title: STK11_p.L245F_rep7_TA.OE014_A549_96H_X8_B19:C02


title: SERPINB5_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:D02

status: Public on Jun 28 2016

type: RNA

city: Cambridge

first: Jesse

middle: S.

last: Boehm

address: 415 Main Street

country: USA

institute: Broad Institute

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 (LXB) 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 (Q2NORM). Z-scores are then calculated for each feature with respect to the population of all samples on the plate (Z-SCORES).

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.

growth_protocol: Cells are grown in 384-well plates.

extract_protocol: Cells are lysed in TCL lysate buffer and transferred to Turbocapture plates, which bind the mRNA in the lysate.

treatment_protocol: Cells are grown, treated with virus then lysed.  Lysate is analyzed using the L1000 assay.

tag: cell line

tag: genetic modification


title: EGFP_rep64_TA.OE014_A549_96H_X8_B19:C03

value: EGFP


title: ABCB9_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:C01


title: MRPS16_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B19


title: BMP4_WT_V5_rep7_TA.OE014_A549_96H_X8_B19:B20


title: RNH1_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B21


title: MVP_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B18

value: MVP


title: STK11_p.G242W_rep8_TA.OE014_A549_96H_X8_B19:B13


title: NFE2L2_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B17


title: ZBTB24_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B11


title: EGFR_p.R222L_rep8_TA.OE014_A549_96H_X8_B19:B14


title: DNAJC15_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B15


title: CDC45_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B16


title: PTEN_WT_rep7_TA.OE014_A549_96H_X8_B19:B10

value: PTEN


title: EGFR_p.S645C_rep8_TA.OE014_A549_96H_X8_B19:B08


title: CTNNB1_p.V600G_rep8_TA.OE014_A549_96H_X8_B19:C09


title: CTNNB1_p.S33N_rep8_TA.OE014_A549_96H_X8_B19:B07


title: EGFP_rep63_TA.OE014_A549_96H_X8_B19:B06


title: DNMT3A_WT_V5_rep7_TA.OE014_A549_96H_X8_B19:B23


title: TRAP1_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:B03


title: MTERFD1_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:A19


title: DECR1_WT_V5_rep6_TA.OE014_A549_96H_X8_B19:B22


title: PYGL_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:A18

value: PYGL


title: MFSD10_WT_rep8_TA.OE014_A549_96H_X8_B19:B04


title: AURKB_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:A17

value: AURKB


title: NUP88_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:A15


title: ABCB9_WT_rep8_TA.OE014_A549_96H_X8_B19:A07


title: GRB7_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:A16


title: CCND1_WT_rep8_TA.OE014_A549_96H_X8_B19:A10


title: RBM10_WT_rep8_TA.OE014_A549_96H_X8_B19:A09


title: ACAT2_WT_V5_rep8_TA.OE014_A549_96H_X8_B19:A03


title: HCRED_rep55_TA.OE014_A549_96H_X8_B19:A06

value: HCRED


title: AKT1_WT_rep6_TA.OE014_A549_96H_X7_B19:P23


title: PIK3R3_p.P127L_rep8_TA.OE014_A549_96H_X8_B19:A13


title: FAM173B_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:P19


title: SERPINB5_WT_rep7_TA.OE014_A549_96H_X7_B19:P13


title: EGFP_rep62_TA.OE014_A549_96H_X7_B19:P15


title: RBM10_p.Y580F_rep6_TA.OE014_A549_96H_X7_B19:P11


title: EGFR_p.769_770insASV_rep5_TA.OE014_A549_96H_X7_B19:P12


title: BFP_rep53_TA.OE014_A549_96H_X7_B19:P16

value: BFP


title: STK11_p.D194Y_rep7_TA.OE014_A549_96H_X7_B19:P20


title: LUCIFERASE_rep49_TA.OE014_A549_96H_X8_B19:B05

value: LUCIFERASE


title: KRAS_p.G13V_rep7_TA.OE014_A549_96H_X7_B19:P14


title: KEAP1_p.E117K_rep7_TA.OE014_A549_96H_X7_B19:P09


title: TPK1_p.G48C_rep7_TA.OE014_A549_96H_X7_B19:P08


title: RBM34_WT_rep7_TA.OE014_A549_96H_X7_B19:P21


title: FCGR3B_p.K179T_rep6_TA.OE014_A549_96H_X7_B19:P03


title: ARAF_p.S214F_rep7_TA.OE014_A549_96H_X7_B19:P10


title: KEAP1_p.G419W_rep7_TA.OE014_A549_96H_X7_B19:P04


title: SERPINB5_p.D141A_rep7_TA.OE014_A549_96H_X7_B19:P02


title: PIK3R3_p.R245C_rep7_TA.OE014_A549_96H_X7_B19:O21


title: ZBTB24_WT_rep7_TA.OE014_A549_96H_X7_B19:O24


title: DCAF8_WT_rep7_TA.OE014_A549_96H_X7_B19:O19


title: EGFP_rep61_TA.OE014_A549_96H_X7_B19:O16


title: RBM45_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:O14


title: MAX_p.R60del_rep7_TA.OE014_A549_96H_X7_B19:O13


title: KEAP1_p.L268P_rep7_TA.OE014_A549_96H_X7_B19:O11


title: KRAS_p.D33E_rep7_TA.OE014_A549_96H_X7_B19:O08


title: MYC_p.E366Q_rep7_TA.OE014_A549_96H_X7_B19:O07


title: EGFR_p.T790M, p.L858R_rep23_TA.OE014_A549_96H_X7_B19:N23

value: EGFR_p.T790M, p.L858R


title: PTEN_p.H123Y_rep7_TA.OE014_A549_96H_X7_B19:O02


title: EGFR_p.L858R_rep28_TA.OE014_A549_96H_X7_B19:N22


title: CTNNB1_p.G367V_rep7_TA.OE014_A549_96H_X7_B19:O06


title: STK11_p.G251V_rep7_TA.OE014_A549_96H_X7_B19:O01


title: KEAP1_p.R601W_rep7_TA.OE014_A549_96H_X7_B19:O17


title: EGFP_rep60_TA.OE014_A549_96H_X7_B19:N14


title: LUCIFERASE_rep48_TA.OE014_A549_96H_X7_B19:O15


title: STK11_WT_rep28_TA.OE014_A549_96H_X7_B19:N15


title: KRAS_p.G12V_rep24_TA.OE014_A549_96H_X7_B19:N16


title: HCRED_rep54_TA.OE014_A549_96H_X7_B19:N13


title: PIK3R3_p.M295T_rep7_TA.OE014_A549_96H_X7_B19:N12


title: CTNNB1_p.S45F_rep7_TA.OE014_A549_96H_X7_B19:N11


title: ARAF_p.S214C.p.D429A_rep6_TA.OE014_A549_96H_X7_B19:N08


title: HAVCR2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:O09


title: EGFR_p.D837A_rep6_TA.OE014_A549_96H_X7_B19:N03


title: STK11_p.D176H_rep7_TA.OE014_A549_96H_X7_B19:N07


title: ARAF_WT_rep7_TA.OE014_A549_96H_X7_B19:N09

value: ARAF


title: DCAF8_p.P156S_rep7_TA.OE014_A549_96H_X7_B19:N04


title: HAVCR2_p.P6S_rep7_TA.OE014_A549_96H_X7_B19:N05


title: KEAP1_WT_rep27_TA.OE014_A549_96H_X7_B19:M24


title: TP53_p.P278A_rep24_TA.OE014_A549_96H_X7_B19:M22


title: CTNNB1_p.F777S_rep7_TA.OE014_A549_96H_X7_B19:N10


title: KRAS_p.G12V_rep25_TA.OE014_A549_96H_X7_B19:N21


title: EGFR_WT_rep27_TA.OE014_A549_96H_X7_B19:N20

value: EGFR


title: KEAP1_WT_rep28_TA.OE014_A549_96H_X7_B19:N18


title: EGFR_p.L858R_rep27_TA.OE014_A549_96H_X7_B19:N19


title: EGFR_WT_rep26_TA.OE014_A549_96H_X7_B19:M20


title: NFE2L2_WT_rep28_TA.OE014_A549_96H_X7_B19:M21


title: EGFR_p.L858R_rep26_TA.OE014_A549_96H_X7_B19:M18


title: NFE2L2_WT_rep27_TA.OE014_A549_96H_X7_B19:M16


title: MDM2_WT_rep28_TA.OE014_A549_96H_X7_B19:M15


title: STK11_WT_rep27_TA.OE014_A549_96H_X7_B19:M17


title: KEAP1_p.R204P_rep7_TA.OE014_A549_96H_X7_B19:M05


title: STC2_WT_rep7_TA.OE014_A549_96H_X7_B19:M03


title: EGFP_rep59_TA.OE014_A549_96H_X7_B19:M13


title: BFP_rep52_TA.OE014_A549_96H_X7_B19:M14


title: KEAP1_p.T142M_rep7_TA.OE014_A549_96H_X7_B19:M06


title: ARAF_p.V145L_rep7_TA.OE014_A549_96H_X7_B19:M02


title: EGFR_p.T790M, p.L858R_rep22_TA.OE014_A549_96H_X7_B19:M23


title: PIK3R3_p.F380L_rep7_TA.OE014_A549_96H_X7_B19:M11


title: BFP_rep51_TA.OE014_A549_96H_X7_B19:L11


title: KEAP1_p.G417R_rep7_TA.OE014_A549_96H_X7_B19:L20


title: PIK3R3_WT_rep6_TA.OE014_A549_96H_X7_B19:L02


title: STK11_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:L06


title: RARA_WT_rep7_TA.OE014_A549_96H_X7_B19:K20

value: RARA


title: KEAP1_p.R470S_rep7_TA.OE014_A549_96H_X7_B19:L08


title: KEAP1_p.D389Y_rep7_TA.OE014_A549_96H_X7_B19:M01


title: SERPINB5_p.A42F_rep7_TA.OE014_A549_96H_X7_B19:K23


title: KEAP1_p.P278S_rep7_TA.OE014_A549_96H_X7_B19:L09


title: LUCIFERASE_rep47_TA.OE014_A549_96H_X7_B19:L12


title: TPK1_p.K111M_rep7_TA.OE014_A549_96H_X7_B19:K21


title: TPK1_p.E81Q_rep7_TA.OE014_A549_96H_X7_B19:L17


title: ZBTB24_p.G568C_rep7_TA.OE014_A549_96H_X7_B19:L24


title: TPK1_p.P152T_rep7_TA.OE014_A549_96H_X7_B19:K15


title: ZBTB24_p.M78I_rep7_TA.OE014_A549_96H_X7_B19:K18


title: TPK1_p.T213S_rep7_TA.OE014_A549_96H_X7_B19:M08


title: MYC_WT_rep7_TA.OE014_A549_96H_X7_B19:K13

value: MYC


title: STC2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:K09


title: KEAP1_p.G603W_rep7_TA.OE014_A549_96H_X7_B19:K03


title: EGFR_p.774_775insHV_rep7_TA.OE014_A549_96H_X7_B19:J24


title: LUCIFERASE_rep45_TA.OE014_A549_96H_X7_B19:K11


title: SERPINB5_p.A7T_rep7_TA.OE014_A549_96H_X7_B19:L03


title: EGFR_p.773_774insH_rep7_TA.OE014_A549_96H_X7_B19:J23


title: EGFR_WT_rep25_TA.OE014_A549_96H_X7_B19:M19


title: KEAP1_p.R470H_rep7_TA.OE014_A549_96H_X7_B19:K06


title: EGFR_p.K754E_rep7_TA.OE014_A549_96H_X7_B19:K01


title: KRAS_p.G13C_rep6_TA.OE014_A549_96H_X7_B19:J22


title: ARAF_p.S214C_rep7_TA.OE014_A549_96H_X7_B19:K17


title: LUCIFERASE_rep46_TA.OE014_A549_96H_X7_B19:K12


title: KRAS_p.G13D_rep7_TA.OE014_A549_96H_X7_B19:J16


title: GOPC_WT_rep7_TA.OE014_A549_96H_X7_B19:J14

value: GOPC


title: EGFR_p.ELREA746del_rep7_TA.OE014_A549_96H_X7_B19:J18


title: CTNNB1_p.S37C_rep7_TA.OE014_A549_96H_X7_B19:J06


title: KRAS_p.G12S_rep7_TA.OE014_A549_96H_X7_B19:I19


title: CCND1_p.E172K_rep7_TA.OE014_A549_96H_X7_B19:J11


title: KRAS_p.G12C_rep7_TA.OE014_A549_96H_X7_B19:J17


title: RARA_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:K08


title: AKT1_p.D323Y_rep7_TA.OE014_A549_96H_X7_B19:J12


title: KRAS_p.G12A_rep7_TA.OE014_A549_96H_X7_B19:J15


title: EGFR_p.L833F_rep6_TA.OE014_A549_96H_X7_B19:I16


title: FCGR3B_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:J13


title: RBM10_p.E4K_rep7_TA.OE014_A549_96H_X7_B19:J02


title: LUCIFERASE_rep44_TA.OE014_A549_96H_X7_B19:J09


title: EGFR_p.ELREA746del,p.T790M_rep7_TA.OE014_A549_96H_X7_B19:I24


title: EGFP_rep58_TA.OE014_A549_96H_X7_B19:I10


title: HCRED_rep53_TA.OE014_A549_96H_X7_B19:J10


title: EGFR_p.H1129Y_rep7_TA.OE014_A549_96H_X7_B19:I06


title: CTNNB1_p.I140T_rep7_TA.OE014_A549_96H_X7_B19:J03


title: HAT1_WT_V5_rep6_TA.OE014_A549_96H_X7_B19:H23


title: NRAS_p.Q61L_rep7_TA.OE014_A549_96H_X7_B19:I23


title: DCAF8_p.G588C_rep7_TA.OE014_A549_96H_X7_B19:I11


title: KRAS_p.G12R_rep7_TA.OE014_A549_96H_X7_B19:I18


title: KRAS_p.G12D_rep7_TA.OE014_A549_96H_X7_B19:I15


title: KRAS_p.G12F_rep7_TA.OE014_A549_96H_X7_B19:J21


title: MAX_WT_rep7_TA.OE014_A549_96H_X7_B19:I12

value: MAX


title: KEAP1_p.G333C_rep7_TA.OE014_A549_96H_X7_B19:I07


title: BFP_rep50_TA.OE014_A549_96H_X7_B19:I09


title: KRAS_p.G12Y_rep7_TA.OE014_A549_96H_X7_B19:I21


title: BRP44_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:H20


title: DHRS7_WT_V5_rep6_TA.OE014_A549_96H_X7_B19:H22


title: BFP_rep49_TA.OE014_A549_96H_X7_B19:H08


title: LAGE3_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:H17


title: STK11_p.G251F_rep7_TA.OE014_A549_96H_X7_B19:H11


title: ARAF_p.D429A_rep7_TA.OE014_A549_96H_X7_B19:H14


title: TSTA3_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:H15


title: EGFP_rep57_TA.OE014_A549_96H_X7_B19:H07


title: RBM45_p.M126I_rep7_TA.OE014_A549_96H_X7_B19:H13


title: DAXX_WT_V5_rep6_TA.OE014_A549_96H_X7_B19:G23

value: DAXX


title: HLA-DRA_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:G20

value: HLA-DRA


title: NRAS_WT_rep7_TA.OE014_A549_96H_X7_B19:H03

value: NRAS


title: PIK3R3_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:H01


title: ID2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:H19


title: PPARG_WT_V5_rep5_TA.OE014_A549_96H_X7_B19:G22

value: PPARG


title: STC2_p.R5W_rep7_TA.OE014_A549_96H_X7_B19:H06


title: SENP6_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:G16


title: GABPB1_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:H16


title: PCCB_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:G17

value: PCCB


title: PSMG1_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:G24


title: KRAS_WT_rep7_TA.OE014_A549_96H_X7_B19:G11

value: KRAS


title: SOX2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:G19


title: TPK1_p.T205S_rep7_TA.OE014_A549_96H_X7_B19:G12


title: PSME2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:G15


title: KEAP1_p.D479G_rep7_TA.OE014_A549_96H_X7_B19:G13


title: CTNNB1_WT_rep7_TA.OE014_A549_96H_X7_B19:H05


title: KEAP1_p.E611D_rep7_TA.OE014_A549_96H_X7_B19:G10


title: ABCB9_p.R281L_rep7_TA.OE014_A549_96H_X7_B19:G05


title: DCAF8_p.E63K_rep7_TA.OE014_A549_96H_X7_B19:H02


title: TP53_p.P278A_rep23_TA.OE014_A549_96H_X7_B19:F24


title: MDM2_WT_rep27_TA.OE014_A549_96H_X7_B19:F20


title: HCRED_rep52_TA.OE014_A549_96H_X7_B19:G07


title: RBM45_p.D434Y_rep7_TA.OE014_A549_96H_X7_B19:G02


title: SHC1_WT_V5_rep6_TA.OE014_A549_96H_X7_B19:H18


title: BFP_rep48_TA.OE014_A549_96H_X7_B19:G08


title: NFE2L2_WT_rep26_TA.OE014_A549_96H_X7_B19:F19


title: STK11_WT_rep26_TA.OE014_A549_96H_X7_B19:F18


title: EGFR_WT_rep24_TA.OE014_A549_96H_X7_B19:F21


title: NFE2L2_WT_rep25_TA.OE014_A549_96H_X7_B19:F16


title: EGFR_p.T790M, p.L858R_rep21_TA.OE014_A549_96H_X7_B19:F22


title: RBM10_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:G01


title: MDM2_WT_rep26_TA.OE014_A549_96H_X7_B19:F15


title: MAX_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:F08


title: TP53_p.P278A_rep22_TA.OE014_A549_96H_X7_B19:F23


title: KEAP1_WT_rep26_TA.OE014_A549_96H_X7_B19:F17


title: LUCIFERASE_rep43_TA.OE014_A549_96H_X7_B19:F06


title: PTEN_p.M35I_rep7_TA.OE014_A549_96H_X7_B19:F01


title: TERT_p.L593F_rep7_TA.OE014_A549_96H_X7_B19:F14


title: RBM10_p.W658Y_rep7_TA.OE014_A549_96H_X7_B19:F09


title: STK11_WT_rep25_TA.OE014_A549_96H_X7_B19:E24


title: EGFR_p.Q1020H_rep7_TA.OE014_A549_96H_X7_B19:F12


title: EGFR_p.T790M, p.L858R_rep20_TA.OE014_A549_96H_X7_B19:E22


title: EGFR_p.L858R_rep25_TA.OE014_A549_96H_X7_B19:E19


title: KRAS_p.G12V_rep23_TA.OE014_A549_96H_X7_B19:E20


title: KRAS_p.G12V_rep22_TA.OE014_A549_96H_X7_B19:E17


title: KEAP1_WT_rep25_TA.OE014_A549_96H_X7_B19:E15


title: MDM2_WT_rep25_TA.OE014_A549_96H_X7_B19:E18


title: SERPINB5_p.I159S_rep7_TA.OE014_A549_96H_X7_B19:E08


title: TPK1_WT_rep7_TA.OE014_A549_96H_X7_B19:E13


title: RBM45_WT_rep7_TA.OE014_A549_96H_X7_B19:E11


title: STK11_p.G56V_rep7_TA.OE014_A549_96H_X7_B19:E07


title: HCRED_rep51_TA.OE014_A549_96H_X7_B19:F05


title: KEAP1_p.W497L_rep6_TA.OE014_A549_96H_X7_B19:E03


title: HAVCR2_WT_rep7_TA.OE014_A549_96H_X7_B19:E09


title: EGFP_rep56_TA.OE014_A549_96H_X7_B19:E06

value: EGFP


title: KEAP1_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:D14


title: KEAP1_p.G524C_rep7_TA.OE014_A549_96H_X7_B19:D17


title: EGFR_p.T790M_rep7_TA.OE014_A549_96H_X7_B19:D24


title: HCRED_rep50_TA.OE014_A549_96H_X7_B19:E05

value: HCRED


title: KEAP1_p.S144F_rep7_TA.OE014_A549_96H_X7_B19:D13


title: BFP_rep47_TA.OE014_A549_96H_X7_B19:D03

value: BFP


title: DCAF8_p.R559P_rep7_TA.OE014_A549_96H_X7_B19:D06


title: FAM173B_p.R187P_rep7_TA.OE014_A549_96H_X7_B19:D05


title: HCRED_rep49_TA.OE014_A549_96H_X7_B19:D04


title: ZBTB24_p.Q669R_rep7_TA.OE014_A549_96H_X7_B19:D08


title: SERPINB5_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:D02


title: KEAP1_p.S102L_rep7_TA.OE014_A549_96H_X7_B19:D12


title: FCGR3B_WT_rep5_TA.OE014_A549_96H_X7_B19:C20


title: FCGR3B_p.L218P_rep7_TA.OE014_A549_96H_X7_B19:E10


title: MAX_p.R35L_rep7_TA.OE014_A549_96H_X7_B19:C13


title: TPK1_p.L185I_rep7_TA.OE014_A549_96H_X7_B19:C18


title: CTNNB1_p.V600G_rep7_TA.OE014_A549_96H_X7_B19:C09


title: ZBTB24_p.K123M_rep7_TA.OE014_A549_96H_X7_B19:C08


title: RBM34_WT_V5_rep6_TA.OE014_A549_96H_X7_B19:D21


title: CTNNB1_p.G34V_rep7_TA.OE014_A549_96H_X7_B19:C07


title: HCRED_rep48_TA.OE014_A549_96H_X7_B19:C04


title: ARAF_p.S214F.p.D429A_rep5_TA.OE014_A549_96H_X7_B19:C05


title: EGFP_rep55_TA.OE014_A549_96H_X7_B19:C03


title: STK11_p.L245F_rep6_TA.OE014_A549_96H_X7_B19:C02


title: ABCB9_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:C01


title: ZBTB24_p.G693S_rep6_TA.OE014_A549_96H_X7_B19:C22


title: MRPS16_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B19


title: RNH1_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B21


title: MVP_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B18

value: MVP


title: FAIM_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B24

value: FAIM


title: BMP4_WT_V5_rep6_TA.OE014_A549_96H_X7_B19:B20


title: DNMT3A_WT_V5_rep6_TA.OE014_A549_96H_X7_B19:B23


title: SERPINB5_p.A165T_rep5_TA.OE014_A549_96H_X7_B19:C23


title: STK11_p.G242W_rep7_TA.OE014_A549_96H_X7_B19:B13


title: ZBTB24_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B11


title: CDC45_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B16


title: EGFR_p.R222L_rep7_TA.OE014_A549_96H_X7_B19:B14


title: DNAJC15_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B15


title: DECR1_WT_V5_rep5_TA.OE014_A549_96H_X7_B19:B22


title: NFE2L2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B17


title: EGFR_p.S645C_rep7_TA.OE014_A549_96H_X7_B19:B08


title: CTNNB1_p.S33N_rep7_TA.OE014_A549_96H_X7_B19:B07


title: EGFP_rep54_TA.OE014_A549_96H_X7_B19:B06


title: LUCIFERASE_rep42_TA.OE014_A549_96H_X7_B19:B05

value: LUCIFERASE


title: MFSD10_WT_rep7_TA.OE014_A549_96H_X7_B19:B04


title: TRAP1_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:B03


title: DNTTIP2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A23


title: RHEB_WT_V5_rep5_TA.OE014_A549_96H_X7_B19:A24

value: RHEB


title: EXOSC4_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A22


title: PIH1D1_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A20


title: CCL2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A21


title: MTERFD1_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A19


title: PYGL_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A18

value: PYGL


title: AURKB_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A17

value: AURKB


title: NUP88_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A15


title: GRB7_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A16


title: RBM10_WT_rep7_TA.OE014_A549_96H_X7_B19:A09


title: CCND1_WT_rep7_TA.OE014_A549_96H_X7_B19:A10


title: ABCB9_WT_rep7_TA.OE014_A549_96H_X7_B19:A07


title: PIK3R3_p.P127L_rep7_TA.OE014_A549_96H_X7_B19:A13


title: HCRED_rep47_TA.OE014_A549_96H_X7_B19:A06


title: BFP_rep46_TA.OE014_A549_96H_X7_B19:A05


title: BFP_rep45_TA.OE014_A549_96H_X6_B19:P16


title: EBNA1BP2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A04


title: ACAT2_WT_V5_rep7_TA.OE014_A549_96H_X7_B19:A03


title: STK11_p.D194Y_rep6_TA.OE014_A549_96H_X6_B19:P20


title: AKT1_WT_rep5_TA.OE014_A549_96H_X6_B19:P23


title: RBM34_WT_rep6_TA.OE014_A549_96H_X6_B19:P21


title: KRAS_p.G13V_rep6_TA.OE014_A549_96H_X6_B19:P14


title: EGFR_p.769_770insASV_rep4_TA.OE014_A549_96H_X6_B19:P12


title: EGFP_rep53_TA.OE014_A549_96H_X6_B19:P15


title: ARAF_p.S214F_rep6_TA.OE014_A549_96H_X6_B19:P10


title: FAM173B_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:P19


title: RBM10_p.Y580F_rep5_TA.OE014_A549_96H_X6_B19:P11


title: SERPINB5_WT_rep6_TA.OE014_A549_96H_X6_B19:P13


title: KEAP1_p.E117K_rep6_TA.OE014_A549_96H_X6_B19:P09


title: TPK1_p.G48C_rep6_TA.OE014_A549_96H_X6_B19:P08


title: DCAF8_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:P07


title: KEAP1_p.G419W_rep6_TA.OE014_A549_96H_X6_B19:P04


title: SERPINB5_p.D141A_rep6_TA.OE014_A549_96H_X6_B19:P02


title: FCGR3B_p.K179T_rep5_TA.OE014_A549_96H_X6_B19:P03


title: ZBTB24_WT_rep6_TA.OE014_A549_96H_X6_B19:O24


title: DCAF8_WT_rep6_TA.OE014_A549_96H_X6_B19:O19


title: KEAP1_p.R601W_rep6_TA.OE014_A549_96H_X6_B19:O17


title: EGFP_rep52_TA.OE014_A549_96H_X6_B19:O16


title: RBM45_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:O14


title: LUCIFERASE_rep41_TA.OE014_A549_96H_X6_B19:O15


title: KRAS_p.D33E_rep6_TA.OE014_A549_96H_X6_B19:O08


title: CTNNB1_p.G367V_rep6_TA.OE014_A549_96H_X6_B19:O06


title: HAVCR2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:O09


title: MYC_p.E366Q_rep6_TA.OE014_A549_96H_X6_B19:O07


title: KEAP1_p.L268P_rep6_TA.OE014_A549_96H_X6_B19:O11


title: STK11_p.G251V_rep6_TA.OE014_A549_96H_X6_B19:O01


title: EGFR_p.T790M, p.L858R_rep19_TA.OE014_A549_96H_X6_B19:N23

value: EGFR_p.T790M, p.L858R


title: KRAS_p.G12V_rep21_TA.OE014_A549_96H_X6_B19:N21


title: EGFR_p.L858R_rep24_TA.OE014_A549_96H_X6_B19:N22


title: EGFR_WT_rep23_TA.OE014_A549_96H_X6_B19:N20

value: EGFR


title: EGFR_p.L858R_rep23_TA.OE014_A549_96H_X6_B19:N19


title: PTEN_p.H123Y_rep6_TA.OE014_A549_96H_X6_B19:O02


title: KRAS_p.G12V_rep20_TA.OE014_A549_96H_X6_B19:N16


title: KEAP1_WT_rep24_TA.OE014_A549_96H_X6_B19:N18


title: PIK3R3_p.R245C_rep6_TA.OE014_A549_96H_X6_B19:O21


title: STK11_WT_rep24_TA.OE014_A549_96H_X6_B19:N15


title: PIK3R3_p.M295T_rep6_TA.OE014_A549_96H_X6_B19:N12


title: CTNNB1_p.S45F_rep6_TA.OE014_A549_96H_X6_B19:N11


title: CTNNB1_p.F777S_rep6_TA.OE014_A549_96H_X6_B19:N10


title: ARAF_WT_rep6_TA.OE014_A549_96H_X6_B19:N09

value: ARAF


title: EGFP_rep51_TA.OE014_A549_96H_X6_B19:N14


title: EGFR_p.D837A_rep5_TA.OE014_A549_96H_X6_B19:N03


title: DCAF8_p.P156S_rep6_TA.OE014_A549_96H_X6_B19:N04


title: HAVCR2_p.P6S_rep6_TA.OE014_A549_96H_X6_B19:N05


title: ARAF_p.S214C.p.D429A_rep5_TA.OE014_A549_96H_X6_B19:N08


title: STK11_p.D176H_rep6_TA.OE014_A549_96H_X6_B19:N07


title: NFE2L2_WT_rep24_TA.OE014_A549_96H_X6_B19:M21


title: EGFR_WT_rep21_TA.OE014_A549_96H_X6_B19:M19


title: EGFR_p.L858R_rep22_TA.OE014_A549_96H_X6_B19:M18


title: TP53_p.P278A_rep20_TA.OE014_A549_96H_X6_B19:M22


title: EGFR_WT_rep22_TA.OE014_A549_96H_X6_B19:M20


title: EGFR_p.T790M, p.L858R_rep18_TA.OE014_A549_96H_X6_B19:M23


title: KEAP1_WT_rep23_TA.OE014_A549_96H_X6_B19:M24


title: NFE2L2_WT_rep23_TA.OE014_A549_96H_X6_B19:M16


title: HCRED_rep46_TA.OE014_A549_96H_X6_B19:N13


title: MAX_p.R60del_rep6_TA.OE014_A549_96H_X6_B19:O13


title: BFP_rep44_TA.OE014_A549_96H_X6_B19:M14


title: STK11_WT_rep23_TA.OE014_A549_96H_X6_B19:M17


title: MDM2_WT_rep24_TA.OE014_A549_96H_X6_B19:M15


title: EGFP_rep50_TA.OE014_A549_96H_X6_B19:M13


title: TP53_p.P278A_rep21_TA.OE014_A549_96H_X7_B19:E23


title: TPK1_p.T213S_rep6_TA.OE014_A549_96H_X6_B19:M08


title: KEAP1_p.R204P_rep6_TA.OE014_A549_96H_X6_B19:M05


title: KEAP1_p.T142M_rep6_TA.OE014_A549_96H_X6_B19:M06


title: STC2_WT_rep6_TA.OE014_A549_96H_X6_B19:M03


title: ARAF_p.V145L_rep6_TA.OE014_A549_96H_X6_B19:M02


title: KEAP1_p.G417R_rep6_TA.OE014_A549_96H_X6_B19:L20


title: ZBTB24_p.G568C_rep6_TA.OE014_A549_96H_X6_B19:L24


title: TPK1_p.E81Q_rep6_TA.OE014_A549_96H_X6_B19:L17


title: KEAP1_p.D389Y_rep6_TA.OE014_A549_96H_X6_B19:M01


title: PIK3R3_p.F380L_rep6_TA.OE014_A549_96H_X6_B19:M11


title: LUCIFERASE_rep40_TA.OE014_A549_96H_X6_B19:L12


title: STK11_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:L06


title: BFP_rep43_TA.OE014_A549_96H_X6_B19:L11


title: KEAP1_p.R470S_rep6_TA.OE014_A549_96H_X6_B19:L08


title: SERPINB5_p.A42F_rep6_TA.OE014_A549_96H_X6_B19:K23


title: RARA_WT_rep6_TA.OE014_A549_96H_X6_B19:K20

value: RARA


title: TPK1_p.P152T_rep6_TA.OE014_A549_96H_X6_B19:K15


title: KEAP1_p.P278S_rep6_TA.OE014_A549_96H_X6_B19:L09


title: TPK1_p.K111M_rep6_TA.OE014_A549_96H_X6_B19:K21


title: SERPINB5_p.A7T_rep6_TA.OE014_A549_96H_X6_B19:L03


title: ARAF_p.S214C_rep6_TA.OE014_A549_96H_X6_B19:K17


title: LUCIFERASE_rep38_TA.OE014_A549_96H_X6_B19:K11


title: STC2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:K09


title: KEAP1_p.R470H_rep6_TA.OE014_A549_96H_X6_B19:K06


title: MYC_WT_rep6_TA.OE014_A549_96H_X6_B19:K13

value: MYC


title: RARA_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:K08


title: EGFR_p.K754E_rep6_TA.OE014_A549_96H_X6_B19:K01


title: EGFR_p.774_775insHV_rep6_TA.OE014_A549_96H_X6_B19:J24


title: KEAP1_p.G603W_rep6_TA.OE014_A549_96H_X6_B19:K03


title: KRAS_p.G13C_rep5_TA.OE014_A549_96H_X6_B19:J22


title: EGFR_p.773_774insH_rep6_TA.OE014_A549_96H_X6_B19:J23


title: PIK3R3_WT_rep5_TA.OE014_A549_96H_X6_B19:L02


title: ZBTB24_p.M78I_rep6_TA.OE014_A549_96H_X6_B19:K18


title: KRAS_p.G13D_rep6_TA.OE014_A549_96H_X6_B19:J16


title: KRAS_p.G12C_rep6_TA.OE014_A549_96H_X6_B19:J17


title: EGFR_p.ELREA746del_rep6_TA.OE014_A549_96H_X6_B19:J18


title: KRAS_p.G12F_rep6_TA.OE014_A549_96H_X6_B19:J21


title: FCGR3B_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:J13


title: LUCIFERASE_rep39_TA.OE014_A549_96H_X6_B19:K12


title: GOPC_WT_rep6_TA.OE014_A549_96H_X6_B19:J14

value: GOPC


title: AKT1_p.D323Y_rep6_TA.OE014_A549_96H_X6_B19:J12


title: HCRED_rep45_TA.OE014_A549_96H_X6_B19:J10


title: CTNNB1_p.I140T_rep6_TA.OE014_A549_96H_X6_B19:J03


title: EGFR_p.ELREA746del,p.T790M_rep6_TA.OE014_A549_96H_X6_B19:I24


title: RBM10_p.E4K_rep6_TA.OE014_A549_96H_X6_B19:J02


title: KRAS_p.G12Y_rep6_TA.OE014_A549_96H_X6_B19:I21


title: NRAS_p.Q61L_rep6_TA.OE014_A549_96H_X6_B19:I23


title: DCAF8_p.G588C_rep6_TA.OE014_A549_96H_X6_B19:I11


title: MAX_WT_rep6_TA.OE014_A549_96H_X6_B19:I12

value: MAX


title: EGFP_rep49_TA.OE014_A549_96H_X6_B19:I10


title: KRAS_p.G12D_rep6_TA.OE014_A549_96H_X6_B19:I15


title: BFP_rep42_TA.OE014_A549_96H_X6_B19:I09


title: KEAP1_p.G333C_rep6_TA.OE014_A549_96H_X6_B19:I07


title: EGFR_p.H1129Y_rep6_TA.OE014_A549_96H_X6_B19:I06


title: EGFR_p.L833F_rep5_TA.OE014_A549_96H_X6_B19:I16


title: HAT1_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:H23


title: LUCIFERASE_rep37_TA.OE014_A549_96H_X6_B19:J09


title: KRAS_p.G12A_rep6_TA.OE014_A549_96H_X6_B19:J15


title: CCND1_p.E172K_rep6_TA.OE014_A549_96H_X6_B19:J11


title: BRP44_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:H20


title: ID2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:H19


title: CTNNB1_p.S37C_rep6_TA.OE014_A549_96H_X6_B19:J06


title: DHRS7_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:H22


title: ARAF_p.D429A_rep6_TA.OE014_A549_96H_X6_B19:H14


title: TSTA3_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:H15


title: KRAS_p.G12S_rep6_TA.OE014_A549_96H_X6_B19:I19


title: LAGE3_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:H17


title: SHC1_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:H18


title: KRAS_p.G12R_rep6_TA.OE014_A549_96H_X6_B19:I18


title: CTNNB1_WT_rep6_TA.OE014_A549_96H_X6_B19:H05


title: STK11_p.G251F_rep6_TA.OE014_A549_96H_X6_B19:H11


title: STC2_p.R5W_rep6_TA.OE014_A549_96H_X6_B19:H06


title: NRAS_WT_rep6_TA.OE014_A549_96H_X6_B19:H03

value: NRAS


title: DCAF8_p.E63K_rep6_TA.OE014_A549_96H_X6_B19:H02


title: PSMG1_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:G24


title: PIK3R3_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:H01


title: HLA-DRA_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:G20

value: HLA-DRA


title: GABPB1_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:H16


title: PPARG_WT_V5_rep4_TA.OE014_A549_96H_X6_B19:G22

value: PPARG


title: DAXX_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:G23

value: DAXX


title: SOX2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:G19


title: SENP6_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:G16


title: PSME2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:G15


title: RBM45_p.M126I_rep6_TA.OE014_A549_96H_X6_B19:H13


title: KEAP1_p.D479G_rep6_TA.OE014_A549_96H_X6_B19:G13


title: PCCB_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:G17

value: PCCB


title: KRAS_WT_rep6_TA.OE014_A549_96H_X6_B19:G11

value: KRAS


title: KEAP1_p.E611D_rep6_TA.OE014_A549_96H_X6_B19:G10


title: EGFP_rep48_TA.OE014_A549_96H_X6_B19:H07

value: EGFP


title: BFP_rep41_TA.OE014_A549_96H_X6_B19:H08

value: BFP


title: BFP_rep40_TA.OE014_A549_96H_X6_B19:G08


title: TPK1_p.T205S_rep6_TA.OE014_A549_96H_X6_B19:G12


title: HCRED_rep44_TA.OE014_A549_96H_X6_B19:G07

value: HCRED


title: RBM45_p.D434Y_rep6_TA.OE014_A549_96H_X6_B19:G02


title: RBM10_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:G01


title: TP53_p.P278A_rep18_TA.OE014_A549_96H_X6_B19:F23


title: Black poplar leaf grown under control condition (2 ppm)_rep1

city: TOKAT

first: KUBILAY

last: YILDIRIM

address: TASLICIFTLIK

department: BIOENGINEERING

country: Turkey

institute: GAZIOSMANPASA UNIVERSITY

description:
Gene expression data from the leaves of boron toxicity tolerant Black poplar genotype
P.n_Cont_Leaf 1_(Poplar)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Poplar Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Robust Multiarray Analysis (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

organism: Populus nigra

source_name: Black poplar leaf_control condition (2 ppm)control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 15 cm cuttings (60 cuttings /clone) were grown in 5 L plastic bags on 15 April 2014. When the rooted cuttings  had 15-20 mature leaves, the best growing 35 ones/clone were selected and transferred  to 20 L plastic pots (one sapling for one pot) filled with 5 kg homogenized soil and perlite mixture(4:1). The soil was clay loam (pH 7.4) with 0.0062 dS/m EC, 1.9 % organic carbon and 2.02 mg/kg total B content. The pots were moved to a semi-controlled greenhouse at the Gaziosmanpasa University (Tokat /Turkey). The day temperature of the greenhouse ranged between 26–34 °C with a night temperature range of 18–24 °C. The water holding capacity of pots’ soil was measured approximately 1.1kg water/ kg soil at this field capacity. After transferring the seedling into pots, they were continued to be irrigated with tap water (B content; 0.068ppm) at field capacity for two weeks to ensure their adequate root development and acclimation to pot conditions.

extract_protocol: Leaves and roots collected from control (2ppm soil boron content) and toxic (15 ppm soil boron content) soil conditions were were utilized for total RNA isolation as described in Chang et al. (1993) with minor modifications as described in Le-Provost et al (2007).

treatment_protocol: Seven elevated B toxicity treatment was applied to sapling grown in pots by adding 0, 5, 10, 20, 40, 80 and 160 ppm boric acid to irrigation water. Each B treatment was applied to 5 rotted cuttings/clone (replication) at the field capacity

tag: clone id

tag: phentoype

value: tolerant to boron toxicity and accumulation

tag: age

value: one year old rooted cuttings

tag: treated with

value: 2ppm boron (control condition)

tag: tissue

value: leaf


title: Black poplar root grown under boron toxicity (15 ppm)_rep1

description:
Gene expression data from the roots of boron toxicity tolerant Black poplar genotype
P.n_160_Root 1_(Poplar)

source_name: Black poplar root_boron toxicity (15 ppm)control

value: 15 ppm boron (boron toxicity)

value: root


title: Black poplar root grown under control condition (2 ppm)_rep1

description:
Gene expression data from the roots of boron toxicity tolerant Black poplar genotype
P.n_Cont_Root 1_(Poplar)

source_name: Black poplar root_control condition (2 ppm)control


title: Black poplar root grown under boron toxicity (15 ppm)_rep2

description:
Gene expression data from the roots of boron toxicity tolerant Black poplar genotype
P.n_160_Root 2_(Poplar)


title: ABCB9_p.R281L_rep6_TA.OE014_A549_96H_X6_B19:G05


title: Black poplar root grown under control condition (2 ppm)_rep2

description:
Gene expression data from the roots of boron toxicity tolerant Black poplar genotype
P.n_Cont_Root 2_(Poplar)


title: Black poplar leaf grown under boron toxicity (15 ppm)_rep2

description:
Gene expression data from the leaves of boron toxicity tolerant Black poplar genotype
P.n_160_Leaf 2_(Poplar)

source_name: Black poplar leaf_boron toxicity (15 ppm)control


title: Black poplar leaf grown under control condition (2 ppm)_rep2

description:
Gene expression data from the leaves of boron toxicity tolerant Black poplar genotype
P.n_Cont_Leaf 2_(Poplar)


title: MDM2_WT_rep23_TA.OE014_A549_96H_X6_B19:F20


title: TBTO_48h_Exp2

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: Amplified, biotinylated and fragmented targets were then hybridized on to the arrays.

scan_protocol: After hybridization, arrays were washed and stained using an Affymetrix fluidics station and scanned by use of an Affymetrix GeneArray scanner. A total of 189 RNA samples was prepared and analyzed on GeneChip arrays (treated and control samples from each time point were at least in triplicate). Normalization quality controls, including scaling factors, average intensities, present calls, background intensities, noise, and raw Q values, appeared to be within acceptable limits for all chips. Hybridization controls BioB, BioC, BioD, and CreX were called present on all chips and yielded the expected increases in intensities.

data_processing: All raw datasets from generated CEL files were first imported into R2.11.0 and run through an in-house quality control pipeline (available through ArrayAnalysis.org (Eijssen et al, 2013)) and then used for statistical analysis. R package is freely available for academic use from the Comprehensive R Archive Network (http://www.cran.r-project.org/). The probe sets were re-annotated by use of custom Cell Definition Files (CDF) (version 12.1.0. http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/12.1.0/entrezg.asp). This resulted in a list of 16,331 unique gene IDs. After re-annotation, data were normalized by Robust Multichip Average (RMA) normalization and log2 transformed using the R package “affy”. Low expression genes were filtered out by using a log[intensity cutoff] >5. This cutoff was based on the 1st quartile of the distribution of average intensities of all reporters.

organism: Mus musculus

label_protocol: High-density oligonucleotide GeneChips from Affymetrix were used to measure gene expression levels (Mouse Genome 430 2.0 array (45101 probes)). Targets for these arrays were prepared from 250 ng of total RNA by means of the GeneChip 3’ IVT Express Kit according to the Affymetrix protocol (Affymetrix UK Ltd, High Wycombe, UK).

growth_protocol: PMH were isolated from adult male C57BL/6 mice using a perfusion method and cultured between a collagen-collagen sandwich formation in two six wells plates as described before.

extract_protocol: At the end of treatment the medium was removed and PMH were harvested in Qiazol (QIAGEN Benelux B.V., Venlo, The Netherlands). Total RNA was isolated using a miRNeasy Mini Kit (QIAGEN Benelux B.V., Venlo, The Netherlands) according to the manufacturer’s protocol and followed by DNase I (Qiagen, Inc) treatment. Following purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific, Wilmington, USA) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies Netherlands B.V., Amstelveen, The Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 8 were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After a recovery period of 40-42h, the Dulbecco's Modified Eagle's (Gibco BRL, Breda, The Netherlands) culture medium was replaced by culture medium containing either one of the 21 compounds or a vehicle control (0.5% of DMSO, PBS, EtOH). Seventeen chemicals were obtained through Sigma-Aldrich, TCDD through Cerilliant, DMBA through ICN, E2 through Steraloids Inc. and PhB through Brocacef Intramuraal bv. A dose causing minimal cytotoxicity after 24h of exposure thus resulting in ±80% viability, was established by the MTT assay (Mosmann, 1983). Next, cells were treated with an IC20-24h dose of di(2-ethylhexyl)phthalate(DEHP),4-Acetylaminofluorene(4AAF),Curcumin(Cur),Phenobarbital(PhB),Reserpine(Res),7,12-Dimethylbenzanthracene (DMBA),Resorcinol(Resorcinol),Para-cresidine(pCres),Phenacetin(Phen),Diclofenac(diclo),Wy 14643(Wy),Tributyltinoxide(TBTO),Benzo[a]pyrene(BaP),8-Hydroxyquinoline [AKA 8-quinolinol](8HQ),17-b-estradiol(E2),ampicillin(AmpC),cisplatin(CisPl),Aflatoxin B1(AFB1),Cyclosporin A(CsA),2,3,7,8-Tetrachlorodibenzo-p-dioxin(TCDD),Quercetin(Que) for 24 or 48 h before being harvested. Independent biological experiments (at least in triplicate) with hepatocytes from different mice were obtained for every time point.

tag: studymainsource

value: Mouse liver

tag: studytype

value: Single Dose Toxicity

tag: assaytype

value: ex vivo

tag: strain

tag: compound

value: Tributyltinoxide

tag: dose

tag: doseunit

value: µM

tag: doseduration

tag: durationunit

value: h

tag: dosefrequency

value: once

tag: vehicle

value: ETOH

tag: route

value: medium


title: TBTO_48h_Exp3


title: STK11_WT_rep22_TA.OE014_A549_96H_X6_B19:F18

tag: cell line

tag: genetic modification


title: NFE2L2_WT_rep22_TA.OE014_A549_96H_X6_B19:F19


title: KEAP1_WT_rep22_TA.OE014_A549_96H_X6_B19:F17


title: TBTO_48h_Exp1


title: NFE2L2_WT_rep21_TA.OE014_A549_96H_X6_B19:F16


title: TBTO_24h_Exp3


title: Black poplar leaf grown under boron toxicity (15 ppm)_rep1

description:
Gene expression data from the leaves of boron toxicity tolerant Black poplar genotype
P.n_160_Leaf 1_(Poplar)

tag: clone id

tag: phentoype

tag: age


title: MDM2_WT_rep22_TA.OE014_A549_96H_X6_B19:F15


title: EGFR_p.T790M, p.L858R_rep17_TA.OE014_A549_96H_X6_B19:F22

value: EGFR_p.T790M, p.L858R


title: Resorcinol_48h_Exp3

description: ETOH_48h_Exp3_DL-Mouse A3

tag: studymainsource

value: Resorcinol


title: Resorcinol_48h_Exp2

description: ETOH_48h_Exp2_DL-Mouse A2

tag: studytype


title: Resorcinol_24h_Exp3

description: ETOH_24h_Exp3_DL-Mouse A3

tag: assaytype


title: TBTO_24h_Exp2

tag: strain


title: Resorcinol_48h_Exp1

description: ETOH_48h_Exp1_DL-Mouse A1

tag: compound


title: TBTO_24h_Exp1

tag: dose


title: TERT_p.L593F_rep6_TA.OE014_A549_96H_X6_B19:F14


title: TP53_p.P278A_rep19_TA.OE014_A549_96H_X6_B19:F24


title: MAX_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:F08

value: MAX


title: HCRED_rep43_TA.OE014_A549_96H_X6_B19:F05

value: HCRED


title: RBM10_p.W658Y_rep6_TA.OE014_A549_96H_X6_B19:F09


title: PTEN_p.M35I_rep6_TA.OE014_A549_96H_X6_B19:F01


title: EGFR_p.T790M, p.L858R_rep16_TA.OE014_A549_96H_X6_B19:E22


title: TP53_p.P278A_rep17_TA.OE014_A549_96H_X6_B19:E23


title: KRAS_p.G12V_rep19_TA.OE014_A549_96H_X6_B19:E20


title: Res_48h_Exp2

description: DMSO_48h_Exp2_DL-Mouse A2

value: Reserpine

tag: doseunit

value: DMSO


title: Res_48h_Exp3

description: DMSO_48h_Exp3_DL-Mouse A3

tag: doseduration


title: Res_24h_Exp3

description: DMSO_24h_Exp3_DL-Mouse A3

tag: durationunit


title: Resorcinol_24h_Exp1

description: ETOH_24h_Exp1_DL-Mouse A1

tag: dosefrequency


title: EGFR_p.L858R_rep21_TA.OE014_A549_96H_X6_B19:E19


title: EGFR_p.Q1020H_rep6_TA.OE014_A549_96H_X6_B19:F12


title: Res_48h_Exp1

description: DMSO_48h_Exp1_DL-Mouse A1

tag: vehicle


title: Res_24h_Exp2

description: DMSO_24h_Exp2_DL-Mouse A2

tag: route


title: LUCIFERASE_rep36_TA.OE014_A549_96H_X6_B19:F06

tag: cell line

value: LUCIFERASE


title: Resorcinol_24h_Exp2

description: ETOH_24h_Exp2_DL-Mouse A2


title: Que_48h_Exp3

value: Quercetin

value: uM


title: Que_48h_Exp2

value: Mouse liver

value: Single Dose Toxicity


title: KEAP1_WT_rep21_TA.OE014_A549_96H_X6_B19:E15

tag: genetic modification


title: TPK1_WT_rep6_TA.OE014_A549_96H_X6_B19:E13


title: MDM2_WT_rep21_TA.OE014_A549_96H_X6_B19:E18


title: RBM45_WT_rep6_TA.OE014_A549_96H_X6_B19:E11


title: STK11_WT_rep21_TA.OE014_A549_96H_X6_B19:E24


title: FCGR3B_p.L218P_rep6_TA.OE014_A549_96H_X6_B19:E10


title: Que_48h_Exp1

value: ex vivo


title: Que_24h_Exp3


title: Res_24h_Exp1

description: DMSO_24h_Exp1_DL-Mouse A1

value: µM


title: HAVCR2_WT_rep6_TA.OE014_A549_96H_X6_B19:E09


title: SERPINB5_p.I159S_rep6_TA.OE014_A549_96H_X6_B19:E08


title: EGFP_rep47_TA.OE014_A549_96H_X6_B19:E06

value: EGFP


title: Que_24h_Exp1

value: h

value: once


title: STK11_p.G56V_rep6_TA.OE014_A549_96H_X6_B19:E07


title: Que_24h_Exp2

value: medium


title: Phen_48h_Exp3

description: ETOH_48h_Exp3_DL-Mouse A3

value: Phenacetin

value: ETOH


title: HCRED_rep42_TA.OE014_A549_96H_X6_B19:E05


title: Phen_24h_Exp2

description: ETOH_24h_Exp2_DL-Mouse A2


title: KEAP1_p.W497L_rep5_TA.OE014_A549_96H_X6_B19:E03


title: EGFR_p.T790M_rep6_TA.OE014_A549_96H_X6_B19:D24


title: Phen_24h_Exp3

description: ETOH_24h_Exp3_DL-Mouse A3


title: Phen_48h_Exp1

description: ETOH_48h_Exp1_DL-Mouse A1


title: PhB_48h_Exp3

description: DMSO_48h_Exp3_DL-Mouse A3

value: Phenobarbital


title: Phen_24h_Exp1

description: ETOH_24h_Exp1_DL-Mouse A1


title: PhB_48h_Exp2

description: DMSO_48h_Exp2_DL-Mouse A2


title: KEAP1_p.G524C_rep6_TA.OE014_A549_96H_X6_B19:D17


title: PhB_24h_Exp3

description: DMSO_24h_Exp3_DL-Mouse A3


title: KEAP1_p.S144F_rep6_TA.OE014_A549_96H_X6_B19:D13


title: PhB_48h_Exp1

description: DMSO_48h_Exp1_DL-Mouse A1


title: RBM34_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:D21


title: KEAP1_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:D14


title: PhB_24h_Exp1

description: DMSO_24h_Exp1_DL-Mouse A1


title: PhB_24h_Exp2

description: DMSO_24h_Exp2_DL-Mouse A2


title: Phen_48h_Exp2

description: ETOH_48h_Exp2_DL-Mouse A2


title: KEAP1_p.S102L_rep6_TA.OE014_A549_96H_X6_B19:D12


title: FAM173B_p.R187P_rep6_TA.OE014_A549_96H_X6_B19:D05


title: pCres_48h_Exp3

description: ETOH_48h_Exp3_DL-Mouse A3

value: Para-cresidine


title: pCres_48h_Exp1

description: ETOH_48h_Exp1_DL-Mouse A1


title: ZBTB24_p.Q669R_rep6_TA.OE014_A549_96H_X6_B19:D08


title: BFP_rep39_TA.OE014_A549_96H_X6_B19:D03

value: BFP


title: pCres_48h_Exp2

description: ETOH_48h_Exp2_DL-Mouse A2


title: DCAF8_p.R559P_rep6_TA.OE014_A549_96H_X6_B19:D06


title: SERPINB5_p.A165T_rep4_TA.OE014_A549_96H_X6_B19:C23


title: pCres_24h_Exp2

description: ETOH_24h_Exp2_DL-Mouse A2


title: pCres_24h_Exp1

description: ETOH_24h_Exp1_DL-Mouse A1


title: SERPINB5_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:D02


title: HCRED_rep41_TA.OE014_A549_96H_X6_B19:D04

value: HCRED


title: ZBTB24_p.G693S_rep5_TA.OE014_A549_96H_X6_B19:C22


title: FCGR3B_WT_rep4_TA.OE014_A549_96H_X6_B19:C20


title: EtOH_48h_Exp3_LR_10071

value: ethanol


title: TPK1_p.L185I_rep6_TA.OE014_A549_96H_X6_B19:C18


title: ETOH_48h_Exp3_PvK_5

value: Ethanol


title: EtOH_48h_Exp2_LR_10016


title: ETOH_48h_Exp2_PvK_4


title: ETOH_48h_Exp3_DL_Mouse_A3


title: ETOH_48h_Exp2_DL_Mouse_A2


title: CTNNB1_p.V600G_rep6_TA.OE014_A549_96H_X6_B19:C09


title: pCres_24h_Exp3

description: ETOH_24h_Exp3_DL-Mouse A3


title: ETOH_48h_Exp1_PvK_3


title: EtOH_48h_Exp1_LR_10015


title: CTNNB1_p.G34V_rep6_TA.OE014_A549_96H_X6_B19:C07


title: ETOH_48h_Exp1_DL_Mouse_A1


title: ARAF_p.S214F.p.D429A_rep4_TA.OE014_A549_96H_X6_B19:C05


title: HCRED_rep40_TA.OE014_A549_96H_X6_B19:C04


title: MAX_p.R35L_rep6_TA.OE014_A549_96H_X6_B19:C13


title: STK11_p.L245F_rep5_TA.OE014_A549_96H_X6_B19:C02


title: ABCB9_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:C01


title: FAIM_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B24

value: FAIM


title: DNMT3A_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:B23


title: ZBTB24_p.K123M_rep6_TA.OE014_A549_96H_X6_B19:C08


title: EtOH_24h_Exp3_LR_10070

value: Mouse liver


title: ETOH_24h_Exp3_DL_Mouse_A3

value: Single Dose Toxicity


title: EtOH_24h_Exp2_LR_10014

value: ex vivo


title: ETOH_24h_Exp2_DL_Mouse_A2


title: DECR1_WT_V5_rep4_TA.OE014_A549_96H_X6_B19:B22


title: MRPS16_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B19


title: MVP_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B18

value: MVP


title: EtOH_24h_Exp1_LR_10013


title: RNH1_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B21


title: ETOH_24h_Exp1_DL_Mouse_A1


title: E2_48h_Exp3

value: uM

value: DMSO


title: E2_48h_Exp1

value: h

value: once


title: ETOH_24h_Exp3_PvK_5

value: medium


title: BMP4_WT_V5_rep5_TA.OE014_A549_96H_X6_B19:B20


title: E2_48h_Exp2


title: E2_24h_Exp3


title: E2_24h_Exp1


title: NFE2L2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B17


title: DNAJC15_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B15


title: EGFP_rep46_TA.OE014_A549_96H_X6_B19:C03

value: EGFP


title: CDC45_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B16


title: E2_24h_Exp2


title: EGFR_p.R222L_rep6_TA.OE014_A549_96H_X6_B19:B14


title: DMSO_48h_Exp3_DL_Mouse_A3

value: dimethylsulfoxide


title: ETOH_24h_Exp2_PvK_4

value: ETOH


title: STK11_p.G242W_rep6_TA.OE014_A549_96H_X6_B19:B13


title: EGFR_WT_rep20_TA.OE014_A549_96H_X6_B19:F21

value: EGFR


title: ZBTB24_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B11


title: ETOH_24h_Exp4_PvK_6


title: DMSO_48h_Exp2_LR_10033


title: DMSO_48h_Exp3_LR_10034


title: DMSO_48h_Exp2_PvK_4


title: PTEN_WT_rep6_TA.OE014_A549_96H_X6_B19:B10

value: PTEN


title: LUCIFERASE_rep35_TA.OE014_A549_96H_X6_B19:B05

value: LUCIFERASE


title: EGFR_p.S645C_rep6_TA.OE014_A549_96H_X6_B19:B08


title: DMSO_48h_Exp2_LR_10086


title: RHEB_WT_V5_rep4_TA.OE014_A549_96H_X6_B19:A24

value: RHEB


title: CTNNB1_p.S33N_rep6_TA.OE014_A549_96H_X6_B19:B07


title: EGFP_rep45_TA.OE014_A549_96H_X6_B19:B06


title: MFSD10_WT_rep6_TA.OE014_A549_96H_X6_B19:B04


title: DMSO_48h_Exp1_PvK_3


title: DNTTIP2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A23


title: TRAP1_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:B03


title: PIH1D1_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A20


title: DMSO_48h_Exp2_DL_Mouse_A2


title: CCL2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A21


title: DMSO_48h_Exp1_LR_10023


title: DMSO_48h_Exp1_LR_10085


title: GRB7_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A16


title: EXOSC4_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A22


title: PYGL_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A18

value: PYGL


title: MTERFD1_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A19


title: NUP88_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A15


title: DMSO_48h_Exp1_DL_Mouse_A1

value: Mouse liver


title: DMSO_24h_Exp3_PvK_3

value: Single Dose Toxicity


title: DMSO_24h_Exp3_LR_10032

value: ex vivo


title: DC live t=36h D7_224

city: San Francisco

first: Mark

last: Voorhies

state: CA

address: 513 Parnassus, S472

department: Microbiology and Immunology

institute: University of California

hyb_protocol: Probes were hybridized to MEEBO (mouse exonic evidence-based oligonucleotide) microarrays (http://alizadehlab.stanford.edu/) using a pooled reference strategy in which Cy5-labeled aRNA samples corresponding to each time point were competitively hybridized against a Cy-3 labeled reference pool containing equal amounts of all infected and uninfected samples. Arrays were hybridized for 36 hours at 63C.

scan_protocol: Arrays were scanned on a GenePix 4000B scanner (Axon Instruments).

data_processing:
Arrays were gridded using GenePix Pro, version 6.0 (Molecular Devices)
and median normalized using NOMAD 2.0 (http://nomad2.ucsf.edu/).  To
eliminate elements with low signal, we analyzed only elements for
which the sum of the medians for the 635 nm and 532 nm channels was >=
500 intensity units.  Median normalized ratios for elements passing this
threshold are given in the VALUE column.

source_name: DC live t=36h D7_224

label_protocol:
Microarray probes were generated by coupling aRNA to Cy5 or Cy3
    monofunctional dyes (Amersham).

extract_protocol:
Total RNA was isolated
at various time points post-infection using the RNeasy Mini Extraction
Kit (Qiagen) and amplified using the Amino Allyl MessageAmp II aRNA
Amplification Kit (Applied Biosystems).

source_name: pooled reference


title: PIK3R3_p.P127L_rep6_TA.OE014_A549_96H_X6_B19:A13


title: DMSO_24h_Exp3_DL_Mouse_A3


title: DC live t=24h D7_221

source_name: DC live t=24h D7_221


title: DC live t=12h D7_180

source_name: DC live t=12h D7_180


title: DMSO_24h_Exp2_LR_10084


title: DC live t=6h D7_238

source_name: DC live t=6h D7_238


title: DC live t=3h D7_124

source_name: DC live t=3h D7_124


title: AURKB_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A17

value: AURKB


title: HCRED_rep39_TA.OE014_A549_96H_X6_B19:A06

value: HCRED


title: DC live t=1h D7_226

source_name: DC live t=1h D7_226


title: CCND1_WT_rep6_TA.OE014_A549_96H_X6_B19:A10


title: DC UV t=36h D7_225


title: DC UV t=24h D7_222


title: BFP_rep38_TA.OE014_A549_96H_X6_B19:A05

value: BFP


title: ABCB9_WT_rep6_TA.OE014_A549_96H_X6_B19:A07


title: RBM10_WT_rep6_TA.OE014_A549_96H_X6_B19:A09


title: DMSO_24h_Exp2_LR_10027

value: h

value: DMSO


title: ACAT2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A03


title: EBNA1BP2_WT_V5_rep6_TA.OE014_A549_96H_X6_B19:A04


title: AKT1_WT_rep4_TA.OE014_A549_96H_X5_B19:P23


title: RBM34_WT_rep5_TA.OE014_A549_96H_X5_B19:P21


title: STK11_p.D194Y_rep5_TA.OE014_A549_96H_X5_B19:P20


title: FAM173B_WT_V5_rep5_TA.OE014_A549_96H_X5_B19:P19


title: DMSO_24h_Exp1_LR_10083

value: once

value: medium


title: BFP_rep37_TA.OE014_A549_96H_X5_B19:P16


title: EGFP_rep44_TA.OE014_A549_96H_X5_B19:P15

value: EGFP


title: DMSO_24h_Exp1_LR_10020

value: dimethylsulfoxide


title: DMSO_24h_Exp1_DL_Mouse_A1


title: DC UV t=12h D7_216


title: DMSO_24h_Exp2_DL_Mouse_A2


title: DMBA_48h_Exp3

description: DMSO_48h_Exp3_DL-Mouse A3

value: µM


title: KRAS_p.G13V_rep5_TA.OE014_A549_96H_X5_B19:P14


title: DC UV t=6h D7_230

source_name: DC UV t=6h D7_230


title: DC untreated t=36h D7_232

source_name: DC untreated t=36h D7_232


title: DC UV t=3h D7_209

source_name: DC UV t=3h D7_209


title: DC untreated t=24h D7_220

source_name: DC untreated t=24h D7_220


title: DC UV t=1h D7_122

source_name: DC UV t=1h D7_122


title: SERPINB5_WT_rep5_TA.OE014_A549_96H_X5_B19:P13


title: RBM10_p.Y580F_rep4_TA.OE014_A549_96H_X5_B19:P11


title: EGFR_p.769_770insASV_rep3_TA.OE014_A549_96H_X5_B19:P12


title: ARAF_p.S214F_rep5_TA.OE014_A549_96H_X5_B19:P10


title: KEAP1_p.E117K_rep5_TA.OE014_A549_96H_X5_B19:P09


title: KEAP1_p.G419W_rep5_TA.OE014_A549_96H_X5_B19:P04


title: TPK1_p.G48C_rep5_TA.OE014_A549_96H_X5_B19:P08


title: DC untreated t=6h D7_237

source_name: DC untreated t=6h D7_237


title: FCGR3B_p.K179T_rep4_TA.OE014_A549_96H_X5_B19:P03


title: SERPINB5_p.D141A_rep5_TA.OE014_A549_96H_X5_B19:P02


title: ZBTB24_WT_rep5_TA.OE014_A549_96H_X5_B19:O24


title: DMBA_24h_Exp3

description: DMSO_24h_Exp3_DL-Mouse A3


title: PIK3R3_p.R245C_rep5_TA.OE014_A549_96H_X5_B19:O21


title: blastocysts IVC BASAL vs IVC HIGH COMBI_rep4

type: genomic

city: Wilrijk

first: Karolien

middle: LJ

last: Desmet

state: Antwerpen

address: Universiteitsplein 1

department: Veterinary Sciences

country: Belgium

institute: University of Antwerp

description: NEFA IVC MET repl4

hyb_protocol: one Cy3 labeled DNA sample and one Cy5 DNA sample were combined and hybridized to one area of a 2x444,000 Agilent EmbryoGene microarray slide.

scan_protocol: Slides were scanned using Agilent’s High-Resolution Scanner (Agilent Technologies, CA, USA).

data_processing:
The Limma Bioconductor package was used to apply loess intra-array normalization followed by Quantile inter-array scale normalization to draw the intensities. Normalized intensities were then fitted to a linear model and Bayesian statistics of differential expression were obtained. Probes that exhibited a P-value < 0.05 and an absolute log2 fold-change of at least 1.5 were considered differentially methylated.
The file Normalized_data_all_data.txt contains the lowess normalized log2 ratio representing test/reference.

molecule: genomic DNA

organism: Bos taurus

source_name: blastocysts BASAL IVC

label_protocol: 2µg amplified gDNA was labelled using with either Cy-3 or Cy-5 dyes using ULS Fluorescent gDNA labelling kit (Kreatech Biotechnology) according to the manufacturer's protocol.

growth_protocol: Grade I cumulus oocyte complexes (COCs) were matured in groups of 50-60 in 500 μl serum-free maturation medium containing TCM199 supplemented with fatty acid-free 0.75% BSA, 0.4 mM glutamine, 0.2 mM sodium pyruvate, 0.1 mM cysteamine, 50 mg/ml gentamycin and murine epidermal growth factor (mEGF, 20 ng/ml) for 24 h in humidified air with 5% CO2 at 38.5°C. In the IVM experiment, oocytes were randomly divided in equal groups between treatment-specific maturation media. In the IVC experiment, oocytes were matured in serum-free maturation medium as mentioned above. After IVM, COCs were co-incubated in groups of 100-120 with spermatozoa at a final concentration of 106/ml for 22 h at 38.5°C in 500 μl fertilization medium (containing 114 mM NaCl, 3.1 mM KCl, 0.3 mM Na2HPO4, 2.1 mM CaCl2-2H2O, 0.4 mM MgCl2-6H2O, 25 mM bicarbonate, 1 mM pyruvate, 36 mM lactate, 2 μL/ml phenol red, 6 mg/mL fatty acid-free BSA, 50 μg/mL gentamycin and 0.72U/mL heparin) in a humidified 5% CO2 incubator. Presumptive zygotes were cultured in groups of 25 ± 4. During the IVM experiment, the presumptive zygotes were cultured in 50 μl droplets of mSOF medium with a mineral oil overlay (modular incubator: 38.5 °C, 5% CO2, 5% O2 and 90% N2) until the day of analysis. During the IVC experiment, the presumptive zygotes were incubated in a reduced surface 96-well dish containing 75 µl medium without mineral oil overlay (modular incubator: 38.5°C, 5% CO2, 5% O2 and 90% N2). The mSOF medium contained 108 mM NaCl, 7.2 mM KCl, 1.2 mM KH2PO4, 0.8 mM MgSO4.7H2O, 0.6mM sodium lactate, 25 mM NaHCO3, 0.0266 mM phenol red, 0.73 mM sodium pyruvate, 1.78 mM CaCl2.2H2O, 0.34 mM trisodium citrate, 2.755 mM myoinositol, 3% v/v BME 50x, 1% v/v MEM 100x, 0.4 mM glutamine, 5% fetal bovine serum and 50 μg/mL gentamycin. For the IVC experiment, NEFAs were added to the mSOF medium at concentrations according to the treatment.

extract_protocol: Genomic DNA (gDNA) and total RNA were extracted from pools of 10 blastocysts (per treatment of each replicate) using the Allprep DNA/RNA micro kit (Qiagen) according to the manufacturer's protocol.

treatment_protocol: In the IVM experiment, oocytes were exposed to the following conditions: 1) BASAL: physiological NEFA concentrations (72 μM total NEFA containing 28 μM stearic acid (SA), 23 μM palmitic acid (PA) and 21 μM oleic acid (OA)). 2) HIGH COMBI: a combination of elevated NEFA concentrations equivalent to those measured in the follicular fluid during severe lipolytic conditions (425 μM total NEFA, containing 75 μM SA, 150 μM PA and 200 μM OA). In the IVC experiment, embryos were exposed to the following conditions: 1) BASAL: physiological NEFA concentrations (72 μM total NEFA containing 28 μM SA, 23 μM PA, and 21 μM OA). 2) HIGH COMBI: a combination of elevated NEFA concentrations equivalent to those measured in serum under high lipolytic conditions (720 μM total NEFA, containing 280 μM SA, 230 μM PA, and 210 μM OA).

tag: tissue

value: day 7.5 embryo

tag: nefa concentration

value: BASAL

tag: nefa exposure stage

value: in vitro cultured embryo

source_name: blastocysts HIGH COMBI IVC

value: HIGH COMBI


title: DCAF8_WT_rep5_TA.OE014_A549_96H_X5_B19:O19


title: EGFP_rep43_TA.OE014_A549_96H_X5_B19:O16


title: DMBA_24h_Exp2

description: DMSO_24h_Exp2_DL-Mouse A2

tag: studymainsource

value: Mouse liver


title: KEAP1_p.R601W_rep5_TA.OE014_A549_96H_X5_B19:O17


title: DMBA_48h_Exp2

description: DMSO_48h_Exp2_DL-Mouse A2

tag: studytype

value: Single Dose Toxicity


title: diclo_48h_Exp2

tag: assaytype

value: ex vivo

value: Diclofenac


title: DMBA_24h_Exp1

description: DMSO_24h_Exp1_DL-Mouse A1

tag: strain


title: diclo_48h_Exp1

tag: compound


title: MO live t=36h D7_118

source_name: MO live t=36h D7_118


title: MO live t=12h D7_112

source_name: MO live t=12h D7_112


title: MO live t=24h D7_115

source_name: MO live t=24h D7_115


title: blastocysts IVC BASAL vs IVC HIGH COMBI_rep3

description: NEFA IVC MET repl3


title: DC untreated t=3h D7_123

source_name: DC untreated t=3h D7_123

source_name: pooled reference


title: MO live t=6h D7_109

source_name: MO live t=6h D7_109


title: DC untreated t=1h D7_120

source_name: DC untreated t=1h D7_120


title: DC untreated t=12h D7_231

source_name: DC untreated t=12h D7_231


title: diclo_24h_Exp3

tag: dose


title: diclo_24h_Exp2

tag: doseunit


title: DMBA_48h_Exp1

description: DMSO_48h_Exp1_DL-Mouse A1

tag: doseduration


title: blastocysts IVC BASAL vs IVC HIGH COMBI_rep2

description: NEFA IVC MET repl2


title: MAX_p.R60del_rep5_TA.OE014_A549_96H_X5_B19:O13


title: KEAP1_p.L268P_rep5_TA.OE014_A549_96H_X5_B19:O11


title: MO live t=1h D7_233

source_name: MO live t=1h D7_233


title: blastocysts IVM BASAL vs IVM HIGH COMBI_rep3

description: NEFA IVM MET repl3

source_name: blastocysts BASAL IVM

value: in vitro matured oocyte

source_name: blastocysts HIGH COMBI IVM


title: LUCIFERASE_rep34_TA.OE014_A549_96H_X5_B19:O15

value: LUCIFERASE


title: HAVCR2_WT_V5_rep5_TA.OE014_A549_96H_X5_B19:O09


title: RBM45_WT_V5_rep5_TA.OE014_A549_96H_X5_B19:O14


title: MO UV t=36h D7_119


title: DEHP_48h_Exp3

description: DMSO_48h_Exp3_DL-Mouse A3

tag: durationunit

value: h


title: blastocysts IVM BASAL vs IVM HIGH COMBI_rep2

description: NEFA IVM MET repl2


title: DEHP_48h_Exp2

description: DMSO_48h_Exp2_DL-Mouse A2

tag: dosefrequency

value: DMSO


title: blastocysts IVM BASAL vs IVM HIGH COMBI_rep4

description: NEFA IVM MET repl4


title: diclo_24h_Exp1

value: once

tag: vehicle


title: blastocysts IVC BASAL vs IVC HIGH COMBI_rep1

description: NEFA IVC MET repl1


title: MO live t=3h D7_106

source_name: MO live t=3h D7_106


title: CTNNB1_p.G367V_rep5_TA.OE014_A549_96H_X5_B19:O06


title: MO UV t=12h D7_236


title: MO UV t=24h D7_116


title: MYC_p.E366Q_rep5_TA.OE014_A549_96H_X5_B19:O07


title: DEHP_24h_Exp3

description: DMSO_24h_Exp3_DL-Mouse A3

tag: route

value: medium


title: MO UV t=1h D7_234

source_name: MO UV t=1h D7_234


title: MO untreated t=36h D7_117

source_name: MO untreated t=36h D7_117


title: MO UV t=6h D7_235

source_name: MO UV t=6h D7_235


title: MO UV t=3h D7_107

source_name: MO UV t=3h D7_107


title: KRAS_p.D33E_rep5_TA.OE014_A549_96H_X5_B19:O08

tag: cell line


title: EGFR_p.L858R_rep20_TA.OE014_A549_96H_X5_B19:N22

tag: genetic modification


title: EGFR_WT_rep19_TA.OE014_A549_96H_X5_B19:N20

value: EGFR


title: DEHP_24h_Exp1

description: DMSO_24h_Exp1_DL-Mouse A1


title: DEHP_48h_Exp1

description: DMSO_48h_Exp1_DL-Mouse A1


title: STK11_p.G251V_rep5_TA.OE014_A549_96H_X5_B19:O01


title: PTEN_p.H123Y_rep5_TA.OE014_A549_96H_X5_B19:O02


title: KEAP1_WT_rep20_TA.OE014_A549_96H_X5_B19:N18


title: MO untreated t=24h D7_114

source_name: MO untreated t=24h D7_114


title: Cur_24h_Exp3

description: DMSO_24h_Exp3_DL-Mouse A3

value: Curcumin


title: Cur_48h_Exp2

description: DMSO_48h_Exp2_DL-Mouse A2

value: µM


title: MO untreated t=12h D7_111

source_name: MO untreated t=12h D7_111


title: STK11_WT_rep20_TA.OE014_A549_96H_X5_B19:N15


title: Cur_48h_Exp3

description: DMSO_48h_Exp3_DL-Mouse A3


title: diclo_48h_Exp3


title: Cur_48h_Exp1

description: DMSO_48h_Exp1_DL-Mouse A1


title: MO untreated t=1h D7_72

source_name: MO untreated t=1h D7_72


title: MO untreated t=3h D7_105

source_name: MO untreated t=3h D7_105


title: KRAS_p.G12V_rep18_TA.OE014_A549_96H_X5_B19:N16


title: EGFP_rep42_TA.OE014_A549_96H_X5_B19:N14

value: EGFP


title: MO untreated t=6h D7_108

source_name: MO untreated t=6h D7_108


title: DEHP_24h_Exp2

description: DMSO_24h_Exp2_DL-Mouse A2


title: AmpC_48h_Exp3

value: ampicillin

value: uM


title: Cur_24h_Exp2

description: DMSO_24h_Exp2_DL-Mouse A2


title: PIK3R3_p.M295T_rep5_TA.OE014_A549_96H_X5_B19:N12


title: HCRED_rep38_TA.OE014_A549_96H_X5_B19:N13

value: HCRED


title: EGFR_p.L858R_rep19_TA.OE014_A549_96H_X5_B19:N19


title: CTNNB1_p.S45F_rep5_TA.OE014_A549_96H_X5_B19:N11


title: AmpC_48h_Exp1

value: Mouse liver


title: ARAF_WT_rep5_TA.OE014_A549_96H_X5_B19:N09

value: ARAF


title: CTNNB1_p.F777S_rep5_TA.OE014_A549_96H_X5_B19:N10


title: AmpC_24h_Exp3

value: Single Dose Toxicity

value: ex vivo


title: Cur_24h_Exp1

description: DMSO_24h_Exp1_DL-Mouse A1


title: AmpC_24h_Exp2


title: STK11_p.D176H_rep5_TA.OE014_A549_96H_X5_B19:N07


title: AmpC_24h_Exp1


title: HAVCR2_p.P6S_rep5_TA.OE014_A549_96H_X5_B19:N05


title: EGFR_p.D837A_rep4_TA.OE014_A549_96H_X5_B19:N03


title: 8HQ_48h_Exp1

value: 8-Hydroxyquinoline [AKA 8-quinolinol]

value: ETOH


title: AmpC_48h_Exp2

value: h


title: 8HQ_24h_Exp3


title: DCAF8_p.P156S_rep5_TA.OE014_A549_96H_X5_B19:N04


title: MatA Cells Treated with IP-1 after 30 minutes Replicate 1

city: Mexico DF

first: Gabriel

last: Del Rio

state: DF

address: Circuito exterior s/n, Delegacion Coyacan

department: Biochemistry and Structural Biology

country: Mexico

institute: Instituto de Fisiologia Celular, UNAM

description:
raw data file: YOMWG_10_05.txt
MatA IP1 30 min Rep1
RNA extracted from cells grown for 30 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 30 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.

scan_protocol: Acquisition and quantification of array images was performed in ScanArray 4000 with its accompanying software ScanArray 4000 from Packard BioChips. All images were captured using 60% PMT gain, 70 to 75% laser power and 10µm resolution at 50% scan rate

data_processing: For each spot the density mean, background mean and normalized signal mean values were calculated with software ArrayPro Analyzer from Media Cybernetics.

organism: Saccharomyces cerevisiae

source_name: MatA cells grown for 30 minutes

label_protocol: 10 μg of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 or dUTP-Cy5 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Cy3 and 655 for Cy5. Equal quantities of labeled cDNA were hybridized using hybridization solution HybIT2 (TeleChem International INC), to the collection of yeast arrays for 14 h at 42°C. dUTP-Cy3 was used to labeled RNA extracted from cells not exposed to the peptide (control) and dUTP-Cy5 to label for RNA extracted from cells treated with Iztli peptide 1

growth_protocol: Cells were grown in YPD media (1% yeast extract, 2% peptone, 2% glucose/dextrose) to reach 0.4 OD at 600 nm; 10 microM of IP-1 was added to the culture and after 30 minutes cells were treated with x to stop reaction and prepare cells to extract RNA.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: BY4741 MatA

tag: passage

source_name: MatA cells exposed for 30 minutes to IP-1

tag: exposed to

value: IP-1 for 30 minutes


title: 8HQ_48h_Exp2

value: once

value: medium


title: MatA Cells Treated with IP-1 after 30 minutes Replicate 2

description:
raw data file: YOMWG_10_05.txt
MatA IP1 30 min Rep2
RNA extracted from cells grown for 30 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 30 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.

hyb_protocol: Equal quantities of labeled cDNA were hybridized using hybridization solution HybIT2 (TeleChem International INC), to the collection of yeast arrays for 14 h at 42°C

treatment_protocol: 10 μg of total RNA were used for cDNA synthesis incorporating dUTP-Cy3 or dUTP-Cy5 employing the CyScribe Firs-Strand cDNA labeling kit (Amersham). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Cy3 and 655 for Cy5


title: 8HQ_24h_Exp2


title: NFE2L2_WT_rep20_TA.OE014_A549_96H_X5_B19:M21


title: KEAP1_WT_rep19_TA.OE014_A549_96H_X5_B19:M24


title: MatA Cells Treated with IP-1 after 15 minutes Replicate 2

description:
raw data file: YOMWG_10_04.txt
MatA IP1 15 min Rep2
RNA extracted from cells grown for 15 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 15 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.

source_name: MatA cells grown for 15 minutes

growth_protocol: Cells were grown in YPD media (1% yeast extract, 2% peptone, 2% glucose/dextrose) to reach 0.4 OD at 600 nm; 10 microM of IP-1 was added to the culture and after 15 minutes cells were treated with x to stop reaction and prepare cells to extract RNA.

source_name: MatA cells exposed for 15 minutes to IP-1

value: IP-1 for 15 minutes


title: 8HQ_48h_Exp3


title: EGFR_WT_rep18_TA.OE014_A549_96H_X5_B19:M20

value: EGFR


title: MatA Cells Treated with IP-1 after 7 minutes Replicate 2

description:
raw data file: YOMWG_10_03.txt
MatA IP1 7 min Rep2
RNA extracted from cells grown for 7 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 7 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.

source_name: MatA cells grown for 7 minutes

growth_protocol: Cells were grown in YPD media (1% yeast extract, 2% peptone, 2% glucose/dextrose) to reach 0.4 OD at 600 nm; 10 microM of IP-1 was added to the culture and after 7 minutes cells were treated with x to stop reaction and prepare cells to extract RNA.

source_name: MatA cells exposed for 7 minutes to IP-1

value: IP-1 for 7 minutes


title: EGFR_WT_rep17_TA.OE014_A549_96H_X5_B19:M19


title: EGFR_p.L858R_rep18_TA.OE014_A549_96H_X5_B19:M18


title: 4AAF_48h_Exp1

description: DMSO_48h_Exp1_DL-Mouse A1

value: µM

value: DMSO


title: 4AAF_48h_Exp2

description: DMSO_48h_Exp2_DL-Mouse A2


title: MatA Cells Treated with IP-1 after 3.5 minutes Replicate 2

description:
raw data file: YOMWG_10_02.txt
MatA IP1 3.5 min Rep2
RNA extracted from cells grown for 3.5 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 3.5 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.

source_name: MatA cells grown for 3.5 minutes

growth_protocol: Cells were grown in YPD media (1% yeast extract, 2% peptone, 2% glucose/dextrose) to reach 0.4 OD at 600 nm; 10 microM of IP-1 was added to the culture and after 3.5 minutes cells were treated with x to stop reaction and prepare cells to extract RNA.

source_name: MatA cells exposed for 3.5 minutes to IP-1

value: IP-1 for 3.5 minutes


title: NFE2L2_WT_rep19_TA.OE014_A549_96H_X5_B19:M16


title: 8HQ_24h_Exp1

value: Mouse liver

value: uM


title: MatA Cells Treated with IP-1 after 3.5 minutes Replicate 1

description:
raw data file: YOMWG_10_02.txt
MatA IP1 3.5 min Rep1
RNA extracted from cells grown for 3.5 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 3.5 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.


title: 4AAF_24h_Exp3

description: DMSO_24h_Exp3_DL-Mouse A3

value: Single Dose Toxicity


title: 4AAF_24h_Exp1

description: DMSO_24h_Exp1_DL-Mouse A1

value: ex vivo


title: MatA Cells Treated with IP-1 after 7 minutes Replicate 1

description:
raw data file: YOMWG_10_03.txt
MatA IP1 7 min Rep1
RNA extracted from cells grown for 7 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 7 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.


title: 4AAF_24h_Exp2

description: DMSO_24h_Exp2_DL-Mouse A2


title: Liver_Control_rep4

status: Public on Jun 27 2016

city: Hangzhou

first: Kunkai

last: Su

address: 79 Qingchun Road

country: China

institute: Zhejiang University

description:
B8
Eight-week-old male pathogen-free BALB/c mice were treated with saline as a control.

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual.

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that had intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering.

source_name: Liver, saline

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

growth_protocol: All mice were raised in a pathogen-free room and the room was maintained at a constant temperature of 23±1℃ with a 12 h light/dark cycle. Food and water were available ad libitum in the home cages.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer's instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity were measured by using Nanodrop spectrophotometer (ND-1000, Nanodrop Technologies), and RNA Integrity was determined by gel electrophoresis.

treatment_protocol: Mice were sacrificed after 2 hours challenge of the Con A. Livers were excised immediately after sacrifice. Part of the livers were immediately snap-frozen in liquid nitrogen and kept at -80°C for total RNA isolation and microRNA microarray analysis.

tag: strain/background

value: BALB/c

tag: gender

value: male

tag: age

value: 8 weeks

tag: tissue

value: liver

tag: treatment

value: saline (same volume to Con A solution)


title: 4AAF_48h_Exp3

description: DMSO_48h_Exp3_DL-Mouse A3

tag: studymainsource

tag: studytype

tag: assaytype

tag: strain

tag: compound

value: h

value: once


title: Liver_Control_rep2

description:
B6
Eight-week-old male pathogen-free BALB/c mice were treated with saline as a control.


title: MatA Cells Treated with IP-1 after 15 minutes Replicate 1

description:
raw data file: YOMWG_10_04.txt
MatA IP1 15 min Rep1
RNA extracted from cells grown for 15 min in YPD and labeled with Cy3 were hybridized against the S. cereviseae ORF probes fixed in the microarray plate. Two experimental replicates were included per plate. In the same plate, RNA extracted from cells exposed to IP-1 for 15 min grown in YPD and labeled with Cy5 were hybridized against the S. cereviseae ORF probes fixed in the plate. Two experimental replicates were included per plate.

value: BY4741 MatA

value: IP-1 for 15 minutes


title: Liver_Control_rep1

description:
B5
Eight-week-old male pathogen-free BALB/c mice were treated with saline as a control.


title: Liver_Control_rep3

description:
B7
Eight-week-old male pathogen-free BALB/c mice were treated with saline as a control.


title: STK11_WT_rep19_TA.OE014_A549_96H_X5_B19:M17


title: Liver_Con A_rep3

description:
A4
Eight-week-old male pathogen-free BALB/c mice were used for the induction of Con A-induced hepatitis.

source_name: Liver, Con A

value: concanavalin A (20 mg/kg) for 2hr


title: Liver_Con A_rep2

description:
A3
Eight-week-old male pathogen-free BALB/c mice were used for the induction of Con A-induced hepatitis.


title: Liver_Con A_rep1

description:
A1
Eight-week-old male pathogen-free BALB/c mice were used for the induction of Con A-induced hepatitis.


title: Liver_Con A_rep4

description:
A9
Eight-week-old male pathogen-free BALB/c mice were used for the induction of Con A-induced hepatitis.


title: GMPder_noDOX_48h_B6-2

city: Basel

first: Antoine

last: Peters

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research (FMI)

hyb_protocol: Following fragmentation, 2.75 ug of ssDNA were hybridized to Mouse Gene 1.0 GeneChips for 16 hours at 45 °C. Gene Chips were washed and stained at the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using am Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed using the affy and limma package of the statistical language R (version 3.1.1) in the Bioconductor environment.

source_name: in vitro immortalized GMP der. -dox 48h, biological rep1

label_protocol: 19 ng of RNA in 5 ul volume was used for the Ovation Pico WTA System (NuGen) according to manufacturer's instructions to generate SPIA cDNA. 3 ug of SPIA cDNA was used to generate sense target cDNA with the WT Ovation Exon module according to manufacturer's instructions. 5.5 ug single-stranded DNA was fragmented and labelled using the Affymetrix GeneChip WT Terminal Labelling kit according to manufacturer's instructions.

growth_protocol: The respective cells or tissue were collected as described above.

extract_protocol: Total RNA was isolated with the Pico Pure extraction kit from Applied Biosystems (Catalog number KIT0204).

treatment_protocol: The samples were washed in PBS buffer, resuspended in 100 ul Pico Pure lysis buffer and frozen to -80°C until RNA isolation.

value: cells harvested from liquid medium


title: GMPder_noDOX_48h_B6-3

source_name: in vitro immortalized GMP der. -dox 48h, biological rep2


title: GMPder_DOX_48h_B6-1

source_name: in vitro immortalized GMP der. +dox 48h, biological rep4


title: GMPder_noDOX_48h_F6-6

source_name: in vitro immortalized GMP der. -dox 48h, biological rep3


title: GMPder_DOX_48h_B6-2

source_name: in vitro immortalized GMP der. +dox 48h, biological rep1


title: GMPder_DOX_48h_B6-3

source_name: in vitro immortalized GMP der. +dox 48h, biological rep2


title: GMPder_DOX_48h_F6-6

source_name: in vitro immortalized GMP der. +dox 48h, biological rep3


title: LTHSCder_noDOX_48h_B6-1

source_name: in vitro immortalized LT-HSC der. -dox 48h, biological rep3


title: KO, Lipid A

city: Bunkyo-ku

first: Rumi

last: Hachiya

state: Tokyo

address: 1-5-45 Yushima

department: Molecular Endocrinology and Metabolism

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression data from peritoneal macrphages

hyb_protocol: Following fragmentation, cRNA were hybridized on Mouse Genome 430 2.0. GeneChips were washed and stained in the GeneChip Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software Version 1.4.0.036 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: KO macrophages stimulated with Lipid A

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Extraction of total RNA was performed using RNeasy Plus Universal Mini Kit.

treatment_protocol: Peritoneal macrophages from WT and KO mice were stimulated by lipid A  10 ug/ml or vehicle for 4 h.

tag: cell type

value: Peritoneal macrophages

tag: genotype

value: Setdb1 KO


title: WT, vehicle

source_name: WT macrophages stimulated with vehicle

value: wildtype


title: LTHSCder_noDOX_72h_B6-3

source_name: in vitro immortalized LT-HSC der. -dox 72h, biological rep2


title: Lung_WT_12moDT_rep1

city: Obu

first: Masataka

last: Sugimoto

state: Aichi

address: 7-430 Morioka-cho

department: Cellular Pathology

institute: National Center for Geriatrics and Gerontology

description: Gene expression in adult wild type lung

hyb_protocol: Probe fragmentation (600ng) was performed at 60 degree for 30 minutes, and hybridized to Agilent SurePrint G3 Mouse GE microarrays (G4852A) at 65 degree, 10rpm for 17 hours in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 degree with GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using Scan Control, version A.8.5.1. Scanning parameters were as follow: Dye channel - green, Scan region - Agilent HD (61x21.6 mm), TIFF file dinamic range - 20bit, R/G PMT gain - 100%, Scan resolution 3um.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20131202).

source_name: Wild type, adult, treated with DT

label_protocol: cRNA was synthesized using T7 RNA polymerase and labeled with Cyanine 3 dye (Agilent Technologies) followed by purification with Rneasy mini kit (Qiagen).

extract_protocol: Lungs were homogenized using ULTRA-TURRAX T8 (IKA) prior to RNA extraction. RNA was extracted using Rneasy mini kit (Qiagen) and treated with Rnase-Free Dnase Set (Qiagen).

treatment_protocol: 12-month-old female ARF-DTR or wild type mice were intraperitoneally administrated with PBS or DT (50 microgram/kg bodyweight) with two week interval for one month. 2-month-old ARF-DTR were sacrificed without treatment.

value: Lung

value: Female

value: 12 month

tag: genotype/variation

value: wild type

value: DT


title: LTHSCder_noDOX_48h_B6-3

source_name: in vitro immortalized LT-HSC der. -dox 48h, biological rep2


title: Lung_ARF-DTR_12moDT_rep3

description: Gene expression in adult ARF-DTR lung treated with DT

source_name: ARF-DTR, adult, treated with DT

value: ARF-DTR


title: Lung_WT_12mo_rep2

description: Gene expression in adult wild type lung

source_name: Wild type, adult, control (PBS)

value: PBS


title: WT, Lipid A

source_name: WT macrophages stimulated with Lipid A


title: Lung_ARF-DTR_12moDT_rep1


title: Lung_WT_12mo_rep1

description: Gene expression in adult wild type lung treated with DT


title: Lung_ARF-DTR_12mo_rep3

description: Gene expression in adult ARF-DTR lung

source_name: ARF-DTR, adult, control (PBS)


title: KO, vehicle

source_name: KO macrophages stimulated with vehicle


title: LTHSCder_DOX_72h_B6-3

source_name: in vitro immortalized LT-HSC der. +dox 72h, biological rep2


title: LTHSCder_DOX_72h_B6-1

source_name: in vitro immortalized LT-HSC der. +dox 72h, biological rep3


title: LTHSCder_noDOX_72h_B6-1

source_name: in vitro immortalized LT-HSC der. -dox 72h, biological rep3


title: Lung_WT_12moDT_rep2

description: Gene expression in adult wild type lung


title: LTHSCder_DOX_48h_B6-3

source_name: in vitro immortalized LT-HSC der. +dox 48h, biological rep2


title: Lung_ARF-DTR_12moDT_rep4


title: Lung_ARF-DTR_12mo_rep4

description: Gene expression in adult ARF-DTR lung


title: Lung_ARF-DTR_12moDT_rep2


title: blastocysts IVM BASAL vs IVM HIGH COMBI_rep1

description: NEFA IVM MET repl1

source_name: blastocysts BASAL IVM

value: day 7.5 embryo

tag: nefa concentration

value: BASAL

tag: nefa exposure stage

value: in vitro matured oocyte

source_name: blastocysts HIGH COMBI IVM

value: HIGH COMBI


title: Lung_ARF-DTR_12mo_rep2

description: Gene expression in adult ARF-DTR lung


title: LTHSCder_noDOX_72h_B6-2

source_name: in vitro immortalized LT-HSC der. -dox 72h, biological rep1


title: LTHSCder_noDOX_48h_B6-2

source_name: in vitro immortalized LT-HSC der. -dox 48h, biological rep1


title: Lung_ARF-DTR_2mo_rep3

description: Gene expression in young ARF-DTR lung

source_name: ARF-DTR, young

value: 2 month


title: LTHSCder_DOX_72h_B6-2

source_name: in vitro immortalized LT-HSC der. +dox 72h, biological rep1


title: wt_GMP4

source_name: in vivo sorted wt GMP, biological rep4

value: FACS sorted cells from bone marrow


title: wt_GMP_3

source_name: in vivo sorted wt GMP, biological rep3


title: Lung_ARF-DTR_2mo_rep1

description: Gene expression in young ARF-DTR lung


title: Lung_ARF-DTR_2mo_rep2

description: Gene expression in young ARF-DTR lung


title: wt_LTHSC_4

source_name: in vivo sorted wt LT-HSC, biological rep4


title: wt_LTHSC_3

source_name: in vivo sorted wt LT-HSC, biological rep3


title: wt_LTHSC_2

source_name: in vivo sorted wt LT-HSC, biological rep2


title: Lung_ARF-DTR_12mo_rep1

description: Gene expression in adult ARF-DTR lung

source_name: ARF-DTR, adult, control (PBS)


title: wt_GMP_2

source_name: in vivo sorted wt GMP, biological rep2


title: Hippocampus_Mock_3

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: Mock EE4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The image-derived data were processed with Illumina GenomeStudio (v2011)

source_name: Hippocampus, Mock, Good spatial learning

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Mice were injected intracranially with 10uL of saline (Mock) or 10^4 plaque forming units of mutant West Nile Virus (WNV)-NS5-E218A at 8 weeks of age.  Between days 21 and 24 post-infection, mice were assessed for behavior on the open field test and the Barnes Maze spatial memory test and scored based on number of errors commited during the second day of Barnes Maze testing.

extract_protocol: RNA was extracted with Tri-reagent, followed by clean-up with ambion kit in accordance with the prescribed protocol provided with the kit. DNase I and RNAse-out treatment (invitrogen)was then performed following manufacturer's protocols.

treatment_protocol: At Day 25 post-infection (12 weeks of age), mice were anaesthetized and then perfused transcardially with PBS, followed by dissection of the hippocampi. Hippocampi were then dropped in Tri-Reagent and snap-frozen at -80 degrees celsius.

value: hippocampus

value: male

value: 12 weeks

tag: infection

value: Mock

tag: group

value: control


title: Hippocampus_Mock_2

description: Mock II2


title: Hippocampus_WNVGood_2

description: WNV Good LL2

source_name: Hippocampus, West Nile Virus-NS5-E218A, Good spatial learning

value: West Nile Virus-NS5-E218A

value: Fewer than 8 errors on Barnes Maze


title: LTHSCder_DOX_48h_B6-2

source_name: in vitro immortalized LT-HSC der. +dox 48h, biological rep1

value: cells harvested from liquid medium


title: wt_GMP_1

source_name: in vivo sorted wt GMP, biological rep1


title: Hippocampus_WNVPoor_2

description: WNV Poor JJ1

source_name: Hippocampus, West Nile Virus-NS5-E218A, Poor spatial learning

value: Greater than 10 errors on Barnes Maze


title: wt_LTHSC_1

source_name: in vivo sorted wt LT-HSC, biological rep1


title: Hippocampus_Mock_4

description: Mock EE2


title: Hippocampus_WNV_1

description: WNV JJ3

source_name: Hippocampus, West Nile Virus-NS5-E218A

value: other WNV-infected mouse


title: Hippocampus_WNVGood_3

description: WNV Good DD1


title: Hippocampus_WNV_2

description: WNV DD4


title: Hippocampus_Mock_1

description: Mock EE5


title: Hippocampus_WNVPoor_1

description: WNV Poor DD2


title: Hippocampus_WNVPoor_3

description: WNV Poor DD3


title: Hippocampus_WNVGood_1

description: WNV Good LL1


title: 35S-P53_rep3

status: Public on Jun 26 2016

city: Shanghai

first: Shui

last: Wang

state: Shanghai

address: 100 Guilin Rd

department: College of Life Sciences

institute: Shanghai Normal University

description: cRNA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on Affymetrix ATH1 GeneChip (Santa Clara, CA, U.S.A).

scan_protocol: GeneChips were scanned using the Axon Genepix Scanner (Genepix 4000B).

data_processing: The raw data refer to the linear data which has been summarized using a summarization algorithm (RMA16, PLIER 16 and Iterative PLIER 16). All summarization algorithms also do variance stabilization by adding 16.The normalized data are generated after the log transformation and baseline transformation step.

organism: Arabidopsis thaliana

label_protocol: RNA probes were labelled using the Ambion MessageAmp Premier.

growth_protocol: Arabidopsis seedlings were grown at 21-24°C, 16-hour day length, 60% relative humidity

extract_protocol: Total RNA was isolated from the frozen material using Invitrogen TRIzol.

treatment_protocol: 10-day-old wild type (Col-0) and 35S:P53-transgenic plants. Replicates are derived from three independent biological experiments.

value: seedling

value: 35S:P53 transgenic

tag: ecotype


title: RNA-seq for CLL patient 3873, sample 1-5-606

type: SRA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 3873, sample 1-5-606

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair per million created
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair per million; narrowPeak files contain peaks called by MACS2

source_name: Primary peripheral blood mononucleated cells (PBMC) from chronic lymphocytic leukemia patient with high leukemic cell count

extract_protocol:
All patients were diagnosed and treated at the Royal Bournemouth Hospital (UK) according to the revised guidelines of the International Workshop Chronic Lymphocytic Leukemia/National Cancer Institute (IWCLL/NCI). Patients were selected to reflect the clinical and biological heterogeneity of the disease. Sequential samples were included for a total of 24 patients. All samples contained more than 80% leukemic cells.
For ATAC-seq, accessible chromatin mapping was performed using the ATAC-seq method as previously described (Buenrostro 2013, doi:10.1038/nmeth.2688), with minor adaptations. In each experiment, 105 cells were washed once in 50 µl PBS, resuspended in 50 µl ATAC-seq lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL CA-630) and centrifuged for 10 min at 4°C. Upon centrifugation, the pellet was washed briefly in 50 µl MgCl2 buffer (10 mM Tris, pH 8.0, and 5 mM MgCl2) before incubating in the transposase reaction mix (12.5 µl 2x TD buffer, 2 µl transposase (Illumina) and 10.5 µl nuclease-free water) for 30 min at 37°C. After DNA purification with the MinElute kit, 1 µl of the eluted DNA was used in a qPCR reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 basepairs. DNA concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers (Buenrostro 2013, doi:10.1038/nmeth.2688). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 25 basepair paired-end configuration; For RNA-seq, total RNA was isolated using the AllPrep DNA/RNA Mini Kit (Qiagen). RNA amount was measured using Qubit 2.0 Fluorometric Quantitation (Life Technologies), and the RNA integrity number (RIN) was determined using Experion Automated Electrophoresis System (Bio-Rad). RNA-seq libraries were prepared using a Sciclone NGS Workstation (PerkinElmer) and a Zepyhr NGS Workstation (PerkinElmer) with the TruSeq Stranded mRNA LT sample preparation kit (Illumina). Library amount and quality were determined using Qubit 2.0 Fluorometric Quantitation (Life Technologies) and Experion Automated Electrophoresis System (Bio-Rad). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 3000/4000 platform and the 50 basepair single-read configuration; For ChIPmentation, it was carried out as previously described (Schmidl 2015, doi:10.1038/nmeth.3542), with minor adaptions. Briefly, cells were washed once with PBS and fixed with 1% paraformaldehyde in up to 1 ml PBS for 10 minutes at room temperature. Glycine was added to stop the reaction. Cells were collected at 500 x g for 10 minutes at 4°C (subsequent work was performed on ice and used cool buffers and solutions unless otherwise specified) and washed twice with up to 0.5 ml ice-cold PBS supplemented with 1 μM PMSF. The pellet was lysed in sonication buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 0.25% SDS, 1x protease inhibitors (Sigma), 1 µM PMSF) and sonicated with a Covaris S220 sonicator for 20-30 minutes in a milliTUBE or microTUBE until the size of most fragments was in the range of 200-700 basepairs. Lysates were centrifuged at full speed for 5 minutes at 4°C, and the supernatant containing the sonicated chromatin was transferred to a new tube. The lysate was then brought to RIPA buffer conditions (final concentration: 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 140 mM NaCl, 1% Triton x-100, 0.1% SDS, 0.1% DOC, 1x protease inhibitors (Sigma), 1 µM PMSF) in a volume of 200 µl/immunoprecipitation For each immunoprecipitation, 10 μl magnetic Protein A (Life Technologies) were washed twice and resuspended in PBS supplemented with 0.1% BSA. The antibody was added and bound to the beads by rotating 2 hours at 4°C. Used antibodies were H3K4me1 (0.5 μg/immunoprecipitation, Diagenode pAb-194-050), H3K27ac (1 µg/immunoprecipitation, Diagenode pAB-196-050), H3K27me3 (1 µg/immunoprecipitation, Millipore 07-499). For control libraries an IP with 2.5 µg of a nonspecific IgG rabbit antibody was used. Blocked antibody-conjugated beads were then placed on a magnet, supernatant was removed, and the sonicated lysate was added to the beads followed by incubation for 3-4 hours at 4°C on a rotator. Beads were washed subsequently with RIPA (twice), RIPA-500 (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 500 mM NaCl, 1% Triton x-100, 0.1% SDS, 0.1% DOC,) (twice), and RIPA-LiCl (10 mM Tris- HCl, pH 8.0, 1 mM EDTA, pH 8.0, 250 mM LiCl, 1% Triton X-100, 0.5% DOC, 0.5% NP40) (twice). Beads were washed once with cold Tris-Cl pH 8.0 to remove detergent, salts, and EDTA. Beads were washed once more with cold Tris-Cl pH 8.0 but the reaction was not placed on a magnet to discard supernatant immediately. Instead, the whole reaction including beads was transferred to a new tube, and then placed on a magnet to remove supernatant to decrease tagmentation of unspecific chromatin fragments sticking to the tube wall. Beads were then carefully resuspended in 25 μl of the tagmentation reaction mix (10 mM Tris pH 8.0, 5 mM MgCl2, 10% v/v dimethylformamide) containing 1 μl Tagment DNA Enzyme from the Nextera DNA Sample Prep Kit (Illumina) and incubated at 37°C for 1-3 minutes in a thermocycler. The beads were washed with RIPA (twice) and once with cold Tris-Cl pH 8. Beads were washed once more with cold Tris-Cl pH 8.0 but the reaction was not placed on a magnet to discard supernatant immediately. Instead, the whole reaction including beads was again transferred to a new tube, and then placed on a magnet to remove supernatant to remove unspecific tagmented chromatin fragments. Beads were then incubated with 70 μl elution buffer (0.5% SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris-HCl pH 8.0) containing 2 μl of Proteinase K (NEB) for 1 hour at 55°C and 8 hours at 65°C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Finally, DNA was purified with SPRI AMPure XP beads (sample-to-beads ratio 1:2) or Qiagen MinElute columns. 1 μl of each library was amplified in a 10-μl qPCR reaction containing 0.15 μM primers, 1× SYBR Green and 5 μl Kapa HiFi HotStart ReadyMix (Kapa Biosystems) to estimate the optimum number of enrichment cycles with the following program: 72°C for 5 min; 98°C for 30 s; 24 cycles of 98°C for 10 s, 63°C for 30 s; and 72°C for 30 s; and a final elongation at 72°C for 1 min. Kapa HiFi HotStart ReadyMix was incubated at 98°C for 45 s before preparation of all PCR reactions (qPCR and final enrichment PCR) to activate the hot-start enzyme for successful nick translation in the first PCR step. Final enrichment of the libraries was performed in a 50 μl reaction using 0.75 μM primers and 25 μl Kapa HiFi HotStart ReadyMix. Libraries were amplified for N+1 cycles, where N is equal to the rounded-up Cq value determined in the qPCR reaction. Enriched libraries were purified with size selection using SPRI AMPure XP beads at a beads-to-sample ratio of 1:1, followed by a size selection using AMPure XP beads to recover libraries with a fragment length of 200-400 basepairs. Library preparation was performed using custom Nextera primers as previously described for ATAC-seq (Buenrostro 2013, doi:10.1038/nmeth.2688). The libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq3000/4000 platform and the 50 basepair single-read configuration.

value: F

value: unmutated


title: RNA-seq for CLL patient 2613, sample 1-5-6916

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 2613, sample 1-5-6916

value: M

value: mutated


title: RNA-seq for CLL patient 4784, sample 1-5-52817

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 4784, sample 1-5-52817


title: RNA-seq for CLL patient 4080, sample 1-5-27302

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 4080, sample 1-5-27302


title: RNA-seq for CLL patient 4189, sample 1-5-48773

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 4189, sample 1-5-48773


title: RNA-seq for CLL patient 4333, sample 1-5-11319

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 4333, sample 1-5-11319


title: RNA-seq for CLL patient 5263, sample 1-5-60462

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 5263, sample 1-5-60462


title: Lung_ARF-DTR_2mo_rep4

description: Gene expression in young ARF-DTR lung

source_name: ARF-DTR, young

value: Lung

tag: gender

value: Female

value: 2 month

value: ARF-DTR


title: RNA-seq for CLL patient 680, sample 1-5-10787

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 680, sample 1-5-10787


title: ChIPmentation of IgG for CLL patient 5263, sample 1-5-60462

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5263, sample 1-5-60462

library_source: genomic

tag: antibody

value: IgG


title: 35S-P53_rep2

description: cRNA

tag: tissue


title: ChIPmentation of H3K4me1 for CLL patient 5263, sample 1-5-60462

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5263, sample 1-5-60462


title: ChIPmentation of H3K27me3 for CLL patient 5263, sample 1-5-60462

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5263, sample 1-5-60462


title: ChIPmentation of IgG for CLL patient 4784, sample 1-5-52817

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4784, sample 1-5-52817


title: WT_rep1

description: cRNA

value: WT


title: WT_rep3

description: cRNA


title: 35S-P53_rep1

description: cRNA


title: ChIPmentation of H3K27ac for CLL patient 4784, sample 1-5-52817

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4784, sample 1-5-52817


title: ChIPmentation of H3K4me1 for CLL patient 4784, sample 1-5-52817

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4784, sample 1-5-52817


title: RNA-seq for CLL patient 3240, sample 1-5-47651

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 3240, sample 1-5-47651


title: ChIPmentation of IgG for CLL patient 4189, sample 1-5-48773

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4189, sample 1-5-48773


title: ChIPmentation of H3K27me3 for CLL patient 4189, sample 1-5-48773

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4189, sample 1-5-48773


title: ChIPmentation of H3K4me1 for CLL patient 4189, sample 1-5-48773

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4189, sample 1-5-48773


title: ChIPmentation of H3K27ac for CLL patient 4189, sample 1-5-48773

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4189, sample 1-5-48773


title: ChIPmentation of IgG for CLL patient 4080, sample 1-5-27302

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4080, sample 1-5-27302


title: ChIPmentation of H3K27ac for CLL patient 5263, sample 1-5-60462

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 5263, sample 1-5-60462


title: ChIPmentation of H3K4me1 for CLL patient 4080, sample 1-5-27302

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4080, sample 1-5-27302


title: RNA-seq for CLL patient 1781, sample 1-5-1614

description: RNA-seq of primary peripheral blood mononucleated cells (PBMC) from CLL patient 1781, sample 1-5-1614


title: WT_rep2

description: cRNA


title: ChIPmentation of H3K27ac for CLL patient 4080, sample 1-5-27302

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4080, sample 1-5-27302


title: ChIPmentation of H3K4me1 for CLL patient 3873, sample 1-5-606

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3873, sample 1-5-606


title: ChIPmentation of H3K27ac for CLL patient 3240, sample 1-5-47651

description: ChIPmentation of H3K27ac in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3240, sample 1-5-47651


title: ChIPmentation of H3K4me1 for CLL patient 3240, sample 1-5-47651

description: ChIPmentation of H3K4me1 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3240, sample 1-5-47651


title: ChIPmentation of IgG for CLL patient 3240, sample 1-5-47651

description: ChIPmentation of IgG in primary peripheral blood mononucleated cells (PBMC) from CLL patient 3240, sample 1-5-47651


title: ChIPmentation of H3K27me3 for CLL patient 4080, sample 1-5-27302

description: ChIPmentation of H3K27me3 in primary peripheral blood mononucleated cells (PBMC) from CLL patient 4080, sample 1-5-27302