by cellranger.

extract_protocol:
RNA-seq: RNA was harvested using ZYMO RESEARCH Direct-zol RNA Mini Prep. 1.5 ug of total RNA was used for the construction of sequencing libraries. scRNA-seq: single cells were suspended in PBS containing 0.04% BSA. About 6,000 cells were added to each channel, and the target cell will be recovered was estimated to be about 3,000 cells. Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53°C for 45 min, followed by 85°Cfor 5 min, and hold at 4°C. The cDNA was generated and then amplified, and quality assessed using an Agilent 4200.
RNA-seq: mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. scRNA-seq: Libraries were constructed using Single Cell 3’Library and Gel Bead Kit V3.1.

tag: strain


title: sgCDK6left_54_SEM_KRAB-Rep2


title: HOXA9-SEM-TRE3G-HoxAID-HA-zeo-minuxDox-Rep3


title: RNAseq, 11_B3-1_Hepatoblast1


title: TPC1

city: Brussels

first: Pierre

middle: P

last: Roger

address: 808 Route de Lennik, Campus Erasme Bat.C - C1.132

country: Belgium

institute: IRIBHM, Université Libre de Bruxelles

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases using "Trimmomatic v.0.36".
Clean paired sequences were aligned to the human reference genome GRCh38 using “STAR” software v.2.5.3.
The number of reads per gene were obtained using "HTSeq" v.0.9.1.
Raw counts were normalized to obtain counts per 20 millions of reads (CP20M).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing matrix of counts normalized to 20 millions of reads for all genes in all samples.

source_name: Thyroid

growth_protocol: Cell lines were maintained in basal standard conditions

extract_protocol:
Total RNA was harvested using the RNeasy Mini Kit according to the manufacturer's protocol. RNA quality was checked using a Fragment Analyzer 5200
cDNA libraries were prepared from 100 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New Englands Biolabs) following manufacturer's recommendations. Paired-end sequencing was performed with a NovaSeq 6000 (Illumina).

value: Thyroid

value: Papillary thyroid carcinoma-derived cell line


title: BCPAP

value: BCPAP

value: Poorly-differentiated thyroid carcinoma-derived cell line


title: ASH3

value: Anaplastic thyroid carcinoma-derived cell line


title: CAL-62


title: 8305C


title: TT2609-C02

value: Follicular thyroid carcinoma-derived cell line


title: IHH4


title: ML1


title: HTCC3


title: C643


title: Lenti_Puro_CFP_SEM_KRAB-Rep1

value: SEM

value: Lenti


title: 8505C


title: BHT101


title: WRO

value: WRO


title: FTC-238


title: MCF-7 PR, MITF, ChIP 3

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

institute: George Washington University

data_processing:
Basecalls were performed using bcl2fastq v.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score>30, using Trimmomactic v0.33, discarding reads left with <20bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches was retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150bp to represent sequenced fragments.
Peaks were called using MACS v2.1.0 with the significane cut-off q-value <=0.01
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: Human breast

growth_protocol: All cells were maintained in DMEM supplemented with 10% FBS at 37 °C with 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator
ChIP-Seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes. 10ng of DNA was used as starting material for the Input and IP samples. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Human breast

value: MCF-7 PR

value: Human breast cancer

value: PR

value: Palbociclib


title: MCF-7 PR, MITF, ChIP 1


title: MCF-7 PR, MITF, ChIP 2


title: K1


title: MCF-7 WT, MITF, ChIP 2

value: MCF-7 WT

value: WT

value: No


title: MCF-7 WT, MITF, ChIP 3


title: Skeletal Muscle, PAD3, snRNA-seq

city: Gainesville

first: Terence

middle: E.

last: Ryan

state: Florida

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v7.0.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: snRNA-seq

molecule: nuclear RNA

source_name: Gastrocnemius

extract_protocol:
Nuclei were isolated using the 10x Genomics Chromium nuclei isolation kit.
Library was performed according to the manufacter's instructions (Chromium Next GEM Single Cell 3’ HT Reagent kits v3.1, 10x Genomics).

value: Skeletal Muscle

value: Gastrocnemius


title: FTC-133

value: Thyroid


title: Skeletal Muscle, nonPAD2, snRNA-seq

description: 10x Genomics


title: Skeletal Muscle, PAD2, snRNA-seq

description: 10x Genomics


title: scRNAseq, S4_Hepatoblast2

description: 10x Genomics


title: Skeletal Muscle, PAD1, snRNA-seq

description: 10x Genomics


title: scRNAseq, S3_Hepatoblast1

description: 10x Genomics


title: RNAseq, H10_hiHEP_GJY-10.7

source_name: Mature Hepatocyte

value: Mature Hepatocyte


title: RNAseq, H2_hiHEP_0409-C16


title: RNAseq, H6_hiHEP_0409-C19


title: RNAseq, H11_hiHPC_GJY-10.7_P15

source_name: Hepatic Progenitor Cell

value: Hepatic Progenitor Cell


title: RNAseq, H3_hiHPC_0409-C16_P15


title: RNAseq, H5_hiHPC_0409-C19_P5


title: RNAseq, C15_CiPSC_GJY-10.7

source_name: CiPSC

value: CiPSC


title: RNAseq, H1_hiHPC_0409-C16_P5


title: RNAseq, H9_hiHPC_GJY-10.7_P5


title: RNAseq, C13_CiPSC_0409-C16


title: RNAseq, H7_hiHPC_0409-C19_P15


title: WDR13_C2 [ATAC-Seq]

data_processing:
We trimmed adaptor sequences using CTA (v0.1.2; https://github.com/ParkerLab/cta).
We aligned the trimmed reads to the GRCh38 genome assembly using BWA-MEM v0.7.17-r1194 with the -M option (Li & Durbin 2009).
We called peaks using MACS2 v2.2.7.1 (Zhang et al. 2008) with options “--nomodel --shift -100 --extsize 200 -B --keep-dup all”.
We merged peaks across libraries, and then generated a master peak across libraries.
We quantified read counts per master peak per library and generated the raw read count matrix.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include read counts per genomic peak region per sample

extract_protocol:
50,000  hESC-beta cells were washed them with 1000 μl of ice-cold PBS, and resuspended the pellets in 25 μl of ice cold 1X ATAC Buffer [20mM Tris-HCl (pH 7.4), 20mM NaCl and 6mM MgCl2]. We incubated the samples for 5 minutes on ice, thoroughly mixed in 25 μl of ice cold ATAC-Detergent-buffer [20mM Tris-HCl (pH 7.4), 20 mM NaCl and 6 mM MgCl2, 0.2% Igepal CA-630, 0.2% Tween 20 and 0.02% Digitonin, and continued incubating the samples on ice for another 3 minutes. After incubation, we centrifuged the samples and collected the pellets.
ATAC libraries for ATAC-seq were prepared  according to Weill Cornell Medicine Epigenetics Core facility protocol <https://epicore.med.cornell.edu/services.php?option=atacseqdescription#seq> protocols.

value: MEL1 (INSGFP/W)

value: human embryonic stem cell

value: WDR13 knockout

value: beta-cell differentiation

value: Day 24


title: WFS1_C3 [ATAC-Seq]

value: WFS1 knockout


title: WFS1_C2 [ATAC-Seq]


title: Skeletal Muscle, nonPAD1, snRNA-seq

description: 10x Genomics


title: MCF-7 WT, MITF, ChIP 1

value: Human breast

value: Human breast cancer


title: RNAseq, C14_CiPSC_0409-C19


title: WFS1_C4 [ATAC-Seq]


title: WT2_C3 [ATAC-Seq]

value: Wild type


title: WDR13_C3 [ATAC-Seq]


title: TMCC2_C2 [ATAC-Seq]

value: TMCC2 knockout


title: WT2_C1 [ATAC-Seq]


title: TMCC2_C1 [ATAC-Seq]


title: TMCC2_C3 [ATAC-Seq]


title: WFS1_C1 [ATAC-Seq]


title: WDR13_C1 [ATAC-Seq]


title: WT2_C2 [ATAC-Seq]


title: TLE4_C3 [ATAC-Seq]

value: TLE4 knockout


title: TGFB1_C2 [ATAC-Seq]

value: TGFB1 knockout


title: TLE4_C2 [ATAC-Seq]


title: TGFB1_C3 [ATAC-Seq]


title: TGFB1_C1 [ATAC-Seq]


title: TLE4_C1 [ATAC-Seq]


title: TCF7L2_C2 [ATAC-Seq]

value: TCF7L2 knockout


title: SLC30A8_C2 [ATAC-Seq]

value: SLC30A8 knockout


title: SLC30A8_C1 [ATAC-Seq]


title: SLC16A11_C1 [ATAC-Seq]

value: SLC16A11 knockout


title: SLC16A11_C3 [ATAC-Seq]


title: SLC30A8_C3 [ATAC-Seq]


title: SLC16A11_C2 [ATAC-Seq]


title: WT1_C1 [ATAC-Seq]


title: KCNJ11_C2 [ATAC-Seq]

value: KCNJ11 knockout


title: KCNJ11_C3 [ATAC-Seq]


title: WT1_C3 [ATAC-Seq]


title: KCNJ11_C1 [ATAC-Seq]


title: IGF2BP2_C3 [ATAC-Seq]

value: IGF2BP2 knockout


title: IGF2BP2_C2 [ATAC-Seq]

value: MEL1 (INSGFP/W)


title: IGF2BP2_C1 [ATAC-Seq]

value: human embryonic stem cell


title: HNF4A_C2 [ATAC-Seq]

value: HNF4A knockout


title: HNF4A_C3 [ATAC-Seq]

value: beta-cell differentiation


title: HTT_C3 [ATAC-Seq]

value: HTT knockout

value: Day 24


title: HTT_C2 [ATAC-Seq]


title: TCF7L2_C1 [ATAC-Seq]


title: HNF4A_C1 [ATAC-Seq]


title: TCF7L2_C3 [ATAC-Seq]


title: HNF1A_C3 [ATAC-Seq]

value: HNF1A knockout


title: HNF1A_C1 [ATAC-Seq]


title: GCKR_C3 [ATAC-Seq]

value: GCKR knockout


title: GCKR_C1 [ATAC-Seq]


title: GIPR_C1 [ATAC-Seq]

value: GIPR knockout


title: HNF1A_C2 [ATAC-Seq]


title: WT1_C2 [ATAC-Seq]

value: Wild type


title: GIPR_C3 [ATAC-Seq]


title: HTT_C1 [ATAC-Seq]


title: CDKAL1_C1 [ATAC-Seq]

value: CDKAL1 knockout


title: CDC123_C2 [ATAC-Seq]

value: CDC123 knockout


title: CDC123_C1 [ATAC-Seq]


title: GIPR_C2 [ATAC-Seq]


title: GCKR_C2 [ATAC-Seq]


title: COBLL1_C1 [ATAC-Seq]

value: COBLL1 knockout


title: COBLL1_C2 [ATAC-Seq]


title: COBLL1_C3 [ATAC-Seq]


title: CDKAL1_C2 [ATAC-Seq]


title: APOE_C3 [ATAC-Seq]

value: APOE knockout


title: ABCC8_C1 [ATAC-Seq]

value: ABCC8 knockout


title: ABCC8_C3 [ATAC-Seq]


title: WFS1_C3

data_processing:
We aligned the raw reads to the GRCh38 genome assembly using STAR v2.73a (Dobin et al. 2013) with default parameters.
We quantified expression levels of Gencode v19 genes (Ensembl release 103) using QoRTs v1.3.6, (Hartley & Mullikin 2015).
Finally, we generated a raw read count matrix of gene by library.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file include read counts per gene per sample

extract_protocol:
RNA of  purified hESC-beta cells was harvested using the Absolutely RNA Nanoprep kit (Agilent Technologies, Santa Clara, CA). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample Prep Kit  (Illumina, San Diego, CA) following manufacturer's protocols.

value: WFS1 knockout


title: CDC123_C3 [ATAC-Seq]


title: APOE_C1 [ATAC-Seq]


title: ABCC8_C2 [ATAC-Seq]


title: WFS1_C1


title: CDKAL1_C3 [ATAC-Seq]


title: WFS1_C4


title: WFS1_C2


title: APOE_C2 [ATAC-Seq]


title: WDR13_C2

value: WDR13 knockout


title: WDR13_C1

value: MEL1 (INSGFP/W)


title: WDR13_C3

value: human embryonic stem cell


title: WT2_C3


title: WT2_C2


title: TMCC2_C4

value: TMCC2 knockout


title: TMCC2_C1

value: beta-cell differentiation


title: WT2_C1


title: TLE4_C3

value: TLE4 knockout


title: TLE4_C1

value: Day 24


title: TGFB1_C3

value: TGFB1 knockout


title: TGFB1_C1


title: TGFB1_C2


title: TCF7L2_C1

value: TCF7L2 knockout


title: SLC30A8_C3

value: SLC30A8 knockout


title: SLC30A8_C2


title: SLC30A8_C1


title: SLC16A11_C3

value: SLC16A11 knockout


title: SLC16A11_C1


title: SLC16A11_C2


title: WT1_C1

value: Wild type


title: WT1_C2


title: KCNJ11_C3

value: KCNJ11 knockout


title: KCNJ11_C2


title: TMCC2_C2


title: HTT_C3

value: HTT knockout


title: WT1_C3


title: IGF2BP2_C1

value: IGF2BP2 knockout


title: TLE4_C2


title: TCF7L2_C2


title: IGF2BP2_C3


title: HTT_C2


title: HNF4A_C3

value: HNF4A knockout


title: IGF2BP2_C2


title: HTT_C1


title: KCNJ11_C1


title: TCF7L2_C3


title: HNF4A_C1


title: GIPR_C4

value: GIPR knockout


title: GIPR_C2


title: GIPR_C3


title: HNF1A_S32

value: HNF1A knockout


title: HNF1A_C4

value: MEL1 (INSGFP/W)


title: GCKR_C1

value: human embryonic stem cell

value: GCKR knockout


title: GCKR_C2

value: beta-cell differentiation


title: COBLL1_C2

value: COBLL1 knockout


title: CDKAL1_C3

value: CDKAL1 knockout

value: Day 24


title: COBLL1_C1


title: HNF4A_C2


title: COBLL1_C3


title: CDKAL1_C2


title: CDKAL1_C1


title: CDC123_C3

value: CDC123 knockout


title: APOE_C3

value: APOE knockout


title: CDC123_C1


title: HNF1A_C3


title: APOE_C1


title: ABCC8_C2

value: ABCC8 knockout


title: APOE_C2


title: ABCC8_C1


title: BE2C-shAhR_2-3

city: Buffalo

first: Mark

middle: D

last: Long

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
ATAC-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33
ATAC-seq reads were aligned to the UCSC hg19 genome using bwa version 0.7.17. Only uniquely mapping reads were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
CPM normalized bigWig files were generated using the deepTools v3.1.3. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: Cells were grown in RPMI media supplemented with 10% FBS and 1% antibiotics

extract_protocol:
50K cells in triplicates were collected in cold PBS and spun down. Pellet were gently resuspended in 50ul cold lysis buffer and nuceli were spun at 2,100rpm, 10min at 4C. Supernatant was discarded and pellets were placed on ice for the trasposition reaction
ATAC-seq libraries were prepared by incubating nuceli pellets with TD 2x buffer and TDE1 transposase by Illumina for 30min at 37C, followed bysample purification with Qiagen MinElute PCR purification kit. Transposed DNA fragemnts were amplified with 10 PCR cycles using a PCR primer (Ad1_noMX ,IDT) and a barcoded PCR primer (Ad_index primer, IDT) with a NEBNextHighFidelity 2x PCR Master Mix (NEB)

treatment_protocol: Cells were transduced with lentiviral supernatant for empty vector (pLKO) or 2 distinct shRNA against AHR

value: Neuroblastoma


title: BE2C-shAhR_2-1


title: Kelly-shAhR_2-3

source_name: Kelly

value: Kelly


title: Kelly-shAhR_2-1


title: GCKR_C3


title: Kelly-shAhR_2-2


title: BE2C-PLKO-1-3

value: pLKO


title: BE2C-shAhR_2-2


title: CDC123_C2


title: BE2C-shAhR_1-1


title: BE2C-PLKO-1-1


title: BE2C-PLKO-1-2


title: BE2C-shAhR_1-2


title: Kelly-shAhR_1-3


title: Kelly-shAhR_1-1


title: Kelly-shAhR_1-2


title: Kelly-PLKO-1-2


title: Kelly-shAhR2-3

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.7.9a).
The number of fragments in each known gene from GENCODE (version 33) was quantified using STAR QuantMode (GeneCounts) function.
Assembly: GRCh38.p7
Supplementary files format and content: The first column represents gene symbol. The other columns are raw counts for all the samples.

extract_protocol:
Total and small RNA was isolated and purified using the miRNeasy mini kit (Qiagen, Cat # 217084) according to the manufacturer’s directions.
The sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) (Roche Sequencing Solutions) using 500 ng of total RNA.

value: neuroblastoma cell line

value: AhR knockdown


title: ABCC8_C3


title: Kelly-shAhR2-1


title: Kelly-shAhR1-2


title: Kelly-PLKO-1-3


title: Kelly-shAhR2-2


title: Kelly-pLKO-GFP-3

value: control


title: Kelly-shAhR1-3


title: BE2C-shAhR_1-3


title: Kelly-shAhR1-1


title: Kelly-pLKO-GFP-2


title: BE2C-pLKO-GFP-2


title: BE2C-pLKO-GFP-3


title: BE2C-shAhR2-3


title: BE2C-shAhR2-1


title: Kelly-pLKO-GFP-1


title: BE2C-shAhR1-2


title: BE2C-shAhR1-1


title: BE2C-shAhR1-3


title: BE2C-shAhR2-2


title: ConH48hA

city: Chicago

first: Trevor

middle: R

last: Leonardo

state: Illinois

address: 801 South Paulina Street

department: Medicine

institute: University of Illinois at Chicago

data_processing:
Quality control was performed using fastp to remove adapter contaminated or poly-N sequences and reads of low quality.
Cleaned, high quality reads were mapped to the Homo Sapiens reference genome (GRCh38/hg38) using Spliced Transcripts Alignment to a Reference (STAR) software.
Reads were annotated using FeatureCounts, and Fragments Per Kilobase of exon model per Million mapped reads (FPKM) was calculated.
Assembly: GRCh38/hg38
Supplementary files format and content: ENSG names with gene symbols, counts data

source_name: Gingiva

growth_protocol: DMEM-SILAC Flex medium with insulin, L-Glutamine, epinephrine, apo-transferrin, TGF-α, pituitary extract, hydrocortisone hemisuccinate, L-lysine , and D-Glucose (6mM or 48mM) at 37C with 5% CO2

extract_protocol:
Cells were dissociated from 6-well plates using TrypLE, washed twice with cold 1x PBS, and centrifuged at 175g for 5 minutes at 4C. Total RNA was extracted, and genomic DNA was removed using the RNeasy Plus Mini kit (Qiagen, Catalog # 74034).
NEBNext Ultra Library Prep Kit for Illumina following manufacturer’s recommendations. Briefly, RNA concentrations and RNA integrity were assessed by Novogene America using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies). One microgram of RNA per sample was used as input for sequencing library generation using the NEBNext Ultra Library Prep Kit for Illumina (NEB, USA). The quality of the prepared libraries was assessed using the Agilent Bioanalyzer 2100 DNA Assay Kit (Agilent Technologies) before being run on an Illumina sequencing platform (Illumina). For each sample, approximately 6GB of raw data of 150bp paired-end reads were generated.

treatment_protocol: TIGK were treated with 500uM L-Arginine under 48mM high glucose condition for 24 and 48 hours.

value: Gingiva

value: TIGK

value: Gigival keratinoctyes

value: hTERT transfected

value: 48mM glucose without L-Arginine

value: 48 hours


title: ConH48hB


title: ConH48hC


title: ConH24hC

value: 24 hours


title: ArgH24hA

value: 48mM glucose and 500uM L-Arginine


title: ArgH48hA


title: ArgH48hB


title: ConH24hB


title: ArgH24hC


title: Kelly-PLKO-1-1


title: INPUT-SJMLL066702_C2-SEM

data_processing:
Single-end reads of 100bp were mapped human genome hg19(GRCh37-lite) by BWA (version 0.7.12-r1039, default parameter), duplicated reads were then marked with Picard(version 2.6.0-SNAPSHOT) and only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1024” version 1.2).
We followed ENCODE guideline for quality control and confirmed high quality (>50 million uniquely mapped reads each sample).
We extend reads to fragment size detected by SPP(v1.1) and generate bigwig files normalized to 15 million reads.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Patient-Derived Xenograft

extract_protocol:
A frozen cell pellet containing 10 million cells was sent to Active Motif for ChIP and library preparation. The sample was divided into an aliquot for ChIP using an antibody to H3K27Ac (Active Motif AM, cat# 39133) and an input control.
Libraries were constructed according to standard protocols for ChIP

value: SEM

tag: antibody

value: INPUT(none)


title: ConH24hA


title: H3K27Ac-AB1-SJMLL066704_C2-OCI-AML2


title: H3K27Ac-AB1-SJMLL066703_C2-MOLM13


title: INPUT-SJMLL066704_C2-OCI-AML2


title: INPUT-SJMLL015091_X2-MLL-AF4


title: INPUT-SJMLL066703_C2-MOLM13


title: ArgH48hC


title: H3K27Ac-AB1-SJMLL066702_C2-SEM


title: BE2C-pLKO-GFP-1


title: H3K27Ac-AB1-SJMLL015091_X2-MLL-AF4


title: SEM_sgNT

data_processing:
Paired-end reads of 150bp were first trimmed for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 6 -O 25 ”).
Then trimmed seqeunces were processed by HiC-Pro using human genome hg19 with restriction fragments annotation based on MboI(^GATC).
We then generate bigwig files using make_viewpoints.py script from HiC-Pro. We used “chr13:28674037-28674157(P5)” or "chr13:28674930-28675050(P6)" or both as viewpoint for Foxp3 promoter. bigwig tracks height was normalized to 100k contact within 5 million bp, that is we double the track height if we observed a sample have 50k contact within 5 million bp from viewpoint
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: Capture-C

growth_protocol: SEM (ACC-546, DSMZ) cells were maintained in RPMI-1640 medium (Lonza) containing 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (Thermo Fisher Scientific).

extract_protocol:
Suspension cells (SEM) cells were collected at 10 million cells per reaction while adherent cells were trypsinized before collection. Cells were fixed and lysed in 15 mL conical tubes before storage in -80°C for up to 1 month before library construction.
Cells were thawed on ice and spun down for 5 minutes at 4000rpm, 4°C. The remaining lysis buffer was removed and discarded. The pellets were re-suspended in 1 mL of 1x DpnII buffer and transferred to a 2 mL tube for homogenization with a pestle. The homogenized samples were then centrifuged for 14,000 rpm at 5 mins in 4°C. The supernatant was removed and discarded. After decrosslinking, phenol-chloroform-isoamylalcohol DNA extraction, and sodium acetate precipitation, a small portion of DNA was run on a gel to check for digest and ligation efficiency. Once the 3C library was construction was complete, 5-6ug of the 3C DNA in a total volume of 130ug per covaris tube (microTUBE AFA Fiber Crimp-Cap 6X16mm, catalog). Each 2ug of 3C library generated one Capture.NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles.The Nimblegen SeqCap EZ Hybridization and Wash Buffer Kit (Roche) was used for subsequent hybridization and wash steps. Constructed library was sequenced on Miseq for paired-end 150bp.  NEBNext Ultra II DNA library kit for Illumina (NEB 7645S) was used for end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. NEBNext Mulitplex Oligos (Dual Index Primers Set 1) was used for indexing for four cycles. Agencourt AMPure XP beads were used at 0.8x for all cleanup steps.

value: sgNT


title: ArgH24hB


title: DMSO, Con0, Optimization plate 4, Well A17 [S4881Nr4_A17]

data_processing:
Transcriptomic profiling was performed in batches of 382 samples. Each batch contained 22 negative-control (i.e. DMSO-treated) samples, and 15 blocks of compound-treated samples. Every block included 8 compound concentrations, each in triplicate.
Reads were mapped to the human genome (genome-build GRCh38.p13 – accession GCA_000001405.28) using STAR (version 2.7.9a).
Multi-mapped reads, reads with mapping to inter-genic regions (with respect to Ensembl gene annotation information version 104) and reads with ambiguous mapping location (i.e. location associated with more than one gene) were discarded, and UMI-based deduplication was performed.
Sequencing files were demultiplexed and barcodes were stripped.
Assembly: GRCh38.p13 – accession GCA_000001405.28
Supplementary files format and content: processed_data_counts.txt: RNA unique moecular identifier (UMI) counts per gene. The column EnsemblID provides the unique gene identifier. One column is included per sample with column names matching the column "description" in the table "SAMPLES".

source_name: hiPSC-CM

extract_protocol:
High-throughput transcriptomics was performed using Evotec’s (semi)-automated ScreenSeqTM platform. Cell lysis was performed in a 384-well plate format followed by well-specific labeling of samples.
Plate RNASeq of polyA RNA (ScreenSeqTM); Purified mRNAs were labeled with a unique molecular identifier (UMI). After pooled cDNA synthesis, adapters containing Illumina’s unique dual indexes were attached for final library preparation and sequenced on a NovaSeq 6000 system.

value: hiPSC-CM

value: WT

value: DMSO, Con0


title: Lidocaine, Con5, Optimization plate 4, Well A12 [S4881Nr4_A12]

value: Lidocaine, Con5


title: DMSO, Con0, Optimization plate 4, Well A18 [S4881Nr4_A18]


title: Lidocaine, Con5, Optimization plate 4, Well B12 [S4881Nr4_B12]


title: DMSO, Con0, Optimization plate 4, Well B18 [S4881Nr4_B18]


title: Lidocaine, Con1, Optimization plate 4, Well C16 [S4881Nr4_C16]

value: Lidocaine, Con1


title: Lidocaine, Con5, Optimization plate 4, Well C12 [S4881Nr4_C12]


title: Lidocaine, Con6, Optimization plate 4, Well C11 [S4881Nr4_C11]

value: Lidocaine, Con6


title: DMSO, Con0, Optimization plate 4, Well C18 [S4881Nr4_C18]


title: DMSO, Con0, Optimization plate 4, Well B17 [S4881Nr4_B17]


title: Lidocaine, Con4, Optimization plate 4, Well B13 [S4881Nr4_B13]

value: Lidocaine, Con4


title: Lidocaine, Con3, Optimization plate 4, Well B14 [S4881Nr4_B14]

value: Lidocaine, Con3


title: Lidocaine, Con1, Optimization plate 4, Well B16 [S4881Nr4_B16]


title: Lidocaine, Con6, Optimization plate 4, Well A11 [S4881Nr4_A11]