title: urine microalbuminuria 2° pair (M2)

city: Turin

first: Gabriella

last: Gruden

address: C/so AM Dogliotti 14

department: Medical Science

institute: University of Turin

description: test

data_processing:
Raw Ct value were calculated, standardised to U6 snRNA [2^-deltaCt, where deltaCt = (Ct_Target − Ct_U6)], and expressed as fold change  [2^-ΔΔCt, where -ΔΔCt = -[ΔCtmicro -ΔCtnormo] using the SDS software 2.3. Flags have been applied to delete problematic data from plate document and RQ study analysis.
Fold Change file reports test/control (i.e., micro/normo) ratios in both pairs of patients

label: FAM

source_name: urinary exosomes

extract_protocol: Total RNA was extracted using the Triazol reagent

tag: source

value: urinary exosomes

tag: diabetic nephropathy stage

value: microalbuminuria

tag: glucose control (hba1c)


title: urine normoalbuminuria 2° pair (N2)

status: Public on Feb 14 2014

type: RNA

country: Italy

description: control

molecule: total RNA

organism: Homo sapiens

value: normoalbuminuria


title: urine normoalbuminuria 1° pair (N1)

description: control


title: urine microalbuminuria 1° pair (M1)

description: test


title: Bulgarian4

type: genomic

city: Oxford

first: George

last: Busby

state: OXON

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

hyb_protocol: Followed Illumina Standard Protocol

scan_protocol: Followed Illumina Standard Protocol

data_processing: Image was analyzed using Illumina GenomeStudio v2009.2.0.29803

label: biotin

molecule: genomic DNA

source_name: saliva

label_protocol: Followed Illumina Standard Protocol

extract_protocol: Extraction of genomic DNA from saliva and blood using common laboratory protocols.

tag: gender

value: male

tag: nationality

value: Bulgarian


title: Bulgarian13


title: Bulgarian6


title: THP1-MLL/AF9_knockdown-siRNA4

status: Public on Feb 13 2014

city: Munich

first: Katrin

middle: K

last: Fleischmann

address: Lindwurmstrasse 2a

department: Children’s Research Center

country: Germany

institute: Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Univeristät München

hyb_protocol: 1.65 µg of each Cy3-labeled cRNA sample was fragmented and prepared for hybridization (Gene Expression Hybridization Kit, Agilent Technologies, Santa Clara, CA, USA). cRNA samples were hybridized at 65°C for 17 hours on seperate Whole Human Genome Microarrays (4x44K format). Afterwards microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies, Santa Clara, CA, USA) followed by drying with acetonitrile (Sigma-Aldrich, St. Louis, MO, USA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.4.1 Software on the Agilent DNA Microarray Scanner and extracted from the images using Feature Extraction 10.5.1.1 Software (both Agilent Technologies, Santa Clara, CA, USA). Analysis of the Agilent One-Color RNA Spike-In Plot was used to ensure equal and good performance of each single labeling and hybridization experiment.

data_processing:
Green channel intensities from each data file were read for further analysis. Quality weights for each spot on every array were assigned, based on several quality measures (e.g. saturation, uniformity, population outlier) produced by Agilent Feature Extraction v10.5.1.1 (FE). Background correction was performed by FE and scaling was used for between array normalization.
Hierarchical clustering of arrays and principal component analyses were performed in collaboration with Dr. Philipp Pagel (Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universität München) with the statistical language R (R Development Core Team 2008) using packages from the Bioconductor framework (Gentleman, et al. 2004). Analysis of differential expression between knockdown and control treatments was carried out in R with the limma package (Smyth 2004) which fits a linear model for each gene and computes a moderated t-statistic and its p-value (Smyth 2005). Limma is part of the Bioconductor project (Gentleman, et al. 2004). Adjustment for multiple testing was done using the method by Benjamini and Hochberg (Benjamini, et al. 1995). Thus, logarithmic fold-change (logFC =  ), p-value of the moderated t test and p-value after correcting for multiple testing were generated.
The unnormalized data showed an almost perfect log intensity distribution which was more uniform than the BG-corrected or the BG-corrected and normalized data. In hierarchical clustering of arrays based on the Euclidean distance of log intensity profiles the two treatments (knockdown and control) clearly cluster together. In principal component (PC) analysis of arrays based on their expression profiles clearly the first PC is the knock-down, which is in good agreement with the hierarchical clustering results. No clear improvement is seen in PC analysis through BG-correction and normalization. Additionally unnormalized data seem to be more consistent, e.g. more identical replicate probes are within the top regulated probes. Due to these findings unnormalized data were used for the differential expression analysis.
To evaluate the reliability of the results and to decide on a threshold p-value, a t test was performed over identical replicate probe sets for differentially expressed probes up to p < 0.05. Here, probe sets showing a p-value below 0.05 were regarded as reliably differentially expressed. The percentage of significant replicates was plotted against the p-value threshold. This showed a plateau of high percentage of significant identical replicates up to p < 0.03, with an almost linear decline between p < 0.03 and 0.06. Thus, to include the highest number of differentially expressed transcripts without raising the false positive rate, a cutoff p-value of the moderated t test below 0.03 was set. Within these, probes which did not show significant alteration over all identical replicates were removed from the results. According to experimental design strategies, probes which did not show a uniform regulation between knockdown and control treatments (i.e. both knockdown samples yielding either higher or lower FI values than the controls) were removed from the final results. This concerned five of 1350 deregulated probes.

source_name: THP1 cell line, MLL/AF9_knockdown via siRNA4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) employing T7 RNA polymerase.

growth_protocol: THP1 cells were cultured in RPMI1640, 10%FCS and 1%Pen/Strep up to day 6 of experiments and in DMEM/Ham's F12, 0.5%FCS from day 6 of experiments onwards.

extract_protocol: total RNA was isolated via miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.

treatment_protocol: THP1 cells were treated on day 0, day 3 and day 6 with siRNAs. RNA was harvested on day 8 of experiments.

tag: cell line

value: AML M5 cell line THP1

tag: sirna

tag: genotype/variation

value: MLL-AF9 knockdown


title: THP1-MLL/AF9_knockdown-siRNA3

source_name: THP1 cell line, MLL/AF9_knockdown via siRNA3


title: THP1-control_non_targeting_siRNA1

source_name: THP1 cell line, control non-targeting-siRNA1

value: control non-targeting-siRNA1

value: control


title: T_CD3+ [5342595013_C]

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

description: T cell

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2-transformed and normalized using quantile normalization with Partek Genomics Suite

source_name: peripheral blood

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: initial differentiation

tag: activation stimuli

value: unstimulated

tag: time

tag: donor


title: T_CD3+ [5342595013_F]

description: T cell


title: T_CD3+ [4676163038_L]

description: T cell

value: MB_883 ND221 CS25 pos.SATB1 stim.16h

value: SATB1-transfected + 16 hrs CD3/CD28

value: 14 days


title: THP1-control_non_targeting_siRNA2

source_name: THP1 cell line, control non-targeting-siRNA2

value: control non-targeting-siRNA2


title: SouthItalian18

source_name: blood

value: SouthItalian


title: T_CD3+ [4676163038_H]

description: T cell


title: Bulgarian3


title: T_CD3+ [4676163038_F]

description: T cell


title: T_CD3+ [4676163038_G]

description: T cell

value: MB_873 ND221 CS25 pos.control stim.16h

value: control-transfected + 16 hrs CD3/CD28


title: SouthItalian13


title: T_CD3+ [4676163038_J]

description: T cell


title: Bulgarian1


title: T_CD3+ [4676163038_K]

description: T cell

value: MB_881 ND221 CS25 pos.DsRed stim.16h

value: dsRed-transfected + 16 hrs CD3/CD28


title: Bulgarian2


title: SouthItalian17


title: SouthItalian16


title: T_CD3+ [4676163038_C]

description: T cell


title: Treg [4233291048_B]

description: T cell


title: SouthItalian15


title: SouthItalian7


title: SouthItalian14


title: SouthItalian9


title: SouthItalian10


title: Tmemory [4233291046_E]

description: T cell


title: Tstim [4233291043_B]

description: T cell


title: SouthItalian12


title: Tresting [4233291043_A]

description: T cell


title: Tconv [4233291046_C]

description: T cell


title: iTreg_IL-2 [4233291043_D]

description: T cell


title: iTreg [4233291046_A]

description: T cell

value: CD3/28 + TGF


title: Tnaive [4233291046_F]

description: T cell


title: iTreg_IL-2 [4233291007_F]

description: T cell


title: Treg [4233291046_D]

description: T cell


title: Treg [4233291043_F]

description: T cell


title: T_CD3+ [4676163038_D]

description: T cell


title: Tconv [4233291043_E]

description: T cell


title: iTreg_IL-2 [4233291046_B]

description: T cell


title: iTreg [4233291043_C]

description: T cell


title: SouthItalian6

value: male


title: Tconv [4233291048_A]

description: T cell


title: T_CD3+ [4676163038_B]

description: T cell


title: Tstim [4233291007_D]

description: T cell


title: iTreg [4233291007_E]

description: T cell


title: SouthItalian11


title: Tnaive [4233291007_B]

description: T cell


title: SouthItalian8


title: Tresting [4233291007_C]

description: T cell


title: NK_cells [5342595027_K]

description: NK cell


title: Tmemory [4233291007_A]

description: T cell


title: NK_cells [5342595027_C]

description: NK cell


title: SouthItalian4


title: SouthItalian5


title: SouthItalian3


title: Monocyte_CD14+ [5342595027_B]

description: Monocyte


title: Monocyte_CD14+ [5376074044_E]

description: Monocyte


title: Monocyte_CD14+ [5376074044_H]

description: Monocyte

value: HDL 2mg/ml


title: Monocyte_CD14+ [5342595013_A]

description: Monocyte


title: Monocyte_CD14+ [5376074045_B]

description: Monocyte

value: MCD 10uM


title: Monocyte_CD14+ [5376074044_B]

description: Monocyte


title: Monocyte_CD14+ [5376074044_I]

description: Monocyte


title: Monocyte_CD14+ [5376074044_C]

description: Monocyte


title: SouthItalian1


title: NK_cells [5342595013_B]

description: NK cell


title: M_MCSF_IL4_72h [5376074056_K]

description: Macrophage

value: M-CSF


title: M_MCSF_IL4_72h [5376074056_J]

description: Macrophage


title: M_GMCSF_IL4_upLPS_72h [5376074056_H]

description: Macrophage

value: GM-CSF


title: Monocyte_CD14+ [5376074044_F]

description: Monocyte


title: Monocyte_CD14+ [5342595027_F]

description: Monocyte


title: Monocyte_CD14+ [5376074044_K]

description: Monocyte


title: M_GMCSF_upLPS_72h [5376074056_G]

description: Macrophage

value: upLPS


title: M_MCSF_upLPS_72h [5376074056_F]

description: Macrophage


title: Monocyte_CD14+ [5376074044_D]

description: Monocyte

value: unstimulated


title: Monocyte_CD14+ [5376074045_G]

description: Monocyte


title: M_GMCSF_IL4_72h [5376074056_I]

description: Macrophage


title: Monocyte_CD14+ [5376074045_D]

description: Monocyte


title: M_MCSF_IL4_upLPS_72h [5376074056_L]

description: Macrophage


title: M_GMCSF_IL4_upLPS_72h [5376074056_E]

description: Macrophage


title: M0_GMCSF_0h [5376074056_B]

description: Macrophage

value: con


title: M0_MCSF_0h [5376074056_C]

description: Macrophage


title: M_MCSF_upLPS_72h [5376074056_D]

description: Macrophage


title: M0_GMCSF_0h [5376074054_A]

description: Macrophage


title: SouthItalian2


title: M_GMCSF_HDL_6h [5376074045_H]

description: Macrophage


title: M_GMCSF_OA_24h [5376074054_H]

description: Macrophage

value: OA


title: M0_MCSF_0h [5376074054_F]

description: Macrophage


title: M_MCSF_OA_24h [5376074054_C]

description: Macrophage


title: Monocyte_CD14+ [5376074044_G]

description: Monocyte


title: M_GMCSF_HDL_6h [5376074045_K]

description: Macrophage


title: M_GMCSF_HDL_6h [5376074045_J]

description: Macrophage


title: M_GMCSF_OA_24h [5376074054_L]

description: Macrophage


title: M0_GMCSF_0h [5376074045_E]

description: Macrophage


title: M_GMCSF_HDL_6h [5376074045_L]

description: Macrophage


title: M0_GMCSF_0h [5376074045_C]

description: Macrophage


title: M_GMCSF_OA_24h [5376074040_L]

description: Macrophage


title: M_GMCSF_LiA_24h [5376074040_K]

description: Macrophage

value: LiA


title: M_GMCSF_PA_24h [5376074040_J]

description: Macrophage

value: PA


title: Degroot_144_Plate210

city: Houston

first: Roel

last: Verhaak

state: TX

address: 1400 Pressler street

country: USA

institute: UT MD Anderson Cancer Center

description: GLIOBLASTOMA

hyb_protocol: Refer to the Illumina whole genome DASL array Manual

data_processing: Raw data was transformed to log2 scale and normalized by quantile method using Bioconductor package beadarray. For genes with multiple probes, the probe with maximum value was used to represent the gene.

source_name: Surgical Case

growth_protocol: Clinical samples

extract_protocol: standard TriZol method (Invitrogen)

treatment_protocol: De novo, non-treated.

tag: cell type

value: Astrocytoma

tag: grade

value: GradeIV

tag: Sex

value: M

tag: age


title: Degroot_139_Plate210

description: Oligodendroglioma

scan_protocol: Refer to the Illumina whole genome DASL array Manual

value: Oligodendroglioma

value: GradeII

value: F


title: Degroot_140_Plate210

description: Glioblastoma multiforme

label_protocol: Refer to the Illumina whole genome DASL array Manual


title: M_GMCSF_PA_24h [5376074054_I]

description: Macrophage


title: Degroot_141_Plate210

description: Glioblastoma multiforme


title: Degroot_138_Plate210

description: Glioblastoma multiforme


title: Degroot_142_Plate210

description: Glioblastoma multiforme


title: M0_GMCSF_0h [5376074045_A]

description: Macrophage


title: M0_GMCSF_0h [5376074045_F]

description: Macrophage


title: Degroot_143_Plate210

description: GLIOBLASTOMA


title: M_GMCSF_LA_24h [5376074040_H]

description: Macrophage

value: LA


title: M_GMCSF_LA_24h [5376074040_I]

description: Macrophage


title: M_GMCSF_LA_24h [5376074040_G]

description: Macrophage


title: M_GMCSF_LiA_24h [5376074040_F]

description: Macrophage


title: Degroot_132_Plate210

description: Glioblastoma multiforme


title: M_GMCSF_PA_24h [5376074040_B]

description: Macrophage


title: M_GMCSF_PA_24h [5376074040_D]

description: Macrophage


title: Degroot_135_Plate210

description: GLIOBLASTOMA


title: Degroot_134_Plate210

description: Glioblastoma multiforme


title: Degroot_136_Plate210

description: Astrocytoma


title: Degroot_131_Plate210

description: Glioblastoma multiforme


title: Degroot_133_Plate210

description: Anaplastic astrocytoma

value: GradeIII


title: M_MCSF_SA_24h [5376074039_L]

description: Macrophage

value: SA


title: Degroot_137_Plate210

description: Glioblastoma multiforme


title: Degroot_130_Plate210

description: Anaplastic astrocytoma


title: Degroot_126_Plate210

description: Astrocytoma, low grade


title: Degroot_129_Plate210

description: ANAPLASTIC OLIGODENDROGLIOMA


title: Degroot_125_Plate210

description: Glioblastoma multiforme


title: Degroot_127_Plate210

description: Glioblastoma multiforme


title: M_GMCSF_OA_24h [5376074040_E]

description: Macrophage


title: M_GMCSF_OA_24h [5376074040_A]

description: Macrophage


title: M_MCSF_PA_24h [5376074039_J]

description: Macrophage

value: M-CSF


title: M_GMCSF_upLPS_72h [5376074056_A]

description: Macrophage

value: GM-CSF


title: M_GMCSF_LiA_24h [5376074040_C]

description: Macrophage


title: M_GMCSF_TPP_IFNb_72h [5376074038_J]

description: Macrophage

value: IFNb 100U/ml + TNFa 800 u/ml+ PGE2 1µg/ml+ P3C 1µg/ml


title: M_GMCSF_IFNb_72h [5376074038_G]

description: Macrophage

value: IFNb 100U/ml


title: M_GMCSF_IFNb_72h [5376074038_I]

description: Macrophage


title: M_GMCSF_TPP_IFNb_72h [5376074038_L]

description: Macrophage


title: M0_MCSF_0h [5376074039_F]

description: Macrophage

value: con


title: Degroot_123_Plate210

description: Glioblastoma multiforme


title: Degroot_128_Plate210

description: Glioblastoma multiforme


title: Degroot_124_Plate210

description: DIFFUSE GLIOMA with oligo like features

value: Oligo/Astrocytoma


title: M_GMCSF_TPP_IFNb_72h [5376074038_H]

description: Macrophage


title: M_GMCSF_TPP_IFNb_IFNg_72h [5376074038_K]

description: Macrophage

value: IFNb 100U/ml + TNFa 800 u/ml+ PGE2 1µg/ml+ P3C 1µg/ml + IFNg 200U/ml


title: Degroot_119_Plate210

description: Glioblastoma multiforme


title: Degroot_118_Plate210

description: ANAPLASTIC GLIONEURONAL NEOPLASM


title: Degroot_122_Plate210

description: Oligodendroglioma


title: Degroot_120_Plate210

description: ANAPLASTIC DIFFUSE GLIOMA


title: Degroot_115_Plate210

description: Anaplastic astrocytoma


title: M_GMCSF_TPP_IFNb_IFNg_72h [5376074038_C]

description: Macrophage


title: Degroot_116_Plate210

description: Glioblastoma multiforme


title: M_GMCSF_IFNb_72h [5376074038_E]

description: Macrophage


title: M0_GMCSF_0h [5376074038_F]

description: Macrophage


title: Degroot_117_Plate210

description: Glioblastoma multiforme


title: Degroot_114_Plate210

description: Glioblastoma multiforme


title: M0_GMCSF_0h [5376074038_A]

description: Macrophage


title: M_GMCSF_TPP_IFNb_IFNg_72h [5376074038_D]

description: Macrophage


title: Degroot_113_Plate210

description: Anaplastic astrocytoma


title: M0_GMCSF_0h [5376074038_B]

description: Macrophage


title: Degroot_121_Plate210

description: Diffuse Glioma


title: Degroot_111_Plate210

description: Glioblastoma multiforme


title: Degroot_112_Plate210

description: Astrocytoma, low grade


title: M_MCSF_SA_24h [5376074035_L]

description: Macrophage


title: M_GMCSF_SA_24h [5376074035_J]

description: Macrophage


title: Degroot_110_Plate210

description: Glioblastoma multiforme


title: M0_GMCSF_0h [5376074035_I]

description: Macrophage


title: M_MCSF_SA_24h [5376074035_E]

description: Macrophage


title: M_GMCSF_OA_24h [5376074035_G]

description: Macrophage

value: OA


title: M0_GMCSF_0h [5376074035_K]

description: Macrophage


title: M_GMCSF_PA_24h [5376074035_B]

description: Macrophage

value: PA


title: Degroot_108_Plate210

description: Glioblastoma multiforme

value: Astrocytoma

value: GradeIV


title: Degroot_103_Plate210

description: Glioblastoma multiforme

value: M


title: Degroot_109_Plate210

description: Glioblastoma multiforme


title: M0_MCSF_0h [5376074035_A]

description: Macrophage


title: M0_GMCSF_0h [5376074033_F]

description: Macrophage


title: Degroot_106_Plate210

description: Glioblastoma multiforme


title: Degroot_104_Plate210

description: Anaplastic astrocytoma


title: Degroot_100_Plate210

description: Glioblastoma multiforme


title: Degroot_105_Plate210

description: Anaplastic astrocytoma


title: Degroot_98_Plate210

description: Glioblastoma multiforme


title: Degroot_107_Plate210

description: Glioblastoma multiforme


title: M_GMCSF_TPP_72h [5376074033_G]

description: Macrophage


title: M_GMCSF_PGE2_72h [5376074033_D]

description: Macrophage


title: Degroot_102_Plate210

description: Glioblastoma multiforme


title: Degroot_97_Plate210

description: Glioblastoma multiforme


title: M_GMCSF_TPP_72h [5376074033_J]

description: Macrophage


title: M_GMCSF_TNFa_PGE2_72h [5376074033_H]

description: Macrophage


title: Degroot_96_Plate209

description: Glioblastoma multiforme


title: Degroot_101_Plate210

description: DIFFUSE GLIOMA (ANAPLASTIC MIXED OLIGOASTROCYTOMA)  WHO GRADE 3


title: Degroot_99_Plate210

description: Glioblastoma multiforme


title: M_GMCSF_TNFa_PGE2_72h [5376074033_K]

description: Macrophage


title: M_GMCSF_P3C_PGE2_72h [5376074032_L]

description: Macrophage


title: M_GMCSF_TNFa_PGE2_72h [5376074033_C]

description: Macrophage


title: M_GMCSF_PGE2_72h [5376074033_I]

description: Macrophage


title: M_GMCSF_P3C_72h [5376074033_B]

description: Macrophage


title: M0_GMCSF_0h [5376074033_E]

description: Macrophage


title: M_GMCSF_TNFa_72h [5376074033_L]

description: Macrophage

value: TNFa


title: M_GMCSF_TNFa_P3C_72h [5376074032_K]

description: Macrophage


title: M_GMCSF_P3C_72h [5376074032_J]

description: Macrophage


title: Degroot_95_Plate209

description: DIFFUSE ASTROCYTOMA

value: GradeII


title: Degroot_94_Plate209

description: Glioma, NOS

value: NotDefined


title: M_GMCSF_PGE2_72h [5376074033_A]

description: Macrophage


title: M_GMCSF_TNFa_72h [5376074032_H]

description: Macrophage


title: Degroot_91_Plate209

description: Glioblastoma multiforme

value: F


title: Degroot_90_Plate209

description: Glioblastoma multiforme


title: Degroot_87_Plate209

description: Glioblastoma multiforme


title: Degroot_88_Plate209

description: DIFFUSE ASTROCYTOMA, WHO GRADE IV, OR GLIOBLASTOMA


title: Degroot_92_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TNFa_72h [5376074032_I]

description: Macrophage


title: M_GMCSF_P3C_PGE2_72h [5376074032_F]

description: Macrophage


title: M_GMCSF_TNFa_P3C_72h [5376074032_G]

description: Macrophage


title: Degroot_93_Plate209

description: Glioblastoma multiforme


title: Degroot_86_Plate209

description: Gliosarcoma


title: Degroot_84_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_P3C_72h [5376074032_A]

description: Macrophage


title: M_GMCSF_TPP_72h [5376074032_B]

description: Macrophage


title: M_GMCSF_SA_24h [5376074031_I]

description: Macrophage

value: SA


title: M_GMCSF_TNFa_P3C_72h [5376074032_E]

description: Macrophage


title: Degroot_89_Plate209

description: Astrocytoma, low grade


title: M_GMCSF_P3C_PGE2_72h [5376074032_C]

description: Macrophage


title: Degroot_82_Plate209

description: Glioblastoma multiforme


title: Degroot_81_Plate209

description: Glioblastoma multiforme


title: Degroot_85_Plate209

description: Anaplastic astrocytoma

value: GradeIII


title: Degroot_83_Plate209

description: Glioblastoma multiforme


title: M_MCSF_PA_24h [5376074031_J]

description: Macrophage

value: M-CSF


title: M_MCSF_OA_24h [5376074031_L]

description: Macrophage


title: M_GMCSF_SA_24h [5376074031_H]

description: Macrophage

value: GM-CSF


title: M0_GMCSF_0h [5376074032_D]

description: Macrophage


title: Degroot_78_Plate209

description: Glioblastoma multiforme


title: Degroot_79_Plate209

description: Glioblastoma multiforme


title: Degroot_76_Plate209

description: Glioblastoma multiforme


title: Degroot_73_Plate209

description: Anaplastic oligodendroglioma

value: Oligodendroglioma


title: M_GMCSF_PA_24h [5376074031_F]

description: Macrophage


title: M0_GMCSF_0h [5376074023_L]

description: Macrophage

value: con


title: M0_MCSF_0h [5376074023_J]

description: Macrophage


title: M_MCSF_OA_24h [5376074031_D]

description: Macrophage


title: Degroot_74_Plate209

description: DIFFUSE ASTROCYTOMA, WHO GRADE 3, OR ANAPLASTIC ASTROCYTOMA


title: Degroot_75_Plate209

description: Glioblastoma multiforme


title: Degroot_77_Plate209

description: Glioblastoma multiforme


title: Degroot_71_Plate209

description: Glioblastoma multiforme


title: M_MCSF_IL4_upLPS_72h [5376074023_K]

description: Macrophage


title: Degroot_70_Plate209

description: Glioblastoma multiforme


title: M_MCSF_IL4_upLPS_72h [5376074023_E]

description: Macrophage


title: M_MCSF_IL4_72h [5376074023_G]

description: Macrophage


title: Degroot_72_Plate209

description: Glioblastoma multiforme


title: Degroot_69_Plate209

description: Anaplastic astrocytoma


title: Degroot_67_Plate209

description: Glioblastoma multiforme


title: Degroot_66_Plate209

description: GLIOBLASTOMA


title: M_GMCSF_IL4_upLPS_72h [5376074023_D]

description: Macrophage


title: M_GMCSF_upLPS_72h [5376074023_C]

description: Macrophage

value: upLPS


title: Degroot_68_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_IL4_72h [5376074023_A]

description: Macrophage


title: M0_MCSF_0h [5376074023_B]

description: Macrophage


title: M0_GMCSF_0h [5376074023_H]

description: Macrophage


title: Degroot_64_Plate209

description: Glioblastoma multiforme


title: M_MCSF_upLPS_72h [5376074023_I]

description: Macrophage


title: M_GMCSF_IL4_72h [5376074023_F]

description: Macrophage


title: M_GMCSF_PA_24h [5342595026_L]

description: Macrophage

value: BC 86


title: Degroot_65_Plate209

description: Glioblastoma multiforme


title: Degroot_80_Plate209

description: Anaplastic astrocytoma


title: M_GMCSF_OA_24h [5342595026_J]

description: Macrophage

value: OA

value: BC 84


title: M_GMCSF_LA_24h [5342595026_K]

description: Macrophage

value: LA

value: BC 65


title: M_GMCSF_LA_24h [5342595026_H]

description: Macrophage


title: Degroot_62_Plate209

description: Anaplastic astrocytoma

value: Astrocytoma


title: Degroot_60_Plate209

description: Gliosarcoma

value: GradeIV

value: M


title: Degroot_59_Plate209

description: Anaplastic astrocytoma


title: Degroot_61_Plate209

description: Glioblastoma multiforme


title: M_MCSF_PA_24h [5376074031_B]

description: Macrophage

value: PA


title: M_GMCSF_LA_24h [5342595026_F]

description: Macrophage


title: Degroot_63_Plate209

description: Anaplastic astrocytoma


title: M_GMCSF_OA_24h [5342595026_I]

description: Macrophage


title: Degroot_57_Plate209

description: Glioblastoma multiforme

value: F


title: Degroot_56_Plate209

description: Anaplastic astrocytoma


title: Degroot_55_Plate209

description: Glioblastoma multiforme


title: Degroot_53_Plate209

description: ANAPLASTIC ASTROCYTOMA, GRADE III (WHO)


title: Degroot_52_Plate209

description: Glioblastoma multiforme


title: Degroot_54_Plate209

description: ANAPLASTIC OLIGODENDROGLIOMA


title: M_GMCSF_PA_24h [5342595026_E]

description: Macrophage


title: Degroot_58_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_LiA_24h [5342595026_G]

description: Macrophage

value: LiA


title: Degroot_48_Plate209

description: Anaplastic astrocytoma

value: GradeIII


title: Degroot_51_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_PA_24h [5342595026_A]

description: Macrophage


title: M_GMCSF_LiA_24h [5342595026_C]

description: Macrophage


title: M_GMCSF_TPP_4h [5342595020_K]

description: Macrophage


title: Degroot_49_Plate209

description: Glioblastoma multiforme


title: Degroot_50_Plate209

description: Glioblastoma multiforme


title: Degroot_47_Plate209

description: GLIOBLASTOMA (WHO GRADE 4)


title: M_GMCSF_OA_24h [5342595026_D]

description: Macrophage


title: M_GMCSF_IFNg_TNFa_72h [5342595020_J]

description: Macrophage

value: IFNg + TNFa


title: M0_GMCSF_0h [5342595020_H]

description: Macrophage

value: GM-CSF


title: M_GMCSF_TPP_2h [5342595020_F]

description: Macrophage


title: M_GMCSF_LiA_24h [5342595026_B]

description: Macrophage


title: M0_GMCSF_0h [5342595020_L]

description: Macrophage


title: M_GMCSF_TPP_1h [5342595020_E]

description: Macrophage


title: Degroot_43_Plate209

description: Glioblastoma multiforme


title: Degroot_45_Plate209

description: Glioblastoma multiforme


title: Degroot_46_Plate209

description: OLIGODENDROGLIOMA (WHO GRADE 2)

value: Oligodendroglioma

value: GradeII


title: Degroot_42_Plate209

description: ANAPLASTIC ASTROCYTOMA (WHO GRADE III)


title: Degroot_41_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TPP_1h [5342595020_D]

description: Macrophage


title: M_GMCSF_TPP_4h [5342595020_C]

description: Macrophage


title: Degroot_44_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TPP_30min [5342595001_L]

description: Macrophage


title: Degroot_37_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TPP_30min [5342595001_K]

description: Macrophage


title: M0_GMCSF_0h [5342595020_B]

description: Macrophage

value: con


title: Degroot_38_Plate209

description: Glioblastoma multiforme


title: Degroot_36_Plate209

description: Glioblastoma multiforme


title: Degroot_35_Plate209

description: Anaplastic oligodendroglioma


title: M_GMCSF_TPP_6h [5342595001_H]

description: Macrophage


title: M_GMCSF_TPP_4h [5342595020_A]

description: Macrophage


title: Degroot_39_Plate209

description: Anaplastic astrocytoma


title: M_GMCSF_TPP_2h [5342595001_J]

description: Macrophage


title: Degroot_40_Plate209

description: Anaplastic astrocytoma


title: M_GMCSF_IFNg_TNFa_72h [5342595001_F]

description: Macrophage


title: Degroot_34_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TPP_30min [5342595001_G]

description: Macrophage


title: Degroot_32_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TPP_6h [5342595001_D]

description: Macrophage


title: Degroot_33_Plate209

description: Gliosarcoma


title: M_GMCSF_IFNg_TNFa_72h [5342595001_C]

description: Macrophage


title: M_GMCSF_TPP_1h [5342595001_I]

description: Macrophage


title: M_GMCSF_TPP_2h [5342595001_E]

description: Macrophage


title: Degroot_27_Plate209

description: Anaplastic astrocytoma


title: Degroot_26_Plate209

description: Oligodendroglioma


title: Degroot_31_Plate209

description: Glioblastoma multiforme


title: Degroot_29_Plate209

description: Glioblastoma multiforme


title: Degroot_21_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TPP_6h [5342595001_B]

description: Macrophage


title: Degroot_25_Plate209

description: Glioblastoma multiforme


title: Degroot_28_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_IL4_30min [4958478053_K]

description: Macrophage


title: Degroot_22_Plate209

description: Glioblastoma multiforme


title: Degroot_30_Plate209

description: Glioblastoma multiforme


title: M0_GMCSF_0h [4958478053_I]

description: Macrophage


title: M_GMCSF_IL4_6h [4958478053_L]

description: Macrophage


title: M_GMCSF_TNFa_72h [4958478053_F]

description: Macrophage

value: TNFa


title: M_GMCSF_IL4_1h [4958478053_H]

description: Macrophage


title: Degroot_20_Plate209

description: Anaplastic astrocytoma


title: M_GMCSF_TNFa_72h [4958478053_B]

description: Macrophage


title: M_GMCSF_IL4_4h [4958478053_J]

description: Macrophage


title: Degroot_23_Plate209

description: Anaplastic astrocytoma


title: M_GMCSF_IL4_2h [4958478053_C]

description: Macrophage


title: M_GMCSF_TNFa_72h [4958478053_A]

description: Macrophage


title: M_GMCSF_TPP_24h [4958478053_D]

description: Macrophage


title: Degroot_18_Plate209

description: Anaplastic oligodendroglioma


title: Degroot_19_Plate209

description: INFILTRATING DIFFUSE ASTROCYTOMA, WHO GRADE 3, OR ANAPLASTIC ASTROCYTOMA


title: Degroot_16_Plate209

description: Glioblastoma multiforme


title: Degroot_13_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_TPP_24h [4958478053_G]

description: Macrophage


title: Degroot_14_Plate209

description: Oligodendroglioma


title: Degroot_24_Plate209

description: Glioblastoma multiforme


title: Degroot_15_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_IFNg_2h [4958478044_H]

description: Macrophage

value: IFNg


title: M_GMCSF_IFNg_4h [4958478044_K]

description: Macrophage


title: Degroot_17_Plate209

description: Glioblastoma multiforme


title: Degroot_11_Plate209

description: Glioblastoma multiforme


title: M0_GMCSF_0h [4958478044_J]

description: Macrophage


title: M_GMCSF_IFNg_6h [4958478033_J]

description: Macrophage


title: M0_GMCSF_0h [4958478033_L]

description: Macrophage


title: M_GMCSF_IFNg_1h [4958478044_D]

description: Macrophage


title: M_GMCSF_IFNg_1h [4958478044_G]

description: Macrophage


title: Degroot_8_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_IFNg_6h [4958478044_F]

description: Macrophage


title: ORC-ChIP replicate 7

city: Minneapolis

first: Hung-Ji

last: Tsai

state: MN

address: 6-170 MCB, 420 Washington Ave. SE

institute: University of Minnesota

hyb_protocol: Standard Agilent protocol

scan_protocol: Agilent Technologies Scanner G2505C, with  Agilent Feature Extraction Software version 10.5.1.1

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Candida albicans

label_protocol: Standard Agilent protocol

growth_protocol: 3 hrs sub-culture from 30 degree YPD from overnight Candida culture to OD ~0.8-1

extract_protocol: Standard ChIP protocol (Ezhkova and Tansey 2006)

tag: growth phase

value: log phase cells

tag: fraction

tag: antibody

value: polyclonal ORC antibody

tag: antibody provider

value: gift from Stephen Bell Lab


title: M_GMCSF_IFNg_2h [4958478044_A]

description: Macrophage


title: Degroot_10_Plate209

description: Anaplastic astrocytoma

value: Astrocytoma


title: ORC-ChIP replicate 6


title: M_GMCSF_IFNg_6h [4958478033_H]

description: Macrophage


title: Degroot_6_Plate209

description: Gliosarcoma

value: GradeIV


title: M0_GMCSF_0h [4958478033_G]

description: Macrophage


title: ORC-ChIP replicate 3


title: M_GMCSF_IFNg_30min [4958478033_K]

description: Macrophage


title: Degroot_12_Plate209

description: Gliosarcoma


title: ORC-ChIP replicate 5


title: Degroot_5_Plate209

description: Glioblastoma


title: M_GMCSF_IFNg_1h [4958478033_I]

description: Macrophage


title: Degroot_7_Plate209

description: Glioblastoma multiforme

value: M


title: ORC-ChIP replicate 4


title: M_GMCSF_IFNg_4h [4958478044_C]

description: Macrophage


title: ORC-ChIP replicate 2


title: ORC-ChIP replicate 1


title: Degroot_4_Plate209

description: Anaplastic astrocytoma


title: M_GMCSF_IFNg_30min [4958478033_D]

description: Macrophage


title: Degroot_2_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_IFNg_2h [4958478033_B]

description: Macrophage


title: M_GMCSF_IFNg_4h [4958478033_F]

description: Macrophage


title: M_GMCSF_IL4_2h [4958478015_L]

description: Macrophage


title: M_GMCSF_IL4_6h [4958478015_K]

description: Macrophage


title: M_GMCSF_IL4_30min [4958478015_G]

description: Macrophage


title: M0_GMCSF_0h [4958478015_C]

description: Macrophage


title: M_GMCSF_IL4_4h [4958478015_I]

description: Macrophage


title: M_GMCSF_IL4_2h [4958478015_E]

description: Macrophage


title: M0_GMCSF_0h [4958478015_J]

description: Macrophage


title: M_GMCSF_IL4_6h [4958478015_H]

description: Macrophage


title: M_GMCSF_IL4_1h [4958478015_F]

description: Macrophage


title: Degroot_1_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_IFNg_30min [4958478033_A]

description: Macrophage


title: Degroot_3_Plate209

description: Astrocytoma, low grade


title: Degroot_9_Plate209

description: Glioblastoma multiforme


title: M_GMCSF_IL4_30min [4958478015_D]

description: Macrophage


title: M_GMCSF_TPP_24h [4958478053_E]

description: Macrophage


title: M_GMCSF_upLPS_72h [4958478013_L]

description: Macrophage

value: upLPS


title: M_GMCSF_IL4_1h [4958478015_B]

description: Macrophage


title: M_GMCSF_IFNg_24h [4958478013_H]

description: Macrophage


title: M_GMCSF_upLPS_72h [4958478013_J]

description: Macrophage


title: M_GMCSF_upLPS_IC_72h [4958478013_F]

description: Macrophage

value: upLPS+IC


title: M_GMCSF_IL4_24h [4958478013_I]

description: Macrophage


title: M_GMCSF_upLPS_IC_72h [4958478013_C]

description: Macrophage


title: M_GMCSF_IFNg_24h [4958478013_G]

description: Macrophage


title: M_GMCSF_IL4_24h [4958478013_E]

description: Macrophage


title: M_GMCSF_upLPS_IC_72h [4958478013_D]

description: Macrophage


title: M_GMCSF_IL4_4h [4958478015_A]

description: Macrophage


title: M_GMCSF_IL4_24h [4958478013_K]

description: Macrophage


title: M_GMCSF_IFNg_72h [4950679045_K]

description: Macrophage


title: M_GMCSF_upLPS_72h [4958478013_A]

description: Macrophage


title: M_GMCSF_IFNg_24h [4958478013_B]

description: Macrophage


title: M0_GMCSF_12h [4950679045_L]

description: Macrophage


title: M_GMCSF_TPP_72h [4950679045_I]

description: Macrophage


title: M_GMCSF_IFNg_24h [4950679045_H]

description: Macrophage


title: M_GMCSF_IL4_72h [4950679045_G]

description: Macrophage


title: M0_GMCSF_24h [4950679045_J]

description: Macrophage


title: M0_GMCSF_72h [4950679045_C]

description: Macrophage


title: M0_GMCSF_6h [4950679045_D]

description: Macrophage


title: M_GMCSF_IL4_24h [4950679045_E]

description: Macrophage


title: M_GMCSF_IL10_72h [4950679045_A]

description: Macrophage


title: M_GMCSF_GC_72h [4950679045_B]

description: Macrophage

value: GC


title: M_GMCSF_GC_72h [4950679013_J]

description: Macrophage


title: M_GMCSF_IL4_24h [4950679013_L]

description: Macrophage


title: M0_GMCSF_48h [4950679013_K]

description: Macrophage


title: M0_GMCSF_12h [4950679013_I]

description: Macrophage


title: M0_GMCSF_72h [4950679013_E]

description: Macrophage


title: M_GMCSF_IL13_72h [4950679013_F]

description: Macrophage


title: M_GMCSF_IL10_72h [4950679013_G]

description: Macrophage


title: M_GMCSF_IL4_72h [4950679013_C]

description: Macrophage


title: M_GMCSF_IL13_72h [4950679013_A]

description: Macrophage


title: M_GMCSF_TPP_48h [4676163034_L]

description: Macrophage


title: M_GMCSF_TPP_48h [4676163034_J]

description: Macrophage


title: M0_GMCSF_6h [4950679013_B]

description: Macrophage


title: embryo_0-24h_UVI750_rep3

city: Shanghai

first: jingmin

last: zhu

address: Room 501,State Key Laboratory of Estuarine and Coastal Research,No.3663,ZhongShan North Road, PuTuo District

country: China

institute: East China Normal University

description:
0-24h UVI750-3
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(750μg/L) during 0-24h after stage10/11.

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Xenopus tropicalis

source_name: embryos_UVI3003 (750μg/L) during 0-24h after stage 10/11

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Xenopus tropicalis adults were obtained from Nasco (Fort Atkinson, WI, USA). Breeding was induced by subcutaneous injection of human chorionic gonadotrophin (hCG) (Zhejiang, China).

extract_protocol: Total RNA was extracted from frozen embryos by using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The experiments were initiated when embryos reached stage 10/11, the embryos were exposed to 250,500,750 µg/L UVI3003 for 0-24 and 24-48 for microarray analysis (n=24).

tag: tissue

value: embroys

value: stage 41/42

tag: exposed to


title: M_GMCSF_TPP_72h [4676163034_K]

description: Macrophage

value: GM-CSF


title: M0_GMCSF_24h [4676163034_I]

description: Macrophage


title: M0_GMCSF_72h [4676163034_H]

description: Macrophage


title: embryo_0-24h_UVI750_rep2

department: State Key Laboratory of Estuarine and Coastal Research

description:
0-24h UVI750-2
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(750μg/L) during 0-24h after stage10/11.

value: UVI3003 (750μg/L) during 0-24h after stage 10/11


title: M_GMCSF_TPP_72h [4676163034_G]

description: Macrophage


title: embryo_0-24h_UVI750_rep1

description:
0-24h UVI750-1
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(750μg/L) during 0-24h after stage10/11.


title: CHM110

city: Fukuoka

first: Kenshi

last: Hayashi

address: Maidashi 3-1-1, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip arrays were scanned using the BeadArray Reader (Illumina).

data_processing: The scanned data files were processed by GenomeStudio (Illumina).

label: Alexa555 and Alexa647

source_name: complete hydatidiform mole

label_protocol: As per manufacturer (Illumina)

extract_protocol: Genomic DNA was extracted from complete hydatidiform mole tissues using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: complete hydatidiform mole


title: CHM114


title: M_GMCSF_IFNg_24h [4676163034_E]

description: Macrophage


title: CHM115


title: embryo_0-24h_UVI500_rep3

description:
0-24h UVI500-3
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(500μg/L) during 0-24h after stage10/11.

source_name: embryos_UVI3003 (500μg/L) during 0-24h after stage 10/11


title: CHM113


title: M0_GMCSF_48h [4676163034_D]

description: Macrophage

value: con


title: CHM105


title: CHM118


title: M0_GMCSF_12h [4676163034_C]

description: Macrophage


title: M_GMCSF_IFNg_72h [4676163034_B]

description: Macrophage


title: CHM117


title: CHM101


title: CHM106


title: CHM098


title: M_GMCSF_IFNg_72h [4676163030_L]

description: Macrophage


title: CHM116


title: CHM104


title: CHM100


title: embryo_0-24h_UVI250_rep3

description:
0-24h UVI250-3
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(250μg/L) during 0-24h after stage10/11.

source_name: embryos_UVI3003 (250μg/L) during 0-24h after stage 10/11


title: M_GMCSF_TPP_48h [4676163034_F]

description: Macrophage


title: M_GMCSF_IL4_72h [4676163030_K]

description: Macrophage


title: M_GMCSF_TPP_72h [4676163030_J]

description: Macrophage


title: CHM103


title: M0_GMCSF_72h [4676163030_I]

description: Macrophage


title: M_GMCSF_IFNg_72h [4676163030_H]

description: Macrophage


title: M_GMCSF_IL4_72h [4676163030_G]

description: Macrophage


title: embryo_0-24h_UVI250_rep1

description:
0-24h UVI250-1
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(250μg/L) during 0-24h after stage10/11.

value: UVI3003 (250μg/L) during 0-24h after stage 10/11


title: CHM094


title: M_GMCSF_TPP_72h [4676163030_F]

description: Macrophage


title: M0_GMCSF_48h [4676163034_A]

description: Macrophage


title: embryo_0-24h_DMS0_rep3

description:
0-24h DMSO-3
Gene expression data from embryos at stage 41/42, which exposed to DMSO during 0-24h after stage10/11.

source_name: embryos_DMSO during 0-24h after stage 10/11

value: DMSO during 0-24h after stage 10/11


title: M0_GMCSF_72h [4676163030_E]

description: Macrophage


title: M_GMCSF_IFNg_72h [4676163030_D]

description: Macrophage

value: IFNg


title: CHM095


title: M_GMCSF_IL4_72h [4676163030_C]

description: Macrophage


title: embryo_0-24h_DMS0_rep2

description:
0-24h DMSO-2
Gene expression data from embryos at stage 41/42, which exposed to DMSO during 0-24h after stage10/11.


title: CHM090


title: M_GMCSF_TPP_72h [4676163030_B]

description: Macrophage


title: M0_GMCSF_72h [4676163030_A]

description: Macrophage


title: CHM099


title: embryo_0-24h_DMS0_rep1

description:
0-24h DMSO-1
Gene expression data from embryos at stage 41/42, which exposed to DMSO during 0-24h after stage10/11.


title: M_GMCSF_GC_72h [4676163025_L]

description: Macrophage


title: CHM088


title: embryo_0-24h_UVI500_rep1

description:
0-24h UVI500-1
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(500μg/L) during 0-24h after stage10/11.

value: UVI3003 (500μg/L) during 0-24h after stage 10/11


title: CHM087


title: embryo_0-24h_UVI250_rep2

description:
0-24h UVI250-2
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(250μg/L) during 0-24h after stage10/11.


title: embryo_24-48h_UVI750_rep3

description:
24-48h UVI750-3
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(750μg/L) during 24-48h after stage10/11.

source_name: embryos_UVI3003 (750μg/L) during 24-48h after stage 10/11


title: CHM093


title: CHM086


title: CHM085


title: embryo_0-24h_UVI500_rep2

description:
0-24h UVI500-2
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(500μg/L) during 0-24h after stage10/11.


title: CHM083


title: embryo_24-48h_UVI500_rep3

description:
24-48h UVI500-3
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(500μg/L) during 24-48h after stage10/11.

source_name: embryos_UVI3003 (500μg/L) during 24-48h after stage 10/11


title: CHM084


title: embryo_24-48h_UVI750_rep1

description:
24-48h UVI750-1
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(750μg/L) during 24-48h after stage10/11.

value: UVI3003 (750μg/L) during 24-48h after stage 10/11


title: M_GMCSF_IL4_24h [4676163025_E]

description: Macrophage


title: M_GMCSF_IFNg_72h [4676163025_H]

description: Macrophage


title: embryo_24-48h_UVI500_rep2

description:
24-48h UVI500-2
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(500μg/L) during 24-48h after stage10/11.

value: UVI3003 (500μg/L) during 24-48h after stage 10/11


title: embryo_24-48h_UVI750_rep2

description:
24-48h UVI750-2
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(750μg/L) during 24-48h after stage10/11.


title: M0_GMCSF_6h [4676163025_I]

description: Macrophage


title: M_GMCSF_IFNg_24h [4676163025_F]

description: Macrophage


title: M_GMCSF_IL4_72h [4676163025_J]

description: Macrophage


title: M_GMCSF_IL10_72h [4676163025_D]

description: Macrophage


title: MCF7_Hypoxia_48h_rep1 [miRNA]

first: Carme

last: Camps

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

description:
Total RNA containing short RNA fraction
Hypoxia_48h_R1

hyb_protocol: The hybridization was performed at 55˚C for 20h and at a constant speed rotation of 20rpm.

scan_protocol: After washing the microarrays with the Agilent Gene Expression Wash Buffer kit, the hybridization signals were detected by the Agilent Microarray scanner (G2565BA)and using the following settings: scan area 61 x 21.6 mm, scan resolution 5µm, 5µm scanning mode Single Pass, eXtended Dynamic range selected, Dye chanel set to green, green PMT set to XDR Hi 100% and XDR Lo 5%.

data_processing: The scanned images were analyzed with Feature Extraction Software version 9.5.1 (Agilent). A GeneView file was generated for each of the samples and used for further analysis. The Total Gene signal from GeneView files was normalised using the vsn package from Bioconductor

label_protocol: 100µg of total RNA were first dephosphorylated using Calf Instestine Alkaline Phosphatase (New England Biolabs). Single molecules of Cyanine 3-pCp provided in the miRNA Labeling Reagent and Hybridization kit (Agilent) were ligated to the 3' end of the dephosphorylated RNA molecules using T4 RNA ligase (New England Biolabs). Labeled RNAs were purified throughout micro Bio-Spin 6 columns (BioRad) and dried down using a speed-vacuum concentrator Savant ISS110 (Thermo Scientific). Samples were resuspended in 18µl of RNAse free water and prepared for hybridization by adding 4.5µl of 10X GE Blocking agent and 22.5µl of 2X Hi-RPM Hybridization Buffer (both in Agilent miRNA Labeling Reagent and hybridization kit).

growth_protocol: MCF-7 cells were grown in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 2mmol/L of L-glutamine

extract_protocol: RNA was extracted from cells using the miRVana miRNA isolation kit (Ambion) in accordance with the prescribed protocol provided with the kit. RNA quality was assessed after extraction using Agilent bioanalyser.

treatment_protocol: Exposure of cell cultures to hypoxia (1% oxygen) was undertaken in an In vivo2 Hypoxia Work Station (Ruskin Technologies) in parallel with cells maintained in normoxic conditions (21% oxygen). Cells were recovered after 16h, 32h and 48h of exposure to hypoxia.

tag: oxygen


title: MCF7_Hypoxia_32h_rep3 [miRNA]

description:
Total RNA containing short RNA fraction
Hypoxia_32h_R3


title: MCF7_Hypoxia_48h_rep3 [miRNA]

description:
Total RNA containing short RNA fraction
Hypoxia_48h_R3


title: MCF7_Hypoxia_48h_rep2 [miRNA]

description:
Total RNA containing short RNA fraction
Hypoxia_48h_R2


title: CHM111


title: embryo_24-48h_UVI500_rep1

description:
24-48h UVI500-1
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(500μg/L) during 24-48h after stage10/11.


title: MCF7_Hypoxia_32h_rep2 [miRNA]

description:
Total RNA containing short RNA fraction
Hypoxia_32h_R2


title: MCF7_Hypoxia_32h_rep1 [miRNA]

description:
Total RNA containing short RNA fraction
Hypoxia_32h_R1


title: M_GMCSF_IL13_72h [4676163025_C]

description: Macrophage


title: MCF7_Hypoxia_16h_rep2 [miRNA]

description:
Total RNA containing short RNA fraction
Hypoxia_16h_R2


title: CHM082


title: CHM081


title: MCF7_Hypoxia_16h_rep1 [miRNA]

description:
Total RNA containing short RNA fraction
Hypoxia_16h_R1


title: embryo_24-48h_UVI250_rep2

description:
24-48h UVI250-2
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(250μg/L) during 24-48h after stage10/11.

source_name: embryos_UVI3003 (250μg/L) during 24-48h after stage 10/11


title: CHM102


title: embryo_24-48h_DMS0_rep3

description:
24-48h DMSO-3
Gene expression data from embryos at stage 41/42, which exposed to DMSO during 24-48h after stage10/11.

source_name: embryos_DMSO during 24-48h after stage 10/11

value: DMSO during 24-48h after stage 10/11


title: M0_GMCSF_24h [4676163025_A]

description: Macrophage


title: MCF7_Normoxia_rep3 [miRNA]

description:
Total RNA containing short RNA fraction
Normoxia_R3


title: M_GMCSF_IL4_12h [4648883071_L]

description: Macrophage


title: embryo_24-48h_UVI250_rep3

description:
24-48h UVI250-3
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(250μg/L) during 24-48h after stage10/11.

value: UVI3003 (250μg/L) during 24-48h after stage 10/11


title: M_GMCSF_IL4_12h [4648883071_K]

description: Macrophage


title: MCF7_Normoxia_rep2 [miRNA]

description:
Total RNA containing short RNA fraction
Normoxia_R2


title: MCF7_Normoxia_rep1 [miRNA]

description:
Total RNA containing short RNA fraction
Normoxia_R1


title: embryo_24-48h_DMS0_rep2

description:
24-48h DMSO-2
Gene expression data from embryos at stage 41/42, which exposed to DMSO during 24-48h after stage10/11.


title: M_GMCSF_IFNg_12h [4648883071_H]

description: Macrophage


title: M_GMCSF_IFNg_12h [4648883071_I]

description: Macrophage


title: CHM078


title: M_GMCSF_TPP_12h [4648883071_J]

description: Macrophage


title: CHM097


title: M_GMCSF_IFNg_12h [4648883071_G]

description: Macrophage


title: 240 Min Treated Cy3 vs. Control Cy5

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

description: 240 Min Dye Swap, 2/2.

hyb_protocol: 760 ng of each Cy3- and Cy5-labelled RNA was fragmented and hybridised to the Agilent-023956 microarray at 65°C for 16 h using the Agilent Hybridisation Chamber and Agilent Hybridisation Kit according to the manufacturer's instructions.

scan_protocol: The array was scanned using the Agilent DNA Microarray Scanner at 5 µm resolution and the raw data were extracted using Agilent Feature Extraction software (V9.5).

data_processing: The data were processed by Bioconductor packages written in R language (http://www.r-project.org). The linear models for microarray analysis (LIMMA) package was used for background correction, Loess normalisation of the two chanels of one array, quantile-normalisation between different arrays and identification of differentially expressed genes.

organism: Streptococcus mutans UA159

source_name: Streptococcus mutans, carolacton treated, 240 min

label_protocol: RNA samples were labelled either with Cy3 or Cy5 using the ULS fluorescent labelling kit (Kreatech, Germany).

growth_protocol: Biofilms were grown in THBS medium for 3.5 hours (initial OD600 = 0.05) in 24-well polystyrene plates (Greiner, Germany). Then, the medium was exchanged against fresh THBS supplemented with and without carolacton (0.25 µg/ml).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Germany).

treatment_protocol: Biofilm cells were treated with 0.25 µg/ml carolacton, control wells without treatment.

tag: strain/background

value: wildtype

value: biofilm cells

tag: treatment

value: carolacton

tag: timepoint

value: 240 min

source_name: Streptococcus mutans, untreated, 240 min


title: embryo_24-48h_DMS0_rep1

description:
24-48h DMSO-1
Gene expression data from embryos at stage 41/42, which exposed to DMSO during 24-48h after stage10/11.

value: embroys

value: stage 41/42


title: N402ΔflbA_mutant_zone_5_replicate_1

city: Utrecht

first: Pauline

last: Krijgsheld

address: Padualaan 8

department: Sciences

country: Netherlands

institute: Utrecht University

hyb_protocol: 15 µg cRNA was fragmented  and half of it was used for hybridization on Affymetrix A. niger GeneChips. (Affymetrix #900720)

scan_protocol: Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1 software.

data_processing: Genedata Expressionist and Genedata Analyst were used for normalization and statistical analysis of the arrays (Genedata, Basel, Switzerland). The arrays were condensed with the RMA algorithm and normalized on the quantile.

label: Biotin

organism: Aspergillus niger

source_name: sandwiched xylose grown colony, peripheral zone 5

label_protocol: The Affymetrix (#901229) 3’ IVT-Express Labeling Kit was used to synthesize Biotin-labeled cRNA. From each RNA sample 100 ng was used as input for the labeling reactions. For the second labeling reaction, 500 ng RNA was used.

growth_protocol: 7-day old sandwiched colonies grown on xylose were used for RNA isolation. Distinct zones of the mycelium (zone 1, 3, and 5) harvested form the colony. Zone 1 represents the youngest or central part of the colony. Zone 5 represents the oldest or peripheral part of the colony, whereas zone 3 represents the intermediate zone.

extract_protocol: Mycelium of zones was harvested from three colonies, frozen with liquid nitrogen, and ground with a TissueLyser (Qiagen, Venlo, The Netherlands) in a 2 ml Eppendorf tube with two metal balls (4.76 in diameter) for 1 min at 25 Hz. The frozen material was taken up in 1 ml TRIzol reagent (Invitrogen, Life technologies, Bleiswijk, Netherlands) by vortexing. Samples were incubated for 2 min after mixing with 200 µl chloroform. This was followed by centrifugation at 10000 g for 10 min. RNA was purified using an RNA clean up column (Machery Nagel, Düren, Germany), after addition of 1 volume 70 % EtOH to the water phase. To this end, the sample was loaded on the column, which was centrifuged for 30 sec at 10000 rpm. This was followed by addition of 600 µl RA3 buffer (provided by the RNA-clean up kit). After 2 min of centrifugation at 10000 g, 250 µl RNA3 was added, followed by another 2 min centrifugation at 10000 g. RNA was eluted after 10 min incubation in two steps with 40 µl and 50 µl RNAse free water.

tag: strain


title: N402ΔflbA_mutant_zone_5_replicate_2


title: 240 Min Treated Cy5 vs. Control Cy3

description: 240 Min Dye Swap, 1/2.

tag: genotype/variation


title: 300 Min Treated Cy5 vs. Control Cy3

description: 300 Min Dye Swap, 1/2.

source_name: Streptococcus mutans, carolacton treated, 300 min

value: 300 min

source_name: Streptococcus mutans, untreated, 300 min


title: N402ΔflbA_mutant_zone_3_replicate_2

source_name: sandwiched xylose grown colony, intermediate zone 3


title: M_GMCSF_IL4_12h [4648883071_F]

description: Macrophage

source_name: peripheral blood

tag: initial differentiation

value: GM-CSF

tag: activation stimuli

tag: time

tag: donor


title: CHM079

value: complete hydatidiform mole


title: N402ΔflbA_mutant_zone_3_replicate_1


title: 200 Min Treated Cy5 vs. Control Cy3

description: 200 Min Dye Swap, 1/2.

source_name: Streptococcus mutans, carolacton treated, 200 min

tag: cell type

value: 200 min

source_name: Streptococcus mutans, untreated, 200 min


title: CHM080

source_name: complete hydatidiform mole


title: 200 Min Treated Cy3 vs. Control Cy5

description: 200 Min Dye Swap, 2/2.


title: N402ΔflbA_mutant_zone_1_replicate_2

source_name: sandwiched xylose grown colony, central zone 1


title: M0_GMCSF_0h [4648883071_D]

description: Macrophage

value: con


title: 160 Min Treated Cy3 vs. Control Cy5

description: 160 Min Dye Swap, 2/2.

source_name: Streptococcus mutans, carolacton treated, 160 min

value: 160 min

source_name: Streptococcus mutans, untreated, 160 min


title: M_GMCSF_TPP_12h [4648883071_C]

description: Macrophage


title: 300 Min Treated Cy3 vs. Control Cy5

description: 300 Min Dye Swap, 2/2.


title: N402ΔflbA_mutant_zone_1_replicate_1


title: M_GMCSF_TPP_12h [4648883071_E]

description: Macrophage


title: CHM073


title: CHM070_2


title: embryo_24-48h_UVI250_rep1

description:
24-48h UVI250-1
Gene expression data from embryos at stage 41/42, which exposed to UVI3003(250μg/L) during 24-48h after stage10/11.

tag: age


title: CHM075


title: 160 Min Treated Cy5 vs. Control Cy3

description: 160 Min Dye Swap, 1/2.


title: CHM072_2


title: wild-type_N402_zone_5_replicate_2


title: M_GMCSF_TPP_24h [4648883071_B]

description: Macrophage


title: wild-type_N402_zone_5_replicate_1


title: CHM074


title: M0_GMCSF_0h [4648883071_A]

description: Macrophage


title: 120 Min Treated Cy3 vs. Control Cy5

description: 120 Min Dye Swap, 2/2.

source_name: Streptococcus mutans, carolacton treated, 120 min

value: 120 min

source_name: Streptococcus mutans, untreated, 120 min


title: 120 Min Treated Cy5 vs. Control Cy3

description: 120 Min Dye Swap, 1/2.


title: M_GMCSF_IFNg_24h [4648883069_K]

description: Macrophage

value: IFNg


title: wild-type_N402_zone_3_replicate_2


title: CHM076


title: wild-type_N402_zone_3_replicate_1


title: 100 Min Treated Cy3 vs. Control Cy5

description: 100 Min Dye Swap, 2/2.

source_name: Streptococcus mutans, carolacton treated, 100 min

value: 100 min

source_name: Streptococcus mutans, untreated, 100 min


title: M_GMCSF_TPP_24h [4648883069_L]

description: Macrophage


title: CHM066


title: M_GMCSF_TPP_24h [4648883069_J]

description: Macrophage


title: 100 Min Treated Cy5 vs. Control Cy3

description: 100 Min Dye Swap, 1/2.


title: CHM063


title: wild-type_N402_zone_1_replicate_2


title: CHM069


title: CHM068


title: CHM067


title: wild-type_N402_zone_1_replicate_1


title: 80 Min Treated Cy3 vs. Control Cy5

description: 80 Min Dye Swap, 2/2.

source_name: Streptococcus mutans, carolacton treated, 80 min

value: 80 min

source_name: Streptococcus mutans, untreated, 80 min


title: 80 Min Treated Cy5 vs. Control Cy3

description: 80 Min Dye Swap, 1/2.


title: 60 Min Treated Cy3 vs. Control Cy5

description: 60 Min Dye Swap, 2/2.

source_name: Streptococcus mutans, carolacton treated, 60 min

value: 60 min

source_name: Streptococcus mutans, untreated, 60 min


title: M1/2_GMCSF_24h [4648883069_H]

description: Macrophage

value: unknown


title: M_GMCSF_TPP_24h [4648883069_I]

description: Macrophage


title: 60 Min Treated Cy5 vs. Control Cy3

description: 60 Min Dye Swap, 1/2.

value: wildtype

value: biofilm cells


title: M1/2_GMCSF_24h [4648883069_F]

description: Macrophage


title: CHM060


title: CHM062


title: 40 Min Treated Cy5 vs. Control Cy3

description: 40 Min Dye Swap, 1/2.

source_name: Streptococcus mutans, carolacton treated, 40 min

value: carolacton

value: 40 min

source_name: Streptococcus mutans, untreated, 40 min


title: 40 Min Treated Cy3 vs. Control Cy5

description: 40 Min Dye Swap, 2/2.


title: CHM059


title: M_GMCSF_IFNg_24h [4648883069_D]

description: Macrophage

source_name: peripheral blood


title: CHM064


title: M_GMCSF_TPP_24h [4648883069_C]

description: Macrophage


title: CHM058


title: 20 Min Treated Cy5 vs. Control Cy3

description: 20 Min Dye Swap, 1/2.

source_name: Streptococcus mutans, carolacton treated, 20 min

value: 20 min

source_name: Streptococcus mutans, untreated, 20 min


title: M_GMCSF_IFNg_24h [4648883069_B]

description: Macrophage


title: 20 Min Treated Cy3 vs. Control Cy5

description: 20 Min Dye Swap, 2/2.


title: 5 Min Treated Cy3 vs. Control Cy5

description: 5 Min Dye Swap, 2/2.

source_name: Streptococcus mutans, carolacton treated, 5 min

value: 5 min

source_name: Streptococcus mutans, untreated, 5 min


title: M_GMCSF_TPP_24h [4648883069_A]

description: Macrophage

value: GM-CSF


title: CHM056

source_name: complete hydatidiform mole

value: complete hydatidiform mole


title: M_GMCSF_IFNg_24h [4648883069_G]

description: Macrophage


title: CHM055


title: CHM057


title: M_GMCSF_IL4_6h [4648883056_K]

description: Macrophage


title: M_GMCSF_TPP_24h [4648883069_E]

description: Macrophage


title: 5 Min Treated Cy5 vs. Control Cy3

description: 5 Min Dye Swap, 1/2.


title: CHM054


title: M_GMCSF_TPP_6h [4648883056_J]

description: Macrophage


title: Yeast_Dal80Δ_LoaOOH-treated_1h_BioRep3_TecRep1

city: Sydney

first: Patrick

middle: John

last: O'Doherty

state: NSW

address: Goldsmith Ave

country: Australia

institute: University of Western Sydney

description: Dal80Δ yeast (OD600 1.0), grown from a single colony, were treated with either methanol or LoaOOH at an arresting concentration (75 µM) for 1 h. At 1h total RNA was isolated. Affymetrix Yeast_2 microarrays were used to probe changes in gene expression.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 h at 45 oC on GeneChip Yeast Genome 2.0 Arrays, Affymetrix. GeneChips were washed and stained with streptavidin-phycoerythrin conjugate in the Affymetrix FS450 fluidics station.

scan_protocol: Yeast_2 GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: Collected fluorescent intensity data (CEL files) were imported into the Partek® Genomic Suite™ version 6.5 (Partek inc.) with processing that included RMA normalisation and masking of all non-S. cerevisiae probes present on the Affymetrix Yeast_2 arrays.

organism: Saccharomyces cerevisiae

source_name: exp growing S. cer treated with oxidant (LoaOOH)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 3, Affymetrix).

growth_protocol: S. cerevisiae (Dal80Δ) was grown in minimal medium, 30 oC, 150 rpm, from a single colony to an optical density of 1.0 (OD600 1.0). Six cultures were prepared in total, three biological replicates for each for control and oxidant conditions.

extract_protocol: Frozen cells were lysed with 1 mL cold (4 oC) TRIzol® reagent (Invitrogen) and mechanically disrupted with 0.75 g of acid washed glass beads (425-600 µm, Sigma) using a bead mill. Total RNA was then isolated according to the manufacturer’s instructions. Total RNA was further purified using a Qiagen Rneasy column purification kit according to the manufacturer's protocol. Following purification, each sample was split to provide a technical duplicate, i.e. total RNA from six samples were run on twelve Affymetrix GeneChips.

treatment_protocol: Yeast cultures at OD600 1.0 were treated with an arresting concentration of LoaOOH (75 µM) or an equivalent volume of methanol (absolute). Growth was then allowed to resume at 30 oC, with orbital shaking (150 rpm) for a further 60 min. A 50 mL aliquot for each replicate was centrifuged twice at 5000 g for 3 min, at room temperature. Cell pellets (x6) were snap-frozen in liquid nitrogen and stored at -80 °C until extraction.

value: LoaOOH (75 µM) for 1 hr

value: Dal80 mutant (parent strain:S288C)

tag: growth phase

value: Exponential (OD600 1.0)


title: M_GMCSF_IL4_6h [4648883056_L]

description: Macrophage


title: CHM051


title: Yeast_Dal80Δ_LoaOOH-treated_1h_BioRep3_TecRep2


title: CHM053


title: M_GMCSF_TPP_24h [4648883056_H]

description: Macrophage


title: Yeast_Dal80Δ_LoaOOH-treated_1h_BioRep2_TecRep2


title: HnRNP L knockdown, biological rep3

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

department: Biochemistry

institute: University of Giessen

description: HeLa  cell line

hyb_protocol: Approximately 5.5ug of labeled DNA target was hybridized to the Affymetrix GeneChip Human Exon 1.0 ST Array at 45oC for 16 hours per manufacturers recommendation. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: .CEL files were background adjusted, quantile normalized netween all 12 samples and summarized in probeset level using RMAExpress.

source_name: HeLa

label_protocol: Ribosomal RNA was depleted from 1µg of total RNA using the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen Corp., Carlsbad, CA). cDNA was generated using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Inc., Santa Clara, CA) per manufacturer's instructions. cDNA was fragmented and end labeled using the GeneChip® WT Terminal Labeling Kit (Affymetrix, Inc.).

growth_protocol: HeLa cell culture under standard conditions

extract_protocol: One day before transfection, HeLa cells were seeded in 6-well culture plates (1.5 x 10e5 cells per well) or 10-cm culture dishes (4.3 x 10e5 cells per dish). siRNA duplex (at a final concentration in culture medium of 30 nM) was transfected with Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. siRNA duplices were from MWG Biotech (Ebersberg, Germany). Four days after siRNA transfection, total RNA was isolated using Trizol (Invitrogen) and RNeasy kit (QIAGEN).

treatment_protocol: transient siRNA transfection, plus cycloheximide treatment

tag: cell line

value: HeLa

value: HnRNP L knockdown


title: M_GMCSF_IFNg_6h [4648883056_G]

description: Macrophage

value: IFNg


title: M_GMCSF_TPP_6h [4648883056_I]

description: Macrophage


title: CHM049


title: M_GMCSF_TPP_6h [4648883056_F]

description: Macrophage


title: luciferase control knockdown, biological rep1

description: HeLa  cell line

value: luciferase control knockdown


title: CHM048


title: HnRNP L knockdown, biological rep2

description: HeLa  cell line


title: HnRNP L knockdown, biological rep1

description: HeLa  cell line


title: luciferase control knockdown, biological rep3

description: HeLa  cell line


title: M_GMCSF_IL4_6h [4648883056_E]

description: Macrophage


title: CHM046


title: CHM047


title: luciferase control knockdown, biological rep2

description: HeLa  cell line


title: CHM042


title: CHM043


title: M_GMCSF_TPP_24h [4648883056_B]

description: Macrophage


title: Yeast_Dal80Δ_Control_1h_BioRep3_TecRep1

source_name: exp growing S. cer treated with solvent (MeOH)

value: control


title: Yeast_Dal80Δ_Control_1h_BioRep3_TecRep2


title: Yeast_Dal80Δ_Control_1h_BioRep2_TecRep1


title: Yeast_Dal80Δ_Control_1h_BioRep2_TecRep2


title: CHM038


title: CHM039


title: CHM041


title: M0_GMCSF_0h [4648883056_C]

description: Macrophage

value: con


title: CHM050


title: Yeast_Dal80Δ_LoaOOH-treated_1h_BioRep2_TecRep1


title: M_GMCSF_IFNg_6h [4648883056_A]

description: Macrophage


title: Yeast_Dal80Δ_LoaOOH-treated_1h_BioRep1_TecRep1


title: Yeast_Dal80Δ_Control_1h_BioRep1_TecRep1


title: CHM033


title: Yeast_Dal80Δ_Control_1h_BioRep1_TecRep2


title: M_GMCSF_IFNg_72h [4487653415_H]

description: Macrophage


title: Yeast_Dal80Δ_LoaOOH-treated_1h_BioRep1_TecRep2


title: M_GMCSF_IL4_72h [4487653415_E]

description: Macrophage


title: M_GMCSF_IFNg_6h [4648883056_D]

description: Macrophage


title: M_GMCSF_TPP_72h [4487653415_G]

description: Macrophage


title: CHM031


title: Th17 culture, PBAB stimulation, biological replicate 2

city: Bethesda

first: Lai

last: Wei

state: MD

address: 10 Center Dr. Room 2B47

institute: NIH/NEI/NCCAM

hyb_protocol: Approximately 10 µg of total labeled RNA was hybridized to GeneChip MEO430 2.0 arrays (Affymetrix) according to the manufacturer’s protocols.

scan_protocol: Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1.

data_processing: All data analysis was performed using GeneSpring GX 11.0 (Agilent Technologies). Expression values for each probe were normalized using Robust Multichip Average (RMA) method.

organism: Mus musculus

source_name: CD4+ T cells

label_protocol: 500 ng total RNA was amplified and biotin-labelled using MessageAmp II-Biotin Enhanced Kit (Ambion).

growth_protocol: Naïve CD4+ T cells were purified from spleen and lymph node cells of 3A9 mice, using T cell columns (R&D). CD4 cells expressing the Tg TCR were sorted by FACSAria II (BD Biosciences), using the clonotypic mAb 1G12, and then were activated and polarized toward Th1, Th9 and Th17 lineage as follows: the CD4 cells were cultured in 12-well plates (Corning) at 25x104/ml cells in a volume of 2 ml of RPMI-1640, supplemented with 10% FCS, antibiotics and 50 μM 2-ME. Activation was induced either by HEL (1 μg/ml for Th9 cell culture, or 2 μg/ml for Th1 and Th17 cell cultures) presented by irradiated (30 Gy) syngeneic wild type naive splenocytes serving as APCs (125x104/ml) (“HA”), or by plate bound anti-CD3 (1 μg/ml) and anti-CD28 (10 μg/ml) Abs (“PbAb”). Polarizing cocktails, added concurrently with the activation process included:  for Th1 lineage, 10 ng/ml IL-12, 10 μg/ml anti-IL-4; for Th9 lineage, 10 ng/ml IL-4, 1 ng/ml TGF-b; and for Th17 lineage, 3 ng/ml TGF-β, 10 ng/ml IL-6, 5 ng/ml IL-1α, 20 μg/ml anti-IFN-γ, 10 μg/ml anti-IL-4, 10 μg/ml anti-IL-12.

extract_protocol: Total RNA was isolated from different Th cells cultured for 4 days using mirVana miRNA isolation kit (Ambion).

value: Th17 culture

value: PBAB stimulation


title: Th17 culture, PBAB stimulation, biological replicate 1


title: DC_upLPS_10_24h [5376074048_L]

description: Dendritic cell

value: GM-CSF + IL4

value: upLPS


title: Th17 culture, HA stimulation, biological replicate 1

value: HA stimulation


title: M0_GMCSF_72h [4487653414_E]

description: Macrophage


title: CHM034


title: DC_imm [5376074048_K]

description: Dendritic cell


title: DC_upLPS_10_24h [5376074048_J]

description: Dendritic cell


title: Th17 culture, APC alone

value: APC alone


title: CHM035


title: Th17 culture, HA stimulation, biological replicate 2


title: DC_upLPS_10_24h [5376074048_I]

description: Dendritic cell


title: CHM030


title: Th9 culture, PBAB stimulation, biological replicate 2

value: Th9 culture


title: Th9 culture, PBAB stimulation, biological replicate 1


title: DC_upLPS_10_24h [5376074048_H]

description: Dendritic cell


title: DC_imm [5376074048_F]

description: Dendritic cell


title: MC3T3-E1 cells at day 9  treated with Runx2 shRNA, biological replicate 3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

institute: University of Vermont

description: expressin data from differentiating preosteoblast MC3T3-E1 subclone 4 cells with Runx2 depleted by shRNA

hyb_protocol: Labeled cRNA were then hybridized to GeneChip Mouse Gene 1.0 ST Array Rev 4 using GeneChip Hybridization, Wash, and Stain kit.

scan_protocol: Hybridization signals were obtained by GeneChip Scanner (Affymetrix)

data_processing: Microarray data were analyzed using Bioconductor (version 2.11) packages affy and limma in R (http://www.R-project.org, version 2.15.1).Briefly, after performing robust multichip average (RMA) normalization of microarray expression levels and filtering, differential expression was detected using a Bayesian moderated t-test.

source_name: differentiating MC3T3-E1 cells treated with Runx2-specific shRNA

label_protocol: RNA isolated from MC3T3-E1 cells (day 0 and 9 scramble shRNA, and day 9 Runx2 shRNA) were reversely transcribed into cDNA using WT expression Kit (Ambion), labeled and fragmented with GeneChip WT terminal labeling and controls Kit.

growth_protocol: MC3T3-E1 Subclone cells were grown in ascorbic acid-free alpha-MEM (Hyclone) supplemented with 10% fetal bovine serum (FBS; Hyclone), 2 mM L-glutamine, 100 U/ml of penicillin and 100 µg/ml streptomycin (Pen/Strep, Invitrogen). To induce osteogenic differentiation, complete alpha-MEM was supplemented with 280 μM ascorbic acid and 10 mM beta-glycerophosphate (Sigma Aldrich). Cells were maintained at 37C in a humidified 5% CO2 environment and media replaced every 2-3 days for the duration of all experiments.

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

treatment_protocol: Lentiviruses carrying Runx2-shRNA and control Scramble-shRNA was used to infect MC3T3-E1 cells respectively. Infected cells were subsequently sorted by GFP and grown to 90% confluency followed by osteogenic differentiation for 9 days. Knockdown experiments were performed in three biological replicates.

value: calvaria


title: DC_upLPS_10_24h [5376074048_G]

description: Dendritic cell


title: Th9 culture, HA stimulation, biological replicate 2


title: Th9 culture, HA stimulation, biological replicate 1


title: CHM029

value: complete hydatidiform mole


title: MC3T3-E1 cells at day 9  treated with Runx2 shRNA, biological replicate 2


title: CHM032


title: Th9 culture, APC alone


title: DC_imm [5376074048_E]

description: Dendritic cell


title: MC3T3-E1 cells at day 9  treated with Runx2 shRNA, biological replicate 1


title: DC_upLPS_10_24h [5376074048_C]

description: Dendritic cell


title: CHM040


title: Th1 culture, PBAB stimulation, biological replicate 2

value: Th1 culture


title: Th1 culture, HA stimulation, biological replicate 2


title: DC_imm [5376074048_B]

description: Dendritic cell


title: DC_imm [5376074048_D]

description: Dendritic cell


title: CHM023


title: CHM022


title: MC3T3-E1 cells at day 9  treated with scramble shRNA, biological replicate 1

description: expressin data from differentiating preosteoblast MC3T3-E1 subclone 4 cells

source_name: differentiating MC3T3-E1 cells treated with control scramble shRNA


title: MC3T3-E1 cells at day 9  treated with scramble shRNA, biological replicate 3


title: DC_imm [5376074048_A]

description: Dendritic cell


title: Th1 culture, HA stimulation, biological replicate 1


title: MC3T3-E1 cells at day 0  treated with scramble shRNA, biological replicate 3

description: expressin data from proliferating preosteoblast MC3T3-E1 subclone 4 cells

source_name: proliferating MC3T3-E1 cells treated with control scramble shRNA


title: CHM026


title: Th1 culture, PBAB stimulation, biological replicate 1


title: CHM024


title: CHM019


title: MC3T3-E1 cells at day 9  treated with scramble shRNA, biological replicate 2


title: DC_imm [5376074046_K]

description: Dendritic cell


title: Ovarian surface epithelium scraping [OV 30]

city: Oslo

first: Bente

middle: Vilming

last: Elgaaen

address: Ullernchausseen 70

department: Department of Gynecological Oncology

country: Norway

institute: Oslo University Hospital

description: OV 30

hyb_protocol: Labeled RNAs was hybridized to the GeneChip miRNA 2.0 Array (Affymetrix, Santa Clara, CA) as recommended by the vendor. The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA). The scanned images were processed using the AGCC (Affymetrix GeneChip Command Console) software.

data_processing: The CEL files were imported into Partek Genomics Suite software (Partek, Inc. MO, USA). The Robust Multichip Analysis (RMA) algorithm was applied for generation of signal values and normalization.For expression comparisons of different groups, profiles  were compared using a 1-way ANOVA model. The results were expressed as FC (fold change) with p-values and calculation of FDR (false discovery rate).

source_name: Ovarian surface epithelium scraping

label_protocol: 400 ng of total RNA was used for labeling of microRNA by the Genisphere FlashTag HSR kit following the manufacturer's recommendations (Genisphere, Hatfield, PA).

extract_protocol: Frozen tissue specimens of less than 50 mg were homogenized directly for 3 minutes in 700 µl QIAzol using a TissueLyzer (Qiagen.com). Total RNA was extracted using the miRNeasy Mini Kit (Qiagen, Hilden Germany) and Phase Lock Gel™ Heavy (5 PRIME GmbH, Hamburg, Germany). RNA was quantified with a NanoDrop® ND-1000 Spectrophotometer (Saveen Werner, Malmö, Sweden), and quality assessed on an Agilent 2100 Bioanalyzer RNA 6000 Nano Kits (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Cancer tissue samples and OSE scrapings from normal ovaries were immediately harvested from removed ovaries at surgery and snap-frozen in liquid nitrogen or transferred to TRIzol solution (Invitrogen.com), respectively. The samples were stored at -80⁰C until processed.

value: ovary

tag: disease status

value: Ovarian surface epithelium scraping


title: DC_imm [5376074046_J]

description: Dendritic cell


title: MC3T3-E1 cells at day 0  treated with scramble shRNA, biological replicate 1

tag: tissue


title: CHM020


title: DC_imm [5376074046_I]

description: Dendritic cell


title: Ovarian surface epithelium scraping [OV 29]

description: OV 29


title: DC_upLPS_10_24h [5376074046_L]

description: Dendritic cell


title: Th1 culture, APC alone


title: CHM028


title: CHM021


title: 2nd kidney tumor 3

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

description:
2nd KT3
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99℃ for 5 minutes, then 45℃ for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing:
Data were processed using Genespring software.
summarization algorithm : RMA16
Technology : Affymetrix.ExonExprChip.MoGene-1_0-st-v1_na32_mm9_2011-10-07

source_name: transplanted secondary kidney tumors in the subcutaneous tissues of immnodeficient mice

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNeasy Plus Mini kit

value: transplanted secondary kidney tumors


title: CHM018


title: 2nd kidney tumor 2

description:
2nd KT2
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: Ovarian surface epithelium scraping [OV 27]

description: OV 27


title: CHM016


title: CHM014


title: 2nd kidney tumor 1

description:
2nd KT1
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: liver tumor 3

description:
LT3
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.

source_name: liver tumor

value: liver tumor


title: DC_upLPS_10_24h [5376074046_H]

description: Dendritic cell


title: Ovarian surface epithelium scraping [OV 26]

description: OV 26


title: CHM011


title: DC_imm [5376074046_F]

description: Dendritic cell


title: Ovarian surface epithelium scraping [OV 25]

description: OV 25


title: DC_imm [5376074046_G]

description: Dendritic cell


title: DC_upLPS_10_24h [5376074046_E]

description: Dendritic cell


title: CHM009


title: liver tumor 2

description:
LT2
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: Ovarian surface epithelium scraping [OV 24]

description: OV 24


title: CHM012


title: Ovarian surface epithelium scraping [OV 28]

description: OV 28


title: Ovarian surface epithelium scraping [OV 23]

description: OV 23


title: CHM010_2


title: Ovarian surface epithelium scraping [OV 22]

description: OV 22


title: normal liver 3

description:
NL3
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.

source_name: normal liver

value: normal liver


title: DC_upLPS_10_24h [5376074046_D]

description: Dendritic cell

source_name: peripheral blood


title: CHM013


title: DC_imm [5376074046_A]

description: Dendritic cell


title: normal liver 2

description:
NL2
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: DC_upLPS_10_24h [5376074046_C]

description: Dendritic cell


title: MC3T3-E1 cells at day 0  treated with scramble shRNA, biological replicate 2


title: DC_upLPS_10_24h [5376074046_B]

description: Dendritic cell


title: normal liver 1

description:
NL1
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: CHM008


title: CHM006


title: CHM007


title: Clear cell ovarian carcinoma [OV 18]

description: OV 18

source_name: Clear cell ovarian carcinoma

value: Clear cell ovarian carcinoma

tag: progression (0=no, 1=yes)

tag: time (months) until progression or last follow-up

tag: death (0=no, 1=yes)

tag: time (months) until death or last follow-up


title: Clear cell ovarian carcinoma [OV 20]

description: OV 20


title: DC_reg [5342595027_J]

description: Dendritic cell

value: TNFa 800 u/ml+ PGE2 1µg/ml+ P3C 1µg/ml


title: DC_reg [5342595027_E]

description: Dendritic cell


title: Clear cell ovarian carcinoma [OV 19]

description: OV 19


title: normal kidney 2

description:
NK2
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.

source_name: normal kidney

value: normal kidney


title: Clear cell ovarian carcinoma [OV 17]

description: OV 17


title: kidney tumor 2

description:
KT2
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.

source_name: kidney tumor

value: kidney tumor


title: DC_imm [5342595027_H]

description: Dendritic cell

value: GM-CSF + IL4


title: kidney tumor 3

description:
KT3
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: normal kidney 3

description:
NK3
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: DC_imm [5342595027_A]

description: Dendritic cell


title: Clear cell ovarian carcinoma [OV 16]

description: OV 16


title: Clear cell ovarian carcinoma [OV 15]

description: OV 15


title: DC_mat [5342595027_D]

description: Dendritic cell

value: TNFa 800 u/ml


title: kidney tumor 1

description:
KT1
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: DC_mat [5342595013_L]

description: Dendritic cell


title: CHM015


title: M454 SKM-Tg

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description:
M454 + QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

hyb_protocol: 2.2 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC, washing and staining of microarrays was performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Arrays were processed in Bioconductor, using RMA background correction, quantile normalization and RMA summarization.

source_name: SKM-Tg

label_protocol: 25 ng total RNA per sample was processed using isothermal amplification SPIA Biotin System (NuGEN Technologies, Inc.)

growth_protocol: Mice were kept under a 12h dark-light period and provided with a standard chow-diet and water ad libitum

extract_protocol: RNA from quadriceps muscles was extracted using a protocol combining TRIzol reagent (Invitrogen) and RNAeasy® minikit columns (Qiagen) following manufacturer's instructions

treatment_protocol: Quadriceps muscles were extracted and directly frozen in liquid nitrogen

tag: gender

value: male

value: SKM-Tg

value: Skeletal muscle (quadriceps)


title: Clear cell ovarian carcinoma [OV 14]

description: OV 14


title: normal kidney 1

description:
NK1
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: M473 SKM-Tg

description:
M473 + QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

tag: strain


title: M474 SKM-Tg

description:
M474 + QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

tag: genotype/variation


title: liver tumor 1

description:
LT1
Since mice had been generated with the ESC line, mouse tissues are in 129xC57BL6 F1 or mixed (129 and C57BL6) genetic background. We analyzed tumors developed in chimeric mice, so tumor samples may contain ICR cells as well.


title: M452 SKM-Tg

description:
M452 + QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse


title: High-grade serous ovarian carcinomas [OV 12]

description: OV 12

source_name: High-grade serous ovarian carcinoma

value: High-grade serous ovarian carcinoma


title: Clear cell ovarian carcinoma [OV 13]

description: OV 13


title: DC_mat [5342595013_H]

description: Dendritic cell

tag: initial differentiation


title: DC_imm [5342595013_E]

description: Dendritic cell

tag: activation stimuli


title: CHM005

source_name: complete hydatidiform mole

value: complete hydatidiform mole


title: M479 Wt

description:
M479 - QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

source_name: Wt

value: Wt


title: B cell [5342595027_I]

description: B cell

value: unstimulated

tag: time


title: DC_reg [5342595013_D]

description: Dendritic cell

tag: donor


title: ES cell

description:
ESC1
We used ES cells with 129xC57BL6 F1 genetic background.

source_name: ES cell

tag: cell type

value: ES


title: M465 Wt

description:
M465 - QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

tag: age


title: High-grade serous ovarian carcinomas [OV 9]

description: OV 9

value: ovary


title: AML1 no IL-3 16h

city: Adelaide

first: Chung

middle: H

last: Kok

state: South Australia

address: North Terrace

institute: South Australia Health and Medical Research Institute

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner.

data_processing: Raw CEL files were normalised with RMA method using aroma.affymetrix.

source_name: Primary AML MNCs

label_protocol: Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

growth_protocol: Mononuclear AML cells were thawed and recovered overnight in IMDM with 20% FBS and DNase (50U/mL). Non-viable cells were subsequently removed using Lymphoprep (Axis-Shield PLC). AML cells were then cultured in IMDM with 10% FBS and stimulated with IL-3 as described below.

extract_protocol: Total RNA was purified using the miRNeasy protocol (Qiagen)

treatment_protocol: Mononuclear AML cells thawed overnight and cultured in IMDM with 10% FBS were treated +/- 15ng/mL hIL-3 for 6 or 16h.

value: Primary AML MNCs

tag: treatment

value: no IL-3 16h

tag: disease

value: Acute myeloid leukaemia

tag: cytogenetics


title: B cell [5342595013_I]

description: B cell


title: M327 SKM-KO

description:
M327 QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

source_name: SKM-KO

value: SKM-KO

tag: tissue


title: AML3 + IL-3 6h

value: normal


title: Clear cell ovarian carcinoma [OV 21]

description: OV 21

tag: disease status

value: Clear cell ovarian carcinoma

tag: progression (0=no, 1=yes)


title: AML3 no IL-3 6h

value: no IL-3 6h


title: High-grade serous ovarian carcinomas [OV 8]

description: OV 8

tag: time (months) until progression or last follow-up

tag: death (0=no, 1=yes)


title: High-grade serous ovarian carcinomas [OV 11]

description: OV 11

tag: time (months) until death or last follow-up


title: M322 SKM-KO

description:
M322 QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

tag: strain

tag: gender


title: B cell [5342595013_G]

description: B cell

tag: initial differentiation


title: High-grade serous ovarian carcinomas [OV 10]

description: OV 10


title: AML4 no IL-3 6h


title: M325 C

description:
M325 QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

source_name: C

tag: genotype/variation

value: C


title: M304 SKM-KO

description:
M304 QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

value: male


title: SKR6LR cells, biological replicate 3

city: Boston

first: Shannon

middle: Terrell

last: Bailey

state: MA

address: 450 Brookline Avenue, D728

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data of SKR6LR cells, which are SKR6 cells that were treated with increasing lapatinib concentrations (0.2 to 5 μM) for several months to derive a resistant cell population.

hyb_protocol: The biotinylated complementary RNA (cRNA) was purified from the IVT reaction mixture using magnetic particles, and it was quantified spectrophotometrically. The purity of the cRNA was also assessed by spectrophometric measurements.  The purified cRNA was first fragmented to facilitate hybridization, and the fragmented cRNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control) and hybridized to a microarray chip overnight at 45Â°C after which the hybridization solution was removed. The chips were transferred to a fluidics instrument that washed away and cRNA that did not hybridized to its complementary oligonucleotide probe. The bound cRNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluorophores were then added using a biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: Each cRNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The expression data were normalized using the robust multichip average (RMA) method and processed using linear models for microarray data (Limma) using R.

source_name: SKR6LR cells

label_protocol: RNA was converted into cDNA using a T7 promoter-tailed oligo-dT primer to synthesize the first cDNA strand and a second strand cDNA synthesis was then performed.  The double-stranded cDNA was used as a template for an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containing biotinylated CTP and UTP in addition to the four unmodified ribonucleoside triphosphates.

growth_protocol: The SKR6, SKR6-Vector, SKR6CA, and SKR6LR cells were seeded in RPMI 1640 medium supplemented with 10% fetal bovine serum and grown for 48 hours prior to total RNA extraction. The SKLR cells were maintained in the presence of 0.2 uM lapatinib.

extract_protocol: A hybrid Trizol/Qiagen Rneasy protocol was used to isolate total RNA

tag: parental cell line


title: CHM002


title: AML2 no IL-3 6h


title: High-grade serous ovarian carcinomas [OV 7]

description: OV 7


title: CHM001


title: SKR6LR cells, biological replicate 2

value: SKR6LR cells, which are SKR6 cells that were treated with increasing lapatinib concentrations (0.2 to 5 μM) for several months to derive a resistant cell population.


title: M323 C

description:
M323 QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse

value: Skeletal muscle (quadriceps)


title: M464 Wt

description:
M464 - QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse


title: AML1 + IL-3 6h


title: AML4 + IL-3 6h


title: M303 C

description:
M303 QV RNA
Gene expression data from quadriceps muscle of 4-month-old male mouse


title: AML4 + IL-3 16h


title: SKR6LR cells, biological replicate 1


title: High-grade serous ovarian carcinomas [OV 4]

description: OV 4

value: High-grade serous ovarian carcinoma


title: High-grade serous ovarian carcinomas [OV 5]

description: OV 5


title: AML2 + IL-3 6h


title: High-grade serous ovarian carcinomas [OV 6]

description: OV 6


title: SKR6CA cells, biological replicate 3

description: Gene expression data of SKR6CA cells, which are SKR6 cells that were retrovirally transduced with constitutively active NF-κB relA/p65 (CAp65) and selected with puromycin

source_name: SKR6CA cells


title: CHM003

value: complete hydatidiform mole


title: SKR6CA cells, biological replicate 2

value: SKR6CA cells, which are SKR6 cells that were retrovirally transduced with constitutively active NF-κB relA/p65 (CAp65) and selected with puromycin


title: MCF7_Hypoxia_48h_rep2 [mRNA]

city: Oxford

address: Roosevelt Drive

description:
Hypoxia_48h_R2
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalised (quantile normalisation) using preprocessCore package from Bioconductor

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit.

growth_protocol: MCF-7 cells were grown in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 2mmol/L of L-glutamine.

tag: oxygen

tag: time of exposure


title: MCF7_Hypoxia_48h_rep1 [mRNA]

description:
Hypoxia_48h_R1
replicate 1


title: MCF7_Hypoxia_48h_rep3 [mRNA]

description:
Hypoxia_48h_R3
replicate 3


title: AML4 no IL-3 16h

tag: cell type


title: AML3 + IL-3 16h

tag: treatment


title: AML2 no IL-3 16h

tag: disease


title: SKR6-Vector cells, biological replicate 2

description: Gene expression data of SKR6-Vector cells, which are SKR6 cells that were retrovirally transduced with the pQCXIP empty retroviral vector and selected with puromycin

source_name: SKR6-Vector cells


title: MCF7_Hypoxia_32h_rep2 [mRNA]

description:
Hypoxia_32h_R2
replicate 2


title: MCF7_Hypoxia_32h_rep3 [mRNA]

description:
Hypoxia_32h_R3
replicate 3


title: High-grade serous ovarian carcinomas [OV 1]

description: OV 1


title: MCF7_Hypoxia_16h_rep3 [mRNA]

description:
Hypoxia_16h_R3
replicate 3