title: COV362:Ctrl_1

description: vehicle


title: OV56:ERI_2

status: Public on Oct 02 2014

type: RNA

city: Andover

first: Zoltan

last: Dezso

state: MA

address: 4 Corporate dr

country: USA

institute: Eisai Inc

description: drug

hyb_protocol: We used manufacture recommened protocol (Affymetrix). Arrays were washed and stained using Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Gene chips were analyzed using Affymetrix Microarray Analysis Suite (MAS) version 5. RMA normalization was performed using Affymetrix Power Tools version 1.12.0.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: OV56 Eribulin 24h

label_protocol: Biotinylated fragmenetd cRNA was used.

growth_protocol: Cell lines were growing in growth media recommanded by ATCC.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen).

treatment_protocol: Treated with eribulin and paclitaxel at 10xIC50 conc. for 24 hours. IC50 determinded in growth inhibitation assay for cell line separately.

tag: cell line

tag: cell type

value: ovarian cancer


title: OV56:PTX_3

description: drug

source_name: OV56 Paclitaxel 24h


title: HT29 cell treated by control for nutrient starvation

city: Xi'an

first: Ni

last: Hou

state: Shaanxi Province

address: 76 Western Yanta Road

department: Department of Genetics and Molecular Biology

country: China

institute: Xi'an Jiaotong University

description: Ctrl

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (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. Four replicated spots of each miRNA probe were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs were identified through Fold Change filtering (>=2).

source_name: HT-29 cell

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: HT29 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum at 37 °C in a humidified atmosphere of 5% CO2/ 95% air with medium changes every two days. Cells in mid-log phase were used in this study.

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 was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: For 5-FU treatment, HT29s were treated with 5 μM of 5-FU for 24 h. For nutrient starvation, HT29s were incubated in Krebs-Ringer buffer (120 mM NaCl, 5 mM KCl, , 24 mM NaHCO3, 5.6 mM glucose, 2mM CaCl2, pH 7.6) at 37 °C for 7 h.

value: colorectal carcinoma cells


title: OV56:ERI_1

description: drug


title: COV362:Ctrl_2

description: vehicle

source_name: COV362 Control


title: COV504:Ctrl_3

description: vehicle

source_name: COV504 Control


title: OV56:Ctrl_2

description: vehicle

source_name: OV56 Control


title: TOV-112D:PTX_2

description: drug

source_name: TOV-112D Paclitaxel 24h


title: TOV-112D:ERI_2

description: drug

source_name: TOV-112D Eribulin 24h


title: OV56:Ctrl_1

description: vehicle


title: OV56:PTX_2

description: drug


title: TOV-112D:PTX_3

description: drug


title: TOV-112D:ERI_1

description: durg


title: TOV-112D:Ctrl_3

description: vehicle

source_name: TOV-112D Control


title: CONTROL-11

city: Rotterdam

first: Martin

middle: Anne

last: Rijlaarsdam

address: Wytemaweg 80

department: Pathology

country: Netherlands

institute: Erasmus MC

data_processing: Raw data files (.eds) were imported and analyzed in using ExpressionSuite v1.0.4 (Life Technologies), a software data analysis tool that can easily import and analyze large raw data files. In these experiments the Cq is defined as the fractional cycle at which the amplification plot crosses the fluorescence threshold (Ct). The baseline was set automatically and the threshold was manually set at 0.2. For gene expression analysis a Ct cutoff that provides reliable results for low expressing targets is identified. The cutoff will depend on the platform, number of replicates (technical and biological) and number of preamplification cycles if preamplification was included. For TaqMan Array cards without preamplification, a Ct <30 is generally considered positive and indicates expression;  Ct between 30 – 32 are considered low but detectable. Ct between 32-40 represent very low expression. A  larger number of replicates or low standard deviation of Ct increases the confidence and power of results in this range. To capture as many differentially expressed miRNAs as possible the threshold was set at 40 and statistical analysis was applied to identify the most relevant and consistent (i.e. significant) results.   Undetermined values were replaced with the maximal number of cycles (40). Non-human RNAs were removed from the dataset before normalization. Each assay was treated as an independent target. Ct values were normalized using global normalization according to [1]. RNU44, RNU48 and U6.snRNA were removed from the dataset before further analysis because these have been shown to be absent in serum [2]. Batch effects were corrected using Combat as implemented in the sva Bioconductor package (v3.10.0).  1. Mestdagh, P., et al., A novel and universal method for microRNA RT-qPCR data normalization. Genome Biol, 2009. 10(6): p. R64.  2. Gillis, A.J., et al., Targeted serum miRNA (TSmiR) test for diagnosis and follow-up of (testicular) germ cell cancer patients: a proof of principle. Mol Oncol, 2013. 7(6): p. 1083-92.

label: FAM

source_name: serum

label_protocol: For miRNA profiling, Megaplex™ Primer Pools A and B v3.0 (PN 4444750) were used in conjunction with their matching TaqMan® MicroRNA Array Cards (PN 4444913). Each Pool contains either reverse transcription primers or preamplification primers that target 377 unique miRNAs and additional control targets and allows for profiling up to of 754  unique miRNAs across the two pools. Each sample was run separately with Pool A and B according to a modified protocol for blood plasma outlined in the Life Technologies Application Note: “Optimized blood plasma protocol for profiling human miRNAs using the OpenArray® Real-Time PCR System”, 2011, PN 4399721 rev C. Briefly, 3 µl of of the miRNA sample that was isolated with the ABC kit was reverse transcribed with the Megaplex™ RT Primer Pool A or B in a 10 µl final volume. The RT reaction was thermal cycled (2 min at 16˚C, 1 min at 42˚C, 1 sec at 50˚C, for 40 cycles) and the enzyme inactivated at 85˚C for 5 min. The entire RT reaction was combined with its matching Megaplex™ PreAmp Primer Pool and TaqMan® PreAmp Master Mix (PN 4391128) in a final volume of 50 µl. Preamplification was run using the following cycling conditions: 10 min at 95˚C; 2 min at 55˚C; 2 min at 72˚C; 15s at 95˚C, 4 min at 60˚C for 14 cycles; 99˚C for 10 min. The final preamplification product was diluted 1:100 in 1X TaqMan® Universal Master Mix II then loaded onto the matching TaqMan® MicroRNA Array Card and run on a QuantStudio™ 12K Flex System fitted with a TaqMan® Array Card Block under universal cycling. Each sample was run on Card A and Card B.

growth_protocol: Samples were extracted at the Department of Pathology, Erasmus MC, Rotterdam, the Netherlands. Use of tissue samples for scientific reasons was approved by an institutional review board (MEC 02.981 and CCR2041). Samples were used according to the “Code for Proper Secondary Use of Human Tissue in The Netherlands” developed by the Dutch Federation of Medical Scientific Societies (FMWV (Version 2002, update 2011).

extract_protocol: miRNAs were purified from serum sample using TaqMan® ABC Purification Kit -  Human Panel A and B (Life Technologies,  PN 4473087 and 4473088). All reagents are provided in the kit. These panels consist of superparmagnetic Dynabeads® covalently bound to a unique set of ~380 anti-miRNA oligonucleotides for each panel. The miRNAs in each panel match the miRNAs in Megaplex Pools A and B described below. Each panel includes exogenous and endogenous controls. Briefly, for each panel 100ul of lysis buffer was added to 50 µl of serum. 2 µl of 1nM an external control (ath-miR-159a) was added to monitor the extraction process, followed by the addition of 80 µl of beads (  80 X 10^6 beads). The tubes were shaken at 1200 rpm at 30˚C for 40 minutes then washed three times with wash buffer using a magnetic bead separator. The bound miRNAs were eluted from the beads with 100 µl elution buffer and incubation at 70˚C for 3 minutes. The eluted miRNA was stored at -80˚C until ready to use.

tag: sample type

value: serum from patient with normal adult testis tissue with adequate spermatogenesis (johnson score 8-10)


title: CONTROL-9


title: TOV-112D:PTX_1

description: drug


title: SE-14

value: serum from patient with seminoma


title: SE-15


title: TOV-112D:ERI_3

description: drug


title: OV56:Ctrl_3

description: vehicle


title: EFO-27:Ctrl_1

description: vehicle

source_name: EFO-27 Control


title: TOV-112D:Ctrl_2

description: vehicle


title: TOV-112D:Ctrl_1

description: vehicle


title: OVISE:ERI_2

description: drug

source_name: OVISE Eribulin 24h

value: OVISE


title: SE-9


title: SE-10


title: CONTROL-10


title: SE-11


title: SE-12


title: OVISE:PTX_2

description: drug

source_name: OVISE Paclitaxel 24h


title: OVISE:PTX_3

description: drug


title: OVISE:ERI_3

description: drug


title: OVISE:PTX_1

description: drug


title: OVISE:ERI_1

description: drug


title: SE-7


title: SE-6


title: SE-8


title: SE-5


title: SE-4


title: SE-3


title: OVISE:Ctrl_2

description: vehicle

source_name: OVISE Control


title: OVISE:Ctrl_1

description: vehicle


title: TOV-21G:PTX_3

description: drug

source_name: TOV-21G Paclitaxel 24h


title: OVISE:Ctrl_3

description: vehicle


title: TOV-21G:PTX_2

description: drug


title: NS-10

value: serum from patient with embryonal carcinoma + teratoma


title: SE-1


title: SE-2


title: NS-9


title: NS-8

value: serum from patient with embryonal carcinoma + yolk sac tumor


title: TOV-21G:PTX_1

description: drug


title: TOV-21G:ERI_2

description: drug

source_name: TOV-21G Eribulin 24h


title: SK-OV-3:PTX_3

description: drug

source_name: SK-OV-3 Paclitaxel 24h


title: TOV-21G:Ctrl_1

description: vehicle

source_name: TOV-21G Control


title: COLO 720E:ERI_3

description: drug

source_name: COLO 720E Eribulin 24h

value: COLO 720E


title: TOV-21G:ERI_1

description: drug


title: SK-OV-3:PTX_1

description: drug


title: TOV-21G:ERI_3

description: drug


title: SK-OV-3:PTX_2

description: drug


title: TOV-21G:Ctrl_3

description: vehicle


title: SK-OV-3:ERI_2

description: drug

source_name: SK-OV-3 Eribulin 24h


title: NS-6

value: serum from patient with embryonal carcinoma


title: NS-3

value: serum from patient with teratoma


title: NS-5


title: NS-4


title: SK-OV-3:ERI_3

description: drug


title: NS-2

value: serum from patient with yolk sac tumor


title: NS-7


title: CONTROL-7

value: serum from patient with neuro endocrine tumor


title: NS-1


title: TOV-21G:Ctrl_2

description: vehicle


title: SK-OV-3:ERI_1

description: drug


title: CONTROL-4

value: serum from patient with epidermis cyst


title: CONTROL-6


title: CONTROL-3


title: SK-OV-3:Ctrl_1

description: vehicle

source_name: SK-OV-3 Control


title: SNG-M_PTX_3

description: drug

source_name: SNG-M Paclitaxel 24h

value: SNG-M

value: endometrial cancer


title: SNG-M_PTX_2

description: drug


title: SNG-M_PTX_1

description: drug


title: SNG-M_ERI_3

description: drug

source_name: SNG-M Eribulin 24h


title: SK-OV-3:Ctrl_2

description: vehicle


title: SK-OV-3:Ctrl_3

description: vehicle


title: CONTROL-2


title: CONTROL-1

value: serum from patient with epidermoid cyst


title: CONTROL-8

value: serum from patient with paratesticular hemorrhage


title: CONTROL-5

value: serum from patient with low grade liposarcoma


title: SNG-M_control_1

description: vehicle

source_name: SNG-M Control


title: SNG-M_ERI_2

description: drug


title: SNG-M_control_2

description: vehicle


title: SNG-M_ERI_1

description: drug


title: SNG-M_control_3

description: vehicle


title: HEC-1-B_PTX_3

description: drug

source_name: HEC-1-B Paclitaxel 24h


title: HEC-1-B_PTX_1

description: drug


title: HEC-1-B_PTX_2

description: drug


title: HEC-1-B_ERI_3

description: drug

source_name: HEC-1-B Eribulin 24h


title: HEC-1-B_control_3

description: vehicle

source_name: HEC-1-B Control


title: 4-1 vs. 4-2

city: Jeju-si

first: Jeongsik

last: Kim

state: Jeju

address: 102 Jejudaehakroe

department: Faculty of Science Education

country: South Korea

institute: Jeju National University

hyb_protocol: Microarray chips were hybridized using Agilent’s Gene Expression Hybridization Kit and washed with Agilent’s Gene Expression Wash Buffer Kit

scan_protocol: Scanned on an Agilent’s DNA microarray scanner

data_processing: Images were quantified using Agilent Feature Extraction Software and background substration, LOWESS normalization and clustering were performed using Agilent's GeneSpring software.

organism: Arabidopsis thaliana

source_name: Col

label_protocol: Total RNA was aamplified and labled using Agilent's Low RNA Input Linear Amplification kit PLUS.

growth_protocol: Arabidopsis were grown in the 1/2 B5 for 14 days on an 16:8 light-dark (LD) cycle

extract_protocol: Total RNA extracted using RNeasy plant kit (Qiagen) following manufacturer's instructions

treatment_protocol: Plants were harvested at 6 hr after light-on.

tag: strain

value: Col

tag: age

value: 14-day-old seedling

tag: genotype

value: wildtype


title: 1-1 vs. 1-2


title: HEC-1-B_ERI_2

description: drug


title: 3-1 vs. 3-2


title: Hippocampus_retrieval_30 minutes_rep7

city: Spokane

first: Lucia

last: Peixoto

state: WA

address: PO Box 1495

department: College of Medicine

institute: Washington State University, Spokane

hyb_protocol: cRNA was hybridized to a Mouse Gene 1.1 ST 96-Array Plate using GeneTitan Hybridization, Wash and Stain Kit for WT Array Plates. The array plate was washed and stained in the GeneTitan multi-channel instrument.

scan_protocol: Gene 1.1 ST Array Plates were scanned using the GeneTitan® Multi-channel Instrument

data_processing: RMA normalization using Affymetrix powertools

organism: Mus musculus

source_name: Hippocampus_retrieval_30 minutes

label_protocol: Biotinylated cRNA were prepared from 3 ug total RNA at the UPENN molecular profiling core using the Ambion WT Expression Kit

growth_protocol: Mouse Hippomcapus dissected from C57BL/6J mice. .C57BL/6J adult male mice (2 months of age) were obtained from Jackson laboratories and housed individually for a week on a 12 hr/12 hr light/dark schedule with lights on at 7 am (Zeitgeber time (ZT) 0). Food and water were available ad libitum throughout the experiment.

extract_protocol: Hippocampal dissections were performed immediately following the behavioral treatment, and alternated between FC and control animals. Tissue was collected at 30 minutes (FC30), 4 hours (FC4), 12 hours (FC12) and 24 hours after FC (FC24) as well as 30 minutes after testing for retrieval of the memory (RT30). Testing was performed at 24 hours after training over a 5-minute interval. Tissue was immersed in RNAlater (Qiagen) and immediately frozen. Animals that were handled but not trained were dissected at the same time of day to control for variations due to circadian rhythms (CC30, CC4 andCC12). The protocol was repeated over the course of 2 weeks to obtain 9 animals (2 hippocampi) per group, so that 9 independent FC experiments were represented in each time point and all animals for each group were dissected at the exactly the same time of day.RNA extraction was performed using the RNAEasy Microarray Tissue kit from Qiagen

treatment_protocol: To acclimate the mice to the experimenter each animal was handled daily for 3 days prior to contextual fear conditioning (FC). Handling consisted of manipulation of the animals for 1-2 minutes per mouse in the same room as the experimental setting without exposure to the context. The conditioning protocol entailed a single 2-second, 1.5-mA foot shock, terminating at 2.5 minutes after placement of the mouse in the chamber, starting at 10 am (ZT3) daily.

value: 2 months old

tag: Sex

value: male


title: Hippocampus_retrieval_30 minutes_rep5


title: HEC-1-B_control_2

description: vehicle


title: HEC-1-B_ERI_1

description: drug


title: Hippocampus_retrieval_30 minutes_rep9


title: Hippocampus_retrieval_30 minutes_rep6


title: Hippocampus_retrieval_30 minutes_rep3


title: KLE_PTX_3

description: drug

source_name: KLE Paclitaxel 24h

value: KLE


title: Hippocampus_retrieval_30 minutes_rep8


title: HEC-1-B_control_1

description: vehicle


title: KLE_PTX_1

description: drug


title: Hippocampus_retrieval_30 minutes_rep4


title: KLE_PTX_2

description: drug


title: Hippocampus_retrieval_30 minutes_rep2


title: KLE_ERI_3

description: drug

source_name: KLE Eribulin 24h


title: KLE_ERI_1

description: drug


title: KLE_control_3

description: vehicle

source_name: KLE Control


title: Hippocampus_fear_conditioned_24hours_rep9


title: Hippocampus_retrieval_30 minutes_rep1


title: KLE_ERI_2

description: drug


title: Hippocampus_fear_conditioned_24hours_rep8


title: KLE_control_2

description: vehicle


title: Hippocampus_fear_conditioned_24hours_rep2


title: Hippocampus_fear_conditioned_24hours_rep4


title: RL95-2 _ERI_2

description: drug

source_name: RL95-2  Eribulin 24h


title: Hippocampus_fear_conditioned_24hours_rep5


title: Hippocampus_fear_conditioned_24hours_rep3


title: RL95-2 _PTX_2

description: drug

source_name: RL95-2  Paclitaxel 24h


title: RL95-2 _control_3

description: vehicle

source_name: RL95-2  Control


title: Hippocampus_fear_conditioned_12hours_rep9


title: RL95-2 _ERI_1

description: drug


title: Hippocampus_fear_conditioned_12hours_rep6


title: MFE-280_PTX_3

description: drug

source_name: MFE-280 Paclitaxel 24h


title: KLE_control_1

description: vehicle


title: RL95-2 _PTX_3

description: drug


title: Hippocampus_fear_conditioned_12hours_rep7


title: Hippocampus_fear_conditioned_24hours_rep6


title: RL95-2 _control_1

description: vehicle


title: Hippocampus_fear_conditioned_24hours_rep1


title: MFE-280_PTX_2

description: drug


title: Hippocampus_fear_conditioned_12hours_rep5


title: RL95-2 _PTX_1

description: drug


title: Hippocampus_fear_conditioned_12hours_rep4


title: MFE-280_PTX_1

description: drug


title: Hippocampus_fear_conditioned_12hours_rep8


title: MFE-280_ERI_3

description: drug

source_name: MFE-280 Eribulin 24h


title: Hippocampus_fear_conditioned_24hours_rep7


title: RL95-2 _control_2

description: vehicle


title: Hippocampus_fear_conditioned_12hours_rep3


title: Hippocampus_control_12hours_rep9


title: Hippocampus_fear_conditioned_12hours_rep1


title: Hippocampus_control_12hours_rep6


title: MFE-280_control_2

description: vehicle

source_name: MFE-280 Control


title: MFE-280_ERI_2

description: drug


title: Hippocampus_control_12hours_rep4


title: HEC-6_ERI_2

description: drug

source_name: HEC-6 Eribulin 24h


title: Hippocampus_control_12hours_rep7


title: Hippocampus_control_12hours_rep3


title: HEC-6_ERI_3

description: drug


title: HEC-6_PTX_2

description: drug

source_name: HEC-6 Paclitaxel 24h


title: MFE-280_control_1

description: vehicle


title: Hippocampus_fear_conditioned_12hours_rep2


title: Hippocampus_control_12hours_rep8


title: Hippocampus_control_12hours_rep5


title: HEC-6_PTX_3

description: drug


title: HEC-6_PTX_1

description: drug


title: Hippocampus_control_12hours_rep2


title: HEC-6_ERI_1

description: drug


title: MFE-280_control_3

description: vehicle


title: Hippocampus_control_12hours_rep1


title: Hippocampus_fear_conditioned_4hours_rep9


title: HEC-6_control_2

description: vehicle

source_name: HEC-6 Control


title: Hippocampus_fear_conditioned_4hours_rep7


title: HEC-6_control_1

description: vehicle


title: Hippocampus_fear_conditioned_4hours_rep5


title: Hippocampus_fear_conditioned_4hours_rep6


title: HEC-6_control_3

description: vehicle


title: HEC-1_PTX_3

description: drug

source_name: HEC-1 Paclitaxel 24h


title: HEC-1_ERI_3

description: drug

source_name: HEC-1 Eribulin 24h


title: HEC-1_PTX_2

description: drug


title: Hippocampus_fear_conditioned_4hours_rep8


title: Hippocampus_fear_conditioned_4hours_rep4


title: HEC-1_PTX_1

description: drug


title: 2-1 vs. 2-2


title: HEC-1_ERI_2

description: drug


title: HEC-1_control_3

description: vehicle

source_name: HEC-1 Control


title: AN3 CA_PTX_3

description: drug

source_name: AN3 CA Paclitaxel 24h

value: AN3 CA


title: HEC-1_control_2

description: vehicle


title: Hippocampus_fear_conditioned_4hours_rep2


title: HEC-1_ERI_1

description: drug


title: HEC-1_control_1

description: vehicle


title: Hippocampus_control_4hours_rep9


title: Hippocampus_fear_conditioned_4hours_rep3


title: Hippocampus_control_4hours_rep8


title: Hippocampus_fear_conditioned_4hours_rep1


title: Hippocampus_control_4hours_rep7


title: Hippocampus_control_4hours_rep5


title: Hippocampus_control_4hours_rep6


title: Hippocampus_control_4hours_rep4


title: AN3 CA_PTX_1

description: drug


title: AN3 CA_PTX_2

description: drug


title: AN3 CA_ERI_2

description: drug

source_name: AN3 CA Eribulin 24h


title: AN3 CA_ERI_3

description: drug


title: Hippocampus_control_4hours_rep3


title: AN3 CA_ERI_1

description: drug


title: Hippocampus_control_4hours_rep1


title: Hippocampus_fear_conditioned_30minutes_rep7


title: Hippocampus_fear_conditioned_30minutes_rep6


title: Hippocampus_fear_conditioned_30minutes_rep4


title: AN3 CA_control_1

description: vehicle

source_name: AN3 CA Control


title: Hippocampus_fear_conditioned_30minutes_rep9


title: AN3 CA_control_3

description: vehicle


title: Hippocampus_fear_conditioned_30minutes_rep8


title: Hippocampus_control_4hours_rep2


title: Hippocampus_fear_conditioned_30minutes_rep5


title: HEC-265_PTX_3

description: drug

source_name: HEC-265 Paclitaxel 24h


title: HEC-265_PTX_2

description: drug


title: HEC-265_PTX_1

description: drug


title: AN3 CA_control_2

description: vehicle


title: Hippocampus_fear_conditioned_30minutes_rep3


title: HEC-265_ERI_2

description: drug

source_name: HEC-265 Eribulin 24h


title: Hippocampus_fear_conditioned_30minutes_rep1


title: HEC-265_ERI_1

description: drug


title: Hippocampus_fear_conditioned_30minutes_rep2


title: HEC-265_ERI_3

description: drug


title: Hippocampus_control_30minutes_rep9

source_name: Hippocampus, control, 30 minutes


title: Hippocampus_control_30minutes_rep6


title: HEC-265_control_1

description: vehicle

source_name: HEC-265 Control


title: HEC-265_control_2

description: vehicle


title: Hippocampus_control_30minutes_rep5


title: Hippocampus_control_30minutes_rep8


title: Hippocampus_control_30minutes_rep7


title: HEC-50B_PTX_3

description: drug

source_name: HEC-50B Paclitaxel 24h


title: Hippocampus_control_30minutes_rep2


title: HEC-50B_PTX_2

description: drug


title: HEC-50B_ERI_3

description: drug

source_name: HEC-50B Eribulin 24h


title: HEC-50B_ERI_1

description: drug


title: HEC-50B_control_3

description: vehicle

source_name: HEC-50B Control


title: HEC-50B_PTX_1

description: drug


title: HEC-50B_ERI_2

description: drug


title: HEC-50B_control_2

description: vehicle


title: SNG-II_PTX_3

description: drug

source_name: SNG-II Paclitaxel 24h

value: SNG-II


title: Hippocampus_control_30minutes_rep3


title: HEC-50B_control_1

description: vehicle


title: MFE-280_ERI_1

description: drug

source_name: MFE-280 Eribulin 24h


city: RTP

first: Keith

last: Shockley

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: blood sample from patient BH005, highresponder, female, day2, hour 0, baseline

hyb_protocol: Following fragmentation, 10 ug of cDNA was hybridized for 18 hr at 45C. GeneChips were washed and stained in the Affymetrix

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Data were processed using R/affy software. In brief, the RMA method adjusts the background of perfect match (PM) probes, applies a quantile normalization of the corrected PM values, and calculates final expression measures with the Tukey median polish algorithm.

source_name: blood sample from patient BH005, high responder, female, day2, hour 0, baseline

label_protocol: RT/IVT protocol and reagents provided by Affymetrix

extract_protocol: PAXgene protocol was used to extract total RNA

tag: patient

tag: responder

value: high

value: female

tag: day

tag: hour

tag: biological group

value: baseline


description: blood sample from patient BH005, highresponder, female, day3, hour20, sleepdep

source_name: blood sample from patient BH005, high responder, female, day3, hour20, sleepdep

value: sleep deprivation


description: blood sample from patient BH007, highresponder, male, day2, hour 4, baseline

source_name: blood sample from patient BH007, high responder, male, day2, hour 4, baseline


description: blood sample from patient BH005, highresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH005, high responder, female, day2, hour 8, baseline


title: SNG-II_PTX_1

description: drug


title: Hippocampus_control_30minutes_rep4


title: SNG-II_PTX_2

description: drug


description: blood sample from patient BH005, highresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH005, high responder, female, day1, hour 8, baseline


description: blood sample from patient BH005, highresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH005, high responder, female, day3, hour 8, sleepdep


title: SNG-II_ERI_3

description: drug

source_name: SNG-II Eribulin 24h


description: blood sample from patient BH005, highresponder, female, day1, hour16, baseline

source_name: blood sample from patient BH005, high responder, female, day1, hour16, baseline


title: SNG-II_ERI_2

description: drug


description: blood sample from patient BH007, highresponder, male, day3, hour 0, sleepdep

source_name: blood sample from patient BH007, high responder, male, day3, hour 0, sleepdep


title: SNG-II_ERI_1

description: drug


title: SNG-II_control_2

description: vehicle

source_name: SNG-II Control


description: blood sample from patient BH015, highresponder, male, day2, hour12, baseline

source_name: blood sample from patient BH015, high responder, male, day2, hour12, baseline


title: MFE-296_PTX_2

description: drug

source_name: MFE-296 Paclitaxel 24h


description: blood sample from patient BH007, highresponder, male, day2, hour12, baseline

source_name: blood sample from patient BH007, high responder, male, day2, hour12, baseline


description: blood sample from patient BH005, highresponder, female, day4, hour 0, recovery

source_name: blood sample from patient BH005, high responder, female, day4, hour 0, recovery

value: recovery


description: blood sample from patient BH005, highresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH005, high responder, female, day1, hour20, baseline


title: MFE-296_PTX_3

description: drug

value: endometrial cancer


title: MFE-296_PTX_1

description: drug


title: SNG-II_control_3

description: vehicle


title: MFE-296_ERI_3

description: drug

source_name: MFE-296 Eribulin 24h


title: MFE-296_ERI_2

description: drug


description: blood sample from patient BH005, highresponder, female, day2, hour 4, baseline

source_name: blood sample from patient BH005, high responder, female, day2, hour 4, baseline


title: MFE-296_control_3

description: vehicle

source_name: MFE-296 Control


description: blood sample from patient BH007, highresponder, male, day3, hour20, sleepdep

source_name: blood sample from patient BH007, high responder, male, day3, hour20, sleepdep


title: MFE-296_ERI_1

description: drug


title: MFE-296_control_2

description: vehicle


description: blood sample from patient BH004, highresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH004, high responder, female, day1, hour 8, baseline


title: HEC-59_PTX_2

description: drug

source_name: HEC-59 Paclitaxel 24h


title: SNG-II_control_1

description: vehicle


description: blood sample from patient BH016, highresponder, male, day2, hour20, baseline

source_name: blood sample from patient BH016, high responder, male, day2, hour20, baseline


title: MFE-296_control_1

description: vehicle


title: HEC-59_PTX_3

description: drug


description: blood sample from patient BH008, lowresponder, female, day2, hour 4, baseline

source_name: blood sample from patient BH008, low responder, female, day2, hour 4, baseline

value: low


description: blood sample from patient BH004, highresponder, female, day3, hour20, sleepdep

source_name: blood sample from patient BH004, high responder, female, day3, hour20, sleepdep


description: blood sample from patient BH007, highresponder, male, day1, hour20, baseline

source_name: blood sample from patient BH007, high responder, male, day1, hour20, baseline


description: blood sample from patient BH009, lowresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH009, low responder, female, day1, hour20, baseline


title: HEC-59_ERI_3

description: drug

source_name: HEC-59 Eribulin 24h


title: HEC-59_ERI_2

description: drug


title: HEC-59_PTX_1

description: drug


description: blood sample from patient BH004, highresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH004, high responder, female, day4, hour 8, recovery


description: blood sample from patient BH006, lowresponder, male, day3, hour 4, sleepdep

source_name: blood sample from patient BH006, low responder, male, day3, hour 4, sleepdep


description: blood sample from patient BH015, highresponder, male, day3, hour20, sleepdep

source_name: blood sample from patient BH015, high responder, male, day3, hour20, sleepdep


description: blood sample from patient BH008, lowresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH008, low responder, female, day1, hour 8, baseline


title: HEC-59_ERI_1

description: drug


description: blood sample from patient BH026, highresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH026, high responder, female, day3, hour12, sleepdep


title: HEC-59_control_3

description: vehicle

source_name: HEC-59 Control


title: HEC-59_control_2

description: vehicle


title: HEC-59_control_1

description: vehicle


title: HEC-151_PTX_2

description: drug

source_name: HEC-151 Paclitaxel 24h


description: blood sample from patient BH004, highresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH004, high responder, female, day2, hour20, baseline


title: HEC-151_control_3

description: vehicle

source_name: HEC-151 Control


title: Hippocampus_control_30minutes_rep1

source_name: Hippocampus, control, 30 minutes


description: blood sample from patient BH003, lowresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH003, low responder, female, day4, hour 4, recovery


description: blood sample from patient BH006, lowresponder, male, day3, hour 0, sleepdep

source_name: blood sample from patient BH006, low responder, male, day3, hour 0, sleepdep


description: blood sample from patient BH003, lowresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH003, low responder, female, day2, hour 8, baseline


title: HEC-151_ERI_3

description: drug

source_name: HEC-151 Eribulin 24h


description: blood sample from patient BH008, lowresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH008, low responder, female, day3, hour12, sleepdep


title: HEC-151_PTX_3

description: drug


description: blood sample from patient BH013, highresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH013, high responder, female, day1, hour12, baseline


title: HEC-151_PTX_1

description: drug


description: blood sample from patient BH013, highresponder, female, day3, hour 4, sleepdep

source_name: blood sample from patient BH013, high responder, female, day3, hour 4, sleepdep


description: blood sample from patient BH013, highresponder, female, day2, hour12, baseline

source_name: blood sample from patient BH013, high responder, female, day2, hour12, baseline


title: HEC-151_ERI_2

description: drug


description: blood sample from patient BH010, lowresponder, female, day3, hour20, sleepdep

source_name: blood sample from patient BH010, low responder, female, day3, hour20, sleepdep


title: HEC-151_ERI_1

description: drug


title: HEC-151_control_2

description: vehicle


description: blood sample from patient BH006, lowresponder, male, day4, hour 0, recovery

source_name: blood sample from patient BH006, low responder, male, day4, hour 0, recovery


title: HEC-151_control_1

description: vehicle


description: blood sample from patient BH004, highresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH004, high responder, female, day3, hour12, sleepdep


title: HEC-251_PTX_3

description: drug

source_name: HEC-251 Paclitaxel 24h


title: HEC-251_PTX_1

description: drug


description: blood sample from patient BH004, highresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH004, high responder, female, day2, hour16, baseline


title: HEC-251_ERI_1

description: drug

source_name: HEC-251 Eribulin 24h


title: HEC-251_ERI_3

description: drug


title: HEC-251_PTX_2

description: drug


description: blood sample from patient BH013, highresponder, female, day1, hour16, baseline

source_name: blood sample from patient BH013, high responder, female, day1, hour16, baseline


description: blood sample from patient BH010, lowresponder, female, day2, hour12, baseline

source_name: blood sample from patient BH010, low responder, female, day2, hour12, baseline


description: blood sample from patient BH016, highresponder, male, day2, hour 8, baseline

source_name: blood sample from patient BH016, high responder, male, day2, hour 8, baseline


description: blood sample from patient BH007, highresponder, male, day2, hour 8, baseline

source_name: blood sample from patient BH007, high responder, male, day2, hour 8, baseline


description: blood sample from patient BH016, highresponder, male, day3, hour 4, sleepdep

source_name: blood sample from patient BH016, high responder, male, day3, hour 4, sleepdep


description: blood sample from patient BH008, lowresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH008, low responder, female, day2, hour16, baseline


title: HEC-251_ERI_2

description: drug


description: blood sample from patient BH016, highresponder, male, day3, hour 0, sleepdep

source_name: blood sample from patient BH016, high responder, male, day3, hour 0, sleepdep


description: blood sample from patient BH006, lowresponder, male, day3, hour12, sleepdep

source_name: blood sample from patient BH006, low responder, male, day3, hour12, sleepdep


description: blood sample from patient BH010, lowresponder, female, day3, hour 4, sleepdep

source_name: blood sample from patient BH010, low responder, female, day3, hour 4, sleepdep


title: HEC-251_control_1

description: vehicle

source_name: HEC-251 Control


description: blood sample from patient BH003, lowresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH003, low responder, female, day4, hour 8, recovery


description: blood sample from patient BH006, lowresponder, male, day4, hour 4, recovery

source_name: blood sample from patient BH006, low responder, male, day4, hour 4, recovery


description: blood sample from patient BH006, lowresponder, male, day1, hour20, baseline

source_name: blood sample from patient BH006, low responder, male, day1, hour20, baseline


title: ECC-1_PTX_2

description: drug

source_name: ECC-1 Paclitaxel 24h


description: blood sample from patient BH006, lowresponder, male, day2, hour 8, baseline

source_name: blood sample from patient BH006, low responder, male, day2, hour 8, baseline


description: blood sample from patient BH006, lowresponder, male, day2, hour 4, baseline

source_name: blood sample from patient BH006, low responder, male, day2, hour 4, baseline


description: blood sample from patient BH026, highresponder, female, day1, hour16, baseline

source_name: blood sample from patient BH026, high responder, female, day1, hour16, baseline


title: ECC-1_PTX_1

description: drug


title: ECC-1_control_2

description: vehicle

source_name: ECC-1 Control


title: ECC-1_ERI_1

description: drug

source_name: ECC-1 Eribulin 24h


title: ECC-1_control_3

description: vehicle


description: blood sample from patient BH016, highresponder, male, day1, hour 8, baseline

source_name: blood sample from patient BH016, high responder, male, day1, hour 8, baseline


title: ECC-1_ERI_2

description: drug


title: ECC-1_PTX_3

description: drug


title: HEC-1-A_PTX_3

description: drug

source_name: HEC-1-A Paclitaxel 24h


title: HEC-1-A_PTX_2

description: drug


title: HEC-1-A_PTX_1

description: drug


title: ECC-1_control_1

description: vehicle


description: blood sample from patient BH006, lowresponder, male, day2, hour16, baseline

source_name: blood sample from patient BH006, low responder, male, day2, hour16, baseline


title: ECC-1_ERI_3

description: drug


description: blood sample from patient BH003, lowresponder, female, day3, hour20, sleepdep

source_name: blood sample from patient BH003, low responder, female, day3, hour20, sleepdep


title: HEC-1-A_ERI_3

description: drug

source_name: HEC-1-A Eribulin 24h


description: blood sample from patient BH013, highresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH013, high responder, female, day2, hour16, baseline


title: HEC-1-A_ERI_2

description: drug


description: blood sample from patient BH013, highresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH013, high responder, female, day3, hour12, sleepdep


description: blood sample from patient BH007, highresponder, male, day4, hour 4, recovery

source_name: blood sample from patient BH007, high responder, male, day4, hour 4, recovery


description: blood sample from patient BH010, lowresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH010, low responder, female, day1, hour12, baseline


title: HEC-1-A_control_3

description: vehicle

source_name: HEC-1-A Control


title: HEC-1-A_ERI_1

description: drug


description: blood sample from patient BH006, lowresponder, male, day3, hour20, sleepdep

source_name: blood sample from patient BH006, low responder, male, day3, hour20, sleepdep


description: blood sample from patient BH013, highresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH013, high responder, female, day4, hour 8, recovery


title: HEC-108_PTX_2

description: drug

source_name: HEC-108 Paclitaxel 24h


description: blood sample from patient BH010, lowresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH010, low responder, female, day1, hour 8, baseline


title: HEC-108_PTX_3

description: drug


title: HEC-1-A_control_1

description: vehicle


title: HEC-108_PTX_1

description: drug


title: HEC-108_ERI_1

description: drug

source_name: HEC-108 Eribulin 24h


description: blood sample from patient BH003, lowresponder, female, day4, hour 0, recovery

source_name: blood sample from patient BH003, low responder, female, day4, hour 0, recovery


title: HEC-1-A_control_2

description: vehicle


description: blood sample from patient BH006, lowresponder, male, day1, hour16, baseline

source_name: blood sample from patient BH006, low responder, male, day1, hour16, baseline


title: HEC-108_ERI_3

description: drug


title: HEC-251_control_2

description: vehicle

source_name: HEC-251 Control


description: blood sample from patient BH013, highresponder, female, day3, hour 0, sleepdep

source_name: blood sample from patient BH013, high responder, female, day3, hour 0, sleepdep


title: HEC-108_control_2

description: vehicle

source_name: HEC-108 Control


description: blood sample from patient BH013, highresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH013, high responder, female, day4, hour 4, recovery


title: HEC-108_ERI_2

description: drug


description: blood sample from patient BH007, highresponder, male, day4, hour 8, recovery

source_name: blood sample from patient BH007, high responder, male, day4, hour 8, recovery


title: HEC-108_control_3

description: vehicle

source_name: HEC-108  Control


title: HEC-88nu_PTX_2

description: drug

source_name: HEC-88nu Paclitaxel 24h


description: blood sample from patient BH003, lowresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH003, low responder, female, day3, hour12, sleepdep


description: blood sample from patient BH010, lowresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH010, low responder, female, day2, hour 8, baseline


title: HEC-88nu_PTX_3

description: drug


title: HEC-108_control_1

description: vehicle


description: blood sample from patient BH007, highresponder, male, day1, hour12, baseline

source_name: blood sample from patient BH007, high responder, male, day1, hour12, baseline


title: HEC-88nu_ERI_2

description: drug

source_name: HEC-88nu Eribulin 24h


title: HEC-88nu_PTX_1

description: drug


description: blood sample from patient BH003, lowresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH003, low responder, female, day1, hour20, baseline


description: blood sample from patient BH013, highresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH013, high responder, female, day2, hour 8, baseline


title: HEC-88nu_ERI_3

description: drug


description: blood sample from patient BH006, lowresponder, male, day1, hour12, baseline

source_name: blood sample from patient BH006, low responder, male, day1, hour12, baseline


description: blood sample from patient BH003, lowresponder, female, day1, hour16, baseline

source_name: blood sample from patient BH003, low responder, female, day1, hour16, baseline


description: blood sample from patient BH015, highresponder, male, day1, hour 8, baseline

source_name: blood sample from patient BH015, high responder, male, day1, hour 8, baseline


description: blood sample from patient BH013, highresponder, female, day2, hour 0, baseline

source_name: blood sample from patient BH013, high responder, female, day2, hour 0, baseline


description: blood sample from patient BH008, lowresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH008, low responder, female, day1, hour20, baseline


description: blood sample from patient BH008, lowresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH008, low responder, female, day3, hour 8, sleepdep


title: HEC-88nu_ERI_1

description: drug


title: HEC-88nu_control_3

description: vehicle

source_name: HEC-88nu Control


description: blood sample from patient BH010, lowresponder, female, day1, hour16, baseline

source_name: blood sample from patient BH010, low responder, female, day1, hour16, baseline


description: blood sample from patient BH008, lowresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH008, low responder, female, day4, hour 8, recovery


description: blood sample from patient BH013, highresponder, female, day2, hour 4, baseline

source_name: blood sample from patient BH013, high responder, female, day2, hour 4, baseline


title: HEC-88nu_control_1

description: vehicle


title: UACC-812_ERI_3

description: drug

source_name: UACC-812 Eribulin_24h

value: breast cancer


description: blood sample from patient BH008, lowresponder, female, day3, hour 4, sleepdep

source_name: blood sample from patient BH008, low responder, female, day3, hour 4, sleepdep


title: UACC-812_PTX_1

description: drug

source_name: UACC-812 Paclitaxel_24h


description: blood sample from patient BH007, highresponder, male, day2, hour16, baseline

source_name: blood sample from patient BH007, high responder, male, day2, hour16, baseline


description: blood sample from patient BH003, lowresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH003, low responder, female, day1, hour 8, baseline


description: blood sample from patient BH010, lowresponder, female, day2, hour 0, baseline

source_name: blood sample from patient BH010, low responder, female, day2, hour 0, baseline


description: blood sample from patient BH003, lowresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH003, low responder, female, day1, hour12, baseline


title: UACC-812_Ctrl_3

description: vehicle

source_name: UACC-812 Control


title: HCC-70_PTX_2

description: drug

source_name: HCC-70 Paclitaxel_24h


title: UACC-812_ERI_1

description: drug


description: blood sample from patient BH003, lowresponder, female, day3, hour 0, sleepdep

source_name: blood sample from patient BH003, low responder, female, day3, hour 0, sleepdep


description: blood sample from patient BH003, lowresponder, female, day3, hour16, sleepdep

source_name: blood sample from patient BH003, low responder, female, day3, hour16, sleepdep


description: blood sample from patient BH008, lowresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH008, low responder, female, day4, hour 4, recovery


title: UACC-812_PTX_2

description: drug


description: blood sample from patient BH003, lowresponder, female, day2, hour 0, baseline

source_name: blood sample from patient BH003, low responder, female, day2, hour 0, baseline


title: HCC-70_PTX_3

description: drug


title: UACC-812_Ctrl_1

description: vehicle


description: blood sample from patient BH010, lowresponder, female, day2, hour 4, baseline

source_name: blood sample from patient BH010, low responder, female, day2, hour 4, baseline


description: blood sample from patient BH010, lowresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH010, low responder, female, day2, hour20, baseline


title: UACC-812_ERI_2

description: drug


title: HEC-88nu_control_2

description: vehicle

source_name: HEC-88nu Control


description: blood sample from patient BH008, lowresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH008, low responder, female, day2, hour20, baseline


title: UACC-812_Ctrl_2

description: vehicle


title: HCC-70_PTX_1

description: drug


description: blood sample from patient BH016, highresponder, male, day2, hour 0, baseline

source_name: blood sample from patient BH016, high responder, male, day2, hour 0, baseline


title: HCC-70_ERI_3

description: drug

source_name: HCC-70 Eribulin_24h


title: UACC-812_PTX_3

description: drug

source_name: UACC-812 Paclitaxel_24h


description: blood sample from patient BH007, highresponder, male, day4, hour 0, recovery

source_name: blood sample from patient BH007, high responder, male, day4, hour 0, recovery


title: HCC-70_Ctrl_1

description: vehicle

source_name: HCC-70 Control


title: HCC-70_ERI_1

description: drug


description: blood sample from patient BH013, highresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH013, high responder, female, day1, hour20, baseline


title: HCC-70_Ctrl_2

description: vehicle


title: HCC-70_ERI_2

description: drug


description: blood sample from patient BH006, lowresponder, male, day2, hour 0, baseline

source_name: blood sample from patient BH006, low responder, male, day2, hour 0, baseline


description: blood sample from patient BH016, highresponder, male, day3, hour12, sleepdep

source_name: blood sample from patient BH016, high responder, male, day3, hour12, sleepdep


title: HCC-70_Ctrl_3

description: vehicle


title: HCC-1500_PTX_3

description: drug

source_name: HCC-1500 Paclitaxel_24h


title: HCC-1500_PTX_2

description: drug


description: blood sample from patient BH013, highresponder, female, day3, hour20, sleepdep

source_name: blood sample from patient BH013, high responder, female, day3, hour20, sleepdep


description: blood sample from patient BH003, lowresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH003, low responder, female, day3, hour 8, sleepdep


description: blood sample from patient BH008, lowresponder, female, day2, hour12, baseline

source_name: blood sample from patient BH008, low responder, female, day2, hour12, baseline


description: blood sample from patient BH010, lowresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH010, low responder, female, day1, hour20, baseline


title: HCC-1500_ERI_3

description: drug

source_name: HCC-1500 Eribulin_24h


description: blood sample from patient BH006, lowresponder, male, day3, hour 8, sleepdep

source_name: blood sample from patient BH006, low responder, male, day3, hour 8, sleepdep


description: blood sample from patient BH010, lowresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH010, low responder, female, day3, hour 8, sleepdep


title: HCC-1500_PTX_1

description: drug


description: blood sample from patient BH016, highresponder, male, day2, hour12, baseline

source_name: blood sample from patient BH016, high responder, male, day2, hour12, baseline


title: HCC-1500_ERI_2

description: drug


description: blood sample from patient BH007, highresponder, male, day3, hour 8, sleepdep

source_name: blood sample from patient BH007, high responder, male, day3, hour 8, sleepdep


title: HCC-1500_ERI_1

description: drug


title: HCC-1500_Ctrl_3

description: vehicle

source_name: HCC-1500 Control


description: blood sample from patient BH006, lowresponder, male, day1, hour 8, baseline

source_name: blood sample from patient BH006, low responder, male, day1, hour 8, baseline


title: HCC-1500_Ctrl_2

description: vehicle


description: blood sample from patient BH006, lowresponder, male, day4, hour 8, recovery

source_name: blood sample from patient BH006, low responder, male, day4, hour 8, recovery


title: HCC-1500_Ctrl_1

description: vehicle


description: blood sample from patient BH006, lowresponder, male, day3, hour16, sleepdep

source_name: blood sample from patient BH006, low responder, male, day3, hour16, sleepdep


title: HCC-1419_PTX_3

description: drug

source_name: HCC-1419 Paclitaxel_24h


title: HCC-1419_PTX_1

description: drug


description: blood sample from patient BH010, lowresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH010, low responder, female, day2, hour16, baseline


title: HCC-1419_ERI_2

description: drug

source_name: HCC-1419 Eribulin_24h


description: blood sample from patient BH008, lowresponder, female, day2, hour 0, baseline

source_name: blood sample from patient BH008, low responder, female, day2, hour 0, baseline


title: HCC-1419_Ctrl_3

description: vehicle

source_name: HCC-1419 Control


description: blood sample from patient BH013, highresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH013, high responder, female, day1, hour 8, baseline


title: HCC-1419_ERI_3

description: drug


title: HCC-1419_ERI_1

description: drug


title: HCC-1419_PTX_2

description: drug


description: blood sample from patient BH016, highresponder, male, day3, hour20, sleepdep

source_name: blood sample from patient BH016, high responder, male, day3, hour20, sleepdep


description: blood sample from patient BH008, lowresponder, female, day3, hour16, sleepdep

source_name: blood sample from patient BH008, low responder, female, day3, hour16, sleepdep


title: HCC-1419_Ctrl_2

description: vehicle


description: blood sample from patient BH010, lowresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH010, low responder, female, day3, hour12, sleepdep


title: HCC-1419_Ctrl_1

description: vehicle


description: blood sample from patient BH010, lowresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH010, low responder, female, day4, hour 4, recovery


title: MDA-MB-453_PTX_2

description: drug

source_name: MDA-MB-453 Paclitaxel_24h


description: blood sample from patient BH015, highresponder, male, day3, hour16, sleepdep

source_name: blood sample from patient BH015, high responder, male, day3, hour16, sleepdep


title: MDA-MB-453_PTX_3

description: drug


description: blood sample from patient BH013, highresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH013, high responder, female, day2, hour20, baseline


title: MDA-MB-453_PTX_1

description: drug


description: blood sample from patient BH004, highresponder, female, day1, hour16, baseline

source_name: blood sample from patient BH004, high responder, female, day1, hour16, baseline


description: blood sample from patient BH026, highresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH026, high responder, female, day2, hour 8, baseline


title: MDA-MB-453_ERI_2

description: drug

source_name: MDA-MB-453 Eribulin_24h


description: blood sample from patient BH004, highresponder, female, day2, hour 0, baseline

source_name: blood sample from patient BH004, high responder, female, day2, hour 0, baseline


description: blood sample from patient BH013, highresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH013, high responder, female, day3, hour 8, sleepdep


title: MDA-MB-453_ERI_1

description: drug


title: MDA-MB-453_ERI_3

description: drug


description: blood sample from patient BH015, highresponder, male, day1, hour20, baseline

source_name: blood sample from patient BH015, high responder, male, day1, hour20, baseline


description: blood sample from patient BH003, lowresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH003, low responder, female, day2, hour16, baseline


title: MDA-MB-453_Ctrl_1

description: vehicle

source_name: MDA-MB-453 Control


title: MDA-MB-453_Ctrl_2

description: vehicle


description: blood sample from patient BH007, highresponder, male, day3, hour16, sleepdep

source_name: blood sample from patient BH007, high responder, male, day3, hour16, sleepdep


description: blood sample from patient BH026, highresponder, female, day2, hour 0, baseline

source_name: blood sample from patient BH026, high responder, female, day2, hour 0, baseline


title: MDA-MB-453_Ctrl_3

description: vehicle


description: blood sample from patient BH004, highresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH004, high responder, female, day4, hour 4, recovery


title: HCC-1428_PTX_1

description: drug

source_name: HCC-1428 Paclitaxel_24h


title: HCC-1428_PTX_3

description: drug


title: HCC-1428_ERI_3

description: drug

source_name: HCC-1428 Eribulin_24h


title: HCC-1428_PTX_2

description: drug


description: blood sample from patient BH015, highresponder, male, day2, hour 8, baseline

source_name: blood sample from patient BH015, high responder, male, day2, hour 8, baseline


description: blood sample from patient BH015, highresponder, male, day3, hour 8, sleepdep

source_name: blood sample from patient BH015, high responder, male, day3, hour 8, sleepdep


description: blood sample from patient BH015, highresponder, male, day1, hour12, baseline

source_name: blood sample from patient BH015, high responder, male, day1, hour12, baseline


description: blood sample from patient BH004, highresponder, female, day4, hour 0, recovery

source_name: blood sample from patient BH004, high responder, female, day4, hour 0, recovery


description: blood sample from patient BH015, highresponder, male, day2, hour 0, baseline

source_name: blood sample from patient BH015, high responder, male, day2, hour 0, baseline


description: blood sample from patient BH004, highresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH004, high responder, female, day2, hour 8, baseline


title: HCC-1428_Ctrl_3

description: vehicle

source_name: HCC-1428 Control


title: HCC-1428_ERI_2

description: drug


title: HCC-1428_Ctrl_1

description: vehicle


description: blood sample from patient BH010, lowresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH010, low responder, female, day4, hour 8, recovery


title: HCC-1428_Ctrl_2

description: vehicle


title: MDA-MB-468_PTX_1

description: drug

source_name: MDA-MB-468 Paclitaxel_24h


title: HCC-1428_ERI_1

description: drug


description: blood sample from patient BH013, highresponder, female, day4, hour 0, recovery

source_name: blood sample from patient BH013, high responder, female, day4, hour 0, recovery


description: blood sample from patient BH016, highresponder, male, day4, hour 0, recovery

source_name: blood sample from patient BH016, high responder, male, day4, hour 0, recovery


title: MDA-MB-468_ERI_1

description: drug

source_name: MDA-MB-468 Eribulin_24h


description: blood sample from patient BH015, highresponder, male, day2, hour16, baseline

source_name: blood sample from patient BH015, high responder, male, day2, hour16, baseline


title: MDA-MB-468_ERI_3

description: drug


description: blood sample from patient BH004, highresponder, female, day2, hour 4, baseline

source_name: blood sample from patient BH004, high responder, female, day2, hour 4, baseline


description: blood sample from patient BH008, lowresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH008, low responder, female, day1, hour12, baseline


description: blood sample from patient BH026, highresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH026, high responder, female, day1, hour20, baseline


title: MDA-MB-468_PTX_2

description: drug


description: blood sample from patient BH013, highresponder, female, day3, hour16, sleepdep

source_name: blood sample from patient BH013, high responder, female, day3, hour16, sleepdep


title: MDA-MB-468_ERI_2

description: drug


title: MDA-MB-468_PTX_3

description: drug


title: MDA-MB-468_Ctrl_3

description: vehicle

source_name: MDA-MB-468 Control


title: MDA-MB-468_Ctrl_2

description: vehicle


title: MDA-MB-468_Ctrl_1

description: vehicle


description: blood sample from patient BH015, highresponder, male, day3, hour 4, sleepdep

source_name: blood sample from patient BH015, high responder, male, day3, hour 4, sleepdep


description: blood sample from patient BH010, lowresponder, female, day3, hour16, sleepdep

source_name: blood sample from patient BH010, low responder, female, day3, hour16, sleepdep


description: blood sample from patient BH007, highresponder, male, day3, hour12, sleepdep

source_name: blood sample from patient BH007, high responder, male, day3, hour12, sleepdep


title: UACC-893_PTX_3

description: drug

source_name: UACC-893 Paclitaxel_24h


title: UACC-893_PTX_1

description: drug


description: blood sample from patient BH004, highresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH004, high responder, female, day1, hour12, baseline


title: UACC-893_ERI_3

description: drug

source_name: UACC-893 Eribulin_24h


title: UACC-893_ ERI_1

description: drug


title: UACC-893_PTX_2

description: drug


description: blood sample from patient BH003, lowresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH003, low responder, female, day2, hour20, baseline


description: blood sample from patient BH015, highresponder, male, day3, hour12, sleepdep

source_name: blood sample from patient BH015, high responder, male, day3, hour12, sleepdep


title: UACC-893_Ctrl_1

description: vehicle

source_name: UACC-893 Control


description: blood sample from patient BH004, highresponder, female, day3, hour 0, sleepdep

source_name: blood sample from patient BH004, high responder, female, day3, hour 0, sleepdep


description: blood sample from patient BH026, highresponder, female, day4, hour 0, recovery

source_name: blood sample from patient BH026, high responder, female, day4, hour 0, recovery


title: UACC-893_ERI_2

description: drug


description: blood sample from patient BH015, highresponder, male, day1, hour16, baseline

source_name: blood sample from patient BH015, high responder, male, day1, hour16, baseline


title: UACC-893_Ctrl_2

description: vehicle


description: blood sample from patient BH005, highresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH005, high responder, female, day1, hour12, baseline


title: AU565_PTX_3

description: drug

source_name: AU565 Paclitaxel_24h


title: AU565_ERI_3

description: drug

source_name: AU565 Eribulin_24h


title: AU565_PTX_1

description: drug


description: blood sample from patient BH015, highresponder, male, day2, hour20, baseline

source_name: blood sample from patient BH015, high responder, male, day2, hour20, baseline


description: blood sample from patient BH015, highresponder, male, day4, hour 0, recovery

source_name: blood sample from patient BH015, high responder, male, day4, hour 0, recovery


description: blood sample from patient BH015, highresponder, male, day4, hour 8, recovery

source_name: blood sample from patient BH015, high responder, male, day4, hour 8, recovery


description: blood sample from patient BH015, highresponder, male, day2, hour 4, baseline

source_name: blood sample from patient BH015, high responder, male, day2, hour 4, baseline


description: blood sample from patient BH015, highresponder, male, day4, hour 4, recovery

source_name: blood sample from patient BH015, high responder, male, day4, hour 4, recovery


description: blood sample from patient BH008, lowresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH008, low responder, female, day2, hour 8, baseline


title: AU565_ERI_1

description: drug


description: blood sample from patient BH016, highresponder, male, day2, hour16, baseline

source_name: blood sample from patient BH016, high responder, male, day2, hour16, baseline


description: blood sample from patient BH026, highresponder, female, day2, hour12, baseline

source_name: blood sample from patient BH026, high responder, female, day2, hour12, baseline


title: AU565_Ctrl_3

description: vehicle

source_name: AU565 Control


description: blood sample from patient BH016, highresponder, male, day4, hour 8, recovery

source_name: blood sample from patient BH016, high responder, male, day4, hour 8, recovery


title: HCC-38_PTX_1

description: drug

source_name: HCC-38 Paclitaxel_24h


description: blood sample from patient BH009, lowresponder, female, day2, hour12, baseline

source_name: blood sample from patient BH009, low responder, female, day2, hour12, baseline


title: UACC-893_Ctrl_3

description: vehicle

source_name: UACC-893 Control


title: HCC-38_ERI_2

description: drug

source_name: HCC-38 Eribulin_24h


title: AU565_Ctrl_2

description: vehicle


title: HCC-38_Ctrl_3

description: vehicle

source_name: HCC-38 Control


title: HCC-38_ERI_1

description: drug


title: AU565_Ctrl_1

description: vehicle


title: HCC-38_PTX_2

description: drug


description: blood sample from patient BH010, lowresponder, female, day3, hour 0, sleepdep

source_name: blood sample from patient BH010, low responder, female, day3, hour 0, sleepdep


description: blood sample from patient BH026, highresponder, female, day3, hour 0, sleepdep

source_name: blood sample from patient BH026, high responder, female, day3, hour 0, sleepdep


title: AU565_PTX_2

description: drug

source_name: AU565 Paclitaxel_24h


title: HCC-38_PTX_3

description: drug


description: blood sample from patient BH020, lowresponder, male, day4, hour 4, recovery

source_name: blood sample from patient BH020, low responder, male, day4, hour 4, recovery


description: blood sample from patient BH026, highresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH026, high responder, female, day1, hour12, baseline


description: blood sample from patient BH014, lowresponder, male, day2, hour16, baseline

source_name: blood sample from patient BH014, low responder, male, day2, hour16, baseline


description: blood sample from patient BH004, highresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH004, high responder, female, day3, hour 8, sleepdep


title: HCC-38_ERI_3

description: drug


description: blood sample from patient BH026, highresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH026, high responder, female, day4, hour 8, recovery


title: HCC-38_Ctrl_2

description: vehicle


title: HCC-38_Ctrl_1

description: vehicle


description: blood sample from patient BH020, lowresponder, male, day3, hour16, sleepdep

source_name: blood sample from patient BH020, low responder, male, day3, hour16, sleepdep


description: blood sample from patient BH020, lowresponder, male, day4, hour 0, recovery

source_name: blood sample from patient BH020, low responder, male, day4, hour 0, recovery


description: blood sample from patient BH009, lowresponder, female, day4, hour 0, recovery

source_name: blood sample from patient BH009, low responder, female, day4, hour 0, recovery


description: blood sample from patient BH009, lowresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH009, low responder, female, day2, hour20, baseline


title: MDA-MB-231_PTX_1

description: drug

source_name: MDA-MB-231 Paclitaxel_24h


title: AU565_ERI_2

description: drug

source_name: AU565 Eribulin_24h


title: MDA-MB-231_PTX_2

description: drug


description: blood sample from patient BH020, lowresponder, male, day1, hour16, baseline

source_name: blood sample from patient BH020, low responder, male, day1, hour16, baseline


description: blood sample from patient BH020, lowresponder, male, day2, hour20, baseline

source_name: blood sample from patient BH020, low responder, male, day2, hour20, baseline


title: MDA-MB-231_Ctrl_1

description: vehicle

source_name: MDA-MB-231 Control


title: MDA-MB-231_ERI_3

description: drug

source_name: MDA-MB-231 Eribulin_24h


title: MDA-MB-231_Ctrl_2

description: vehicle


title: MDA-MB-231_ERI_2

description: drug


title: MDA-MB-231_ERI_1

description: drug


title: MDA-MB-231_PTX_3

description: drug


description: blood sample from patient BH009, lowresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH009, low responder, female, day3, hour 8, sleepdep


title: HCC-1143_PTX_1

description: drug

source_name: HCC-1143 Paclitaxel_24h


description: blood sample from patient BH009, lowresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH009, low responder, female, day1, hour 8, baseline


description: blood sample from patient BH026, highresponder, female, day3, hour20, sleepdep

source_name: blood sample from patient BH026, high responder, female, day3, hour20, sleepdep


description: blood sample from patient BH026, highresponder, female, day1, hour 8, baseline

source_name: blood sample from patient BH026, high responder, female, day1, hour 8, baseline


title: MDA-MB-231_Ctrl_3

description: vehicle


description: blood sample from patient BH016, highresponder, male, day1, hour12, baseline

source_name: blood sample from patient BH016, high responder, male, day1, hour12, baseline


title: HCC-1143_PTX_2

description: drug


description: blood sample from patient BH014, lowresponder, male, day3, hour12, sleepdep

source_name: blood sample from patient BH014, low responder, male, day3, hour12, sleepdep


title: HCC-1143_PTX_3

description: drug


description: blood sample from patient BH020, lowresponder, male, day1, hour 8, baseline

source_name: blood sample from patient BH020, low responder, male, day1, hour 8, baseline


title: HCC-1143_ERI_3

description: drug

source_name: HCC-1143 Eribulin_24h


description: blood sample from patient BH014, lowresponder, male, day1, hour 8, baseline

source_name: blood sample from patient BH014, low responder, male, day1, hour 8, baseline


description: blood sample from patient BH020, lowresponder, male, day3, hour12, sleepdep

source_name: blood sample from patient BH020, low responder, male, day3, hour12, sleepdep


description: blood sample from patient BH014, lowresponder, male, day2, hour12, baseline

source_name: blood sample from patient BH014, low responder, male, day2, hour12, baseline


title: HCC-1143_Ctrl_2

description: vehicle

source_name: HCC-1143 Control


description: blood sample from patient BH009, lowresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH009, low responder, female, day3, hour12, sleepdep


description: blood sample from patient BH009, lowresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH009, low responder, female, day4, hour 4, recovery


description: blood sample from patient BH020, lowresponder, male, day2, hour16, baseline

source_name: blood sample from patient BH020, low responder, male, day2, hour16, baseline


title: HCC-1937_PTX_3

description: drug

source_name: HCC-1937 Paclitaxel_24h


description: blood sample from patient BH026, highresponder, female, day3, hour 8, sleepdep

source_name: blood sample from patient BH026, high responder, female, day3, hour 8, sleepdep


description: blood sample from patient BH004, highresponder, female, day3, hour 4, sleepdep

source_name: blood sample from patient BH004, high responder, female, day3, hour 4, sleepdep


title: HCC-1143_ERI_2

description: drug


description: blood sample from patient BH009, lowresponder, female, day2, hour 0, baseline

source_name: blood sample from patient BH009, low responder, female, day2, hour 0, baseline


description: blood sample from patient BH009, lowresponder, female, day3, hour16, sleepdep

source_name: blood sample from patient BH009, low responder, female, day3, hour16, sleepdep


description: blood sample from patient BH020, lowresponder, male, day4, hour 8, recovery

source_name: blood sample from patient BH020, low responder, male, day4, hour 8, recovery


description: blood sample from patient BH009, lowresponder, female, day2, hour 8, baseline

source_name: blood sample from patient BH009, low responder, female, day2, hour 8, baseline


description: blood sample from patient BH009, lowresponder, female, day1, hour12, baseline

source_name: blood sample from patient BH009, low responder, female, day1, hour12, baseline


title: HCC-1143_Ctrl_1

description: vehicle


description: blood sample from patient BH020, lowresponder, male, day2, hour 8, baseline

source_name: blood sample from patient BH020, low responder, male, day2, hour 8, baseline


description: blood sample from patient BH020, lowresponder, male, day1, hour12, baseline

source_name: blood sample from patient BH020, low responder, male, day1, hour12, baseline


description: blood sample from patient BH020, lowresponder, male, day3, hour 8, sleepdep

source_name: blood sample from patient BH020, low responder, male, day3, hour 8, sleepdep


description: blood sample from patient BH009, lowresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH009, low responder, female, day2, hour16, baseline


title: HCC-1143_ERI_1

description: drug

source_name: HCC-1143 Eribulin_24h


description: blood sample from patient BH016, highresponder, male, day3, hour16, sleepdep

source_name: blood sample from patient BH016, high responder, male, day3, hour16, sleepdep


description: blood sample from patient BH020, lowresponder, male, day3, hour20, sleepdep

source_name: blood sample from patient BH020, low responder, male, day3, hour20, sleepdep


title: HCC-1937_PTX_1

description: drug


description: blood sample from patient BH026, highresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH026, high responder, female, day2, hour16, baseline


title: HCC-1937_ERI_3

description: drug

source_name: HCC-1937 Eribulin_24h


title: HCC-1937_PTX_2

description: drug

source_name: HCC-1937 Paclitaxel_24h


description: blood sample from patient BH009, lowresponder, female, day3, hour20, sleepdep

source_name: blood sample from patient BH009, low responder, female, day3, hour20, sleepdep


description: blood sample from patient BH014, lowresponder, male, day2, hour 4, baseline

source_name: blood sample from patient BH014, low responder, male, day2, hour 4, baseline


description: blood sample from patient BH020, lowresponder, male, day3, hour 4, sleepdep

source_name: blood sample from patient BH020, low responder, male, day3, hour 4, sleepdep


title: HCC-1937_ERI_2

description: drug


description: blood sample from patient BH026, highresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH026, high responder, female, day4, hour 4, recovery


description: blood sample from patient BH020, lowresponder, male, day2, hour 0, baseline

source_name: blood sample from patient BH020, low responder, male, day2, hour 0, baseline


description: blood sample from patient BH026, highresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH026, high responder, female, day2, hour20, baseline


title: DU4475_PTX_2

description: drug

source_name: DU4475 Paclitaxel_24h


title: HCC-1937_Ctrl_2

description: vehicle

source_name: HCC-1937 Control


title: HCC-1937_Ctrl_3

description: vehicle


description: blood sample from patient BH020, lowresponder, male, day2, hour12, baseline

source_name: blood sample from patient BH020, low responder, male, day2, hour12, baseline


description: blood sample from patient BH020, lowresponder, male, day2, hour 4, baseline

source_name: blood sample from patient BH020, low responder, male, day2, hour 4, baseline


description: blood sample from patient BH016, highresponder, male, day1, hour16, baseline

source_name: blood sample from patient BH016, high responder, male, day1, hour16, baseline


description: blood sample from patient BH026, highresponder, female, day3, hour 4, sleepdep

source_name: blood sample from patient BH026, high responder, female, day3, hour 4, sleepdep


title: HCC-1937_ERI_1

description: drug


description: blood sample from patient BH016, highresponder, male, day3, hour 8, sleepdep

source_name: blood sample from patient BH016, high responder, male, day3, hour 8, sleepdep


title: DU4475_PTX_3

description: drug


description: blood sample from patient BH016, highresponder, male, day1, hour20, baseline

source_name: blood sample from patient BH016, high responder, male, day1, hour20, baseline


description: blood sample from patient BH014, lowresponder, male, day3, hour 0, sleepdep

source_name: blood sample from patient BH014, low responder, male, day3, hour 0, sleepdep


title: HCC-1937_Ctrl_1

description: vehicle


description: blood sample from patient BH014, lowresponder, male, day3, hour16, sleepdep

source_name: blood sample from patient BH014, low responder, male, day3, hour16, sleepdep


description: blood sample from patient BH014, lowresponder, male, day3, hour 4, sleepdep

source_name: blood sample from patient BH014, low responder, male, day3, hour 4, sleepdep


title: DU4475_PTX_1

description: drug


description: blood sample from patient BH020, lowresponder, male, day3, hour 0, sleepdep

source_name: blood sample from patient BH020, low responder, male, day3, hour 0, sleepdep


description: blood sample from patient BH026, highresponder, female, day3, hour16, sleepdep

source_name: blood sample from patient BH026, high responder, female, day3, hour16, sleepdep


title: DU4475_ERI_3

description: drug

source_name: DU4475 Eribulin_24h


description: blood sample from patient BH009, lowresponder, female, day1, hour16, baseline

source_name: blood sample from patient BH009, low responder, female, day1, hour16, baseline


description: blood sample from patient BH014, lowresponder, male, day2, hour20, baseline

source_name: blood sample from patient BH014, low responder, male, day2, hour20, baseline


description: blood sample from patient BH009, lowresponder, female, day3, hour 0, sleepdep

source_name: blood sample from patient BH009, low responder, female, day3, hour 0, sleepdep


title: DU4475_ERI_2

description: drug


description: blood sample from patient BH009, lowresponder, female, day2, hour 4, baseline

source_name: blood sample from patient BH009, low responder, female, day2, hour 4, baseline


description: blood sample from patient BH009, lowresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH009, low responder, female, day4, hour 8, recovery


title: DU4475_ERI_1

description: drug


title: DU4475_Ctrl_2

description: vehicle

source_name: DU4475 Control


description: blood sample from patient BH014, lowresponder, male, day4, hour 8, recovery

source_name: blood sample from patient BH014, low responder, male, day4, hour 8, recovery


description: blood sample from patient BH016, highresponder, male, day4, hour 4, recovery

source_name: blood sample from patient BH016, high responder, male, day4, hour 4, recovery


description: blood sample from patient BH014, lowresponder, male, day1, hour16, baseline

source_name: blood sample from patient BH014, low responder, male, day1, hour16, baseline


description: blood sample from patient BH014, lowresponder, male, day1, hour12, baseline

source_name: blood sample from patient BH014, low responder, male, day1, hour12, baseline


title: DU4475_Ctrl_1

description: vehicle


description: blood sample from patient BH009, lowresponder, female, day3, hour 4, sleepdep

source_name: blood sample from patient BH009, low responder, female, day3, hour 4, sleepdep


title: BT-474_PTX_2

description: drug

source_name: BT-474 Paclitaxel_24h


description: blood sample from patient BH014, lowresponder, male, day3, hour 8, sleepdep

source_name: blood sample from patient BH014, low responder, male, day3, hour 8, sleepdep


title: BT-474_PTX_3

description: drug


description: blood sample from patient BH014, lowresponder, male, day3, hour20, sleepdep

source_name: blood sample from patient BH014, low responder, male, day3, hour20, sleepdep


description: blood sample from patient BH004, highresponder, female, day1, hour20, baseline

source_name: blood sample from patient BH004, high responder, female, day1, hour20, baseline


description: blood sample from patient BH020, lowresponder, male, day1, hour20, baseline

source_name: blood sample from patient BH020, low responder, male, day1, hour20, baseline


title: BT-474_PTX_1

description: drug


title: DU4475_Ctrl_3

description: vehicle


description: blood sample from patient BH014, lowresponder, male, day2, hour 8, baseline

source_name: blood sample from patient BH014, low responder, male, day2, hour 8, baseline


description: blood sample from patient BH014, lowresponder, male, day4, hour 4, recovery

source_name: blood sample from patient BH014, low responder, male, day4, hour 4, recovery


description: blood sample from patient BH005, highresponder, female, day4, hour 4, recovery

source_name: blood sample from patient BH005, high responder, female, day4, hour 4, recovery


description: blood sample from patient BH014, lowresponder, male, day1, hour20, baseline

source_name: blood sample from patient BH014, low responder, male, day1, hour20, baseline


description: blood sample from patient BH014, lowresponder, male, day4, hour 0, recovery

source_name: blood sample from patient BH014, low responder, male, day4, hour 0, recovery


title: BT-474_ERI_3

description: drug

source_name: BT-474 Eribulin_24h


description: blood sample from patient BH005, highresponder, female, day3, hour16, sleepdep

source_name: blood sample from patient BH005, high responder, female, day3, hour16, sleepdep


description: blood sample from patient BH005, highresponder, female, day2, hour12, baseline

source_name: blood sample from patient BH005, high responder, female, day2, hour12, baseline


title: BT-474_ERI_1

description: drug


description: blood sample from patient BH005, highresponder, female, day3, hour12, sleepdep

source_name: blood sample from patient BH005, high responder, female, day3, hour12, sleepdep


description: blood sample from patient BH005, highresponder, female, day4, hour 8, recovery

source_name: blood sample from patient BH005, high responder, female, day4, hour 8, recovery


description: blood sample from patient BH007, highresponder, male, day3, hour 4, sleepdep

source_name: blood sample from patient BH007, high responder, male, day3, hour 4, sleepdep


description: blood sample from patient BH007, highresponder, male, day1, hour16, baseline

source_name: blood sample from patient BH007, high responder, male, day1, hour16, baseline


description: blood sample from patient BH014, lowresponder, male, day2, hour 0, baseline

source_name: blood sample from patient BH014, low responder, male, day2, hour 0, baseline


description: blood sample from patient BH005, highresponder, female, day2, hour20, baseline

source_name: blood sample from patient BH005, high responder, female, day2, hour20, baseline


description: blood sample from patient BH005, highresponder, female, day3, hour 0, sleepdep

source_name: blood sample from patient BH005, high responder, female, day3, hour 0, sleepdep


title: BT-474_Ctrl_3

description: vehicle

source_name: BT-474 Control


description: blood sample from patient BH005, highresponder, female, day2, hour16, baseline

source_name: blood sample from patient BH005, high responder, female, day2, hour16, baseline


title: HCC-2218_PTX_3

description: drug

source_name: HCC-2218 Paclitaxel_24h


title: BT-474_Ctrl_1

description: vehicle


title: RU486 treatment replicate 1

city: Baltiimore

first: Sige

last: Zou

state: MD

address: 251 Bayview Blvd

department: Translational Gerontology Branch

institute: National Institute on Aging

description: Biological replicate 1

hyb_protocol: Samples were added to custom printed long oligo arrays

scan_protocol: The hybridized slides were scanned with the GenePix 4100A Scanner (Axon Instruments, Sunnyvale, CA) and images were analyzed with GenePix Pro 6 software.

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal using BRB-ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.html, Biological research Branch, NCI)

organism: Drosophila melanogaster

source_name: heads of actin-GSG>UAS-ATPSyn-dRNAi

label_protocol: 3.5 ug total RNA was labeled with the 3DNA array kit following manufacturer's instructions  (Genisphere, Hatfield, PA).

growth_protocol: Females were cultured on the diet with 2% sugar and 18% yeast

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

treatment_protocol: Flies were treated with and without 200 uM RU486 until they reached the age of 2-week

tag: tissue

value: head

tag: gender

source_name: Heads of Canton S


title: HCC-2218_PTX_1

description: drug


title: RU486 treatment replicate 3

description: Biological replicate 3


title: BT-474_Ctrl_2

description: vehicle


title: RU486 treatment replicate 2

description: Biological replicate 2


description: blood sample from patient BH005, highresponder, female, day3, hour 4, sleepdep

source_name: blood sample from patient BH005, high responder, female, day3, hour 4, sleepdep


description: blood sample from patient BH007, highresponder, male, day1, hour 8, baseline

source_name: blood sample from patient BH007, high responder, male, day1, hour 8, baseline


title: RU486 treatment replicate 4

description: Biological replicate 4


title: HCC-2218_ERI_1

description: drug

source_name: HCC-2218 Eribulin_24h


title: HCC-2218_ERI_3

description: drug


title: No RU486 treatment replicate 4

description: Biological replicate 4


title: HCC-2218_Ctrl_3

description: vehicle

source_name: HCC-2218 Control


title: HCC-2218_ERI_2

description: drug


title: HCC-2218_PTX_2

description: drug


title: No RU486 treatment replicate 2

description: Biological replicate 2


title: BT-474_ERI_2

description: drug

source_name: BT-474 Eribulin_24h


title: HCC-2218_Ctrl_2

description: vehicle


title: No RU486 treatment replicate 3

description: Biological replicate 3


title: HCC-2218_Ctrl_1

description: vehicle


title: No RU486 treatment replicate 1

description: Biological replicate 1


title: SKBR3_ERI_3

description: drug

source_name: SKBR3 Eribulin_24h


title: SKBR3_PTX_1

description: drug

source_name: SKBR3 Paclitaxel_24h


title: SKBR3_PTX_3

description: drug


title: SKBR3_PTX_2

description: drug


title: Adar2-/-_wholebrain_2

city: Vienna

first: Fritz

last: Sedlazeck

state: Vienna

address: Dr. Bohr-Gasse 9

department: CIBIV

country: Austria

institute: MFPL

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Analysis by KFB Regensburg, Germany using Expression Console™ 1.3.1.187 : Affymetrix GeneChip Command Console (AGCC) and Expression Console Software; Normalization was performed with Robust Multi-chip Analysis (RMA) algorithm: Background Adjustment, Quantile Normalization, and Probe Signal Summarization (Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data, Biostatistics, April 2003; Vol. 4; Number 2: 249–264)

source_name: whole brain

label_protocol: RNA was quality checked and samples for microarray analysis were processed according to the GeneChip® WT Terminal Labeling and Hybridization User Manual

extract_protocol: Female mice were dissected and whloe brain was homogenized. Total RNA was extracted using peqGOLD TriFast reagent according to manufacturer´s instructions (PEQLAB Biotechnologie GmbH, Erlangen, Germany).

value: brain

tag: developmental stage

value: adult


title: wildtype_wholebrain_2


title: wildtype_wholebrain_1


title: SKBR3_ERI_2

description: drug


title: SKBR3_Ctrl_1

description: vehicle

source_name: SKBR3 Control


title: HCC-1806_PTX_2

description: drug

source_name: HCC-1806 Paclitaxel_24h


title: SKBR3_Ctrl_3

description: vehicle


title: HCC-1806_PTX_3

description: drug


title: cm1-3

city: Beijing

first: yuan

middle: Yuan

last: Du

address: Yihe Yuan Road 5

institute: Department of Cell Biology and Genetics, College of Life Sciences, Peking University

hyb_protocol: Hybridized to a mouse Oligo Microarray (Phalanx Mouse OneArray® v2, Phalanx Biotech) according to the manufacturer's protocol.

scan_protocol: After hybridization, arrays were scanned using GenePix 4000B scanner (Molecular Devices) and processed using the GenePix Pro 6.0 software (Molecular Devices).

data_processing: After removing control probes, a 14/33 presence call (SNR>=5 and foreground-background>0) was used to filter probes for the 33 microarrays, resulting in 12733 probes for further quantile normalization. The median of each sample was used for hierarchical clustering. Complete-linkage hierarchical clustering was performed using cluster 3.0 (written by Michael Eisen, Stanford University) with Spearman rank correlation coefficient as gene distances measurement and Pearson correlation coefficient as sample distances measurement.

source_name: cardiomyocyte directly from newborn mouse heart (less than 3days)

label_protocol: Total mRNA from NBF1, NBF2, ICM1, ICM2, cm1, cm2 cells were labeled with Cy5.

extract_protocol: Total cellular RNA was extracted with TRIzol reagent (Sigma). Genomic DNA were removed with DNAase(Ambion), and 1ug RNA of each sample were used for reverse transcription with EasyScript Reverse Transcriptase (TransGen), according to the manufacturer's instructions. PCR amplification was performed using 2× EasyTaq SuperMix (TransGen).

treatment_protocol: In brief, the limbs and tails of neonatal mice were cut off, and the neonatal mouse skin was carefully peeled. The isolated neonatal mouse skin was then incubated in Collagenase type Ⅳ (2mg/ml, Gibco) for 2hrs at 37℃. After incubation, the epiderm was carefully removed from the surface of the skin. The remaining tissues were dissociated and minced into 1mm pieces, which were then resuspended by Dulbecco’s Modified Eagle Medium (DMEM, Hyclone), containing 10% Fetal bovine serum (Hyclone), 2x penicillin/streptomycin (Invitrogen). The isolated neonatal skin fibroblasts were collected by flowing through cell strainers.

value: ICR

value: 3 days

value: skin


title: SKBR3_ERI_1

description: drug


title: ICM2-3

source_name: induced cardiomyocyte from fibroblast


title: HCC-1806_PTX_1

description: drug


title: cm2-1


title: SKBR3_Ctrl_2

description: vehicle


title: cm1-1


title: cm1-2


title: FVB/N AIN76A Low Rep4

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

country: New Zealand

institute: Plant and Food Research Ltd.

hyb_protocol: Labeled cRNAs were hybridised using an In Situ Hybridization Plus Kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s protocols, using 750 ng of experimental and reference cRNA onto 44k mouse oligonucleotide arrays (Agilent Technologies, Santa Clara, CA, USA). After hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

scan_protocol: Slides were scanned using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA) with photomultiplier tube (PMT) voltage of 580 V.  Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices).  All slides were individually checked and manually flagged for abnormalities.

data_processing:
Microarray data were analysed using the Limma package in Bioconductor. Image analyses of the extracted foreground and background fluorescence intensity measurements were evaluated to select the best background correction for the experiment, but no background correction was necessary due to homogeneous hybridisation. Data were normalised using a local linear regression analysis (LOESS). Data with bad flags (-50 = poor or irregular spots, automatically flagged by the GenePix 4200A scanner; and -100, flagged by hand after visual inspection of the images) were not included in the analysis. Control probes (eQC, Bright corners, E1A and Pro25G) were also removed before normalization. Boxplots, density plots and spatial images of the raw and normalized data were examined in order to check the quality of the microarray data, and that no unusual results for any slide were observed. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe using an empirical Bayes approach. The probability values were then corrected for multiple testing using the Benjamini and Hochberg correction, and a false discovery rate (FDR) calculated. Probes that had an FDR of less than 5 % (q<0*05) were considered to be differentially expressed between the Mdr1a-/- mice on the AIN-76A diet and the FVB/N mice on the same diet.
The 'Mdr1a.AIN76A.High_vs_FVB.AIN76A.Low.csv' contains fold changes of the [high inflammation vs. low inflammation] comparison ranked by significance.
Additional processed data files are described in the 'readme.txt'

source_name: reference RNA

label_protocol: cDNA and cRNA were synthesised using the Low RNA Input Linear Amplification kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Reverse transcription used 500 ng of total RNA and oligo-dT primers. cRNA was synthesised and labeled with either cyanine3 (samples) or cyanine5 (reference) dye (Perkin-Elmer/NEN Life Science, Boston, MA, USA) and the dye incorporation evaluated using a Nanodrop ND-1000 spectrophotometer. Samples ranged from 10 to 22 pmol of dye/µg of RNA.

growth_protocol: Mice were raised under conventional conditions, and received standard rodent chow and water ad libitum.

extract_protocol: Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Twenty-four male Mdr1a-/- mice, five to six weeks old, mean weight 23.8 g (SD 2.0 g), and twenty-four male FVB/N mice, five to six weeks old, mean weight 24.9 g (SD 2.3 g), were housed individually in cages with pressed wood chips and a plastic tube for environmental enrichment. The room was climate controlled (22 to 24 ºC, at approximately 60 % humidity) with a 12-hour light:dark cycle. All mice were acclimatized for a week before the start of the experiment. Mice were randomly assigned to one of three treatment groups of 12 animals each. Each treatment group received one of the following diets: Control (AIN-76A powdered diet) - 4 Mdr1a mice with a high histology score (Microarray Slides 251269421243,251269421255, 251269421259 & 251269421253) and 4 FVB/N mice with a low HIS score (Microarray Slides 251269421242, 251269421252, 251269421258 & 251269421384) were selected for microarray analysis. The microarray analysis of these slides has been previously reported (Nones et al 2009, PMID: 18761777). Animals received food and water ad libitum.

tag: strain background

value: Swiss

value: mixed

value: adult and fetal

value: Small intestine, colon, kidney, liver (adult); whole fetus

value: reference RNA

source_name: FVB/N mouse fed control (AIN-76A) diet

growth_protocol: Mice were weighed three times a week throughout the experiment to determine body weight changes. Food intake was measured during two periods of four days at 15 and 18 weeks of age. Food intake was calculated from the amount of food offered during the four days minus the remaining and spilt food at the end of the period. To minimize the variation between the last food intake and sampling, mice were fasted overnight before the tissue sampling and food was returned for two hours before sampling in the morning in staggered groups of six mice. Six mice from each group were euthanised via CO2 asphyxiation and cervical dislocation at 21 weeks of age (sample group 1) and the remaining animals at 24 weeks of age (sample group 2). These time points were selected based on previous results to verify possible time-dependent changes in the colonic inflammation patterns.

value: FVB/N

tag: genotype/variation

value: wild type

value: 21-24 weeks

value: male

tag: diet

value: control (AIN-76A powdered) diet

tag: colonic histological injury score (his)

value: colon


title: Adar2-/-_wholebrain_1

value: female


title: HCC-1806_ERI_3

description: drug

source_name: HCC-1806 Eribulin_24h

tag: cell line

tag: cell type

value: breast cancer


title: ICM2-2

tag: strain

tag: age


title: cm2-2


title: HCC-1806_ERI_1

description: drug


title: HCC-1806_ERI_2

description: drug


title: icm-1-8


title: cm3-3


title: icm1-3


title: FVB/N AIN76A Low Rep3

tag: sample type

value: low


title: HCC-1806_Ctrl_1

description: vehicle

source_name: HCC-1806 Control


title: HCC-1806_Ctrl_3

description: vehicle


title: FVB/N AIN76A Low Rep1


title: HCC-1806_Ctrl_2

description: vehicle


title: fibroblast_cultured_rep2-3

source_name: fibroblast of newborn mouse (less than 3days)

value: ICR


title: Mdr1a AIN76A High Rep4

source_name: Mdr1a-/- mouse fed control (AIN-76A) diet

value: high


title: Mdr1a AIN76A High Rep3


title: HCC-1954_PTX_2

description: drug

source_name: HCC-1954 Paclitaxel_24h


title: ICM2-1

value: 3 days

value: skin


title: fibroblast_cultured_repl3


title: fibroblast_cultured_rep2-1


title: Mdr1a AIN76A High Rep1

value: Swiss

value: mixed


title: fibroblast_cultured_8days_rep7


title: Mdr1a AIN76A High Rep2

value: adult and fetal

value: Small intestine, colon, kidney, liver (adult); whole fetus


title: HCC-1954_PTX_1

description: drug


title: fibroblast_cultured_rep2-2


title: FVB/N AIN76A Low Rep2

value: reference RNA

value: FVB/N


title: fibroblast_cultured_repl2


title: HCC-1954_ERI_2

description: drug

source_name: HCC-1954 Eribulin_24h


title: HCC-1954_PTX_3

description: drug


title: HCC-1954_ERI_1

description: drug


title: HDAC2 siRNA_1_HepG2 [HDAC2 siRNA subset]

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

description: SAMPLE 29

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by means of  Genome Studio v2011.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

label_protocol: Biotinylated cRNA were prepared using Ambion Totalprep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

tag: subset

value: HDAC2 siRNA subset

value: HB cell line HepG2

tag: treatment

value: HDAC2 siRNA


title: HDAC2 siRNA_3_HepG2 [HDAC2 siRNA subset]

description: SAMPLE 31


title: HDAC2 siRNA_2_HepG2 [HDAC2 siRNA subset]

description: SAMPLE 30


title: HCC-1954_ERI_3

description: drug