title: MSA105_A14_chenodeoxycholic acid 10_uM 6_hours 2513-2-4


title: MSA105_A19_phenelzine 10_uM 6_hours 3084-2-2

status: Public on Oct 31 2018

type: RNA

city: Tempe

first: Ben

last: Readhead

state: AZ

address: 797 E. Tyler Street

country: USA

institute: ASU-Banner Neurodegenerative Disease Research Center

description: 24 hiPSC-derived NPCs and 8 CCLs were used (total: 32 cell lines). Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: a) phase 1 had 6/79 drugs from pilot, and 73/79 phase 1 test compounds, b) phase 2 had 6 pilot drugs re-tested, 6/73 phase 1 drugs re-tested, and 67/79 phase 2 compounds. 135 unique compounds were tested.

hyb_protocol: PCR amplicon of each gene is hybridized to barcoded Luminex beads. The barcode incorporated in each amplicon is complementary to a barcode on a Luminex bead, ensuring that each gene from the original lysate mRNA is represented by an amplicon bound to a specific bead.

scan_protocol: Luminex scanners detect individual beads by color, then measure the fluorescent intensity of the SAPE molecules attached to the biotin label on each amplicon-bound bead

data_processing: Raw intensity measurements are deconvoluted to provide intensity values for each landmark gene (the 978 directly measured features). Data is then normalized using a calibration curve based on invariant gene sets, and then quantile normalized.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: mRNA is reverse transcribed and the cDNA product PCR amplified using primers that contain contiguous sequence (barcode) complementary to each L1000 gene; in addition, the upstream primer is biotinylated to enable identification of amplicon-bound beads.

extract_protocol: Cells were lysed with cell lysis buffer (110 µL per well), and stored at -80⁰C

tag: perturbagen

value: phenelzine

tag: cell id

tag: dosage

tag: batch

tag: duration

tag: perturbation type

value: test

tag: well id

tag: plate id


title: MSA105_A16_Aripiprazole 1_uM 6_hours 2513-2-4

value: Aripiprazole


title: MSA105_A12_fendiline 10_uM 6_hours 2513-2-4

value: fendiline


title: MSA105_A11_fendiline 10_uM 6_hours 3084-2-2


title: MSA105_A10_diclofenamide 10_uM 6_hours 2513-2-4

value: diclofenamide


title: MSA105_A06_Chlorpromazine 0.1_uM 6_hours 2513-2-4

value: Chlorpromazine


title: MSA105_A09_diclofenamide 10_uM 6_hours 3084-2-2


title: MSA105_A07_arachidonyltrifluoromethane 10_uM 6_hours 3084-2-2

value: arachidonyltrifluoromethane


title: MSA105_A08_arachidonyltrifluoromethane 10_uM 6_hours 2513-2-4


title: MSA104_P23_Nimodipine 1_uM 6_hours A673

source_name: cancerCells

value: Nimodipine


title: MSA104_P24_Nimodipine 1_uM 6_hours AGS

value: AGS


title: MSA105_A05_Chlorpromazine 0.1_uM 6_hours 3084-2-2


title: MSA105_A04_dihydroergocristine 1_uM 6_hours 2513-2-4

value: dihydroergocristine


title: MSA104_P20_sulconazole 8.6_uM 6_hours AGS

value: sulconazole


title: MSA104_P18_lansoprazole 10_uM 6_hours AGS

value: lansoprazole


title: MSA104_P14_DMSO NA 6_hours AGS

value: DMSO

value: vehicle


title: MSA104_P15_levothyroxine sodium 1_uM 6_hours A673

value: levothyroxine sodium


title: MSA104_P22_sotalol 10_uM 6_hours AGS

value: sotalol


title: MSA105_A03_dihydroergocristine 1_uM 6_hours 3084-2-2


title: MSA104_P21_sotalol 10_uM 6_hours A673


title: MSA104_P19_sulconazole 8.6_uM 6_hours A673


title: MSA104_P13_DMSO NA 6_hours A673


title: MSA104_P16_levothyroxine sodium 1_uM 6_hours AGS


title: MSA104_P11_BUCLADESINE SODIUM 10_uM 6_hours A673

value: BUCLADESINE SODIUM


title: MSA104_P10_niflumic acid 10_uM 6_hours AGS

value: niflumic acid


title: MSA104_P08_flecainide 8.4_uM 6_hours AGS

value: flecainide

value: test


title: MSA104_P12_BUCLADESINE SODIUM 10_uM 6_hours AGS


title: MSA104_P09_niflumic acid 10_uM 6_hours A673


title: MSA104_P07_flecainide 8.4_uM 6_hours A673


title: MSA104_P06_carbimazole 10_uM 6_hours AGS

value: carbimazole


title: MSA104_P17_lansoprazole 10_uM 6_hours A673


title: MSA104_P01_salsolidin 1_uM 6_hours A673

value: salsolidin


title: MSA104_P04_DMSO NA 6_hours AGS


title: MSA104_P05_carbimazole 10_uM 6_hours A673


title: MSA104_P02_salsolidin 1_uM 6_hours AGS


title: MSA104_O24_Nimodipine 1_uM 6_hours 676-2-3


title: MSA104_P03_DMSO NA 6_hours A673


title: MSA104_O21_sotalol 10_uM 6_hours 2607-3-1


title: MSA104_O20_sulconazole 8.6_uM 6_hours 676-2-3


title: MSA104_O22_sotalol 10_uM 6_hours 676-2-3


title: MSA104_O17_lansoprazole 10_uM 6_hours 2607-3-1


title: MSA104_O23_Nimodipine 1_uM 6_hours 2607-3-1


title: MSA104_O19_sulconazole 8.6_uM 6_hours 2607-3-1


title: MSA104_O18_lansoprazole 10_uM 6_hours 676-2-3


title: MSA104_O14_DMSO NA 6_hours 676-2-3


title: MSA104_O15_levothyroxine sodium 1_uM 6_hours 2607-3-1


title: MSA104_O13_DMSO NA 6_hours 2607-3-1


title: MSA104_O06_carbimazole 10_uM 6_hours 676-2-3


title: MSA104_O12_BUCLADESINE SODIUM 10_uM 6_hours 676-2-3


title: MSA104_O07_flecainide 8.4_uM 6_hours 2607-3-1


title: MSA104_O02_salsolidin 1_uM 6_hours 676-2-3


title: MSA104_O11_BUCLADESINE SODIUM 10_uM 6_hours 2607-3-1


title: MSA104_O08_flecainide 8.4_uM 6_hours 676-2-3


title: MSA104_O16_levothyroxine sodium 1_uM 6_hours 676-2-3


title: MSA104_O01_salsolidin 1_uM 6_hours 2607-3-1


title: MSA104_O05_carbimazole 10_uM 6_hours 2607-3-1


title: MSA104_O09_niflumic acid 10_uM 6_hours 2607-3-1


title: MSA104_O10_niflumic acid 10_uM 6_hours 676-2-3


title: MSA104_O04_DMSO NA 6_hours 676-2-3


title: MSA104_O03_DMSO NA 6_hours 2607-3-1


title: MSA104_N24_BAY K8644 1_uM 6_hours AGS

value: BAY K8644


title: MSA104_N23_BAY K8644 1_uM 6_hours A673


title: MSA104_N21_phenyl biguanide 10_uM 6_hours A673

value: phenyl biguanide


title: MSA104_N22_phenyl biguanide 10_uM 6_hours AGS


title: MSA104_N14_pizotifen 1_uM 6_hours AGS

value: pizotifen


title: MSA104_N19_cephaeline 6_uM 6_hours A673

value: cephaeline


title: MSA104_N20_cephaeline 6_uM 6_hours AGS

value: AGS


title: MSA104_N13_pizotifen 1_uM 6_hours A673


title: MSA104_N17_trichostatin NA 6_hours A673

value: trichostatin

value: poscon


title: MSA104_N12_nadolol 10_uM 6_hours AGS

value: nadolol


title: MSA104_N15_trazodone 1_uM 6_hours A673

value: trazodone


title: MSA104_N16_trazodone 1_uM 6_hours AGS


title: MSA104_N10_liothyronine 3.2_uM 6_hours AGS

value: liothyronine


title: MSA104_N18_trichostatin NA 6_hours AGS


title: MSA104_N03_niclosamide 10_uM 6_hours A673

value: niclosamide


title: MSA104_M22_phenyl biguanide 10_uM 6_hours 676-2-3


title: MSA104_M24_BAY K8644 1_uM 6_hours 676-2-3


title: MSA104_N04_niclosamide 10_uM 6_hours AGS


title: MSA104_M23_BAY K8644 1_uM 6_hours 2607-3-1


title: MSA104_M20_cephaeline 6_uM 6_hours 676-2-3


title: MSA104_N07_DMSO NA 6_hours A673

value: DMSO

value: vehicle


title: MSA104_M21_phenyl biguanide 10_uM 6_hours 2607-3-1


title: MSA104_N05_Quetiapine 10_uM 6_hours A673

value: Quetiapine


title: MSA104_N09_liothyronine 3.2_uM 6_hours A673

value: test


title: MSA104_N11_nadolol 10_uM 6_hours A673


title: MSA104_M16_trazodone 1_uM 6_hours 676-2-3


title: MSA104_M19_cephaeline 6_uM 6_hours 2607-3-1


title: MSA104_M15_trazodone 1_uM 6_hours 2607-3-1


title: MSA104_N08_DMSO NA 6_hours AGS


title: MSA104_N06_Quetiapine 10_uM 6_hours AGS


title: MSA104_N01_repaglinide 8.8_uM 6_hours A673

value: repaglinide


title: MSA104_M13_pizotifen 1_uM 6_hours 2607-3-1


title: MSA104_N02_repaglinide 8.8_uM 6_hours AGS


title: MSA104_M18_trichostatin NA 6_hours 676-2-3


title: MSA104_M14_pizotifen 1_uM 6_hours 676-2-3


title: MSA104_M11_nadolol 10_uM 6_hours 2607-3-1


title: MSA104_M10_liothyronine 3.2_uM 6_hours 676-2-3


title: MSA104_M08_DMSO NA 6_hours 676-2-3


title: MSA104_M07_DMSO NA 6_hours 2607-3-1


title: MSA104_M09_liothyronine 3.2_uM 6_hours 2607-3-1


title: MSA104_M12_nadolol 10_uM 6_hours 676-2-3


title: MSA104_M05_Quetiapine 10_uM 6_hours 2607-3-1


title: MSA104_M17_trichostatin NA 6_hours 2607-3-1


title: MSA104_M04_niclosamide 10_uM 6_hours 676-2-3


title: MSA104_M02_repaglinide 8.8_uM 6_hours 676-2-3


title: MSA104_M03_niclosamide 10_uM 6_hours 2607-3-1


title: MSA104_L20_DMSO NA 6_hours AGS


title: MSA104_L16_PK11195 1_uM 6_hours AGS


title: MSA104_M06_Quetiapine 10_uM 6_hours 676-2-3


title: MSA104_L13_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours A673

value: Myeloperoxidase Inhibitor-I


title: MSA104_L22_bergenin 1_uM 6_hours AGS

value: bergenin


title: MSA104_L14_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours AGS


title: MSA104_L21_bergenin 1_uM 6_hours A673


title: MSA104_L11_arcaine 10_uM 6_hours A673

value: arcaine


title: MSA104_L19_DMSO NA 6_hours A673


title: MSA104_L23_MDL100907 0.5_uM 6_hours A673


title: MSA104_L18_celastrol 2.5_uM 6_hours AGS

value: celastrol


title: MSA104_M01_repaglinide 8.8_uM 6_hours 2607-3-1


title: MSA104_L15_PK11195 1_uM 6_hours A673


title: MSA104_L12_arcaine 10_uM 6_hours AGS


title: MSA104_L07_isoniazid 10_uM 6_hours A673

value: isoniazid


title: MSA104_L06_ronidazole 1_uM 6_hours AGS

value: ronidazole

value: AGS


title: MSA104_L24_MDL100907 0.5_uM 6_hours AGS


title: MSA104_L09_Amoxapine 0.1_uM 6_hours A673

value: Amoxapine


title: MSA104_L17_celastrol 2.5_uM 6_hours A673


title: MSA104_K24_MDL100907 0.5_uM 6_hours 676-2-3


title: MSA104_L02_budesonide 9.2_uM 6_hours AGS

value: budesonide


title: MSA104_L10_Amoxapine 0.1_uM 6_hours AGS


title: MSA104_L08_isoniazid 10_uM 6_hours AGS


title: MSA104_L03_tanespimycin NA 6_hours A673

value: tanespimycin

value: poscon


title: MSA104_L01_budesonide 9.2_uM 6_hours A673


title: MSA104_L05_ronidazole 1_uM 6_hours A673


title: MSA104_L04_tanespimycin NA 6_hours AGS


title: MSA104_K22_bergenin 1_uM 6_hours 676-2-3


title: MSA104_K23_MDL100907 0.5_uM 6_hours 2607-3-1


title: MSA104_K16_PK11195 1_uM 6_hours 676-2-3


title: MSA104_K14_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 676-2-3


title: MSA104_K15_PK11195 1_uM 6_hours 2607-3-1


title: MSA104_K07_isoniazid 10_uM 6_hours 2607-3-1


title: MSA104_K03_tanespimycin NA 6_hours 2607-3-1


title: MSA104_K09_Amoxapine 0.1_uM 6_hours 2607-3-1


title: MSA104_K02_budesonide 9.2_uM 6_hours 676-2-3


title: MSA104_K11_arcaine 10_uM 6_hours 2607-3-1


title: MSA104_K12_arcaine 10_uM 6_hours 676-2-3


title: MSA104_K06_ronidazole 1_uM 6_hours 676-2-3


title: MSA104_K19_DMSO NA 6_hours 2607-3-1


title: MSA104_K21_bergenin 1_uM 6_hours 2607-3-1


title: MSA104_K13_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 2607-3-1


title: MSA104_K04_tanespimycin NA 6_hours 676-2-3


title: MSA104_K17_celastrol 2.5_uM 6_hours 2607-3-1


title: MSA104_J24_TCB-2 0.1_uM 6_hours AGS


title: MSA104_J21_lycorine 10_uM 6_hours A673

value: lycorine


title: MSA104_J20_diltiazem 3_uM 6_hours AGS

value: diltiazem


title: MSA104_K08_isoniazid 10_uM 6_hours 676-2-3


title: MSA104_K20_DMSO NA 6_hours 676-2-3

value: DMSO

value: vehicle


title: MSA104_J23_TCB-2 0.1_uM 6_hours A673

value: test


title: MSA104_J22_lycorine 10_uM 6_hours AGS


title: MSA104_K01_budesonide 9.2_uM 6_hours 2607-3-1


title: MSA104_K18_celastrol 2.5_uM 6_hours 676-2-3


title: MSA104_K10_Amoxapine 0.1_uM 6_hours 676-2-3


title: MSA104_K05_ronidazole 1_uM 6_hours 2607-3-1


title: MSA104_J15_DMSO NA 6_hours A673


title: MSA104_J13_suloctidil 10_uM 6_hours A673

value: suloctidil


title: MSA104_J12_vigabatrin 10_uM 6_hours AGS

value: vigabatrin


title: MSA104_J14_suloctidil 10_uM 6_hours AGS


title: MSA104_J19_diltiazem 3_uM 6_hours A673


title: MSA104_J16_DMSO NA 6_hours AGS


title: MSA104_J17_Ziprasidone 0.1_uM 6_hours A673

value: Ziprasidone


title: MSA104_J18_Ziprasidone 0.1_uM 6_hours AGS


title: MSA104_J11_vigabatrin 10_uM 6_hours A673


title: MSA104_J01_DMSO NA 6_hours A673


title: MSA104_J02_DMSO NA 6_hours AGS


title: MSA104_J08_chlorcyclizine 1_uM 6_hours AGS

value: chlorcyclizine


title: MSA104_I22_lycorine 10_uM 6_hours 676-2-3


title: MSA104_J10_spiradoline 0.1_uM 6_hours AGS

value: spiradoline


title: MSA104_J07_chlorcyclizine 1_uM 6_hours A673


title: MSA104_J05_trimethobenzamide 1_uM 6_hours A673

value: trimethobenzamide


title: MSA104_J06_trimethobenzamide 1_uM 6_hours AGS


title: MSA104_J03_mebendazole 10_uM 6_hours A673

value: mebendazole


title: MSA104_I24_TCB-2 0.1_uM 6_hours 676-2-3


title: MSA104_I18_Ziprasidone 0.1_uM 6_hours 676-2-3


title: MSA104_I17_Ziprasidone 0.1_uM 6_hours 2607-3-1


title: MSA104_I19_diltiazem 3_uM 6_hours 2607-3-1


title: MSA104_I20_diltiazem 3_uM 6_hours 676-2-3


title: MSA104_I23_TCB-2 0.1_uM 6_hours 2607-3-1


title: MSA104_J04_mebendazole 10_uM 6_hours AGS

value: AGS


title: MSA104_I16_DMSO NA 6_hours 676-2-3


title: MSA104_I21_lycorine 10_uM 6_hours 2607-3-1


title: MSA104_I14_suloctidil 10_uM 6_hours 676-2-3


title: MSA104_J09_spiradoline 0.1_uM 6_hours A673


title: MSA104_I12_vigabatrin 10_uM 6_hours 676-2-3


title: MSA104_I15_DMSO NA 6_hours 2607-3-1


title: MSA104_I11_vigabatrin 10_uM 6_hours 2607-3-1


title: MSA104_I08_chlorcyclizine 1_uM 6_hours 676-2-3


title: MSA104_I10_spiradoline 0.1_uM 6_hours 676-2-3


title: MSA104_I07_chlorcyclizine 1_uM 6_hours 2607-3-1


title: MSA104_I09_spiradoline 0.1_uM 6_hours 2607-3-1


title: MSA104_I06_trimethobenzamide 1_uM 6_hours 676-2-3


title: MSA104_I13_suloctidil 10_uM 6_hours 2607-3-1


title: MSA104_I05_trimethobenzamide 1_uM 6_hours 2607-3-1


title: MSA104_H24_DMSO NA 6_hours AGS


title: MSA104_I03_mebendazole 10_uM 6_hours 2607-3-1


title: MSA104_I01_DMSO NA 6_hours 2607-3-1


title: MSA104_I04_mebendazole 10_uM 6_hours 676-2-3


title: MSA104_I02_DMSO NA 6_hours 676-2-3


title: MSA104_H20_DL-thiorphan 1_uM 6_hours AGS

value: DL-thiorphan


title: MSA104_H21_3-acetamidocoumarin 10_uM 6_hours A673


title: MSA104_H18_Prestwick-675 10_uM 6_hours AGS


title: MSA104_H19_DL-thiorphan 1_uM 6_hours A673


title: MSA104_H23_DMSO NA 6_hours A673


title: MSA104_H17_Prestwick-675 10_uM 6_hours A673


title: MSA104_H09_trichostatin NA 6_hours A673

value: trichostatin


title: MSA104_H15_prenylamine 9.6_uM 6_hours A673

value: prenylamine


title: MSA104_H14_Primidone 10_uM 6_hours AGS

value: Primidone


title: MSA104_H10_trichostatin NA 6_hours AGS

value: poscon


title: MSA104_H01_diflorasone 8_uM 6_hours A673

value: diflorasone


title: MSA104_H06_melatonin 1_uM 6_hours AGS

value: melatonin


title: MSA104_G24_DMSO NA 6_hours 676-2-3

value: DMSO

value: vehicle


title: MSA104_H22_3-acetamidocoumarin 10_uM 6_hours AGS

value: test


title: MSA104_H07_emetine 7.2_uM 6_hours A673

value: emetine


title: MSA104_H13_Primidone 10_uM 6_hours A673


title: MSA104_H16_prenylamine 9.6_uM 6_hours AGS


title: MSA104_H05_melatonin 1_uM 6_hours A673


title: MSA104_H03_Loxapine 1_uM 6_hours A673

value: Loxapine


title: MSA104_H11_4-hydroxyphenazone 10_uM 6_hours A673


title: MSA104_H12_4-hydroxyphenazone 10_uM 6_hours AGS


title: MSA104_H04_Loxapine 1_uM 6_hours AGS


title: MSA104_G20_DL-thiorphan 1_uM 6_hours 676-2-3


title: MSA104_G19_DL-thiorphan 1_uM 6_hours 2607-3-1


title: MSA104_G21_3-acetamidocoumarin 10_uM 6_hours 2607-3-1


title: MSA104_G22_3-acetamidocoumarin 10_uM 6_hours 676-2-3


title: MSA104_H02_diflorasone 8_uM 6_hours AGS


title: MSA104_G23_DMSO NA 6_hours 2607-3-1


title: MSA104_G16_prenylamine 9.6_uM 6_hours 676-2-3


title: MSA104_G14_Primidone 10_uM 6_hours 676-2-3


title: MSA104_G13_Primidone 10_uM 6_hours 2607-3-1


title: MSA104_G18_Prestwick-675 10_uM 6_hours 676-2-3


title: MSA104_G11_4-hydroxyphenazone 10_uM 6_hours 2607-3-1


title: MSA104_G17_Prestwick-675 10_uM 6_hours 2607-3-1


title: MSA104_G12_4-hydroxyphenazone 10_uM 6_hours 676-2-3


title: MSA104_G08_emetine 7.2_uM 6_hours 676-2-3


title: MSA104_G10_trichostatin NA 6_hours 676-2-3


title: MSA104_G09_trichostatin NA 6_hours 2607-3-1


title: MSA104_G02_diflorasone 8_uM 6_hours 676-2-3


title: MSA104_G07_emetine 7.2_uM 6_hours 2607-3-1


title: MSA104_G05_melatonin 1_uM 6_hours 2607-3-1


title: MSA104_G15_prenylamine 9.6_uM 6_hours 2607-3-1


title: MSA104_G03_Loxapine 1_uM 6_hours 2607-3-1


title: MSA104_G06_melatonin 1_uM 6_hours 676-2-3


title: MSA104_G04_Loxapine 1_uM 6_hours 676-2-3


title: MSA104_F09_nordihydroguaiaretic acid 1_uM 6_hours A673

value: nordihydroguaiaretic acid


title: MSA104_F18_DMSO NA 6_hours AGS


title: MSA104_F22_methylbenzethonium chloride 8.6_uM 6_hours AGS

value: methylbenzethonium chloride


title: MSA104_F13_diphemanil metilsulfate 10_uM 6_hours A673

value: diphemanil metilsulfate


title: MSA104_F11_DMSO NA 6_hours A673


title: MSA104_G01_diflorasone 8_uM 6_hours 2607-3-1


title: MSA104_F24_LY379268 0.1_uM 6_hours AGS


title: MSA104_F16_tyloxapol 4_uM 6_hours AGS

value: tyloxapol


title: MSA104_F23_LY379268 0.1_uM 6_hours A673


title: MSA104_F21_methylbenzethonium chloride 8.6_uM 6_hours A673


title: MSA104_F19_anisomycin 10_uM 6_hours A673

value: anisomycin


title: MSA104_F14_diphemanil metilsulfate 10_uM 6_hours AGS

value: AGS


title: MSA104_F20_anisomycin 10_uM 6_hours AGS


title: MSA104_F15_tyloxapol 4_uM 6_hours A673


title: MSA104_F17_DMSO NA 6_hours A673


title: MSA104_F12_DMSO NA 6_hours AGS


title: MSA104_F07_bumetanide 10_uM 6_hours A673

value: bumetanide


title: MSA104_F10_nordihydroguaiaretic acid 1_uM 6_hours AGS


title: MSA104_F02_phenazone 1_uM 6_hours AGS

value: phenazone


title: MSA104_F03_nefopam 1.38_uM 6_hours A673

value: nefopam


title: MSA104_E24_LY379268 0.1_uM 6_hours 676-2-3


title: MSA104_E20_anisomycin 10_uM 6_hours 676-2-3


title: MSA104_F08_bumetanide 10_uM 6_hours AGS


title: MSA104_E10_nordihydroguaiaretic acid 1_uM 6_hours 676-2-3


title: MSA104_E16_tyloxapol 4_uM 6_hours 676-2-3


title: MSA104_E14_diphemanil metilsulfate 10_uM 6_hours 676-2-3


title: MSA104_F01_phenazone 1_uM 6_hours A673


title: MSA104_E23_LY379268 0.1_uM 6_hours 2607-3-1


title: MSA104_E17_DMSO NA 6_hours 2607-3-1


title: MSA104_E09_nordihydroguaiaretic acid 1_uM 6_hours 2607-3-1


title: MSA104_E08_bumetanide 10_uM 6_hours 676-2-3


title: MSA104_E12_DMSO NA 6_hours 676-2-3


title: MSA104_E15_tyloxapol 4_uM 6_hours 2607-3-1


title: MSA104_E07_bumetanide 10_uM 6_hours 2607-3-1


title: MSA104_E06_furosemide 10_uM 6_hours 676-2-3

value: furosemide


title: MSA104_F04_nefopam 1.38_uM 6_hours AGS


title: MSA104_E13_diphemanil metilsulfate 10_uM 6_hours 2607-3-1


title: MSA104_E21_methylbenzethonium chloride 8.6_uM 6_hours 2607-3-1


title: MSA104_F06_furosemide 10_uM 6_hours AGS


title: MSA104_E02_phenazone 1_uM 6_hours 676-2-3


title: MSA104_E18_DMSO NA 6_hours 676-2-3


title: MSA104_E03_nefopam 1.38_uM 6_hours 2607-3-1


title: MSA104_E22_methylbenzethonium chloride 8.6_uM 6_hours 676-2-3


title: MSA104_E11_DMSO NA 6_hours 2607-3-1


title: MSA104_E05_furosemide 10_uM 6_hours 2607-3-1


title: MSA104_F05_furosemide 10_uM 6_hours A673


title: MSA104_E04_nefopam 1.38_uM 6_hours 676-2-3


title: MSA104_D24_quinpirole 0.1_uM 6_hours AGS

value: quinpirole


title: MSA104_E01_phenazone 1_uM 6_hours 2607-3-1


title: MSA104_D21_hydroquinine 1_uM 6_hours A673

value: hydroquinine


title: MSA104_D22_hydroquinine 1_uM 6_hours AGS


title: MSA104_D20_haloperidol 0.1_uM 6_hours AGS

value: haloperidol


title: MSA104_D18_ethionamide 10_uM 6_hours AGS

value: ethionamide


title: MSA104_D23_quinpirole 0.1_uM 6_hours A673

value: test


title: MSA104_D17_ethionamide 10_uM 6_hours A673


title: MSA104_D16_zardaverine 10_uM 6_hours AGS

value: zardaverine


title: MSA104_D14_tanespimycin NA 6_hours AGS

value: tanespimycin

value: poscon


title: MSA104_D11_BAS-012416453 10_uM 6_hours A673


title: MSA104_D12_BAS-012416453 10_uM 6_hours AGS


title: MSA104_D19_haloperidol 0.1_uM 6_hours A673


title: MSA104_D15_zardaverine 10_uM 6_hours A673


title: MSA104_D13_tanespimycin NA 6_hours A673


title: MSA104_D10_DMSO NA 6_hours AGS

value: DMSO

value: vehicle


title: MSA104_D09_DMSO NA 6_hours A673


title: MSA104_C23_quinpirole 0.1_uM 6_hours 2607-3-1


title: MSA104_D05_DMSO NA 6_hours A673


title: MSA104_D04_alpha-ergocryptine 7_uM 6_hours AGS

value: alpha-ergocryptine


title: MSA104_D08_Vorinostat 1_uM 6_hours AGS

value: Vorinostat


title: MSA104_C21_hydroquinine 1_uM 6_hours 2607-3-1


title: MSA104_D02_moxonidine 1_uM 6_hours AGS

value: moxonidine

value: AGS


title: MSA104_D03_alpha-ergocryptine 7_uM 6_hours A673


title: MSA104_D06_DMSO NA 6_hours AGS


title: MSA104_C22_hydroquinine 1_uM 6_hours 676-2-3


title: MSA104_D01_moxonidine 1_uM 6_hours A673


title: MSA104_C20_haloperidol 0.1_uM 6_hours 676-2-3


title: MSA104_C24_quinpirole 0.1_uM 6_hours 676-2-3


title: MSA104_C18_ethionamide 10_uM 6_hours 676-2-3


title: MSA104_C15_zardaverine 10_uM 6_hours 2607-3-1


title: MSA104_D07_Vorinostat 1_uM 6_hours A673


title: MSA104_C19_haloperidol 0.1_uM 6_hours 2607-3-1


title: MSA104_C16_zardaverine 10_uM 6_hours 676-2-3


title: MSA104_C17_ethionamide 10_uM 6_hours 2607-3-1


title: MSA104_C14_tanespimycin NA 6_hours 676-2-3


title: MSA104_C09_DMSO NA 6_hours 2607-3-1


title: MSA104_C13_tanespimycin NA 6_hours 2607-3-1


title: MSA104_C08_Vorinostat 1_uM 6_hours 676-2-3


title: MSA104_C12_BAS-012416453 10_uM 6_hours 676-2-3


title: MSA104_C01_moxonidine 1_uM 6_hours 2607-3-1


title: MSA104_B24_trimethadione 10_uM 6_hours AGS

value: trimethadione


title: MSA104_C07_Vorinostat 1_uM 6_hours 2607-3-1


title: MSA104_B22_DMSO NA 6_hours AGS


title: MSA104_B21_DMSO NA 6_hours A673


title: MSA104_C10_DMSO NA 6_hours 676-2-3


title: MSA104_C06_DMSO NA 6_hours 676-2-3


title: MSA104_C11_BAS-012416453 10_uM 6_hours 2607-3-1


title: MSA104_C05_DMSO NA 6_hours 2607-3-1


title: MSA104_B14_chenodeoxycholic acid 10_uM 6_hours AGS

value: chenodeoxycholic acid


title: MSA104_C02_moxonidine 1_uM 6_hours 676-2-3


title: MSA104_C03_alpha-ergocryptine 7_uM 6_hours 2607-3-1


title: MSA104_B11_fendiline 10_uM 6_hours A673

value: fendiline


title: MSA104_B20_phenelzine 10_uM 6_hours AGS

value: phenelzine


title: MSA104_C04_alpha-ergocryptine 7_uM 6_hours 676-2-3


title: MSA104_B23_trimethadione 10_uM 6_hours A673


title: MSA104_B19_phenelzine 10_uM 6_hours A673


title: MSA104_B16_Aripiprazole 1_uM 6_hours AGS

value: Aripiprazole


title: MSA104_B15_Aripiprazole 1_uM 6_hours A673


title: MSA104_B17_naringenin 10_uM 6_hours A673

value: naringenin


title: MSA104_B05_Chlorpromazine 0.1_uM 6_hours A673

value: Chlorpromazine


title: MSA104_B04_dihydroergocristine 1_uM 6_hours AGS

value: dihydroergocristine

value: test


title: MSA104_A23_trimethadione 10_uM 6_hours 2607-3-1


title: MSA104_A22_DMSO NA 6_hours 676-2-3


title: MSA104_B13_chenodeoxycholic acid 10_uM 6_hours A673


title: MSA104_B12_fendiline 10_uM 6_hours AGS


title: MSA104_B07_arachidonyltrifluoromethane 10_uM 6_hours A673

value: arachidonyltrifluoromethane


title: MSA104_A20_phenelzine 10_uM 6_hours 676-2-3


title: MSA104_B03_dihydroergocristine 1_uM 6_hours A673


title: MSA104_B18_naringenin 10_uM 6_hours AGS


title: MSA104_B09_diclofenamide 10_uM 6_hours A673

value: diclofenamide


title: MSA104_A24_trimethadione 10_uM 6_hours 676-2-3


title: MSA104_A19_phenelzine 10_uM 6_hours 2607-3-1


title: MSA104_B10_diclofenamide 10_uM 6_hours AGS


title: MSA104_B08_arachidonyltrifluoromethane 10_uM 6_hours AGS


title: MSA104_A15_Aripiprazole 1_uM 6_hours 2607-3-1


title: MSA104_A21_DMSO NA 6_hours 2607-3-1

value: DMSO


title: MSA104_B06_Chlorpromazine 0.1_uM 6_hours AGS


title: MSA104_A14_chenodeoxycholic acid 10_uM 6_hours 676-2-3


title: MSA104_A18_naringenin 10_uM 6_hours 676-2-3


title: MSA104_A13_chenodeoxycholic acid 10_uM 6_hours 2607-3-1


title: MSA104_A12_fendiline 10_uM 6_hours 676-2-3


title: MSA104_A11_fendiline 10_uM 6_hours 2607-3-1


title: MSA104_A17_naringenin 10_uM 6_hours 2607-3-1


title: MSA104_A05_Chlorpromazine 0.1_uM 6_hours 2607-3-1


title: MSA104_A10_diclofenamide 10_uM 6_hours 676-2-3


title: MSA104_A06_Chlorpromazine 0.1_uM 6_hours 676-2-3


title: MSA104_A16_Aripiprazole 1_uM 6_hours 676-2-3


title: MSA104_A07_arachidonyltrifluoromethane 10_uM 6_hours 2607-3-1


title: MSA104_A09_diclofenamide 10_uM 6_hours 2607-3-1


title: MSA103_P24_Nimodipine 1_uM 6_hours 690-2-1

value: Nimodipine


title: MSA104_A03_dihydroergocristine 1_uM 6_hours 2607-3-1


title: MSA104_A04_dihydroergocristine 1_uM 6_hours 676-2-3


title: MSA103_P19_sulconazole 8.6_uM 6_hours 2476-D1-2

value: sulconazole


title: MSA103_P21_sotalol 10_uM 6_hours 2476-D1-2

value: sotalol


title: MSA103_P16_levothyroxine sodium 1_uM 6_hours 690-2-1

value: levothyroxine sodium


title: MSA103_P18_lansoprazole 10_uM 6_hours 690-2-1

value: lansoprazole


title: MSA103_P20_sulconazole 8.6_uM 6_hours 690-2-1


title: MSA103_P23_Nimodipine 1_uM 6_hours 2476-D1-2


title: MSA103_P17_lansoprazole 10_uM 6_hours 2476-D1-2


title: MSA103_P22_sotalol 10_uM 6_hours 690-2-1


title: MSA103_P13_DMSO NA 6_hours 2476-D1-2

value: vehicle


title: MSA103_P14_DMSO NA 6_hours 690-2-1


title: MSA103_P15_levothyroxine sodium 1_uM 6_hours 2476-D1-2


title: MSA104_A08_arachidonyltrifluoromethane 10_uM 6_hours 676-2-3


title: MSA103_P12_BUCLADESINE SODIUM 10_uM 6_hours 690-2-1

value: BUCLADESINE SODIUM


title: MSA103_P11_BUCLADESINE SODIUM 10_uM 6_hours 2476-D1-2


title: MSA103_P10_niflumic acid 10_uM 6_hours 690-2-1

value: niflumic acid


title: MSA103_P07_flecainide 8.4_uM 6_hours 2476-D1-2

value: flecainide


title: MSA103_P09_niflumic acid 10_uM 6_hours 2476-D1-2


title: MSA103_P04_DMSO NA 6_hours 690-2-1


title: MSA103_P08_flecainide 8.4_uM 6_hours 690-2-1


title: MSA103_P05_carbimazole 10_uM 6_hours 2476-D1-2

value: carbimazole


title: MSA103_P03_DMSO NA 6_hours 2476-D1-2


title: MSA103_P01_salsolidin 1_uM 6_hours 2476-D1-2

value: salsolidin


title: WT_t2_rep3

type: SRA

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

country: Germany

institute: University of Oldenburg

description: time point 2 hours

library_source: transcriptomic

data_processing:
Adapter removal with TRIMMOMATIC (version 36, parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
Ribosomal and tRNA sequence filtering with Bowtie2  (version 2.2.9, parameters --fr --un-gz),  using unaligned forward and reverse reads later.
Aligning to A. thaliana genome and Luciferase spike-in sequence to collect expression data: TopHat2 (version 2.1.1, parameters: -p 10 -i 10 -I 1000 --library-type fr-secondstrand).
Collecting unnormalized read counts from alignment with featureCounts (Subead package, version 1.5.2, parameters: -T 6  -F SAF -J -O ), with default parameters, using gene coordinates and adding  Luciferase spike-in sequence.
Differential expression analysis: DESeq2 DESeq2 version 1.16.1 (ref10) with substituting size factors of estimated size factors from the luciferase gene read counts with default parameters. Control was always wild-type.
Model fitting using lmfit package (version 0.9.7) with normalized shrunken log2 fold changes of the expression values from DESeq2 object. Upper limit vas 125%, lower limit was 0 value occurences in average values.
Genome_build: Arabidopsis thaliana: Ensembl Plants release 36 (ftp://ftp.ensemblgenomes.org/pub/release-36/plants/) genome fasta and GTF files, for rRNA/tRNA filering:  Arabidopsis thaliana sequences from tRNA collections (http://gtrnadb2009.ucsc.edu/download/tRNAs/GtRNAdb-all-tRNAs.fa.gz),  Arabidopsis thaliana genes for 5.8S rRNA and 25S rRNA with 18S rRNA fragment (geneBank ID: X52320.1);  sequences from arabidopsis.org: AT2G01010.1 – 18SrRNA, AT2G01020 – 5.8sRNA, ATCG00920 – 16SrRNA, ATCG00950 – 23SrRNA, ATCG00960 – 4.5SrRNA, ATCG01160.1 – 5SrRNA, ATMG00020.1 – 26SrRNA; f Luciferase spike-in sequence (accession number: LT727454.1)
Supplementary_files_format_and_content: “counts_time_course.txt ” output file from featureCounts; “ time_course_normcounts.txt” normalized shrunken log2 fold changes of the expression values from DESeq2 object.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: A. thaliana, whole seedlings, 5 day old

growth_protocol: sterilized seeds (Ethanol) were grown in ½ strength MS on a rocking shaker in constant light for 5 days

extract_protocol:
seedlings were harvested and flash frozen, RNA for library preparation has been extracted using the RNeasy Plant RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s protocol
poly(A)-RNA was isolated using the NEBnext poly(A) mRNA Magnetic Isolation Module (NEB #7490), this was followed by purification of 5-EU labeled RNA with the Click-iT™ Nascent RNA Capture Kit (Thermo Scientific).  A known concentration of a EU containing  RNA was used as spike-in for normalization. Libraries were prepared using ScriptSeq™ v2 RNA-Seq Library Preparation Kit (epicentre). For library preparation mRNA was used as input starting at the fragmentation step in the protocol (step number 5).

treatment_protocol: seedlings were transfered into media containing 0.5 mM 5-ethynyl uridine for 24 hours

tag: ecotype

value: Col 0


title: MSA103_P02_salsolidin 1_uM 6_hours 690-2-1


title: WT_t24_rep3

description:
time point  24 hours
counts_time_course.txt, time_course_normcounts.txt
Time_T66

tag: time point

value: 24 hours


title: MSA103_P06_carbimazole 10_uM 6_hours 690-2-1

value: test


title: WT_t0_rep3

description: time point 0


title: MSA103_O24_Nimodipine 1_uM 6_hours 1835-1-5


title: WT_t12_rep2

description: time point 12 hours


title: MSA103_O21_sotalol 10_uM 6_hours 3651-A-A


title: MSA103_O23_Nimodipine 1_uM 6_hours 3651-A-A


title: MSA103_O20_sulconazole 8.6_uM 6_hours 1835-1-5


title: WT_t12_rep3

description: time point 12 hours


title: WT_t6_rep2

description: time point 6 hours


title: MSA103_O22_sotalol 10_uM 6_hours 1835-1-5


title: MSA103_O19_sulconazole 8.6_uM 6_hours 3651-A-A


title: MSA103_O18_lansoprazole 10_uM 6_hours 1835-1-5


title: MSA103_O15_levothyroxine sodium 1_uM 6_hours 3651-A-A


title: WT_t1_rep3

description: time point 1 hour


title: WT_t2_rep2

description: time point 2 hours


title: WT_t1_rep2

description: time point 1 hour


title: MSA103_O14_DMSO NA 6_hours 1835-1-5


title: WT_t0_rep2

description: time point 0


title: MSA103_O17_lansoprazole 10_uM 6_hours 3651-A-A


title: WT_t12_rep1

description: time point 12 hours


title: WT_t24_rep2

description:
time point  24 hours
counts_time_course.txt, time_course_normcounts.txt
Time_T36


title: MSA103_O13_DMSO NA 6_hours 3651-A-A


title: WT_t6_rep1

description: time point 6 hours


title: WT_t24_rep1

description:
time point  24 hours
counts_time_course.txt, time_course_normcounts.txt
Time_S16


title: WT_t2_rep1

description: time point 2 hours


title: WT_t1_rep1

description: time point 1 hour


title: MSA103_O12_BUCLADESINE SODIUM 10_uM 6_hours 1835-1-5


title: MSA103_O16_levothyroxine sodium 1_uM 6_hours 1835-1-5


title: MSA103_O09_niflumic acid 10_uM 6_hours 3651-A-A


title: WT_all_rep3 [NEU]

description: PulseTotal_3_sorted.bam.featureCounts, counts_all_transcript.txt, counts_transcript_plus.txt, counts_transcript_minus.txt, A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt, A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt, MXE.MATS.ReadsOnTargetAndJunctionCounts.txt, RI.MATS.ReadsOnTargetAndJunctionCounts.txt, SE.MATS.ReadsOnTargetAndJunctionCounts.txt

data_processing:
Adapter removal with TRIMMOMATIC (version 36, parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10  LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
Ribosomal and tRNA sequence filtering with Bowtie2  (version 2.2.9, parameters --fr --un-gz),  using unaligned forward and reverse reads later.
Aligning to A. thaliana genome to collect expression data: TopHat2 (version 2.1.1, parameters: -p 10 -i 10 -I 1000 --library-type fr-secondstrand  -G Arabidopsis_thaliana.TAIR10.36.gtf).
Collecting unnormalized read counts from alignment with featureCounts (Subead package, version 1.5.2, parameters: -T 6  -F SAF -J -O -R  or in case of strand analysis: -T 6 -R --primary -F GTF -J -O -s 1 or -s 2 -t transcript.
Collecting alignment data from featureCounts output using Arabidopsis_thaliana.TAIR10.36_feature.saf for spanning read ratio analysis.
Fisher's exact test for  analysis of spanning read ratio categories (R, version 3.4.1, parameters: Click versus WT all, two.sided/less/greater )
rMATS  for analyzing alternative splicing events (version 3.2.5, only ribosomal and tRNA filtered libraries with the following parameters: -gtf Arabidopsis_thaliana.TAIR10.36.gtf -t single -len 150)
Genome_build: Arabidopsis thaliana: Ensembl Plants release 36 (ftp://ftp.ensemblgenomes.org/pub/release-36/plants/) genome fasta and GTF files, for rRNA/tRNA filering:  Arabidopsis thaliana sequences from tRNA collections (http://gtrnadb2009.ucsc.edu/download/tRNAs/GtRNAdb-all-tRNAs.fa.gz),  Arabidopsis thaliana genes for 5.8S rRNA and 25S rRNA with 18S rRNA fragment (geneBank ID: X52320.1);  sequences from arabidopsis.org: AT2G01010.1 – 18SrRNA, AT2G01020 – 5.8sRNA, ATCG00920 – 16SrRNA, ATCG00950 – 23SrRNA, ATCG00960 – 4.5SrRNA, ATCG01160.1 – 5SrRNA, ATMG00020.1 – 26SrRNA; filtered reference files from the Ensembl release: Arabidopsis_thaliana.TAIR10.36_transcript.saf, Arabidopsis_thaliana.TAIR10.36_feature.saf (only 1st isoforms)
Supplementary_files_format_and_content: “counts_*.txt” output files from featureCounts; *.featureCounts output of detailed read assignment results for spanning read ratio analysis using Arabidopsis_thaliana.TAIR10.36_feature.saf; *.MATS.ReadsOnTargetAndJunctionCounts.txt for alternative splicing analysis; *.saf: filtered reference files
Supplementary_files_format_and_content: PulseClick_1_sorted.bam.featureCounts: detailed read assignment result file
Supplementary_files_format_and_content: PulseClick_2_sorted.bam.featureCounts: detailed read assignment result file
Supplementary_files_format_and_content: PulseClick_3_sorted.bam.featureCounts: detailed read assignment result file
Supplementary_files_format_and_content: PulseTotal_1_sorted.bam.featureCounts: detailed read assignment result file
Supplementary_files_format_and_content: PulseTotal_2_sorted.bam.featureCounts: detailed read assignment result file
Supplementary_files_format_and_content: PulseTotal_3_sorted.bam.featureCounts: detailed read assignment result file
Supplementary_files_format_and_content: Arabidopsis_thaliana.TAIR10.36_transcript.saf: filtered reference file of transcripts (1st isoform)
Supplementary_files_format_and_content: Arabidopsis_thaliana.TAIR10.36_feature.saf: filtered reference file of exonic-intronic features (1st isoform)
Supplementary_files_format_and_content: counts_all_transcript.txt: read count table
Supplementary_files_format_and_content: counts_transcript_plus.txt: read count table
Supplementary_files_format_and_content: counts_transcript_minus.txt: read count table
Supplementary_files_format_and_content: A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt: rMATS unfiltered output table
Supplementary_files_format_and_content: A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt: rMATS unfiltered output table
Supplementary_files_format_and_content: MXE.MATS.ReadsOnTargetAndJunctionCounts.txt: rMATS unfiltered output table
Supplementary_files_format_and_content: RI.MATS.ReadsOnTargetAndJunctionCounts.txt: rMATS unfiltered output table
Supplementary_files_format_and_content: SE.MATS.ReadsOnTargetAndJunctionCounts.txt: rMATS unfiltered output table

extract_protocol:
seedlings were harvested and flash frozen, RNA for library preparation has been extracted using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s protocol.
Ribosomal RNA was removed with the Ribo-Zero rRNA Removal Kit (Plant) of Epicentre (Illumina). A subsample was taken to sequence the steady state level of gene transcription. 5-EU labeled RNA was purified from the remaining ribo-zero treated RNA with the Click-iT™ Nascent RNA Capture Kit (Thermo Scientific). For library preparation mRNA was used as input starting at the fragmentation step in the protocol (step number 5).

treatment_protocol: seedlings were transfered into media containing 0.5 mM 5-ethynyl uridine for 1 hour


title: WT_all_rep2 [NEU]

description: PulseTotal_2_sorted.bam.featureCounts, counts_all_transcript.txt, counts_transcript_plus.txt, counts_transcript_minus.txt, A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt, A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt, MXE.MATS.ReadsOnTargetAndJunctionCounts.txt, RI.MATS.ReadsOnTargetAndJunctionCounts.txt, SE.MATS.ReadsOnTargetAndJunctionCounts.txt


title: MSA103_O06_carbimazole 10_uM 6_hours 1835-1-5


title: MSA103_O07_flecainide 8.4_uM 6_hours 3651-A-A


title: MSA103_O10_niflumic acid 10_uM 6_hours 1835-1-5


title: WT_all_rep1 [NEU]

description: PulseTotal_1_sorted.bam.featureCounts, counts_all_transcript.txt, counts_transcript_plus.txt, counts_transcript_minus.txt, A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt, A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt, MXE.MATS.ReadsOnTargetAndJunctionCounts.txt, RI.MATS.ReadsOnTargetAndJunctionCounts.txt, SE.MATS.ReadsOnTargetAndJunctionCounts.txt


title: WT_t0_rep1

description: time point 0


title: MSA103_O08_flecainide 8.4_uM 6_hours 1835-1-5


title: MSA103_O05_carbimazole 10_uM 6_hours 3651-A-A


title: MSA103_O11_BUCLADESINE SODIUM 10_uM 6_hours 3651-A-A


title: WT_Click_rep2 [NEU]

description:
labeled RNA was seperated from Ribo-Zero treated RNA with Click-iT™ Nascent RNA Capture Kit (Thermo Scientific)
PulseClick_2_sorted.bam.featureCounts, counts_all_transcript.txt, counts_transcript_plus.txt, counts_transcript_minus.txt, A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt, A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt, MXE.MATS.ReadsOnTargetAndJunctionCounts.txt, RI.MATS.ReadsOnTargetAndJunctionCounts.txt, SE.MATS.ReadsOnTargetAndJunctionCounts.txt


title: MSA103_O04_DMSO NA 6_hours 1835-1-5


title: WT_t6_rep3

description: time point 6 hours


title: WT_Click_rep3 [NEU]

description:
labeled RNA was seperated from Ribo-Zero treated RNA with Click-iT™ Nascent RNA Capture Kit (Thermo Scientific)
PulseClick_3_sorted.bam.featureCounts, counts_all_transcript.txt, counts_transcript_plus.txt, counts_transcript_minus.txt, A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt, A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt, MXE.MATS.ReadsOnTargetAndJunctionCounts.txt, RI.MATS.ReadsOnTargetAndJunctionCounts.txt, SE.MATS.ReadsOnTargetAndJunctionCounts.txt


title: MSA103_O03_DMSO NA 6_hours 3651-A-A


title: WT_Click_rep1 [NEU]

description:
labeled RNA was seperated from Ribo-Zero treated RNA with Click-iT™ Nascent RNA Capture Kit (Thermo Scientific)
PulseClick_1_sorted.bam.featureCounts, counts_all_transcript.txt, counts_transcript_plus.txt, counts_transcript_minus.txt, A3SS.MATS.ReadsOnTargetAndJunctionCounts.txt, A5SS.MATS.ReadsOnTargetAndJunctionCounts.txt, MXE.MATS.ReadsOnTargetAndJunctionCounts.txt, RI.MATS.ReadsOnTargetAndJunctionCounts.txt, SE.MATS.ReadsOnTargetAndJunctionCounts.txt


title: MSA103_N21_phenyl biguanide 10_uM 6_hours 2476-D1-2

value: phenyl biguanide


title: MSA103_N24_BAY K8644 1_uM 6_hours 690-2-1

value: BAY K8644


title: MSA103_N23_BAY K8644 1_uM 6_hours 2476-D1-2


title: MSA103_N19_cephaeline 6_uM 6_hours 2476-D1-2

value: cephaeline


title: MSA103_N20_cephaeline 6_uM 6_hours 690-2-1


title: MSA103_O01_salsolidin 1_uM 6_hours 3651-A-A


title: MSA103_N16_trazodone 1_uM 6_hours 690-2-1

value: trazodone


title: MSA103_N15_trazodone 1_uM 6_hours 2476-D1-2


title: MSA103_N18_trichostatin NA 6_hours 690-2-1

value: trichostatin

value: poscon


title: MSA103_O02_salsolidin 1_uM 6_hours 1835-1-5


title: Array 10_vivo_8-cell rep2

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

description: Array 10

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Aligent scanning protocol.

data_processing: Microarray data analysis was performed using the Flex Array software version 1.6. Data were subjected to a simple background correction, a Loess within-array normalization, and a quantile between-array normalization

organism: Bos taurus

source_name: Blastocyst cultured in vivo until 8-cell stage

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol:
Endscopic flushing of in vivo produced embryos from the reproduction tract and transfer to in vitro culture until blastocyst
cultured in groups of 50 in four well dishes each containing 400µL CR1aa medium

extract_protocol: This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 µg of RNA. RNA extraction from larger samples should be done using another kit or technique.

tag: breed (cattle)

value: Simmental

tag: blast staging method

value: Morphological

tag: reproductive status (cattle)

value: Heifer

tag: time of embryo collection

value: 7 dpi (days post-in-vivo insemination)

tag: culture condition

tag: cell type

value: Blastocyst

source_name: InVivo

value: blastocyst


title: MSA103_N17_trichostatin NA 6_hours 2476-D1-2


title: Array 11_vivo_8-cell rep3

description: Array 11

source_name: in vivo control blastocyst


title: MSA103_N22_phenyl biguanide 10_uM 6_hours 690-2-1


title: Array 9_vivo_8-cell rep2

description: Array 9


title: MSA103_N14_pizotifen 1_uM 6_hours 690-2-1

value: pizotifen


title: Array 12_vivo_8-cell rep3

description: Array 12


title: Array 7_vivo_8-cell rep1

description: Array 7


title: Array 8_vivo_8-cell rep1

description: Array 8


title: Dxz4_core_4C

city: Cambridge

first: John

middle: Edward

last: Froberg

state: MA

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

library_source: genomic

data_processing:
Library strategy: 4C-seq
RNA-seq: RNA-seq reads were aligned to the cas (Xa) and mus (Xi) genomes allele-specifically using a previously published pipeline (Kung et al., Molecular Cell 2015)(GSE58242). Following alignment, gene expression levels for each gene were defined using HOMER. Differential expression and fold changes between conditions were calculated using DESeq2. We plotted the cumulative distributions of fold changes for autosomal and X-linked genes and evaluated the significance of any differences between the distributions of the fold changes using the Kolmogorov-Smirnov (KS) test. To examine allele-specific expression from the Xa and the Xi, we summed together allelic reads across both biological replicates and filtered for genes with at least 12 allelic reads in both wild-type and Dxz4∆/∆:FirreXi∆/+and fpm > 0 in all replicates. We also used RNA-seq done in pure hybrid mus or cas fibroblasts to identify and eliminate genes that have incorrect SNP information. We defined escapee genes in a particular condition as genes where at least 10% of allelic reads came from the Xi in either replicate of that condition. We plotted the distribution of expression levels from the Xi (Xi/(Xi+Xa) read counts) for all genes passing our filtered for each replicate. We evaluated the significance in differences of the mean expression level from the Xi using the Wilcoxon Signed Rank Test with Bonferroni correction for multiple hypothesis testing.
ATAC-seq: Attack seq alignment to mm9 was performed exactly as ChIP-seq alignment was performed in (Minajigi et al., Science 2015) (GSE67516). Peaks were called using macs2 with default parameters. Biallelic peaks were identified as peaks with at least 10 alleleic reads in a sample and an Xi:Xa ratio greater than 1/3. Xi-specific peaks were defined as peaks with at least 10 allelic reads and a Xi:Xa ratio less than 1/3. To test whether Xi-specific peaks in wild-type are “restored” (that is: acquire appreciable accessibility on the Xi) in either the Dxz4 or Firre deletion, we plot the wild-type Xa reads on the x-axis and the deletion Xi reads on the y-axis and identify peaks where the deletion Xi/wild-type Xa ratio is greater than ½ (these are peaks where the deletion accessibility level reaches at least half the wild-type accessibility ratio). We also examine the biallelic peaks and plot the wild-type Xi reads on the x-axis and the deletion Xi reads on the y-axis to determine whether the accessibility on the Xi changes for the peaks that are bi-allelic in wild-type.
Hi-C: Hi-C alignment to mm9 was performed according to the method of (Minajigi et al., Science 2015)(GSE67516) The allele-specific Hi-C reads were filtered for quality and uniqueness with HOMER. Custom scripts were used to convert HOMER tag directories into the format accecpted by Juicebox; contact maps were generated using the Juicer tools ‘pre’ command. All Hi-C contact maps visualized in this study are KR-normalized contact maps generated by Juicebox.
Hi-C^2: Reads of each pair were individually mapped to the mus and cas reference genomes using novoalign and merged into Hi-C summary files and filtered using HOMER as previously described (Minajigi et al., Science 2015). For the chrX:70,370,161-71,832,975 captures, 3-4% of mapped and paired reads fell within the target region (0.05% expected based on size of capture region versus genome) and for the chrX:71,832,976-73,511,687 captures, 1-2% of mapped and paired reads fell within the target region (0.06% expected based on size of capture region versus genome). To avoid computational complexities arising from normalization of sparse, non-enriched regions in the Hi-C contact map, only Hi-C interactions falling within the capture region were analyzed further. For each capture, a custom script was used to pull out the filtered Hi-C interactions falling within the target region from the HOMER tag directories. Hi-C contact maps of the capture regions were then generated from these HOMER tags using the ‘pre’ command of Juicer tools. The resulting Hi-C contact maps in .hic format were visualized and normalized with the ‘Coverage (Sqrt)’ option in Juicebox.
4C: 4C analysis was performed using the previously published pipeline in (Chu et al., NSMB 2017) (GSE69887).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files display fragment counts per million reads passing filter for 4C experiments. bigWig files display fpm-normalized ATAC-seq coverage. .hic files can be used to display and generate Hi-C contact maps using the Juicebox toolkit. For bedGraph and bigWig files, "comp" tracks are generated using all unique reads, "mus" tracks are generated using mus-specific reads, "cas" tracks are generated using cas-specific reads and "reps" tracks are generated using non-unique reads (reads with multiple alignments are randomly assigned to one position). genetable*.xlsx files are generated from homer and contain fragment count information for each gene in each experiment.

molecule: genomic DNA

organism: Mus musculus

source_name: fibroblast

extract_protocol: We previously developed a modified 4C protocol (Chu et al., NSMB 2017)  to examine chromatin conformation from repetitive viewpoints. Our protocol has several advantages over existing 4C profiles: 1.) It sequences the genomic region amplified by the 4C primers, ensuring that on-target priming events can be identified and filtered from numerous off-target priming events 2.) Sequencing the viewpoint allows every read to be assigned to a particular allele if the viewpoint is near a variant, 3.) We use a random barcode to identify PCR duplicates, which previously has not been possible in 4C experiments. We performed our modified 4C using the protocol and analysis pipeline previously described for viewpoints within PAR-TERRA repeats (Chu et al., 2017). We used it for several viewpoints within Firre and Dxz4. Some viewpoints were in the core tandem repeats. For these viewpoints, we use the read outside the viewpoint for allelic determination. Others were in unique regions near the tandem repeats; for these we could use known variants to assign every read to the Xa or the Xi. We performed our analysis in two fibroblast lines, one where the mus X is inactive (mus Xi cas Xa), the other where the cas X is inactive (mus Xa cas Xi).

tag: strain

value: CAST/Ei x 129/Sv/Jae

value: c12 (T4, mus-Xi)

tag: genotype

value: T4 (mus-Xi)


title: Array 2_vivo_2-cell rep1

description: Array 2

source_name: Blastocyst cultured in vivo until 2-cell stage


title: Array 4_vivo_2-cell rep2

description: Array 4


title: MSA103_N11_nadolol 10_uM 6_hours 2476-D1-2

tag: perturbagen

value: nadolol

tag: cell id

value: test


title: Array 1_vivo_2-cell rep1

description: Array 1


title: Firre3p_4C_c13

value: c13 (TTF, cas-Xi)


title: Firre3p_4C_c12


title: MSA103_N13_pizotifen 1_uM 6_hours 2476-D1-2

tag: dosage

tag: batch


title: Array 5_vivo_2-cell rep3

description: Array 5


title: Firre_core_4C


title: MSA103_N07_DMSO NA 6_hours 2476-D1-2

value: DMSO

tag: duration

tag: perturbation type

value: vehicle


title: Array 6_vivo_2-cell rep3

description: Array 6


title: Array 3_vivo_2-cell rep2

description: Array 3


title: MSA103_N09_liothyronine 3.2_uM 6_hours 2476-D1-2

value: liothyronine

tag: well id

tag: plate id


title: MSA103_N06_Quetiapine 10_uM 6_hours 690-2-1

value: Quetiapine


title: MSA103_N04_niclosamide 10_uM 6_hours 690-2-1

value: niclosamide


title: MSA103_N08_DMSO NA 6_hours 690-2-1


title: MSA103_N05_Quetiapine 10_uM 6_hours 2476-D1-2


title: MSA103_N01_repaglinide 8.8_uM 6_hours 2476-D1-2

value: repaglinide


title: MSA103_N02_repaglinide 8.8_uM 6_hours 690-2-1


title: MSA103_N03_niclosamide 10_uM 6_hours 2476-D1-2


title: Patient 7 - lesional CDLE plucked hair follicles from scalp

city: Leeds

first: Adewonuola

last: Alase

state: West Yorkshire

address: Beckett St

department: LIRMM

country: United Kingdom

institute: University of Leeds

description: Differential gene expression data obtained from microarray analysis using total RNA extracted from human plucked hair follicles

hyb_protocol: Following fragmentation, 5.5 ug of cDNA was hybridized for 16 hr at 45° C on GeneChip Human 2.0 Arrays. GeneChips were washed and stained using the Affymetrix Fluidics Station 450 using the GeneChip™ Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific).

scan_protocol: Washed and stained GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G

data_processing: Affymetrix CHP data were analysed with Transcriptome Analysis Console 3.1 software using HuGene-2_0-st-v1 library file from Affymetrix. A cut-off level of 1.5 fold change in the expression was used to analyse the differential gene expression when comparing lesional, non-lesional and healthy conditions.

source_name: CDLE patient

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 70ng of  total RNA (Ambion WT Expression Kit and  WT Terminal Labeling and Hybridization Kit, Thermo Fisher Scientific).

extract_protocol: Total RNA was extracted from the cryosectioned plucked hair follicles using ReliaPrep™ RNA Cell Miniprep System, Promega, according to the manufacturer’s protocol

tag: tissue

value: Plucked hair follicle from the scalp

tag: gender

value: Female

tag: disease state

value: lesional CDLE


title: Patient 6 - non lesional CDLE plucked hair follicles from scalp

value: non lesional CDLE


title: Patient 5 - non lesional CDLE plucked hair follicles from scalp


title: MSA103_M24_BAY K8644 1_uM 6_hours 1835-1-5

value: BAY K8644


title: Patient 7 - non lesional CDLE plucked hair follicles from scalp


title: Patient 6 - lesional CDLE plucked hair follicles from scalp


title: MSA103_M23_BAY K8644 1_uM 6_hours 3651-A-A


title: MSA103_M21_phenyl biguanide 10_uM 6_hours 3651-A-A

value: phenyl biguanide


title: MSA103_M22_phenyl biguanide 10_uM 6_hours 1835-1-5


title: Patient 4 - lesional CDLE plucked hair follicles from scalp


title: MSA103_M20_cephaeline 6_uM 6_hours 1835-1-5

value: cephaeline


title: MSA103_M19_cephaeline 6_uM 6_hours 3651-A-A


title: Patient 3 - lesional CDLE plucked hair follicles from scalp


title: MSA103_M17_trichostatin NA 6_hours 3651-A-A

value: trichostatin

value: poscon


title: Patient 2 - non lesional CDLE plucked hair follicles from scalp


title: MSA103_M18_trichostatin NA 6_hours 1835-1-5


title: Patient 4 - non lesional CDLE plucked hair follicles from scalp


title: Patient 1 - non lesional CDLE plucked hair follicles from scalp


title: Patient 5 - lesional CDLE plucked hair follicles from scalp


title: Patient 3 - non lesional CDLE plucked hair follicles from scalp


title: MSA103_M14_pizotifen 1_uM 6_hours 1835-1-5

value: pizotifen

value: test


title: MSA103_M16_trazodone 1_uM 6_hours 1835-1-5

value: trazodone


title: Healthy 2 - male human plucked hair follicles from scalp

source_name: Healthy individual

value: Male

value: healthy


title: MSA103_M13_pizotifen 1_uM 6_hours 3651-A-A


title: Patient 1 - lesional CDLE plucked hair follicles from scalp


title: Healthy 3 - female human plucked hair follicles from scalp


title: Patient 2 - lesional CDLE plucked hair follicles from scalp


title: MSA103_M11_nadolol 10_uM 6_hours 3651-A-A

value: nadolol


title: MSA103_M10_liothyronine 3.2_uM 6_hours 1835-1-5

value: liothyronine


title: MSA103_M12_nadolol 10_uM 6_hours 1835-1-5


title: MSA103_M07_DMSO NA 6_hours 3651-A-A

value: DMSO

value: vehicle


title: Healthy 1 - male human plucked hair follicles from scalp

value: Plucked hair follicle from the scalp


title: Healthy 4 - female human plucked hair follicles from scalp

value: Female


title: MSA103_N12_nadolol 10_uM 6_hours 690-2-1


title: MSA103_M09_liothyronine 3.2_uM 6_hours 3651-A-A


title: MSA103_M08_DMSO NA 6_hours 1835-1-5


title: MSA103_M15_trazodone 1_uM 6_hours 3651-A-A


title: MSA103_M03_niclosamide 10_uM 6_hours 3651-A-A

value: niclosamide


title: MSA103_M04_niclosamide 10_uM 6_hours 1835-1-5


title: MSA103_M02_repaglinide 8.8_uM 6_hours 1835-1-5

value: repaglinide


title: Lactotrope biological replicate 2

city: Philadelphia

first: Michael

middle: Thomas

last: Peel

state: PA

address: 415 Curie Blvd.

department: Genetics

institute: University of Pennsylvania

description: Lactotrope 2

data_processing:
basecalling performed using bcl2fastq version ??? (FGC1127) or bcl2fastq2-v2.17.1.14 (others)
Reads aligned to genome and expression quantified using RUM and moue genome mm9
Differentially expressed genes determined using EdgeR
Expression normalized to FPKM
Differential splicing called using TopHat
Genome_build: mm9
Supplementary_files_format_and_content: FPKM for genes and samples with gene name, RefSeq transcript id, and chromosomal location

source_name: FACS sorted mouse lactotropes

growth_protocol: Female mice were aged to 6-8 weeks before their pituitaries were collected for the experiment

extract_protocol:
Cells were sorted by FACS into Trizol LS and RNA was isolated following the manufacterer's standard instructions.
RNA was amplified using NuGen Ovation V2 kit, then prepared for sequencing using standard Illumina protocols

value: Pituitary

value: CD1 x C57BL/6 hybrid

tag: Sex

value: lactotrope


title: MSA103_M06_Quetiapine 10_uM 6_hours 1835-1-5

value: Quetiapine


title: MSA103_M05_Quetiapine 10_uM 6_hours 3651-A-A


title: Lactotrope biological replicate 1

description: Lactotrope 1


title: MDA-MB-231 sNRP1

city: Kyoto

first: Marina

last: Kiso

address: Sakyoku

country: Japan

institute: Kyoto university

description: gene expression after 48hr culture

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver2.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: soluble NRP1 over expressed MDA-MB-231 breast cancer cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Breast cancer cells were treated with RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum. The cultures were incubated for 48 hours at 37℃ in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the miRNeasy Mini kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agileng Technologies, Santa Clara, CA)

treatment_protocol: Recombinant VEGF treatment was done for 48hours before RNA extraction.

tag: cell line

value: MDA-MB-231 breast cancer cell

tag: treatment


title: MSA103_M01_repaglinide 8.8_uM 6_hours 3651-A-A

value: test


title: Somatotrope biological replicate 3

description: Somatotrope 3

source_name: FACS sorted mouse somatotropes

tag: cell type

value: somatotrope


title: MSA103_L20_DMSO NA 6_hours 690-2-1


title: MSA103_L22_bergenin 1_uM 6_hours 690-2-1

value: bergenin


title: Lactotrope biological replicate 3

description: Lactotrope 3

tag: strain


title: Somatotrope biological replicate 2

description: Somatotrope 2


title: MSA103_L23_MDL100907 0.5_uM 6_hours 2476-D1-2


title: MDA-MB-231 VEGFKO

description: gene expression after 48hr culture

source_name: VEGF-knocked out MDA-MB-231 breast cancer cell

value: VEGFKO


title: MSA103_L21_bergenin 1_uM 6_hours 2476-D1-2


title: JO_06_Control3

city: New York

first: Jordi

last: Ochando

state: New York

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: 2.5ug of fragmented biotin labeled SPIA ST cDNA was 16 hr at 45C on Mouse Gene 2.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing: The data were analyzed with Affymetrix Expression Console using Affymetrix default analysis settings and RMA as normalization method.

label_protocol: 15ng total RNA was converted to fragmented biotin labeled SPIA sense transcript (ST) cDNA using the standard NuGEN pico WTA protocol.

growth_protocol: Graft-infiltrating macrophages were isolated on day 6 post-transplantation by fluorescence-activated cell sorting (FACS).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Transplant recipients were either left untreated (Control) and rejected their allografts or were treated with mTORi-HDL nanobiologics (Sample) as 5mg/kg on days 0, 2, and 5 post-transplantation.

tag: agent

value: untreated


title: MDA-MB-231

description: gene expression after 48hr culture

source_name: MDA-MB-231 breast cancer cell

value: control


title: MSA103_L24_MDL100907 0.5_uM 6_hours 690-2-1

tag: perturbagen


title: MSA103_L18_celastrol 2.5_uM 6_hours 690-2-1

value: celastrol

tag: cell id


title: MSA103_L19_DMSO NA 6_hours 2476-D1-2

value: DMSO

value: vehicle


title: MDA-MB-231 VEGFKO+rhVEGF

description: gene expression after 48hr culture

source_name: rhVEGF treated VEGF -knocked out MDA-MB-231 breast cancer cell

value: VEGFKO+rhVEGF


title: Somatotrope biological replicate 1

description: Somatotrope 1

value: Female


title: JO_02_Sample2

value: mTORi-HDL nanobiologics


title: JO_03_Sample3


title: MSA103_L16_PK11195 1_uM 6_hours 690-2-1

tag: dosage


title: KO

city: Beijing

first: Qianqian

last: Cheng

address: 27 Taiping Road

department: Department of Molecular Immunology

country: China

institute: Institute of Basic Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b).STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample …

source_name: activated CD44hiCD4+ T cells

extract_protocol:
Splenic CD44hiCD4+ T cells were FACS-sorted, and RNA was harvested using Trizol reagent. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA)and quantified using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)and the library preparations were  sequenced on an Illumina platform.

value: spleen

tag: genotype

value: Uba3fl/fl-Lck Cre+


title: JO_05_Control2


title: WT

value: wild type


title: MSA103_L15_PK11195 1_uM 6_hours 2476-D1-2

tag: batch

tag: duration


title: JO_04_Control1


title: JO_01_Sample1


title: MSA103_L17_celastrol 2.5_uM 6_hours 2476-D1-2

tag: perturbation type

tag: well id


title: MSA103_L14_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 690-2-1

value: Myeloperoxidase Inhibitor-I

tag: plate id


title: MSA103_N10_liothyronine 3.2_uM 6_hours 690-2-1

value: liothyronine


title: MSA103_L12_arcaine 10_uM 6_hours 690-2-1

value: arcaine

value: test


title: MSA103_L13_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 2476-D1-2


title: MSA103_L10_Amoxapine 0.1_uM 6_hours 690-2-1

value: Amoxapine


title: MSA103_L11_arcaine 10_uM 6_hours 2476-D1-2


title: MSA103_L06_ronidazole 1_uM 6_hours 690-2-1

value: ronidazole


title: MSA103_L07_isoniazid 10_uM 6_hours 2476-D1-2

value: isoniazid


title: MSA103_L05_ronidazole 1_uM 6_hours 2476-D1-2


title: MSA103_L04_tanespimycin NA 6_hours 690-2-1

value: tanespimycin

value: poscon


title: MSA103_L08_isoniazid 10_uM 6_hours 690-2-1


title: Control mice rep2

city: Tucson

first: Haiquan

last: Li

address: 1657 E Helen Street

department: Medicine

institute: University of Arizona

description: gene expression data

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
Samples were RMA normalized in R (package: “oligo”) and the coefficient of variation was used to remove the least variable 30% of probes.  Transcripts failed to map to HUGO gene symbols were removed from the pathway analysis.
Differentially expressed genes between the two groups were identified using a two-sided, unpaired t-test (p≤ 0.05).
KEGG pathway enrichment was calculated by GSEA (50) with FDR<0.05.

source_name: Control mice

label_protocol: Standard Affymetrix protocol

growth_protocol: Homozygous sickle cell disease model mice (JAX stock #013071 B6;129-Hbatm1(HBA)Tow Hbbtm2(HBG1,HBB*)Tow/tm2(HBG1,HBB*)Tow/J) and non-sickling control (B6;129-Hbatm1(HBA)Tow/tm1(HBA)Tow, Hbbtm3(HBG1,HBB)Tow/tm3(HBG1,HBB)/J were obtained from The Jackson Laboratory and all experiments were performed between the 10-14 weeks of age in male mice.

extract_protocol: LV tissue was dissected from sickle (n=3) and control (n=3) mice, total RNA was isolated.

treatment_protocol: Animals were handled in accordance with the NIH Guide for the Care and Use of Laboratory Animals. All protocols involving animals were approved by the Animal Studies Committee at the University of Illinois at Chicago, University of Wisconsin, Lifespan Animal Welfare Committee in Rhode Island Hospital, and the University of Arizona. Surface electrocardiograms (ECGs) were recorded and ventricular arrhythmia inducibility was determined in WT and sickle mice using described methods (48) under general anesthesia with isofurane. WT and sickle male mice (12-16 weeks) hearts underwent optical mapping. The optical apparatus has been previously described. Sample activation potential traces and activation maps with BCL pacing were made for both the control and sickle cell hearts.

tag: gender

value: male

value: control

tag: tissue

value: Left ventricular tissue


title: Sickle mice rep3

description: gene expression data

source_name: Sickle mice

tag: disease state

value: sickle cell disease


title: MSA103_L09_Amoxapine 0.1_uM 6_hours 2476-D1-2


title: Sickle mice rep1

description: gene expression data


title: Sickle mice rep2

description: gene expression data


title: MSA103_L02_budesonide 9.2_uM 6_hours 690-2-1

value: budesonide


title: MSA103_L03_tanespimycin NA 6_hours 2476-D1-2


title: MSA103_L01_budesonide 9.2_uM 6_hours 2476-D1-2


title: MSA103_K20_DMSO NA 6_hours 1835-1-5

value: DMSO

value: vehicle


title: MSA103_K19_DMSO NA 6_hours 3651-A-A


title: MSA103_K21_bergenin 1_uM 6_hours 3651-A-A

value: bergenin


title: MSA103_K23_MDL100907 0.5_uM 6_hours 3651-A-A


title: MSA103_K18_celastrol 2.5_uM 6_hours 1835-1-5

value: celastrol


title: MSA103_K24_MDL100907 0.5_uM 6_hours 1835-1-5


title: ESCC_GE046T_Nsp

type: genomic

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

description: Hybridized to Affymetrix SNP array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip®Operating Software (GCOS version1.4). Genotype calls were generated by using GTYPE4.1. The raw date[file] were loaded using R/biocunductor and aroma. Affymetrix.For more details, go to htpp://www.aroma-project.org/. We used the CRMA function implemented in the Aroma to preprocess and applied CBS method for segmentation. We combined the segmentation results from two platforms, and imported to Nexus Copy Number 6.1 followed the manual ( www. Biodiscovery.com). We used Q-Bound cut off at 0.5 and G-Score cut off at 1.0. to identify the focal regions of amplification and deletion with FDR q-value 0.25 for copy number using GISTIC 2.0 as recommended.

label: Biotin

source_name: tumor tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: tumor DNA was isolated from frozen tummor tissue using the Allprep Kit (Qiagen) per the manufacturer's instruction. Germline DNA was isolated from the same patient's venous blood. DNA quality and quantity were determined using NanoDrop 2000 (Thermo Scientific).

value: ESCC

tag: case id

value: esophageal squamous cell carcinoma tissue


title: Control mice rep1

description: gene expression data


title: Control mice rep3

description: gene expression data


title: MSA103_K22_bergenin 1_uM 6_hours 1835-1-5

value: test


title: MSA103_K11_arcaine 10_uM 6_hours 3651-A-A

value: arcaine


title: ESCC_GE046B_Nsp

description: Hybridized to Affymetrix SNP array

source_name: whole blood

value: blood from esophageal squamous cell carcinoma patient


title: MSA103_K12_arcaine 10_uM 6_hours 1835-1-5


title: MSA103_K17_celastrol 2.5_uM 6_hours 3651-A-A


title: ESCC_GE044T_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_K13_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 3651-A-A

value: Myeloperoxidase Inhibitor-I


title: MSA103_K10_Amoxapine 0.1_uM 6_hours 1835-1-5

value: Amoxapine


title: MSA103_K08_isoniazid 10_uM 6_hours 1835-1-5

value: isoniazid


title: MSA103_K09_Amoxapine 0.1_uM 6_hours 3651-A-A


title: MSA103_K07_isoniazid 10_uM 6_hours 3651-A-A


title: ESCC_GE043B_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE044B_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_K06_ronidazole 1_uM 6_hours 1835-1-5

value: ronidazole


title: ESCC_GE042T_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE042B_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_K05_ronidazole 1_uM 6_hours 3651-A-A


title: MSA103_K04_tanespimycin NA 6_hours 1835-1-5

value: tanespimycin

value: poscon


title: ESCC_GE040B_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE040T_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE038T_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_K03_tanespimycin NA 6_hours 3651-A-A


title: MSA103_K15_PK11195 1_uM 6_hours 3651-A-A


title: MSA103_K02_budesonide 9.2_uM 6_hours 1835-1-5


title: whole_larva_permethrin_3.125ug/L_rep10 [234_1_3]

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

institute: US Environmental Protection Agency

description: Whole body gene expression after exposure of fathead larvae to 3.125 ug/L of permethrin

hyb_protocol: Individual samples were hybridized onto separate Agilent microarrays, where eight arrays were printed onto a single glass slide. Placement of each treatment within and between slides was balanced as much as possible, given the number of arrays per slide and number of replicates per condition. Samples were fragmented and mixed with a blocking agent per recommended protocols, then quickly added onto the microarrays. Microarrays were hybridized at 65° C for 17 hours with constant rotation, disassembled in Wash Buffer 1, washed in Wash Buffer 1 for one minute, then transferred to Wash Buffer 2 at 65° C for 1 minute, 100% acetonitrile for 10 s, followed by drying and stabilization solution for 30 s.

scan_protocol: Slides were covered with an ozone-barrier slide and scanned in an Agilent C scanner with the following settings: Dye channel: G; scan resolution: 3 µm; TIFF file dynamic range: 20 bit; green PMI gain: 100%. TIFF images were uploaded to the Agilent Feature Extraction program and extracted data were used in downstream analysis.

data_processing: Probe intensities (median foreground spot intensity without background subtraction) from each hybridization were quantile normalized, and probeset intensities for individual hybridizations were calculated as the median (within an array) intensity of the replicated probes constituting that probeset. Probeset intensities were then log-base2 transformed.

organism: Pimephales promelas

source_name: whole larva, permethrin, 3.125 ug/L, replicate 10

label_protocol: Samples were processed according to the Agilent One-color Microarray-Based Gene Expression Analysis protocols (Agilent Technologies, Santa Clara, CA). Isolated total RNA was diluted to 100 ng/µL for labeling. , combined with RNA Spike-in controls and converted to cDNA using Affinity Script Reverse Transcriptase.  cDNA was then converted to cRNA with the inclusion of Cyanine-3 (Cy-3) labeled-CTP.  Labeled cRNA was purified using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and cRNA was eluted twice in a total of 70 µL warm water. Yield and specific activity of purified labeled cRNA were evaluated using the NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop, Wilmington, DE) using the microarray measurement package. Samples with yields <0.825 µg or specific activity <6 pmol Cy3 per µg cRNA were excluded from further analysis. In these cases, an alternative sample was selected for analysis; however, when none were available, failed samples were re-labeled.

growth_protocol: Fathead minnow were raised indoors in labline water. Labline water was produced by passing tempered tap water through a set of activated carbon filters, for the removal of chlorine and organics, and then adding liquid calcium chloride to supplement the hardness. Fish were maintained at 20-25 degC, pH 7.0 to 8.0. dissolved oxygen between 6 and 9 mg/L, and conductivity of 510-660 uS. Fish were fed a mixture of high-protein fin-fish starter food (0.6-0.85 um crumb size) and brine shrimp nauplii. At the start of exposures, fathead larvae were about 48 hours post-hatch.

extract_protocol: Following  48-hour exposure, RNA was isolated separately from 10 pairs of whole larval fish exposed to each of (nominally) two pyrethroid concentrations (Table 1), and DMSO carrier added to water. RNA was isolated using the RiboPure kit (Ambion, Austin, TX) according to the manufacturer’s protocol. RNA was eluted in 60 µL. Following RNA isolation, DNA contamination was removed using Turbo DNA-free (Ambion) according to the manufacturer’s protocol. RNA was concentrated through ethanol precipitation, and integrity was assessed using denaturing gel electrophoresis.

treatment_protocol: 48-hour flow-through exposures were conducted in 10 L tanks, each renewed with exposure media (from continuous mixing of lab water and concentrated pyrethroid stock solution) at a rate of 40 mL/min. The system was pre-equilibrated under flow-through conditions with their respective chemicals nominally at their target concentrations for 24 hours prior to introducing test organisms. Five adult (ranging from six to ten months old) male fathead minnows (FHM; Pimephales promelas) were placed in each tank, as were an exposure vessel containing 10 larval (48 hours post hatch) FHM. The exposure vessels consisted of a three-inch section of 1.5 inch diameter PVC pipe covered on both ends with 400 µm Nitrex mesh. Four exposure experiments were conducted at least one week apart. Each experiment included eight nominal concentrations of a single pyrethroid, and a carrier solvent control (0.002% DMSO; used for the carrier control and as a carrier for pyrethroids, which have very low water solubility). Successive nominal concentrations, targeted to be half the next highest concentration, were achieved by serial dilution. Three replicate tanks were used for each concentration, and chemical concentrations of each tank were measured daily. Tank location in the diluter apparatus was balanced with respect to concentration to minimize location effects. Test organisms were randomly assigned to tanks. Between experiments, water supply lines were replaced, tanks were rinsed with 0.01% DMSO solution overnight, followed by 100% methanol and 24-hour water rinses. Tanks were subsequently scrubbed and rinsed with DMSO and tap water.

value: whole larva

tag: age

value: 48 hours post-hatch

tag: chemical

value: permethrin

value: larva


title: whole_larva_permethrin_3.125ug/L_rep11 [233_2_4]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 11


title: MSA103_J24_TCB-2 0.1_uM 6_hours 690-2-1


title: whole_larva_permethrin_3.125ug/L_rep9 [232_1_1]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 9


title: MSA103_J22_lycorine 10_uM 6_hours 690-2-1

value: lycorine


title: ESCC_GE038B_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_K01_budesonide 9.2_uM 6_hours 3651-A-A

value: budesonide


title: MSA103_J21_lycorine 10_uM 6_hours 2476-D1-2


title: MSA103_J20_diltiazem 3_uM 6_hours 690-2-1

value: diltiazem


title: MSA103_J19_diltiazem 3_uM 6_hours 2476-D1-2


title: whole_larva_permethrin_3.125ug/L_rep7 [229_2_2]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 7


title: ESCC_GE037T_Nsp

description: Hybridized to Affymetrix SNP array

value: ESCC

value: esophageal squamous cell carcinoma tissue


title: MSA103_J23_TCB-2 0.1_uM 6_hours 2476-D1-2

value: test


title: MSA103_J18_Ziprasidone 0.1_uM 6_hours 690-2-1

value: Ziprasidone


title: whole_larva_permethrin_3.125ug/L_rep5 [227_1_3]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 5


title: whole_larva_permethrin_3.125ug/L_rep6 [231_2_4]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 6


title: whole_larva_permethrin_3.125ug/L_rep8 [230_1_3]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 8


title: MSA103_K14_Myeloperoxidase Inhibitor-I 1.1_uM 6_hours 1835-1-5

value: Myeloperoxidase Inhibitor-I


title: MSA103_J17_Ziprasidone 0.1_uM 6_hours 2476-D1-2


title: MSA103_J16_DMSO NA 6_hours 690-2-1

value: DMSO

value: vehicle


title: ESCC_GE036T_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE036B_Nsp

description: Hybridized to Affymetrix SNP array

value: blood from esophageal squamous cell carcinoma patient


title: ESCC_GE037B_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_J14_suloctidil 10_uM 6_hours 690-2-1

value: suloctidil


title: ESCC_GE035T_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_J11_vigabatrin 10_uM 6_hours 2476-D1-2

value: vigabatrin


title: MSA103_J12_vigabatrin 10_uM 6_hours 690-2-1


title: MSA103_J13_suloctidil 10_uM 6_hours 2476-D1-2


title: MSA103_J15_DMSO NA 6_hours 2476-D1-2


title: whole_larva_permethrin_3.125ug/L_rep3 [223_1_4]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 3

value: whole larva


title: MSA103_K16_PK11195 1_uM 6_hours 1835-1-5


title: ESCC_GE035B_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_J10_spiradoline 0.1_uM 6_hours 690-2-1

value: spiradoline


title: MSA103_J07_chlorcyclizine 1_uM 6_hours 2476-D1-2

value: chlorcyclizine


title: MSA103_J06_trimethobenzamide 1_uM 6_hours 690-2-1

value: trimethobenzamide


title: MSA103_J09_spiradoline 0.1_uM 6_hours 2476-D1-2


title: MSA103_J08_chlorcyclizine 1_uM 6_hours 690-2-1


title: MSA103_J05_trimethobenzamide 1_uM 6_hours 2476-D1-2


title: whole_larva_permethrin_3.125ug/L_rep1 [224_2_3]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 1

value: 48 hours post-hatch

value: permethrin

value: larva


title: whole_larva_permethrin_3.125ug/L_rep4 [225_1_4]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 4


title: ESCC_GE034T_Nsp

description: Hybridized to Affymetrix SNP array

value: ESCC


title: whole_larva_permethrin_1.56ug/L_rep10 [221_1_4]

description: Whole body gene expression after exposure of fathead larvae to 1.56 ug/L of permethrin

source_name: whole larva, permethrin, 1.56 ug/L, replicate 10


title: whole_larva_permethrin_3.125ug/L_rep2 [222_2_4]

source_name: whole larva, permethrin, 3.125 ug/L, replicate 2


title: whole_larva_permethrin_1.56ug/L_rep11 [220_2_1]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 11


title: ESCC_GE033T_Nsp

description: Hybridized to Affymetrix SNP array

value: esophageal squamous cell carcinoma tissue


title: ESCC_GE034B_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE043T_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE033B_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_J04_mebendazole 10_uM 6_hours 690-2-1

value: mebendazole

value: test


title: whole_larva_permethrin_1.56ug/L_rep9 [233_1_4]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 9


title: whole_larva_permethrin_1.56ug/L_rep8 [226_2_4]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 8


title: MSA103_I24_TCB-2 0.1_uM 6_hours 1835-1-5


title: MSA103_J03_mebendazole 10_uM 6_hours 2476-D1-2


title: ESCC_GE032T_Nsp

description: Hybridized to Affymetrix SNP array

source_name: tumor tissue


title: MSA103_J02_DMSO NA 6_hours 690-2-1


title: MSA103_I20_diltiazem 3_uM 6_hours 1835-1-5

value: diltiazem


title: MSA103_I21_lycorine 10_uM 6_hours 3651-A-A

value: lycorine


title: whole_larva_permethrin_1.56ug/L_rep7 [232_2_1]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 7


title: MSA103_J01_DMSO NA 6_hours 2476-D1-2

value: DMSO

value: vehicle


title: MSA103_I23_TCB-2 0.1_uM 6_hours 3651-A-A


title: whole_larva_permethrin_1.56ug/L_rep5 [229_1_4]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 5


title: whole_larva_permethrin_1.56ug/L_rep6 [234_2_2]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 6


title: MSA103_I17_Ziprasidone 0.1_uM 6_hours 3651-A-A

value: Ziprasidone


title: MSA103_I18_Ziprasidone 0.1_uM 6_hours 1835-1-5


title: MSA103_I19_diltiazem 3_uM 6_hours 3651-A-A


title: ESCC_GE032B_Nsp

description: Hybridized to Affymetrix SNP array

source_name: whole blood

value: blood from esophageal squamous cell carcinoma patient


title: MSA103_I16_DMSO NA 6_hours 1835-1-5


title: MSA103_I14_suloctidil 10_uM 6_hours 1835-1-5

value: suloctidil


title: ESCC_GE031T_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_I15_DMSO NA 6_hours 3651-A-A


title: MSA103_I13_suloctidil 10_uM 6_hours 3651-A-A


title: whole_larva_permethrin_1.56ug/L_rep4 [230_1_1]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 4

value: whole larva


title: whole_larva_permethrin_1.56ug/L_rep2 [231_1_4]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 2


title: ESCC_GE031B_Nsp

description: Hybridized to Affymetrix SNP array


title: whole_larva_permethrin_1.56ug/L_rep3 [230_2_4]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 3


title: ESCC_GE030T_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE029T_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_I11_vigabatrin 10_uM 6_hours 3651-A-A

value: vigabatrin


title: MSA103_I10_spiradoline 0.1_uM 6_hours 1835-1-5

value: spiradoline


title: whole_larva_permethrin_1.56ug/L_rep1 [227_2_4]

source_name: whole larva, permethrin, 1.56 ug/L, replicate 1

value: 48 hours post-hatch


title: ESCC_GE030B_Nsp

description: Hybridized to Affymetrix SNP array


title: MSA103_I12_vigabatrin 10_uM 6_hours 1835-1-5


title: MSA103_I07_chlorcyclizine 1_uM 6_hours 3651-A-A

value: chlorcyclizine


title: MSA103_I08_chlorcyclizine 1_uM 6_hours 1835-1-5


title: MSA103_I05_trimethobenzamide 1_uM 6_hours 3651-A-A

value: trimethobenzamide


title: ESCC_GE029B_Nsp

description: Hybridized to Affymetrix SNP array

value: ESCC


title: whole_larva_permethrin_0ug/L_rep10 [224_2_4]

description: Whole body gene expression after exposure of fathead larvae to 0 ug/L of permethrin

source_name: whole larva, permethrin, 0 ug/L, replicate 10

value: permethrin

value: larva


title: ESCC_GE028T_Nsp

description: Hybridized to Affymetrix SNP array

value: esophageal squamous cell carcinoma tissue


title: MSA103_I02_DMSO NA 6_hours 1835-1-5


title: MSA103_I09_spiradoline 0.1_uM 6_hours 3651-A-A

value: test


title: MSA103_I03_mebendazole 10_uM 6_hours 3651-A-A

value: mebendazole


title: MSA103_I04_mebendazole 10_uM 6_hours 1835-1-5


title: whole_larva_permethrin_0ug/L_rep9 [223_1_3]

source_name: whole larva, permethrin, 0 ug/L, replicate 9


title: whole_larva_permethrin_0ug/L_rep7 [225_1_1]

source_name: whole larva, permethrin, 0 ug/L, replicate 7


title: whole_larva_permethrin_0ug/L_rep8 [226_2_2]

source_name: whole larva, permethrin, 0 ug/L, replicate 8


title: MSA103_I01_DMSO NA 6_hours 3651-A-A

value: DMSO


title: MSA103_H24_DMSO NA 6_hours 690-2-1

value: vehicle


title: MSA103_I06_trimethobenzamide 1_uM 6_hours 1835-1-5


title: MSA103_H23_DMSO NA 6_hours 2476-D1-2


title: ESCC_GE027B_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE027T_Nsp

description: Hybridized to Affymetrix SNP array


title: whole_larva_permethrin_0ug/L_rep5 [221_1_1]

source_name: whole larva, permethrin, 0 ug/L, replicate 5


title: ESCC_GE026T_Nsp

description: Hybridized to Affymetrix SNP array


title: whole_larva_permethrin_0ug/L_rep4 [220_2_4]

source_name: whole larva, permethrin, 0 ug/L, replicate 4


title: ESCC_GE025T_Nsp

description: Hybridized to Affymetrix SNP array


title: ESCC_GE028B_Nsp

description: Hybridized to Affymetrix SNP array


title: whole_larva_permethrin_0ug/L_rep6 [222_2_2]

source_name: whole larva, permethrin, 0 ug/L, replicate 6


title: MSA103_H21_3-acetamidocoumarin 10_uM 6_hours 2476-D1-2


title: MSA103_H22_3-acetamidocoumarin 10_uM 6_hours 690-2-1


title: whole_larva_permethrin_0ug/L_rep3 [234_2_4]

source_name: whole larva, permethrin, 0 ug/L, replicate 3


title: MSA103_H19_DL-thiorphan 1_uM 6_hours 2476-D1-2

value: DL-thiorphan


title: ESCC_GE026B_Nsp

description: Hybridized to Affymetrix SNP array

value: blood from esophageal squamous cell carcinoma patient


title: MSA103_H17_Prestwick-675 10_uM 6_hours 2476-D1-2


title: whole_larva_permethrin_0ug/L_rep2 [233_1_2]

source_name: whole larva, permethrin, 0 ug/L, replicate 2


title: whole_larva_permethrin_0ug/L_rep1 [223_2_4]

source_name: whole larva, permethrin, 0 ug/L, replicate 1


title: MSA103_H14_Primidone 10_uM 6_hours 690-2-1

value: Primidone


title: PDAC3-Treat-rep1

city: Sendai

first: Toru

last: Furukawa

address: 2-1 Seiryomachi, Aobaku

department: Department of Investigative Pathology

institute: Tohoku University Graduate School of Medicine

description:
human pancreatic cancer cell lines established originally from moderately differenciated liver metastasis of carcinoma of the head of the pancreas
Gene expression 48 hours after incubation with 0.045 % Agaricus blazei Murrill hot water extract

hyb_protocol: After fragmentation, 1.65 µg cRNAs were  hybridized at 65 ºC for 17 hours to an 4×44K Whole Human Genome Microarray slide

scan_protocol: Agilent Scanner Protocol

data_processing: Data were normalized to the 75 percentile.

source_name: pancreatic adenocarcinoma cell line, AbE treated, biological rep1

label_protocol: Cy3 labeled cRNA were prepared according to the Agilent protocol from 500 ng total RNA

growth_protocol: MIA PaCa-2 was cultured with Dulbecco's modified Eagles medium supplemented with 10% fetal bovine serum. PCI-35 and PK-8 were cultured with RPMI1640 medium supplemented with 10% fetal bovine serum. Cells were maintained  at 37°C in 5% CO2 with humid atmosphere.

extract_protocol: total RNA was isolated from PDAC cell lines using RNeasy midi kit (QIAGEN).

treatment_protocol: The cells were treated with 0.045 % AbE contained in appropriate culture media after 24 hours incubation. The culture media were replaced with the media with 0.045 % Agaricus blazei Murill hot water extract (AbE) after 24 hours incubation.

tag: cell line

tag: treatment


title: whole_larva_esfenvalerate_1ug/L_rep3 [232_1_3]

description: Whole body gene expression after exposure of fathead larvae to 1 ug/L of esfenvalerate

source_name: whole larva, esfenvalerate, 1 ug/L, replicate 3

value: whole larva

value: esfenvalerate


title: MSA103_H18_Prestwick-675 10_uM 6_hours 690-2-1

tag: perturbagen


title: MSA103_H13_Primidone 10_uM 6_hours 2476-D1-2

tag: cell id


title: MSA103_H20_DL-thiorphan 1_uM 6_hours 690-2-1

tag: dosage


title: ESCC_GE025B_Nsp

description: Hybridized to Affymetrix SNP array

source_name: whole blood


title: MSA103_H16_prenylamine 9.6_uM 6_hours 690-2-1

value: prenylamine


title: MSA103_H15_prenylamine 9.6_uM 6_hours 2476-D1-2


title: MSA103_H12_4-hydroxyphenazone 10_uM 6_hours 690-2-1


title: MSA103_H10_trichostatin NA 6_hours 690-2-1

value: trichostatin

value: poscon


title: PDAC3-MOCK-rep3

description:
human pancreatic cancer cell lines established originally from moderately differenciated liver metastasis of carcinoma of the head of the pancreas
Gene expression 48 hours after MOCK treatment

source_name: pancreatic adenocarcinoma cell line, control, biological rep3

value: 48 hours after MOCK treatment


title: MSA103_H09_trichostatin NA 6_hours 2476-D1-2

description: 24 hiPSC-derived NPCs and 8 CCLs were used (total: 32 cell lines). Each 96-well plate included: A1 empty well, 12 vehicle wells, and 2 positive control wells (in duplicate) per cell line (i.e., per plate). The remaining 79 wells were used for test compounds: a) phase 1 had 6/79 drugs from pilot, and 73/79 phase 1 test compounds, b) phase 2 had 6 pilot drugs re-tested, 6/73 phase 1 drugs re-tested, and 67/79 phase 2 compounds. 135 unique compounds were tested.


title: whole_larva_esfenvalerate_1ug/L_rep2 [230_1_4]

source_name: whole larva, esfenvalerate, 1 ug/L, replicate 2

value: 48 hours post-hatch


title: MSA103_H11_4-hydroxyphenazone 10_uM 6_hours 2476-D1-2


title: whole_larva_esfenvalerate_1ug/L_rep1 [231_2_2]

source_name: whole larva, esfenvalerate, 1 ug/L, replicate 1


title: MSA103_H08_emetine 7.2_uM 6_hours 690-2-1

value: emetine


title: PDAC3-MOCK-rep1

source_name: pancreatic adenocarcinoma cell line, control, biological rep1


title: PDAC3-MOCK-rep2

source_name: pancreatic adenocarcinoma cell line, control, biological rep2


title: MSA103_H05_melatonin 1_uM 6_hours 2476-D1-2

value: melatonin


title: PDAC2-Treat-rep3

description:
human pancreatic ductal adenocarcinoma cell line
Gene expression 48 hours after incubation with 0.045 % Agaricus blazei Murrill hot water extract

source_name: pancreatic adenocarcinoma cell line, AbE treated, biological rep3


title: MSA103_H03_Loxapine 1_uM 6_hours 2476-D1-2

value: Loxapine


title: PDAC3-Treat-rep2

source_name: pancreatic adenocarcinoma cell line, AbE treated, biological rep2

value: 48 hours after incubation with 0.045 % Agaricus blazei Murrill hot water extract


title: MSA103_H06_melatonin 1_uM 6_hours 690-2-1

value: test


title: MSA103_H04_Loxapine 1_uM 6_hours 690-2-1


title: MSA103_H01_diflorasone 8_uM 6_hours 2476-D1-2

value: diflorasone


title: PDAC2-Treat-rep2


title: whole_larva_esfenvalerate_0.5ug/L_rep9 [226_2_3]

description: Whole body gene expression after exposure of fathead larvae to 0.5 ug/L of esfenvalerate

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 9

value: larva


title: MSA103_G23_DMSO NA 6_hours 3651-A-A

value: DMSO

value: vehicle


title: whole_larva_esfenvalerate_0.5ug/L_rep7 [224_2_2]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 7


title: whole_larva_esfenvalerate_0.5ug/L_rep8 [225_1_3]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 8


title: PDAC2-Treat-rep1


title: whole_larva_esfenvalerate_0.5ug/L_rep5 [223_1_2]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 5


title: MSA103_G24_DMSO NA 6_hours 1835-1-5


title: MSA103_G20_DL-thiorphan 1_uM 6_hours 1835-1-5

value: DL-thiorphan


title: PDAC2-MOCK-rep3

description:
human pancreatic ductal adenocarcinoma cell line
Gene expression 48 hours after MOCK treatment


title: ESCC_GE024T_Nsp

description: Hybridized to Affymetrix SNP array

source_name: tumor tissue

value: ESCC

value: esophageal squamous cell carcinoma tissue


title: whole_larva_esfenvalerate_0.5ug/L_rep6 [227_1_2]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 6

value: whole larva

value: esfenvalerate


title: MSA103_H02_diflorasone 8_uM 6_hours 690-2-1


title: MSA103_G22_3-acetamidocoumarin 10_uM 6_hours 1835-1-5


title: MSA103_G21_3-acetamidocoumarin 10_uM 6_hours 3651-A-A


title: MSA103_G17_Prestwick-675 10_uM 6_hours 3651-A-A


title: PDAC2-MOCK-rep2


title: MSA103_G16_prenylamine 9.6_uM 6_hours 1835-1-5

value: prenylamine


title: MSA103_G15_prenylamine 9.6_uM 6_hours 3651-A-A


title: whole_larva_esfenvalerate_0.5ug/L_rep3 [221_1_3]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 3


title: MSA103_G18_Prestwick-675 10_uM 6_hours 1835-1-5


title: PDAC2-MOCK-rep1

value: 48 hours after MOCK treatment


title: MSA103_G19_DL-thiorphan 1_uM 6_hours 3651-A-A


title: PDAC1-Treat-rep2

description:
human pancreatic cancer cell line established from undifferenciated pancreatic tumor tissue from a 65-year-old Caucasian male
Gene expression 48 hours after incubation with 0.045 % Agaricus blazei Murrill hot water extract


title: MSA103_G13_Primidone 10_uM 6_hours 3651-A-A

value: Primidone


title: MSA103_G14_Primidone 10_uM 6_hours 1835-1-5


title: whole_larva_esfenvalerate_0.5ug/L_rep4 [220_2_3]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 4

value: 48 hours post-hatch


title: MSA103_G12_4-hydroxyphenazone 10_uM 6_hours 1835-1-5


title: MSA103_G10_trichostatin NA 6_hours 1835-1-5

value: trichostatin

value: poscon


title: PDAC1-Treat-rep3

value: 48 hours after incubation with 0.045 % Agaricus blazei Murrill hot water extract


title: MSA103_G09_trichostatin NA 6_hours 3651-A-A


title: whole_larva_esfenvalerate_0.5ug/L_rep1 [233_2_3]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 1


title: MSA103_G11_4-hydroxyphenazone 10_uM 6_hours 3651-A-A

value: test


title: PDAC1-MOCK-rep3

description:
human pancreatic cancer cell line established from undifferenciated pancreatic tumor tissue from a 65-year-old Caucasian male
Gene expression 48 hours after MOCK treatment


title: whole_larva_esfenvalerate_0ug/L_rep10 [229_2_4]

description: Whole body gene expression after exposure of fathead larvae to 0 ug/L of esfenvalerate

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 10


title: whole_larva_esfenvalerate_0ug/L_rep9 [232_2_4]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 9


title: whole_larva_esfenvalerate_0.5ug/L_rep2 [234_1_4]

source_name: whole larva, esfenvalerate, 0.5 ug/L, replicate 2


title: PDAC1-MOCK-rep2


title: PDAC1-MOCK-rep1


title: PDAC1-Treat-rep1

source_name: pancreatic adenocarcinoma cell line, AbE treated, biological rep1


title: whole_larva_esfenvalerate_0ug/L_rep8 [231_1_3]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 8


title: whole_larva_esfenvalerate_0ug/L_rep7 [227_1_4]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 7


title: MSA103_G08_emetine 7.2_uM 6_hours 1835-1-5

value: emetine


title: MSA103_G07_emetine 7.2_uM 6_hours 3651-A-A


title: MSA103_G02_diflorasone 8_uM 6_hours 1835-1-5

value: diflorasone


title: MSA103_G01_diflorasone 8_uM 6_hours 3651-A-A


title: ESCC_GE024B_Nsp

description: Hybridized to Affymetrix SNP array

source_name: whole blood

value: blood from esophageal squamous cell carcinoma patient


title: WT Columnar/Hypertrophic

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

institute: Kyoto University

hyb_protocol: The labeled cRNA were then hybridized on Affimetrix gene chip and stained.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Normakisation and data analyses were performed by using Affymetrix GeneChip Command Console Software 6.

source_name: Columnar and hypertrophic chondrocytes, WT mice cartilage

label_protocol: cRNA labeling was performed according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted by guanidine hydrochloride-phenol-chloroform method and transcribed to cRNA.

tag: cell type

value: Columnar and hypertrophic chondrocytes

tag: strain

value: cartilage

tag: developmental stage

value: E17.5 embryo


title: MSA103_G05_melatonin 1_uM 6_hours 3651-A-A

value: melatonin

tag: batch

tag: duration

tag: perturbation type


title: MSA103_F24_LY379268 0.1_uM 6_hours 690-2-1

tag: well id

tag: plate id


title: whole_larva_esfenvalerate_0ug/L_rep6 [230_1_2]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 6

tag: tissue

value: whole larva

value: larva


title: whole_larva_esfenvalerate_0ug/L_rep5 [226_1_1]

source_name: whole larva, esfenvalerate, 0 ug/L, replicate 5

value: esfenvalerate


title: MSA103_G03_Loxapine 1_uM 6_hours 3651-A-A

value: Loxapine


title: MSA103_F23_LY379268 0.1_uM 6_hours 2476-D1-2


title: MSA103_F22_methylbenzethonium chloride 8.6_uM 6_hours 690-2-1

value: methylbenzethonium chloride


title: MSA103_F19_anisomycin 10_uM 6_hours 2476-D1-2

value: anisomycin