title: PBMC_1

description: Sample name: 7602346012_H

tag: developmental stage

tag: age

tag: bmi

tag: weight

tag: cesd

tag: race

tag: hivdate

tag: fromscyr

tag: smoke

tag: alcohol

tag: cocaine

tag: heroin

tag: halluc

tag: echlor

tag: ghb

tag: anycancer


title: PBM_PM_Nb17

status: Public on Apr 02 2015

type: RNA

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay

scan_protocol: Standard Illumina Scanning protocol

data_processing: With GenomeStudio GX (version 1.5.4) we extracted from each array the background-corrected, summarized expression levels (AVG Signal), standard errors of the bead replicates (BEAD STERR), number of beads used (Avg NBEADS) and detection scores (Detection Pval). Subsequently, we applied a variance stabilizing transformation and a quantile normalization in R, as implemented in the lumi-package from Bioconductor.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood monocytes, metastatic patient

label_protocol: Biotynilated cRNA was prepared with Ambion Illumina TotalPrep RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser, and quantification with Nanodrop.

tag: tumor stage

value: metastatic patient

tag: gender

value: M


title: PBM_P_Nb12

source_name: peripheral blood monocytes, non-metastatic patient

value: non-metastatic patient

value: F

tag: age


title: PBM_PM_Nb3


title: PBM_PM_Nb15


title: PBM_PM_Nb13


title: PBM_P_Nb5


title: PBM_PM_Nb37


title: PBM_HV_Nb40

source_name: peripheral blood monocytes, healthy volunteer

value: healthy volunteer


title: PBM_HV_Nb16


title: PBM_HV_Nb15


title: PBM_HV_Nb14


title: PBM_HV_Nb17


title: PBM_PM_Nb63


title: PBM_HV_Nb39


title: PBM_PM_Nb64


title: PBM_HV_Nb8


title: PBM_P_Nb48


title: PBM_HV_Nb11


title: PBM_P_Nb9


title: PBM_HV_Nb10


title: PBM_HV_Nb13


title: PBM_HV_Nb9


title: PBM_HV_Nb7


title: PBM_HV_Nb5


title: PBM_HV_Nb1


title: PBM_HV_Nb24


title: PBM_HV_Nb26


title: PBM_HV_Nb22


title: PBM_PM_Nb43


title: PBM_HV_Nb25


title: PBM_HV_Nb3


title: PBM_HV_Nb23


title: PBM_HV_Nb2


title: PBM_HV_Nb20


title: PBM_HV_Nb36


title: PBM_HV_Nb33


title: PBM_HV_Nb34


title: PBM_HV_Nb21


title: PBM_HV_Nb38


title: PBM_HV_Nb31


title: PBM_HV_Nb19


title: PBM_HV_Nb32


title: PBM_HV_Nb37


title: PBM_PM_Nb46


title: PBM_HV_Nb6


title: PBM_PM_Nb62


title: PBM_HV_Nb30


title: PBM_HV_Nb28


title: PBM_HV_Nb29


title: PBM_P_Nb42


title: PBM_HV_Nb27


title: PBM_P_Nb41


title: PBM_P_Nb47


title: PBM_PM_Nb36


title: PBM_PM_Nb45


title: PBM_P_Nb34


title: PBM_HV_Nb4


title: PBM_P_Nb26


title: PBM_HV_Nb35


title: PBM_PM_Nb7


title: PBM_P_Nb38


title: PBM_PM_Nb55


title: PBM_PM_Nb61


title: PBM_P_Nb59


title: Kidney_donor_BD_T3_105

city: Groningen

first: Jeffrey

last: Damman

address: Hanzeplein 1

department: Pathology

country: Netherlands

institute: University Medical Center Groningen

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data files were processed using GenomeStudio Software and further analyzed using Genespring GX 12.0 software (Agilent, Santa Clara, USA). Data normalization was performed using the default GeneSpring GX 12.0 median shift normalization to the 75 percentile (applying a log2 transformation) and baseline transformation using the median of all samples.

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina Total Prep RNA kit.

extract_protocol: RNA was extracted with Trizol reagent. Quality was determined by high throughput Caliper GX LabChip RNA kit (Caliper).

tag: tissue

value: kidney biopsy

tag: donor type (0=living, 1=bd, 2=nhb)

tag: timepoint biopsy

tag: deceased paired biopsies

tag: delayed graft function (0=no, 1=yes)


title: Kidney_donor_DCD_T2_53

tag: deceased unpaired biopsies


title: PBM_PM_Nb10


title: PBM_P_Nb2


title: PBM_PM_Nb60


title: Kidney_donor_BD_T3_103


title: Kidney_donor_DCD_T2_52


title: Kidney_donor_DCD_T2_51


title: Kidney_donor_BD_T3_104


title: Kidney_donor_DCD_T2_50


title: Kidney_donor_BD_T2_110


title: PBM_P_Nb56


title: PBM_P_Nb57


title: Kidney_donor_BD_T2_109


title: Kidney_donor_BD_T1_101

tag: deceased donors, only left kidney included in the analysis


title: PBM_PM_Nb49


title: Kidney_donor_BD_T3_102


title: Kidney_donor_BD_T1_98


title: Kidney_donor_BD_T1_100


title: Kidney_donor_BD_T1_97

tag: deceased left and right biopsies same donor (0=left, 1=right)


title: PBM_P_Nb51


title: Kidney_donor_Living_T1_37

tag: living paired biopsies


title: PBM_P_Nb52


title: PBM_PM_Nb54


title: PBM_PM_Nb53


title: Kidney_donor_BD_T2_108


title: Kidney_donor_BD_T3_101


title: Kidney_donor_DCD_T1_50


title: Kidney_donor_DCD_T3_63


title: Kidney_donor_BD_T1_99


title: Kidney_donor_BD_T2_106


title: Kidney_donor_BD_T3_99


title: Kidney_donor_BD_T2_107


title: Kidney_donor_BD_T2_105


title: Kidney_donor_BD_T3_97


title: Kidney_donor_Living_T3_34


title: Kidney_donor_BD_T2_101


title: Kidney_donor_BD_T3_96


title: Kidney_donor_BD_T3_100


title: Kidney_donor_BD_T3_98


title: Kidney_donor_DCD_T3_64


title: Kidney_donor_DCD_T1_49


title: Kidney_donor_DCD_T2_48


title: Kidney_donor_BD_T2_100


title: Kidney_donor_BD_T2_104


title: Kidney_donor_BD_T2_99


title: Kidney_donor_BD_T2_103


title: Kidney_donor_DCD_T3_62


title: Kidney_donor_BD_T2_98


title: Kidney_donor_BD_T1_96


title: Kidney_donor_BD_T2_102


title: Kidney_donor_BD_T2_97


title: Kidney_donor_BD_T3_92


title: Kidney_donor_Living_T1_35


title: Kidney_donor_Living_T1_36


title: Kidney_donor_BD_T3_93


title: Kidney_donor_DCD_T2_49


title: Kidney_donor_DCD_T3_60


title: PBM_PM_Nb58


title: Kidney_donor_BD_T3_94


title: Kidney_donor_DCD_T2_47


title: Kidney_donor_BD_T2_96


title: Kidney_donor_BD_T3_95


title: Kidney_donor_BD_T3_91


title: Kidney_donor_DCD_T1_46


title: Kidney_donor_BD_T1_95


title: Kidney_donor_DCD_T1_47


title: Kidney_donor_DCD_T1_48


title: Kidney_donor_BD_T2_95


title: Kidney_donor_DCD_T1_45


title: Kidney_donor_BD_T1_94


title: Kidney_donor_BD_T1_92


title: Kidney_donor_BD_T2_94


title: Kidney_donor_DCD_T3_58


title: Kidney_donor_DCD_T1_44


title: Kidney_donor_DCD_T3_57


title: Kidney_donor_BD_T2_91


title: Kidney_donor_DCD_T1_43


title: Kidney_donor_Living_T3_31


title: Kidney_donor_BD_T1_93


title: Kidney_donor_BD_T2_92


title: Kidney_donor_DCD_T3_61


title: Kidney_donor_DCD_T3_55


title: Kidney_donor_Living_T1_34


title: Kidney_donor_BD_T2_90


title: Kidney_donor_Living_T3_33


title: Kidney_donor_Living_T1_33


title: Kidney_donor_BD_T2_88


title: Kidney_donor_BD_T2_89


title: Kidney_donor_BD_T3_87


title: Kidney_donor_DCD_T3_53


title: Kidney_donor_BD_T1_87


title: Kidney_donor_BD_T3_85


title: Kidney_donor_Living_T3_30


title: Kidney_donor_DCD_T3_59


title: Kidney_donor_BD_T3_84


title: Kidney_donor_BD_T1_86


title: Kidney_donor_BD_T3_90


title: Kidney_donor_BD_T1_90


title: Kidney_donor_DCD_T3_52


title: Kidney_donor_BD_T3_86


title: Kidney_donor_BD_T2_87


title: Kidney_donor_Living_T3_32


title: Kidney_donor_DCD_T1_42


title: Kidney_donor_DCD_T3_56


title: Kidney_donor_BD_T1_85


title: Kidney_donor_Living_T3_29


title: Kidney_donor_DCD_T2_43


title: Kidney_donor_BD_T1_91


title: Kidney_donor_BD_T3_89


title: Kidney_donor_DCD_T3_49


title: Kidney_donor_BD_T1_83


title: Kidney_donor_BD_T1_89


title: Kidney_donor_BD_T1_84


title: Kidney_donor_DCD_T3_54


title: Kidney_donor_DCD_T2_44


title: Kidney_donor_BD_T3_81


title: Kidney_donor_DCD_T3_51


title: Kidney_donor_DCD_T2_45


title: Kidney_donor_BD_T2_85


title: Kidney_donor_BD_T1_88


title: Kidney_donor_DCD_T2_46


title: Kidney_donor_BD_T2_86


title: Kidney_donor_DCD_T1_41


title: Kidney_donor_BD_T3_88


title: Kidney_donor_BD_T3_83


title: Kidney_donor_BD_T3_82


title: Kidney_donor_BD_T2_93


title: Kidney_donor_DCD_T3_50


title: Kidney_donor_BD_T3_80


title: Kidney_donor_BD_T3_79


title: Kidney_donor_BD_T1_80


title: Kidney_donor_Living_T1_32


title: Kidney_donor_BD_T2_84


title: Kidney_donor_BD_T1_82


title: Kidney_donor_Living_T3_28


title: Kidney_donor_Living_T1_31


title: Kidney_donor_DCD_T1_39


title: Kidney_donor_DCD_T1_40


title: Kidney_donor_DCD_T2_42


title: Kidney_donor_BD_T3_77


title: Kidney_donor_DCD_T3_48


title: Kidney_donor_DCD_T2_41


title: Kidney_donor_BD_T1_78


title: Kidney_donor_DCD_T3_46


title: Kidney_donor_BD_T1_79


title: Kidney_donor_BD_T1_77


title: Kidney_donor_DCD_T3_45


title: Kidney_donor_BD_T3_78


title: Kidney_donor_BD_T3_76


title: Kidney_donor_BD_T3_74


title: Kidney_donor_BD_T2_80


title: Kidney_donor_BD_T3_72


title: Kidney_donor_Living_T3_27


title: Kidney_donor_BD_T2_83


title: Kidney_donor_BD_T2_82


title: Kidney_donor_DCD_T2_40


title: Kidney_donor_Living_T1_30


title: Kidney_donor_DCD_T3_47


title: Kidney_donor_DCD_T1_38


title: Kidney_donor_BD_T3_75


title: Kidney_donor_DCD_T2_39


title: Kidney_donor_DCD_T1_37


title: Kidney_donor_BD_T3_71


title: Kidney_donor_DCD_T3_44


title: Kidney_donor_BD_T3_70


title: Kidney_donor_BD_T3_73


title: Kidney_donor_BD_T1_74


title: Kidney_donor_BD_T2_78


title: Kidney_donor_Living_T3_26


title: Kidney_donor_DCD_T1_35


title: Kidney_donor_BD_T2_79


title: Kidney_donor_DCD_T1_36


title: Kidney_donor_BD_T3_69


title: Kidney_donor_Living_T1_29


title: Kidney_donor_Living_T1_28


title: Kidney_donor_BD_T2_76


title: Kidney_donor_BD_T2_75


title: Kidney_donor_BD_T3_67


title: Kidney_donor_DCD_T3_41


title: Kidney_donor_BD_T1_73


title: Kidney_donor_BD_T2_71


title: Kidney_donor_BD_T1_72


title: Kidney_donor_DCD_T1_33


title: Kidney_donor_DCD_T1_34


title: Kidney_donor_BD_T3_68


title: Kidney_donor_DCD_T3_42


title: Kidney_donor_BD_T1_75


title: Kidney_donor_BD_T3_66


title: Kidney_donor_BD_T2_72


title: Kidney_donor_BD_T2_73


title: Kidney_donor_BD_T2_81


title: Kidney_donor_BD_T1_81


title: Kidney_donor_Living_T3_24


title: Kidney_donor_BD_T2_70


title: Kidney_donor_Living_T1_27


title: Kidney_donor_BD_T1_76


title: Kidney_donor_BD_T3_65


title: Kidney_donor_BD_T1_71


title: Kidney_donor_BD_T2_74


title: Kidney_donor_DCD_T2_38


title: Kidney_donor_BD_T2_77


title: Kidney_donor_BD_T1_70


title: Kidney_donor_Living_T1_26


title: Kidney_donor_Living_T3_25


title: Kidney_donor_DCD_T3_40


title: Kidney_donor_BD_T3_64


title: Kidney_donor_DCD_T1_32


title: Kidney_donor_DCD_T3_39


title: Kidney_donor_BD_T2_69


title: Kidney_donor_BD_T3_60


title: Kidney_donor_DCD_T2_36


title: Kidney_donor_BD_T3_62


title: Kidney_donor_BD_T2_68


title: Kidney_donor_DCD_T3_38


title: Kidney_donor_DCD_T3_43


title: Kidney_donor_BD_T3_61


title: Kidney_donor_DCD_T2_37


title: Kidney_donor_BD_T2_65


title: Kidney_donor_BD_T3_63


title: Kidney_donor_BD_T1_67


title: Kidney_donor_DCD_T3_37


title: Kidney_donor_BD_T2_67


title: Kidney_donor_BD_T2_64


title: Kidney_donor_BD_T3_59


title: Kidney_donor_DCD_T1_31


title: Kidney_donor_DCD_T3_36


title: Kidney_donor_Living_T3_23


title: Kidney_donor_BD_T1_68


title: Kidney_donor_DCD_T3_34


title: Kidney_donor_Living_T1_25


title: Kidney_donor_BD_T1_69


title: Kidney_donor_DCD_T3_33


title: Kidney_donor_BD_T3_56


title: Kidney_donor_BD_T1_66


title: Kidney_donor_DCD_T2_35


title: Kidney_donor_BD_T2_66


title: Kidney_donor_DCD_T1_30


title: Kidney_donor_BD_T2_63


title: Kidney_donor_BD_T3_58


title: Kidney_donor_DCD_T3_35


title: Kidney_donor_BD_T2_61


title: Kidney_donor_Living_T3_22


title: Kidney_donor_DCD_T2_34


title: Kidney_donor_BD_T2_62


title: Kidney_donor_BD_T3_54


title: Kidney_donor_DCD_T2_33


title: Kidney_donor_DCD_T3_31


title: Kidney_donor_BD_T3_55


title: Kidney_donor_BD_T2_57


title: Kidney_donor_Living_T1_24


title: Kidney_donor_BD_T2_60


title: Kidney_donor_BD_T1_62


title: Kidney_donor_BD_T2_58


title: Kidney_donor_BD_T1_64


title: Kidney_donor_DCD_T3_32


title: Kidney_donor_DCD_T1_29


title: Kidney_donor_BD_T3_53


title: Kidney_donor_BD_T3_51


title: Kidney_donor_BD_T2_59


title: Kidney_donor_BD_T2_56


title: Kidney_donor_BD_T1_61


title: Kidney_donor_BD_T1_65


title: Kidney_donor_BD_T2_55


title: Kidney_donor_Living_T1_23


title: Kidney_donor_BD_T1_63


title: Kidney_donor_BD_T1_60


title: Kidney_donor_DCD_T2_32


title: Kidney_donor_BD_T3_50


title: Kidney_donor_BD_T3_52


title: Kidney_donor_DCD_T2_31


title: Kidney_donor_DCD_T1_28


title: Kidney_donor_BD_T1_59


title: Kidney_donor_Living_T1_21


title: Kidney_donor_BD_T1_58


title: Kidney_donor_Living_T3_21


title: Kidney_donor_DCD_T3_30


title: Kidney_donor_Living_T1_22


title: Kidney_donor_Living_T3_20


title: Kidney_donor_DCD_T2_30


title: Kidney_donor_BD_T3_48


title: Kidney_donor_BD_T1_56


title: Kidney_donor_DCD_T2_29


title: Kidney_donor_BD_T3_49


title: Kidney_donor_BD_T2_54


title: Kidney_donor_DCD_T1_25


title: Kidney_donor_BD_T2_52


title: Kidney_donor_BD_T2_51


title: Kidney_donor_DCD_T2_27


title: Kidney_donor_DCD_T3_29


title: Kidney_donor_DCD_T1_27


title: Kidney_donor_BD_T2_50


title: Kidney_donor_DCD_T2_28


title: Kidney_donor_BD_T3_47


title: Kidney_donor_DCD_T3_28


title: Kidney_donor_BD_T2_53


title: Kidney_donor_BD_T1_57


title: Kidney_donor_DCD_T1_26


title: Kidney_donor_BD_T3_45


title: Kidney_donor_BD_T3_57


title: Kidney_donor_BD_T1_55


title: Kidney_donor_BD_T2_49


title: Kidney_donor_BD_T3_46


title: Kidney_donor_DCD_T3_27


title: Kidney_donor_BD_T1_54


title: Kidney_donor_BD_T2_48


title: Kidney_donor_DCD_T2_26


title: Kidney_donor_BD_T1_53


title: Kidney_donor_Living_T1_20


title: Kidney_donor_DCD_T2_24


title: Kidney_donor_BD_T2_46


title: Kidney_donor_DCD_T2_25


title: Kidney_donor_Living_T3_19


title: Kidney_donor_Living_T1_18


title: Kidney_donor_BD_T3_42


title: Kidney_donor_Living_T1_19


title: Kidney_donor_Living_T1_17


title: Kidney_donor_DCD_T3_26


title: Kidney_donor_BD_T1_52


title: Kidney_donor_DCD_T1_24


title: Kidney_donor_DCD_T1_23


title: Kidney_donor_Living_T3_17


title: Kidney_donor_BD_T2_45


title: Kidney_donor_BD_T3_44


title: Kidney_donor_BD_T3_43


title: Kidney_donor_Living_T3_18


title: Kidney_donor_BD_T2_47


title: Kidney_donor_DCD_T2_23


title: Kidney_donor_BD_T1_51


title: Kidney_donor_BD_T3_40


title: Kidney_donor_DCD_T3_25


title: Kidney_donor_Living_T3_16


title: Kidney_donor_BD_T3_39


title: Kidney_donor_BD_T2_43


title: Kidney_donor_BD_T2_44


title: Kidney_donor_BD_T1_49


title: Kidney_donor_BD_T2_42


title: Kidney_donor_BD_T1_47


title: Kidney_donor_DCD_T1_21


title: Kidney_donor_BD_T3_38


title: Kidney_donor_BD_T2_41


title: Kidney_donor_BD_T1_48


title: Kidney_donor_DCD_T2_22


title: Kidney_donor_BD_T1_45


title: Kidney_donor_DCD_T1_22


title: Kidney_donor_BD_T3_36


title: Kidney_donor_BD_T1_46


title: Kidney_donor_DCD_T3_22


title: Kidney_donor_BD_T1_43


title: Kidney_donor_BD_T3_37


title: Kidney_donor_Living_T3_14


title: Kidney_donor_Living_T3_13


title: Kidney_donor_Living_T3_15


title: Kidney_donor_DCD_T3_24


title: Kidney_donor_BD_T1_42


title: Kidney_donor_BD_T3_35


title: Kidney_donor_BD_T1_44


title: Kidney_donor_DCD_T3_23


title: Kidney_donor_BD_T2_39


title: Kidney_donor_DCD_T1_20


title: Kidney_donor_BD_T3_33


title: Kidney_donor_BD_T1_40


title: Kidney_donor_BD_T2_38


title: Kidney_donor_BD_T3_28


title: Kidney_donor_BD_T1_38


title: Kidney_donor_BD_T3_41


title: Kidney_donor_BD_T3_34


title: Kidney_donor_Living_T3_12


title: Kidney_donor_BD_T3_32


title: Kidney_donor_BD_T1_41


title: Kidney_donor_BD_T1_39


title: Kidney_donor_DCD_T1_19


title: Kidney_donor_Living_T3_11


title: Kidney_donor_DCD_T1_18


title: Kidney_donor_DCD_T3_20


title: Kidney_donor_BD_T2_37


title: Kidney_donor_BD_T1_37


title: Kidney_donor_DCD_T3_21


title: Kidney_donor_BD_T1_36


title: Kidney_donor_Living_T1_16


title: Kidney_donor_BD_T3_31


title: Kidney_donor_BD_T3_30


title: Kidney_donor_DCD_T1_17


title: Kidney_donor_BD_T3_29


title: Kidney_donor_DCD_T2_21


title: Kidney_donor_DCD_T3_19


title: Kidney_donor_DCD_T3_18


title: Kidney_donor_BD_T2_36


title: Kidney_donor_Living_T1_15


title: Kidney_donor_BD_T1_35


title: Kidney_donor_BD_T1_34


title: Kidney_donor_BD_T2_32


title: Kidney_donor_DCD_T2_18


title: Kidney_donor_DCD_T3_14


title: Kidney_donor_DCD_T3_15


title: Kidney_donor_BD_T2_34


title: Kidney_donor_Living_T1_14


title: Kidney_donor_DCD_T1_16


title: Kidney_donor_BD_T3_25


title: Kidney_donor_DCD_T3_17


title: Kidney_donor_Living_T1_13


title: Kidney_donor_BD_T3_26


title: Kidney_donor_BD_T2_33


title: Kidney_donor_DCD_T3_13


title: Kidney_donor_BD_T3_24


title: Kidney_donor_BD_T1_33


title: Kidney_donor_BD_T2_31


title: Kidney_donor_BD_T2_40


title: Kidney_donor_BD_T2_35


title: Kidney_donor_DCD_T3_16


title: Kidney_donor_Living_T1_12


title: Kidney_donor_DCD_T2_19


title: Kidney_donor_BD_T3_27


title: Kidney_donor_BD_T1_50


title: Kidney_donor_Living_T3_10


title: Kidney_donor_DCD_T1_15


title: Kidney_donor_DCD_T1_14


title: Kidney_donor_BD_T2_30


title: Kidney_donor_Living_T1_11


title: RA Id-415_Nor

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned on a G4900DA scanner (Agilent Technologies)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 11.5)

data_processing: Data extraction from Images was done using Feature Extraction software  and Percentile shift Normalization of the data was done in GeneSpring GX

source_name: Human cadaver eyeball, Categorized in to Normal

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization

extract_protocol: RNA was prepared using Qiagen RNeasy mini kit following the manufacturer's recommendations.The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).  The integrity of the extracted RNA were analysed on the Bioanalyzer (Agilent; 2100). We considered RNA to be of good quality based on the 260/280 values (Nanodrop), rRNA 28S/18S ratios and RNA integrity number (RIN-Bioanalyzer).

treatment_protocol: The Human cadaver eyes were obtained from the Rotary Aravind International Eye Bank, Aravind Eye Hospital, Madurai  from Age Matched Normal, Diabetic and   Diabetic Retinopathy  cadaver eye balls. The time elapsed from death to eye enucleation was 3.0 - 1.9 h.  After enucleation, eye of each donor were maintained in a moist chamber at 4°C until processing for evaluation of ocular pathology as previously outlined.  The eyes was brought to the laboratory within 24 to 48 hours from the time of donor’s death. Once received in the laboratory, tissues were handled under RNAse – free conditions. After enucleation, neural retina were harvested and immersed in RNA later (Qiagen) and frozen at -80°C until they were assayed for downstream process.

tag: phenotype

value: Normal

value: Neural Retina

tag: clinical history

value: Age matched control with no medical history of diabetes  & no evidence of retinal pathology


title: RA Id-383_Nor


title: Kidney_donor_BD_T1_32


title: RA Id-382_Nor


title: Kidney_donor_DCD_T2_20


title: Kidney_donor_DCD_T2_16


title: Kidney_donor_BD_T1_29


title: Kidney_donor_Living_T1_10


title: Kidney_donor_BD_T3_23


title: Kidney_donor_BD_T1_31


title: Kidney_donor_BD_T1_30


title: Kidney_donor_Living_T3_8


title: Kidney_donor_Living_T3_9


title: Kidney_donor_Living_T3_7


title: RA Id-380_Nor


title: RA Id-109_DM

source_name: Human cadaver eyeball, Categorized in to DM

value: Diabetic (DM)

value: Donor with a medical history of diabetes but no signs of diabetic retinopathy


title: Kidney_donor_BD_T2_25


title: Kidney_donor_BD_T2_29


title: Kidney_donor_BD_T2_27


title: Kidney_donor_DCD_T3_12


title: Kidney_donor_BD_T2_28


title: Kidney_donor_BD_T2_24


title: Kidney_donor_DCD_T2_15


title: Kidney_donor_BD_T2_26


title: Kidney_donor_BD_T2_23


title: Kidney_donor_DCD_T3_11


title: Kidney_donor_BD_T1_28


title: Kidney_donor_DCD_T1_13


title: RA Id-105_DM


title: Kidney_donor_DCD_T2_17


title: RA Id-101_DM


title: RA Id-382_Nor_Rep


title: Kidney_donor_BD_T1_27


title: Kidney_donor_DCD_T2_14


title: RA Id-99_DM_Rep


title: RA Id-273_DR_Rep

source_name: Human cadaver eyeball, Categorized in to DR

value: Diabetic (DR)

value: Donor with a medical history of diabetes with the hallmark clinical signs of diabetic retinopathy


title: RA Id-237_DR_Rep


title: RA Id-273_DR


title: RA Id-239_DR


title: RA Id-50_DR


title: Kidney_donor_Living_T3_6


title: RA Id-237_DR


title: Kidney_donor_DCD_T1_12


title: Kidney_donor_BD_T1_25


title: Kidney_donor_BD_T1_26


title: Kidney_donor_DCD_T1_11


title: Kidney_donor_BD_T3_22


title: Kidney_donor_BD_T3_21


title: Kidney_donor_Living_T1_9


title: Kidney_donor_DCD_T2_12


title: Kidney_donor_DCD_T2_13


title: Kidney_donor_BD_T2_22


title: Kidney_donor_BD_T1_24


title: Kidney_donor_Living_T3_4


title: Kidney_donor_BD_T3_20


title: Kidney_donor_Living_T3_5


title: Kidney_donor_BD_T1_23


title: Lung CD11bhi Ly6Chi inf.moDCs rep 2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Gene expression data from C57BL mouse lungs CD11bhi Ly6Chi DCs

hyb_protocol: 5 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 17.5 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1) using the MAS5 algorithm to generate .CHP files.

label: biotin

organism: Mus musculus

source_name: C57BL mouse lungs CD11bhi Ly6Chi DCs

label_protocol: Fifty (50) ng of total RNA was amplified as directed in the WT-Ovation Pico RNA Amplification System protocol, and labeling with biotin following the Encore Biotin Module.

growth_protocol: Eight to twelve weeks old C57BL/6 male mice were used. Twenty mice were used for each biological replicates.

extract_protocol: Total RNA was extracted from purified cells using QIAGEN Rneasy kit according to manufactore's instruction.

treatment_protocol: Mice were given 50ul PBS containing 100ng lipopolysaccharide and 100ug ovalbumin to airway. Sixteen hours later, lungs were removed, and dendritic cells were purified by flow cytometry (purity >93%).

value: male

value: lung

tag: strain

tag: cell population

value: CD11bhi Ly6Chi dendritic cells (DCs)


title: Lung CD11bhi CD14hi moDCs rep 3

description: Gene expression data from C57BL mouse lungs CD11bhi CD14hi DCs

source_name: C57BL mouse lungs CD11bhi CD14hi DCs

value: CD11bhi CD14hi dendritic cells (DCs)


title: Lung CD11bhi CD14lo cDCs rep 3

description: Gene expression data from C57BL mouse lungs CD11bhi CD14lo DCs

source_name: C57BL mouse lungs CD11bhi CD14lo DCs

value: CD11bhi CD14lo dendritic cells (DCs)


title: Lung CD11bhi CD14lo cDCs rep 1


title: Lung CD11bhi Ly6Chi inf.moDCs rep 3


title: Kidney_donor_BD_T3_19


title: Lung CD11bhi Ly6Chi inf.moDCs rep 1


title: Lung CD11bhi CD14lo cDCs rep 2


title: Kidney_donor_BD_T1_21


title: Lung CD11bhi CD14hi moDCs rep 2


title: Kidney_donor_BD_T1_22


title: Lung CD103+ cDCs rep 3

description: Gene expression data from C57BL mouse lungs CD103+ DCs

source_name: C57BL mouse lungs CD103+ DCs

value: CD103+ dendritic cells (DCs)


title: Lung CD11bhi CD14hi moDCs rep 1


title: RA Id-99_DM

value: M


title: Kidney_donor_BD_T1_20


title: Kidney_donor_BD_T2_20


title: Multi-walled carbon nanotubes (Mitsui-7) 2 48h biological rep2

city: Solna

first: Penny

last: Nymark

state: Stockholm

address: Nobels väg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Sample preparation, hybridisation, washing, staining and scanning of Affymetrix Human GeneChip HT HG-U133 Plus 24-Array Plates were conducted according to the manufacturers’ standard manuals (Affymetrix GeneChip 3’ IVT Express Kit User Manual, the GeneTitan Manual)

data_processing: Quality control and RMA normalization was performed using the ArrayAnalysis.org (www.arrayanalysis.org) web service

extract_protocol: Total RNA was extracted using 0.5 ml TRIZOL (Life Technologies, Carlsbad, CA, USA) according to the manufacturer’s instructions and purified using miRNeasy® Mini Kits (kit 217004, Qiagen, miRNeasy Mini Handbook).

treatment_protocol: Material dispersions were prepared in glass tubes as stock dispersions of 1 mg/ml in cell growth medium (BEGM, Clonetics, Walkerwille, MD, USA) with 0.6 mg/ml of bovine serum albumin (BSA; Sigma-Aldrich, Steinheim, Germany) and sonicated for 20 min at 37 °C in a bath sonicator (Branson 2200, 40 kHz). The freshly prepared and sonicated stock dispersions were further serially diluted to obtain the final dispersions of 0.25, 2 and 10 μg/cm2 (corresponding to 2, 16 and 80 μg/ml), sonicated again and directly applied onto the cells.

tag: cell type

value: epithelial

tag: cell line passage

tag: treatment


title: Multi-walled carbon nanotubes (Mitsui-7) 2 48h biological rep3

scan_protocol: Sample preparation, hybridisation, washing, staining and scanning of Affymetrix Human GeneChip HT HG-U133 Plus 24-Array Plates were conducted according to the manufacturers’ standard manuals (Affymetrix GeneChip 3’ IVT Express Kit User Manual, the GeneTitan Manual)


title: Kidney_donor_DCD_T1_10


title: Kidney_donor_BD_T3_18


title: Multi-walled carbon nanotubes (Mitsui-7) 025 48h biological rep2

label_protocol: Sample preparation, hybridisation, washing, staining and scanning of Affymetrix Human GeneChip HT HG-U133 Plus 24-Array Plates were conducted according to the manufacturers’ standard manuals (Affymetrix GeneChip 3’ IVT Express Kit User Manual, the GeneTitan Manual)


title: Glass wool (MMVF10) 2 48h biological rep3

value: Glass wool (MMVF10) 2 48h


title: Multi-walled carbon nanotubes (Mitsui-7) 025 48h biological rep3


title: Kidney_donor_BD_T3_17

value: kidney biopsy


title: Kidney_donor_DCD_T2_11


title: WT vs. Skp2-null

city: Houston

first: JING

last: WANG

state: TX

address: 1515 Holcombe BLVD

department: Molecular and Cellular Oncology

institute: The University of Texas, MD Anderson Cancer Center

description: Pooled BM cells from 3 mice together

hyb_protocol: 17h hyb @ 65C as protocol 5.0.1  17h hyb @ 65C as protocol 5.0.1

scan_protocol: Agilent G2505B scanner  Agilent G2505B scanner

data_processing: Agilent Feature Extraction 9.5.3.1 was used to collect feature intensity

source_name: wild type mouse HSC

label_protocol: 1 microgram total RNA as described in Agilent two-color microarray protocol 5.0.1. Sent the RNA sample to the core facility for microarray analysis

growth_protocol: BM cell were collected from WT and Skp2-null, three from each group.

extract_protocol: Total RNA was extracted with kit from Ambion according to the instruction.

tag: age

value: 8 to 12 weeks old

source_name: Skp2-null mouse HSC


title: Glass wool (MMVF10) 2 48h biological rep2

tag: tissue


title: Kidney_donor_BD_T3_16

tag: donor type (0=living, 1=bd, 2=nhb)


title: Lung CD103+ cDCs rep 1

tag: gender


title: Glass wool (MMVF10) 025 48h biological rep2

value: Glass wool (MMVF10) 025 48h


title: Kidney_donor_BD_T2_19

tag: timepoint biopsy

tag: deceased paired biopsies


title: Lung CD103+ cDCs rep 2


title: Kidney_donor_DCD_T3_10

tag: delayed graft function (0=no, 1=yes)


title: Kidney_donor_Living_T1_8

tag: deceased donors, only left kidney included in the analysis


title: Glass wool (MMVF10) 2 48h biological rep1


title: Glass wool (MMVF10) 025 48h biological rep1


title: Kidney_donor_BD_T1_18

tag: deceased left and right biopsies same donor (0=left, 1=right)


title: Control (Cy3) x Lavender Oil Blood (Cy5)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description: Rat Lavender Oil (LO) Blood

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

organism: Rattus norvegicus

source_name: Blood Cont Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: F334 rats were purchased from Japan SCL (Hamamatsu, Japan). Twelve male rats (7 weeks old; ~142.8 to 167.5g body weight) were housed at the Animal Institution in Showa University. Thay were maintained in individual cages in isolated animal rooms with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights were turned on at 8:00 AM) and had access to laboratory chow and tap water ad libitum. All animal experiments were started after period of acclimation of at least one week. And all animal care and experimental procedures were approved by the Institutional Animal Care and Use Committee of Showa University.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Lavender oil (LO; Lavandula angustifolia, Biofloral, France) was administered to rats (n=6 per each group) directly into the stomach at a dose of 0 (10% ethanol; diluent: control group), 5 mg/kg (in 10% ethanol : LO administrated group), once a day in the afternoon (11:25-13:50) for 13 days. Fourteen days after treatment, the rats were dissected under the ether anesthesia. The venous blood was taken from the heart and portal vein, and immediately transferred to a sterile tube and immersed in liquid nitrogen and stored at -80 degrees C in a deep freezer.

value: Wistar

source_name: Blood LO Cy5


title: Glass wool (MMVF10) 025 48h biological rep3


title: Kidney_donor_BD_T1_19


title: Kidney_donor_BD_T3_15


title: Control (Cy5) x Lavender Oil Blood (Cy3)

description: Rat Lavender Oil (LO) Blood

source_name: Blood LO Cy3

source_name: Blood Cont Cy5


title: Control 48h biological rep2

value: Control 48h


title: Control 48h biological rep3


title: Control 48h biological rep1


title: Kidney_donor_BD_T1_17


title: Kidney_donor_BD_T2_18

tag: deceased unpaired biopsies


title: Kidney_donor_BD_T1_16


title: Crocidolite asbestos 2 48h biological rep1

value: Crocidolite asbestos 2 48h


title: Kidney_donor_BD_T2_21


title: Kidney_donor_BD_T2_17


title: Crocidolite asbestos 2 48h biological rep2


title: Kidney_donor_Living_T3_3

tag: living paired biopsies


title: Crocidolite asbestos 2 48h biological rep3


title: Kidney_donor_BD_T1_15


title: Kidney_donor_BD_T3_14


title: Kidney_donor_DCD_T2_10


title: Kidney_donor_Living_T1_7


title: Multi-walled carbon nanotubes (Mitsui-7) 2 24h biological rep3


title: Crocidolite asbestos 025 48h biological rep2

value: Crocidolite asbestos 025 48h


title: Kidney_donor_DCD_T1_9


title: Kidney_donor_BD_T2_16


title: Kidney_donor_BD_T1_14


title: Kidney_donor_Living_T3_2


title: Kidney_donor_DCD_T2_9


title: Kidney_donor_DCD_T3_9


title: ARF6-T157A D19_1

city: Los Angeles

first: Minhyung

last: Kim

state: CA

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: SinRep5/ARF6-T157A-6xHis virus expression in matured neurons.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028279 SurePrint G3 Rat GE Microarray 8x60K for 17 hours at 65°C in a rotating SureHyb chamber. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028279_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: primary cultured hippocampal neurons from E18 fetal rats, matured, ARF6

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Hippocampi were dissected from embryonic day 18 Spraque-Dawley fetal rats, dissociated with papain, and triturated with a polished half-pore Pasteur pipette. Cells (2.5 x 10^5) in minimum Eagle’s medium supplemented with 0.6% glucose, 1 mM pyruvate, 2 mM L-glutamine, 10% fetal bovine serum, and antibiotics were plated on poly-D-lysine coated glass coverslips in a 60 mm Petri dish. Four hours after plating, the medium was replaced with Neurobasal (Invitrogen) supplemented with 2% B-27 and 0.5 mM L-glutamine.

extract_protocol: Samples were lysed and RNA isolation was carried out using the RNA-spin total RNA extraction kit (iNtRON Biotechnology, Sungnam, Kyungki-Do, South Korea) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: To generate the Sindbis viral vectors, the vector plasmids were first transcribed in vitro to generate Sindbis viral vector RNA. The RNA would then be transfected into BHK21 cells, where it would be translated, replicated, and packaged into viral particles, which would be used to infect rat primary cultured hippocampal neurons. Plasmids for the in vitro transcription of Sindbis viral RNAs (SinRep5, SinRep5/ARF6-T157A-6xHis, and DH26S) were prepared with the Promega midiprep kit. The helper DNA template DH26S and a replicon plasmid (SinRep5 or SinRep5/ARF6-T157A-6xHis) were digested with XhoI to linearize the templates. Digested plasmids were purified by phenol-chloroform extraction and ethanol precipitation. In vitro transcription reactions were carried out using the mMESSAGE mMACHINETM high-yield capped RNA transcription kit (SP6 version; Ambion, Inc., Austin, TX) to produce capped mRNA transcripts. The quality of the transcribed RNA was checked on 1% agarose gels. Both DH26S and SinRep5 or SinRep5/ARF6-T157A-6xHis were electroporated into BHK21 cells. Twenty four hours after electroporation, culture supernatants were collected and aliquots (1mL) were stored at -80°C. Cultured hippocampal neurons were infected with recombinant sindbisviruses at 10 DIV (days in vitro) for developing stage and 17 DIV for mature stage, and maintained for additional 48 h. Then, infected neurons were washed twice with PBS and were frozen at -70C for storage.

tag: strain/background

value: Spraque-Dawley

value: matured neurons

tag: infection

value: SinRep5/ARF6-T157A-6xHis virus

tag: total days in vitro


title: Crocidolite asbestos 025 48h biological rep3

value: lung

tag: cell type


title: Multi-walled carbon nanotubes (Mitsui-7) 2 24h biological rep2

tag: cell line passage


title: ARF6-T157A D19_2


title: Control D19_2

description: Control SinRep5 virus expression in matured neurons.

source_name: primary cultured hippocampal neurons from E18 fetal rats, matured, control

value: control SinRep5 virus


title: Kidney_donor_DCD_T3_8


title: Control D19_1


title: ARF6-T157A D12_2

description: SinRep5/ARF6-T157A-6xHis virus expression in developing neurons.

source_name: primary cultured hippocampal neurons from E18 fetal rats, developing, ARF6

value: developing neurons


title: Kidney_donor_BD_T2_15


title: Multi-walled carbon nanotubes (Mitsui-7) 2 48h biological repl3

hyb_protocol: Sample preparation, hybridisation, washing, staining and scanning of Agilent Human miRNA Microarrays (8x60K) were conducted according to the manufacturers’ standard manuals (the Agilent miRNA Microarray System Manual)

data_processing: Foreground and background intensity, spot saturation, spot mean-median ratio and level above background was evaluated using an in-house developed pipeline in R. Pre-processing of the miRNA data was performed by the R/Bioconductor package AgiMicroRNA. Total Gene Signals were quantile-normalized, log2 transformed and filtered on isGeneDetected flag according to the script.

tag: treatment


title: Kidney_donor_BD_T1_12


title: Kidney_donor_DCD_T1_8


title: Multi-walled carbon nanotubes (Mitsui-7) 025 12h biological repl1

scan_protocol: Sample preparation, hybridisation, washing, staining and scanning of Agilent Human miRNA Microarrays (8x60K) were conducted according to the manufacturers’ standard manuals (the Agilent miRNA Microarray System Manual)


title: Kidney_donor_BD_T1_13


title: Kidney_donor_BD_T3_13


title: Kidney_donor_DCD_T2_8


title: Kidney_donor_DCD_T3_7


title: ARF6-T157A D12_1


title: Crocidolite asbestos 2 12h biological repl3

label_protocol: Sample preparation, hybridisation, washing, staining and scanning of Agilent Human miRNA Microarrays (8x60K) were conducted according to the manufacturers’ standard manuals (the Agilent miRNA Microarray System Manual)

value: Crocidolite asbestos 2 12h


title: Control 24h biological repl3

value: Control 24h


title: Kidney_donor_BD_T3_12


title: Control D12_1

description: Control SinRep5 virus expression in developing neurons.

source_name: primary cultured hippocampal neurons from E18 fetal rats, developing, control


title: Kidney_donor_BD_T2_13


title: Control D12_2


title: Kidney_donor_BD_T3_10


title: Crocidolite asbestos 2 24h biological repl2

value: epithelial

value: Crocidolite asbestos 2 24h


title: Kidney_donor_BD_T1_10

value: kidney biopsy


title: Kidney_donor_BD_T2_14


title: Kidney_donor_DCD_T1_7


title: Kidney_donor_BD_T1_11


title: Kidney_donor_BD_T3_11


title: Kidney_donor_BD_T2_12


title: Multi-walled carbon nanotubes (Mitsui-7) 025 24h biological repl2


title: Glass wool (MMVF10) 025 24h biological repl2

value: Glass wool (MMVF10) 025 24h


title: Glass wool (MMVF10) 2 24h biological repl2

value: Glass wool (MMVF10) 2 24h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 24h biological repl2


title: Kidney_donor_DCD_T3_6


title: Kidney_donor_Living_T1_6


title: Kidney_donor_BD_T3_9


title: Kidney_donor_BD_T2_10


title: Control 24h biological repl2


title: Control 12h biological repl2

value: Control 12h


title: Kidney_donor_BD_T2_11


title: Multi-walled carbon nanotubes (Mitsui-7) 2 24h biological repl3


title: Kidney_donor_DCD_T3_5


title: Kidney_donor_BD_T1_8


title: Kidney_donor_BD_T2_9


title: Kidney_donor_DCD_T2_7


title: Kidney_donor_BD_T2_8


title: Kidney_donor_BD_T1_9


title: Kidney_donor_BD_T2_7


title: Kidney_donor_DCD_T3_4


title: Kidney_donor_DCD_T2_5


title: Kidney_donor_BD_T3_7


title: Kidney_donor_BD_T1_7


title: Kidney_donor_BD_T3_6


title: Kidney_donor_BD_T2_6


title: Crocidolite asbestos 2 12h biological repl2


title: Kidney_donor_BD_T3_8


title: Crocidolite asbestos 025 12h biological repl2

value: Crocidolite asbestos 025 12h


title: Glass wool (MMVF10) 2 12h biological repl2

value: Glass wool (MMVF10) 2 12h


title: Multi-walled carbon nanotubes (Mitsui-7) 025 12h biological repl2


title: Glass wool (MMVF10) 025 24h biological repl3


title: Kidney_donor_Living_T3_1


title: Kidney_donor_BD_T2_5


title: Control 12h biological repl3


title: Kidney_donor_BD_T1_6


title: Kidney_donor_DCD_T1_5


title: Glass wool (MMVF10) 025 12h biological repl2

value: Glass wool (MMVF10) 025 12h


title: Kidney_donor_DCD_T1_6


title: Kidney_donor_BD_T2_4


title: Kidney_donor_Living_T1_5


title: Kidney_donor_BD_T3_5


title: Kidney_donor_BD_T1_5


title: Kidney_donor_DCD_T1_4


title: Kidney_donor_BD_T3_4


title: Glass wool (MMVF10) 2 6h biological repl3

value: Glass wool (MMVF10) 2 6h


title: Control 6h biological repl3

value: Control 6h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 12h biological repl2


title: Kidney_donor_DCD_T1_3


title: Kidney_donor_BD_T1_4


title: Kidney_donor_BD_T1_3


title: Glass wool (MMVF10) 025 6h biological repl3

value: Glass wool (MMVF10) 025 6h


title: Kidney_donor_DCD_T2_3


title: Kidney_donor_DCD_T3_2


title: Crocidolite asbestos 2 6h biological repl3

value: lung

value: Crocidolite asbestos 2 6h


title: Kidney_donor_Living_T1_4


title: Kidney_donor_DCD_T3_3


title: Multi-walled carbon nanotubes (Mitsui-7) 2 6h biological repl3


title: Crocidolite asbestos 2 24h biological repl3


title: Kidney_donor_DCD_T1_2


title: Kidney_donor_DCD_T2_4


title: Kidney_donor_DCD_T1_1


title: Kidney_donor_DCD_T2_2


title: Kidney_donor_Living_T1_3


title: Multi-walled carbon nanotubes (Mitsui-7) 2 12h biological repl3


title: Kidney_donor_BD_T3_3


title: Kidney_donor_BD_T2_3


title: Crocidolite asbestos 025 24h biological repl2

value: Crocidolite asbestos 025 24h


title: Kidney_donor_DCD_T2_1


title: Kidney_donor_BD_T2_1


title: Kidney_donor_BD_T1_2


title: Glass wool (MMVF10) 2 24h biological repl3


title: Kidney_donor_BD_T2_2


title: Crocidolite asbestos 025 6h biological repl3

value: Crocidolite asbestos 025 6h


title: Kidney_donor_Living_T1_2


title: Kidney_donor_BD_T3_2


title: Kidney_donor_BD_T3_1


title: Kidney_donor_Living_T1_1


title: Glass wool (MMVF10) 2 4h biological repl2

value: Glass wool (MMVF10) 2 4h


title: Control 4h biological repl2

value: epithelial

value: Control 4h


title: Kidney_donor_DCD_T3_1

value: kidney biopsy


title: Crocidolite asbestos 2 1h biological repl2

value: Crocidolite asbestos 2 1h


title: Crocidolite asbestos 2 4h biological repl1

value: Crocidolite asbestos 2 4h


title: Crocidolite asbestos 025 4h biological repl1

value: Crocidolite asbestos 025 4h


title: Glass wool (MMVF10) 025 6h biological repl1


title: Glass wool (MMVF10) 025 12h biological repl3


title: Control 6h biological repl1


title: shH1X_Dox_rep1

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: H1X knock down, T47D-MTVL breast cancer cell line transfected with doxicyclin inducible anti histone H1 shRNA expression vector treated with doxicyclin, replicate 1 of 2

hyb_protocol: Hybridization mix was laid onto each sector of subarray gasket slide and sandwiched against a 8 x 65K format oligonucleotide microarray (Human v1 Sureprint G3 Human GE 8x60k Microarray, Agilent design ID 028004) inside a hybridization chamber which wqs hybridized overnight at 65ºC in a rotisserie oven rotating at 10 rpm for a total of 17 hours. Subsequently array chambers were disassembled submerged in Agilent Gene Expression Buffer 1 and washed 1 minute in another dish with the same solution with a magnetic stirrer at 200 rpm at room temperature, followed by 1 minute in gilent Gene Expression Buffer 2 with a magnetic stirrer at 200 rpm at 37ºC and immediate withdrawal from the solution and air drying.

scan_protocol: Fluorescent signal was captured into TIF images with an Agilent scanner using recommended settings (20 bit, 5 um resolution, 100% PMT and 100% laser power) with Scan Control software (Agilent).

data_processing: Signal intensities were extracted into a tabulated text file using Feature Extraction software (Agilent) using the appropriate array configuration and annotation files. The normalized log2intensities were obtained using quantile method with normexp background correction the Bioconductor Limma package in R.

source_name: breast cancer cell T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter)

label_protocol: For each sample 100 ng of total RNA mixed with 2 ul of 1:10000 Agilent One Color Spike Mix were reversed transcribed into cDNA with a T7 promoter and the cDNA was in vitro transcribed into cRNA in the presence of Cy3-CTP using the Low input quick Amp kit (Agilent). Labelled samples were purified using RNeasy mini spin columns (Qagen) and yield and specific activity wwere assessed by spectrophotometry (Nanodrop) and confirmed to be within specifications (>825 ng and >6 pmol Cy3/ug cRNA). 600 ng of cRNA were preblocked and fragmented in Agilent fragmentation buffer and mixed with  Agilent GEx Hybridization mix.

growth_protocol: Cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol: Total RNA was extracted using High Pure RNA isolation kit (Roche) according to the manufacturer's instructions. cDNA was obtained from 100 ng of total RNA using SuperScript VILO cDNA synthesis (Invitrogen). High RNA integrity was assessed by Bioanalyzer nano 6000 assay with RIN numbers 9.5

treatment_protocol: Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated. Along a 6-day treatment with Dox, cells were passaged at day 3. Serum-containing media was replaced with serum-free media at day 4 for growth arrest.

tag: cell line

value: female

value: breast cancer ductal carcinoma

tag: dox treatment

value: Treated

tag: depletion/expression

value: Histone H1X depletion

tag: expression

value: Histone H1X shRNA vector


title: Crocidolite asbestos 2 6h biological repl1

tag: tissue


title: shH1X_Dox_rep2

description: H1X knock down, T47D-MTVL breast cancer cell line transfected with doxicyclin inducible anti histone H1X shRNA expression vector treated with doxicyclin, replicate 2 of 2

tag: gender


title: Crocidolite asbestos 025 6h biological repl1


title: shH1X_rep1

description: background control for transfection, negative control for induction, T47D-MTVL breast cancer cell line transfected with doxicyclin inducible Histone H1 shRNA expression vector without doxicyclin treatment, replicate 1 of 2

value: Untreated

value: no depletion


title: shH1X_rep2

description: background control for transfection, negative control for induction, T47D-MTVL breast cancer cell line transfected with doxicyclin inducible Histone H1 shRNA expression vector without doxicyclin treatment, replicate 2 of 2


title: Glass wool (MMVF10) 2 6h biological repl1

value: lung

value: Glass wool (MMVF10) 2 6h


title: Kidney_donor_BD_T1_1

tag: donor type (0=living, 1=bd, 2=nhb)

tag: timepoint biopsy

tag: delayed graft function (0=no, 1=yes)


title: Multi-walled carbon nanotubes (Mitsui-7) 2 6h biological repl1


title: Ctrl_Dox

description: negative control for transfection and background control for induction, T47D-MTVL breast cancer cell line transfected with doxicyclin inducible scrambled shRNA expression vector treated with doxicyclin, single experiment (replicate 1 of 1)

value: Random shRNA vector


title: Ctrl_rep2

description: negative control for transfection, T47D-MTVL breast cancer cell line transfected with doxicyclin inducible scrambled shRNA expression vector without doxicyclin treatment, replicate 2 of 2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 6h biological repl1


title: Crocidolite asbestos 025 48h biological repl3

value: Crocidolite asbestos 025 48h


title: Glass wool (MMVF10) 025 48h biological repl3

value: epithelial

value: Glass wool (MMVF10) 025 48h


title: Control 4h biological repl3

value: Control 4h


title: Crocidolite asbestos 2 48h biological repl3

value: Crocidolite asbestos 2 48h


title: Control 48h biological repl1

value: Control 48h


title: Glass wool (MMVF10) 2 48h biological repl1

value: Glass wool (MMVF10) 2 48h


title: Control 48h biological repl2


title: Ctrl_rep1

description: negative control for transfection, T47D-MTVL breast cancer cell line transfected with doxicyclin inducible scrambled shRNA expression vector without doxicyclin treatment, replicate 1 of 2

value: female


title: Glass wool (MMVF10) 025 48h biological repl2


title: Glass wool (MMVF10) 2 48h biological repl2


title: Crocidolite asbestos 2 48h biological repl2


title: Multi-walled carbon nanotubes (Mitsui-7) 2 48h biological repl2


title: Crocidolite asbestos 025 48h biological repl2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 48h biological repl2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 4h biological repl3


title: Glass wool (MMVF10) 2 1h biological repl3

value: Glass wool (MMVF10) 2 1h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 4h biological repl3


title: Crocidolite asbestos 2 4h biological repl3

value: Crocidolite asbestos 2 4h


title: Crocidolite asbestos 025 4h biological repl3

value: Crocidolite asbestos 025 4h


title: Glass wool (MMVF10) 025 4h biological repl3

value: Glass wool (MMVF10) 025 4h


title: Glass wool (MMVF10) 2 4h biological repl3

value: Glass wool (MMVF10) 2 4h


title: Crocidolite asbestos 025 24h biological repl3

value: Crocidolite asbestos 025 24h


title: Multi-walled carbon nanotubes (Mitsui-7) 025 48h biological repl3

value: lung


title: Glass wool (MMVF10) 2 48h biological repl3


title: Glass wool (MMVF10) 025 24h biological rep2

value: Glass wool (MMVF10) 025 24h


title: Crocidolite asbestos 2 48h biological repl1


title: Glass wool (MMVF10) 025 48h biological repl1


title: Control 48h biological repl3


title: Crocidolite asbestos 2 24h biological rep3

value: Crocidolite asbestos 2 24h


title: Multi-walled carbon nanotubes (Mitsui-7) 025 24h biological rep3


title: Kidney_donor_DCD_T2_6

value: kidney biopsy

tag: deceased paired biopsies


title: Control 24h biological rep1

value: epithelial

value: Control 24h


title: Glass wool (MMVF10) 2 24h biological rep2

value: Glass wool (MMVF10) 2 24h


title: Control 24h biological rep2


title: Glass wool (MMVF10) 025 24h biological rep3


title: Glass wool (MMVF10) 025 4h biological repl2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 24h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 24h biological rep1


title: Glass wool (MMVF10) 025 24h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 2 24h biological rep1


title: Glass wool (MMVF10) 2 24h biological rep3


title: Crocidolite asbestos 2 4h biological repl2


title: Crocidolite asbestos 025 4h biological repl2


title: Control 24h biological rep3


title: Crocidolite asbestos 2 24h biological rep2


title: Crocidolite asbestos 025 24h biological rep3


title: Multi-walled carbon nanotubes (Mitsui-7) 025 4h biological repl2


title: Control 4h biological repl1

value: Control 4h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 4h biological repl2


title: Glass wool (MMVF10) 025 4h biological repl1


title: Glass wool (MMVF10) 2 4h biological repl1


title: Crocidolite asbestos 025 24h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 6h biological repl3


title: Control 1h biological repl3

value: Control 1h


title: Glass wool (MMVF10) 2 24h biological rep1


title: Crocidolite asbestos 025 24h biological rep1


title: Glass wool (MMVF10) 025 1h biological repl3

value: Glass wool (MMVF10) 025 1h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 12h biological rep3


title: Crocidolite asbestos 2 24h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 12h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 12h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 12h biological rep3


title: Crocidolite asbestos 025 1h biological repl3

value: Crocidolite asbestos 025 1h


title: Crocidolite asbestos 2 1h biological repl3

value: Crocidolite asbestos 2 1h


title: Glass wool (MMVF10) 2 12h biological rep3

value: Glass wool (MMVF10) 2 12h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 12h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 1h biological repl3


title: Multi-walled carbon nanotubes (Mitsui-7) 025 4h biological repl1


title: Glass wool (MMVF10) 2 12h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 2 12h biological rep2


title: Glass wool (MMVF10) 2 1h biological repl2

value: Glass wool (MMVF10) 2 1h


title: Crocidolite asbestos 025 1h biological repl2


title: Glass wool (MMVF10) 2 12h biological rep1


title: Glass wool (MMVF10) 025 1h biological repl2


title: Control 1h biological repl2


title: Control 12h biological rep3

value: Control 12h


title: Control 12h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 2 1h biological repl3


title: Multi-walled carbon nanotubes (Mitsui-7) 025 1h biological repl2


title: Multi-walled carbon nanotubes (Mitsui-7) 2 4h biological repl1


title: Control 12h biological rep1


title: Glass wool (MMVF10) 025 12h biological rep2

value: Glass wool (MMVF10) 025 12h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 1h biological repl2


title: Glass wool (MMVF10) 025 12h biological rep3


title: Glass wool (MMVF10) 025 12h biological rep1


title: Control 1h biological repl1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 12h biological repl3


title: Crocidolite asbestos 2 12h biological rep2

value: Crocidolite asbestos 2 12h


title: Crocidolite asbestos 2 1h biological repl1

value: lung


title: Glass wool (MMVF10) 025 1h biological repl1


title: Crocidolite asbestos 025 12h biological rep3

value: Crocidolite asbestos 025 12h


title: Crocidolite asbestos 2 12h biological rep3


title: Crocidolite asbestos 025 12h biological rep2


title: Glass wool (MMVF10) 2 1h biological repl1


title: Multi-walled carbon nanotubes (Mitsui-7) 2 1h biological repl1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 1h biological repl1


title: Glass wool (MMVF10) 2 12h biological repl3


title: Multi-walled carbon nanotubes (Mitsui-7) 2 6h biological rep2


title: Crocidolite asbestos 2 12h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 2 6h biological rep3


title: Multi-walled carbon nanotubes (Mitsui-7) 025 6h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 6h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 2 6h biological rep1


title: Crocidolite asbestos 025 1h biological repl1


title: Glass wool (MMVF10) 025 6h biological repl2

value: Glass wool (MMVF10) 025 6h


title: Glass wool (MMVF10) 2 6h biological repl2

value: Glass wool (MMVF10) 2 6h


title: Control 6h biological repl2

value: epithelial

value: Control 6h


title: Crocidolite asbestos 2 6h biological repl2

value: Crocidolite asbestos 2 6h


title: Glass wool (MMVF10) 2 6h biological rep3


title: Multi-walled carbon nanotubes (Mitsui-7) 025 6h biological rep3


title: Crocidolite asbestos 025 6h biological repl2

value: Crocidolite asbestos 025 6h


title: Crocidolite asbestos 025 12h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 2 6h biological repl2


title: Glass wool (MMVF10) 2 6h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 6h biological repl2


title: Glass wool (MMVF10) 025 6h biological rep3


title: Epidermis_control_11

type: genomic

city: Umeå

first: Xiaolian

last: Gu

state: västerbotton

address: Building 6M, 2nd floor, Umeå University

department: Medical Biosciences

institute: Umeå University

description:
control
SAMPLE 46

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: iScan Reader was used to image BeadChips

data_processing: ChAMP pipeline (probe filtering, BMIQ normalization)

label: Cy3 and Cy5

molecule: genomic DNA

source_name: control epidermis 11

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from epidermis using PureLink® Genomic DNA Kits from Life Technologies

treatment_protocol: Skin biopsies were incubated in 3.8% ammonium thiocyanate at room temperature for 20 min for separation of epidermis from dermis

value: Male

value: CONTROL

value: control epidermis


title: Glass wool (MMVF10) 025 6h biological rep2


title: Glass wool (MMVF10) 025 6h biological rep1


title: Epidermis_control_12

description:
control
SAMPLE 47

source_name: control epidermis 12

value: Female


title: Glass wool (MMVF10) 2 6h biological rep1


title: Crocidolite asbestos 025 12h biological repl3


title: Epidermis_control_8

description:
control
SAMPLE 43

source_name: control epidermis 8


title: Epidermis_control_7

description:
control
SAMPLE 42

source_name: control epidermis 7


title: Control 6h biological rep3


title: Control 6h biological rep2


title: Epidermis_control_9

description:
control
SAMPLE 44

source_name: control epidermis 9


title: Control 24h biological repl1

value: Control 24h


title: Epidermis_control_10

description:
control
SAMPLE 45

source_name: control epidermis 10


title: Crocidolite asbestos 2 24h biological repl1

value: Crocidolite asbestos 2 24h


title: Glass wool (MMVF10) 2 24h biological repl1

value: Glass wool (MMVF10) 2 24h


title: Glass wool (MMVF10) 025 24h biological repl1

value: Glass wool (MMVF10) 025 24h


title: Crocidolite asbestos 2 6h biological rep2


title: Crocidolite asbestos 2 6h biological rep3


title: Crocidolite asbestos 025 24h biological repl1

value: Crocidolite asbestos 025 24h


title: Epidermis_control_6

description:
control
SAMPLE 41

source_name: control epidermis 6


title: Multi-walled carbon nanotubes (Mitsui-7) 2 24h biological repl1

value: lung


title: Control 6h biological rep1


title: Crocidolite asbestos 2 6h biological rep1


title: Epidermis_control_5

description:
control
SAMPLE 40

source_name: control epidermis 5


title: Crocidolite asbestos 025 6h biological rep2


title: Epidermis_psoriasis_POST-UV_10

description:
psoriasis
SAMPLE 33

source_name: psoriatic epidermis after phototherapy patient 10

value: POST-UV

value: psoriatic epidermis after phototherapy


title: Crocidolite asbestos 025 6h biological rep3


title: Multi-walled carbon nanotubes (Mitsui-7) 2 4h biological rep3


title: Epidermis_control_4

description:
control
SAMPLE 39

source_name: control epidermis 4


title: Epidermis_psoriasis_POST-UV_12

description:
psoriasis
SAMPLE 35

source_name: psoriatic epidermis after phototherapy patient 12


title: Crocidolite asbestos 025 6h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 2 4h biological rep2


title: Control 12h biological repl1

value: Control 12h


title: Epidermis_psoriasis_POST-UV_11

description:
psoriasis
SAMPLE 34

source_name: psoriatic epidermis after phototherapy patient 11


title: Epidermis_control_2

description:
control
SAMPLE 37

source_name: control epidermis 2


title: Epidermis_control_1

description:
control
SAMPLE 36

source_name: control epidermis 1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 24h biological repl1

value: epithelial


title: Epidermis_control_3

description:
control
SAMPLE 38

source_name: control epidermis 3


title: Glass wool (MMVF10) 2 12h biological repl1

value: Glass wool (MMVF10) 2 12h


title: Crocidolite asbestos 025 12h biological repl1

value: Crocidolite asbestos 025 12h


title: Crocidolite asbestos 2 12h biological repl1

value: Crocidolite asbestos 2 12h


title: Epidermis_psoriasis_POST-UV_8

description:
psoriasis
SAMPLE 31

source_name: psoriatic epidermis after phototherapy patient 8

value: Male


title: Multi-walled carbon nanotubes (Mitsui-7) 025 4h biological rep3


title: Glass wool (MMVF10) 025 12h biological repl1

value: Glass wool (MMVF10) 025 12h


title: Multi-walled carbon nanotubes (Mitsui-7) 2 4h biological rep1


title: Epidermis_psoriasis_POST-UV_9

description:
psoriasis
SAMPLE 32

source_name: psoriatic epidermis after phototherapy patient 9


title: OCT4 overexpressing cell2

city: Marseille

first: michel

last: PUCEAT

address: 27 bd Jean moulin

department: University aix marseille

country: France

institute: INSERM

description: We show that OCT4 when increassing its leval of expression above the one required to maintain pluripotency of ES cells targets mostly chromatin remodeling enzymes, nucleosome packaging actors

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Enriched binding sites were identified based on peak height intensity, peak weight and peak neighboring intensities. To ensure that the identified binding sites is enriched, statistical distributions of log2 fold changes of the enriched binding sites is compared to the distribution of background noise and 5% FDR is used to select enriched binding sites. The identified binding sites were then mapped to the gene promoter sites which are available from Genomatrix (http://www.genomatix.de). Only those enriched ChIP-chip binding sites which were overlapped with the promoter sites were recognized as genes targeted by OCT4iA. Peak and non-peak visualization was carried out with a NimbleGen genome viewer.

source_name: HUES24, nucleofection POU5F1 [ChIP fraction]

label_protocol: Standard Affymetrix protocol

growth_protocol: HUES cells were cuktured in KODMEM + 15% SR and 10 ng/ml FGF2

extract_protocol: Chromatin was extracted following cell and nuclei lysis  and sonicated using a diagenode sonicator (see Zeineddine, D. et al. Oct-3/4 dose dependently regulates specification of embryonic stem cells toward a cardiac lineage and early heart development. Dev Cell. 11, 535-546 (2006)). Sonication 7 min chromatin, IP anti OCT4 santa Cruz Sc9081.

treatment_protocol: cells were nucleofected (AMAXA KIT HUES CELLS) with POU5f1 cDNA or GFP as a control

value: HUES24 ES cell line

tag: genotype/variation

value: mutant (OCT4 overexpression)

tag: chip antibody

value: OCT4 (Santa Cruz, catalog# Sc9081, lot# 12413)


title: Epidermis_psoriasis_POST-UV_6

description:
psoriasis
SAMPLE 29

source_name: psoriatic epidermis after phototherapy patient 6


title: Epidermis_psoriasis_POST-UV_3

description:
psoriasis
SAMPLE 27

source_name: psoriatic epidermis after phototherapy patient 3


title: OCT4 overexpressing cell1


title: control2

source_name: HUES24, cultured with FGF2 [ChIP fraction]

value: wt (control)


title: Epidermis_psoriasis_POST-UV_4

description:
psoriasis
SAMPLE 28

source_name: psoriatic epidermis after phototherapy patient 4


title: control1


title: VWAT_MeDIP_LG-SC07

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2023

hyb_protocol: According to Affymetrix standard protocols

scan_protocol: The tiling arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G according to manufacturer's instruction.

data_processing:
GCOS 1.3 software (Affymetrix) was used to produce .cel files. Data were analyzed using the Partek Genomic Suite Software (PGS) (St. Louis, MO).
Signals were adjusted according to probe sequence and background corrected using the Robust Multiarray method (RMA) . Model-based analysis of tiling-arrays (MAT) was used to identify regions of differential DNA methylation by combining adjacent probes showing significant differences between the groups. A sliding windows of 500 bp was set, according to the average size of the fragments produced in the amplicon preparation step

source_name: VWAT DNA from offspring of mother exposed to late gestational sleep control conditions

growth_protocol: Timed pregnant C57BL/6J female mice (6.5 dpc) were obtained from a commercial supplier (Jackson Laboratory, Bar Harbor, ME). All mice were allowed access to food and water ad libitum, and received standard chow containing 10 kcal% fat (Research Diet, New Brunswick) throughout the experiments.

extract_protocol: Animals were sacrificed after 3 hours fasting and VWAT samples were collected at age 24 weeks, and immediately snap frozen until processing. DNA was isolated using DNeasy Tissue kit (Qiagen, Valencia, CA) and quantified on a Nanodrop 2000 (NanoDrop products, Wilmington, DE). Isolated DNA was stored at -20 °C until use. The methylated fraction of the genome was immunoprecipitated using the MeDIP protocol (Mohn el atl, 2009). The immunoprecipitated DNA was amplified using an adaptor mediated PCR strategy. MeDIP DNA was blunted using T4 DNA polymerase (NEB, Ipswich MA) and universal adaptors were ligated by overnight incubation at 4°C with T4 ligase (NEB, Ipswich MA). Blunt universal adaptors were prepared by annealing two oligonucleotides (oligo 1: GCGGTGACCCGGGAGATCTGAATTC and oligo 2: GAATTCAGATC).Adaptor-ligated DNA was amplified in 25 µL final volume under the following conditions: 1x PCR buffer (Sigma-Aldrich, St. Lous MO) 2.875 mM MgCl2 (Sigma-Aldrich, Sigma-Aldrich, St. Lous MO), 275 µM aminoallyl dNTP mix (Ambion, Austin, TX), 1.6 µM oligo 1 and 25 units Taq DNA polymerase (NEB, Ipswich MA). A "two-cycling" PCR strategy was used. The first PCR program started with an initial extension at 72°C for 5 min followed by 10 cycles of denaturation at 95°C for 1 minute, annealing at 94°C for 40 seconds and elongation at 72°C for 2.5 minutes, with a final extension step at 72°C for 5 minutes. Five mL of the first PCR product were used a template for the second PCR program. The second PCR program was identical to the first program, but used 15 cycles of denaturation/annealing/extension. Amplification was checked by electrophoresis in agarose gels. PCR products were purified using the MinElute kit (Qiagen, Valencia CA) and quantified using a Nanodrop 2000.

treatment_protocol: Pregnant mice were maintained in custom made cages operated under a 12 hour light-dark cycle (7 AM to 7 PM) and exposed to SF, from 15 days post coitus (dpc) until delivery. A custom fabricated device developed in our laboratory was used to induce SF in mice as previously described (Nair et al, 2011).

tag: group

tag: strain

value: male


title: VWAT_MeDIP_LG-SC08

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2024

label_protocol: According to Affymetrix standard protocols

value: late gestational sleep control conditions


title: Epidermis_psoriasis_POST-UV_2

description:
psoriasis
SAMPLE 26

source_name: psoriatic epidermis after phototherapy patient 2

value: Female


title: Multi-walled carbon nanotubes (Mitsui-7) 2 12h biological repl1

value: lung

tag: cell type


title: Glass wool (MMVF10) 2 4h biological rep2

tag: cell line passage

value: Glass wool (MMVF10) 2 4h


title: Epidermis_psoriasis_POST-UV_7

description:
psoriasis
SAMPLE 30

source_name: psoriatic epidermis after phototherapy patient 7

tag: treatment

value: POST-UV

value: psoriatic epidermis after phototherapy


title: VWAT_MeDIP_LG-SC06

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2022


title: Multi-walled carbon nanotubes (Mitsui-7) 025 24h biological repl3

value: epithelial


title: Glass wool (MMVF10) 2 4h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 4h biological rep1


title: Multi-walled carbon nanotubes (Mitsui-7) 025 4h biological rep2


title: Glass wool (MMVF10) 2 4h biological rep3


title: VWAT_MeDIP_LG-SC05

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2021


title: VWAT_MeDIP_LG-SC04

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2020


title: Glass wool (MMVF10) 025 4h biological rep3

value: Glass wool (MMVF10) 025 4h


title: Glass wool (MMVF10) 025 4h biological rep1


title: VWAT_MeDIP_LG-SC03

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2019


title: Glass wool (MMVF10) 025 4h biological rep2


title: Control 4h biological rep3

value: Control 4h


title: Epidermis_psoriasis_MID-UV_7

description:
psoriasis
SAMPLE 19

source_name: psoriatic epidermis during phototherapy patient 7

value: MID-UV

value: psoriatic epidermis during phototherapy


title: Epidermis_psoriasis_MID-UV_9

description:
psoriasis
SAMPLE 21

source_name: psoriatic epidermis during phototherapy patient 9


title: Control 4h biological rep1


title: Control 4h biological rep2


title: VWAT_MeDIP_LG-SC02

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2018


title: VWAT_MeDIP_LG-SF08

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2016

source_name: VWAT DNA from offspring of mother exposed to late gestational sleep fragmentation

value: late gestational sleep fragmentation


title: VWAT_MeDIP_LG-SC01

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2017


title: VWAT_MeDIP_LG-SF07

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2015


title: Epidermis_psoriasis_MID-UV_8

description:
psoriasis
SAMPLE 20

source_name: psoriatic epidermis during phototherapy patient 8

value: Male


title: Epidermis_psoriasis_POST-UV_1

description:
psoriasis
SAMPLE 25

source_name: psoriatic epidermis after phototherapy patient 1


title: Epidermis_psoriasis_MID-UV_11

description:
psoriasis
SAMPLE 23

source_name: psoriatic epidermis during phototherapy patient 11


title: Epidermis_psoriasis_MID-UV_6

description:
psoriasis
SAMPLE 18

source_name: psoriatic epidermis during phototherapy patient 6


title: Crocidolite asbestos 025 4h biological rep3

value: Crocidolite asbestos 025 4h


title: Epidermis_psoriasis_MID-UV_3

description:
psoriasis
SAMPLE 15

source_name: psoriatic epidermis during phototherapy patient 3


title: VWAT_MeDIP_LG-SF05

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2013


title: Crocidolite asbestos 025 4h biological rep2


title: Epidermis_psoriasis_MID-UV_4

description:
psoriasis
SAMPLE 16

source_name: psoriatic epidermis during phototherapy patient 4


title: Epidermis_psoriasis_MID-UV_10

description:
psoriasis
SAMPLE 22

source_name: psoriatic epidermis during phototherapy patient 10


title: Epidermis_psoriasis_MID-UV_5

description:
psoriasis
SAMPLE 17

source_name: psoriatic epidermis during phototherapy patient 5


title: Multi-walled carbon nanotubes (Mitsui-7) 2 1h biological rep1


title: VWAT_MeDIP_LG-SF03

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2011


title: Epidermis_psoriasis_MID-UV_2

description:
psoriasis
SAMPLE 14

source_name: psoriatic epidermis during phototherapy patient 2


title: Epidermis_psoriasis_MID-UV_12

description:
psoriasis
SAMPLE 24

source_name: psoriatic epidermis during phototherapy patient 12


title: Epidermis_psoriasis_PRE-UV_12

description:
psoriasis
SAMPLE 12

source_name: psoriatic epidermis before phototherapy patient 12

value: PRE-UV

value: psoriatic epidermis before phototherapy


title: Crocidolite asbestos 025 4h biological rep1


title: Epidermis_psoriasis_MID-UV_1

description:
psoriasis
SAMPLE 13

source_name: psoriatic epidermis during phototherapy patient 1


title: Multi-walled carbon nanotubes (Mitsui-7) 2 1h biological rep3


title: VWAT_MeDIP_LG-SF02

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2010

value: male


title: Crocidolite asbestos 2 4h biological rep1

value: Crocidolite asbestos 2 4h


title: Epidermis_psoriasis_PRE-UV_11

description:
psoriasis
SAMPLE 11

source_name: psoriatic epidermis before phototherapy patient 11

value: Female


title: VWAT_MeDIP_LG-SF04

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2012


title: VWAT_MeDIP_LG-SF06

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2014


title: Multi-walled carbon nanotubes (Mitsui-7) 2 1h biological rep2

value: lung


title: VWAT_MeDIP_LG-SF01

description: DNA was isolated from visceral white adipose tissue (VWAT). MeDIP was performed according to Mohn et al. 2009


title: Crocidolite asbestos 2 4h biological rep3


title: Crocidolite asbestos 2 4h biological rep2


title: Multi-walled carbon nanotubes (Mitsui-7) 025 1h biological rep3


title: Epidermis_psoriasis_PRE-UV_10

description:
psoriasis
SAMPLE 10

source_name: psoriatic epidermis before phototherapy patient 10


title: Multi-walled carbon nanotubes (Mitsui-7) 025 1h biological rep1


title: Glass wool (MMVF10) 2 1h biological rep3

value: Glass wool (MMVF10) 2 1h


title: Epidermis_psoriasis_PRE-UV_9

description:
psoriasis
SAMPLE 9

source_name: psoriatic epidermis before phototherapy patient 9


title: Epidermis_psoriasis_PRE-UV_6

description:
psoriasis
SAMPLE 6

source_name: psoriatic epidermis before phototherapy patient 6


title: neural-specific Pumilio RNAi, 1 hour pulse, replicate 3

city: Merced

first: Michael

last: Cleary

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

description: TU-RNA present after 1 hour pulse

hyb_protocol: 1.65 micrograms of Cy3 labeled cRNA was combined with the recommended dilution of spike-in control and hybridized following manufacturer's instructions

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B scanner, with pixel size 10, scan power 100%, and 532nm PMTGain set between 500 and 700.

data_processing:
Spot alignments and data measurements were made using GenePix Pro 5.1 software. Post-processing of GenePix Pro data was performed in R.
Signal intensities within a pulse-chase series were normalized using the spike-in control.  Threshold F532 intensity (mean - background) for a spot to be considered present (signal above background) was determined for each pulse-chase series by averaging the signals for maternal mRNAs that should not be present in the TU-RNA samples at any timepoint.  Spots with signals below this average value were removed from analysis.

organism: Drosophila melanogaster

label_protocol: Purified TU-RNA plus a spike-in control (One-Color RNA Spike-In Kit, Agilent) was used to generate Cy3 labeled cRNA (Low Input Quick Amp Labeling Kit, Agilent) and hybridized to Agilent 4x44K Drosophila gene expression microarrays.

growth_protocol: embryos were collected on standard apple juice, agar plates and reared at 18C or 25C to reach stage 12 - 15

extract_protocol: Total RNA was extracted using trizol purification protocols.  TU-RNA was purified as previously described.

treatment_protocol: Embryos were permeabilized and pulse-labeled in tagging media [D22 insect media, 5% FBS, and either 1mM 4-thiouridine (whole embryo tagging) or 1mM 4-thiouracil (neural-specific tagging)] for 1 hour at 30°C. Pulse-labeled embryos were then transferred for 1 or 3 hours to chase media containing uridine [D22 insect media, 5% FBS, 10mM uridine] at 30°C. Embryos were homogenized for 30 seconds and frozen in Trizol (Invitrogen) at -80°C.  Multiple samples for each time-point were pooled for RNA extraction and TU-RNA purification, as previously described

value: embryonic nervous system

tag: genotype

value: Pros-Gal4 X UAS-T.g.UPRT ; UAS-Pum(RNAi)

tag: age

value: stage 12 - 15

tag: timepoint

value: 1 hour pulse


title: neural-specific Pumilio RNAi, 3 hour chase, replicate 2

description: TU-RNA present after 3 hour chase

value: 3 hour chase


title: Epidermis_psoriasis_PRE-UV_5

description:
psoriasis
SAMPLE 5

source_name: psoriatic epidermis before phototherapy patient 5


title: neural-specific Pumilio RNAi, 3 hour chase, replicate 3

description: TU-RNA present after 3 hour chase


title: Glass wool (MMVF10) 2 1h biological rep1

value: epithelial


title: Epidermis_psoriasis_PRE-UV_7

description:
psoriasis
SAMPLE 7

source_name: psoriatic epidermis before phototherapy patient 7


title: neural-specific Pumilio RNAi, 3 hour chase, replicate 1

description: TU-RNA present after 3 hour chase


title: Epidermis_psoriasis_PRE-UV_3

description:
psoriasis
SAMPLE 3

source_name: psoriatic epidermis before phototherapy patient 3


title: neural-specific Pumilio RNAi, 1 hour pulse, replicate 2

description: TU-RNA present after 1 hour pulse


title: Glass wool (MMVF10) 2 1h biological rep2


title: Epidermis_psoriasis_PRE-UV_2

description:
psoriasis
SAMPLE 2

source_name: psoriatic epidermis before phototherapy patient 2


title: neural-specific Pumilio RNAi, 1 hour chase, replicate 3

description: TU-RNA present after 1 hour chase

value: 1 hour chase


title: neural-specific Pumilio RNAi, 1 hour chase, replicate 1

description: TU-RNA present after 1 hour chase


title: CN34-Par-1

city: New York

first: Jason

last: Ross

state: New York

address: 1230 York Ave

department: Systems Cancer Biology

institute: The Rockefeller University

description:
CN34 parental cells-1
replicate 1

hyb_protocol: Biotin-labeled probes were hybridized to Illumina human HT-12 v3 BeadChip using manufactirer's standard conditions.

scan_protocol: After hybridiztion, Illumina HT-12 v3 BeadChips were scanned onto a BeadArray Reader in accordance with manufacturer's instructions.

data_processing: Raw signal intensity for each sample was median-normalized and replicate samples were averaged. Non-normalized values indicate the probe hybrydization signal. Normalized values are median-normalized.

source_name: CN34 parental cells

label_protocol: Total RNA was biotin labeled by converting RNA to cDNA using biotinylated oligo (dT) and random nonamer primers.

extract_protocol: Total RNA from multiple cell lines was extracted using the MiRvana RNA isolation kit (AM1560, Applied Biosystems)

tag: cell line

tag: population

value: parental

value: breast cancer


title: neural-specific Pumilio RNAi, 1 hour chase, replicate 2

description: TU-RNA present after 1 hour chase

tag: tissue


title: CN34-Par-2

description:
CN34 parental cells-2
replicate 2


title: CN34-TE2-1

description:
CN34 tumorigenic-enriched cells-1
replicate 1

source_name: CN34 tumorigenic-enriched cells

value: tumorigenic-enriched


title: Glass wool (MMVF10) 025 1h biological rep2

value: Glass wool (MMVF10) 025 1h


title: CN34-LM1a-2

description:
CN34 lung-metastatic cells-2
replicate 2

source_name: CN34 lung-metastatic cells

value: lung-metastatic


title: MDA-LM2-2

description:
MDA-MB-231 lung-metastatic cells-2
replicate 2

source_name: MDA-MB-231 lung-metastatic cells


title: neural-specific Pumilio RNAi, 1 hour pulse, replicate 1

description: TU-RNA present after 1 hour pulse


title: Epidermis_psoriasis_PRE-UV_4

description:
psoriasis
SAMPLE 4

source_name: psoriatic epidermis before phototherapy patient 4

tag: gender

value: Male

value: PRE-UV

value: psoriatic epidermis before phototherapy


title: Multi-walled carbon nanotubes (Mitsui-7) 025 1h biological rep2

value: lung


title: Glass wool (MMVF10) 025 1h biological rep3


title: Glass wool (MMVF10) 025 1h biological rep1


title: MDA-LM2-1

description:
MDA-MB-231 lung-metastatic cells-1
replicate 1


title: Control 1h biological rep3

value: Control 1h


title: CN34-LM1a-1

description:
CN34 lung-metastatic cells-1
replicate 1


title: neural-specific, 1 hour pulse, replicate 2

description: TU-RNA present after 1 hour pulse

value: embryonic nervous system

value: Pros-Gal4 X UAS-T.g.UPRT


title: neural-specific, 1 hour chase, replicate 2

description: TU-RNA present after 1 hour chase

value: stage 12 - 15


title: Epidermis_psoriasis_PRE-UV_8

description:
psoriasis
SAMPLE 8

source_name: psoriatic epidermis before phototherapy patient 8


title: Epidermis_psoriasis_PRE-UV_1

description:
psoriasis
SAMPLE 1

source_name: psoriatic epidermis before phototherapy patient 1


title: neural-specific, 3 hour chase, replicate 2

description: TU-RNA present after 3 hour chase


title: Crocidolite asbestos 2 1h biological rep2

value: Crocidolite asbestos 2 1h


title: Crocidolite asbestos 2 1h biological rep1


title: neural-specific, 1 hour chase, replicate 1

description: TU-RNA present after 1 hour chase


title: neural-specific, 3 hour chase, replicate 1

description: TU-RNA present after 3 hour chase

value: 3 hour chase


title: neural-specific, 1 hour pulse, replicate 1

description: TU-RNA present after 1 hour pulse

value: 1 hour pulse


title: Crocidolite asbestos 2 1h biological rep3

value: epithelial


title: HB101, exposed to C. elegans and Giardia, biological rep3

city: Calgary

first: Teklu

middle: Kuru

last: Gerbaba

address: 2500 University Drive NW

department: Biological Sciences

country: Canada

institute: University of Calgary

description: Gene expression data from Escherchia coli HB101 exposed to C. elegans and Giardia for 24 hours

hyb_protocol: Following fragmentation and biotinylation, cDNA were hybridized for 16 hr at 45C on GeneChip E. coli Genome 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The microarray data files were processed using statistical software R version 3.0.1 and Bioconductor packages. The Single-Channel Array Normalization (SCAN.UPC) package was used to normalize the microarray data. Batch effects were adjusted by using the Empirical Bayes method implemented in COMBAT software.

organism: Escherichia coli

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

growth_protocol: E. coli HB101 grown in Terrific broth media for 12 hours were washed three times in sdH2O and re-suspended in S-Basal complete medium.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to instructions in the kit.

treatment_protocol: E. coli were incubated in S-Basal complete medium alone or in the presence of C. elegans, Giardia conditioned meida, and both C. elegans and Giardia conditioned media.

value: E. coli [supE44 hsdS20(rB-mB-) recA13 ara-14 proA2 lacY1 galK2 rpsL20 xyl-5 mtl-1]


title: MDA-Par-1

description:
MDA-MB-231 parental cells-1
replicate 1

source_name: MDA-MB-231 parental cells

value: parental

value: breast cancer


title: HB101, exposed to C. elegans and Giardia, biological rep2

source_name: Escherchia coli HB101 exposed to C. elegans and Giardia for 24 hours


title: Crocidolite asbestos 025 1h biological rep3

value: Crocidolite asbestos 025 1h


title: MDA-Par-2

description:
MDA-MB-231 parental cells-2
replicate 2


title: Control 1h biological rep2


title: HB101, exposed to Giardia, biological rep3

description: Gene expression data from Escherchia coli HB101 exposed to Giardia for 24 hours


title: Crocidolite asbestos 025 1h biological rep2


title: MDA-TE3-2

description:
MDA-MB-231 tumorigenic-enriched cells-2
replicate 2

source_name: MDA-MB-231 tumorigenic-enriched cells

value: tumorigenic-enriched


title: MDA-TE3-1

description:
MDA-MB-231 tumorigenic-enriched cells-1
replicate 1


title: Control 1h biological rep1


title: HB101, exposed to Giardia, biological rep2

source_name: Escherchia coli HB101 exposed to Giardia for 24 hours


city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

institute: Universidad de Málaga

description:
10mM WT vs 50mM WT technical replicate 2 biological replicate 1
10mM_WTvs50mMWT_2a

hyb_protocol: Hybridization and slide washing were performed accoding to the manufacturer´s protocol Low Input Quick Amp Labelling Kit - two colour (Agilent Technologies; cat#5190-2306)

scan_protocol: Scanned using GenePix 4100A scanner with a resolution of 5 µm/pixel. Data were extracted from the scanned images using the GenePix v6.0 software.

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. Genes were declared as differentially expressed with adjusted p-value < 0.05 and log FC 1

organism: Populus tremula x Populus alba

source_name: 50mM WT leaves

label_protocol: 200 ng of total RNA was used for each sample. Microarray labelling was performed accoding to the manufacturer´s protocol Low Input Quick Amp Labelling Kit - two colour (Agilent Technologies; cat#5190-2306)

growth_protocol: Untransformed (WT) hybrid poplar (Populus tremula x P. alba, clone INRA 7171-B, Institut National de la Recherche Agronomique, INRA) and a transgenic line overexpressing a glutamine synthetase cytosolic pine (GS1a) under the control of cauliflower mosaic virus 35S promoter (CaMV35S) were produced and maintained in vitro as previously described (Fu et al. 2003. Plant Cell Environ. 26:411-418). Rooted shoots of transformed and WT plants were maintained in plant growth chambers with a photoperiod of 16 h light with light intensity of 295 μmol m2 s-1, a constant temperature 24°C and 80% humidity. Plants were cultivated in plastic pots containing a potting mix and vermiculite in proportions 1:1 and watered with distilled water supplemented with macro and micronutrients for optimal growth (Jing et al. 2004. New Phytol. 164:137-145).

extract_protocol: Total RNA extracted as described by Canales el al. (2010) Amino Acids 39:991-1001.

treatment_protocol: After 8 weeks of growth, plants with similar height (approximately 60 cm) were divided by genotype: Untransformed controls and transgenic poplars (24 individuals per genotype) and each group of plants were then subdivided randomly into 2 groups. One of the groups was irrigated with a nutrient solution enriched with 10 mM nitrate. The remaining group of plants was supplied with 50 mM nitrate. The plants were watered with the nutrient solution once a week by flooding, for a total of 4 weeks. At the end of the growing period plants were harvested.

value: WT (untransformed)

value: leaves

tag: nutrition

value: 50mM Nitrate

source_name: 10mM WT leaves

value: 10mM Nitrate


title: Crocidolite asbestos 025 1h biological rep1

value: lung


description:
10mM WT vs 50mM WT technical replicate 1 biological replicate 1
10mM_WTvs50mMWT_1a


title: HB101, exposed to C. elegans and Giardia, biological rep1


title: HB101, exposed to Giardia, biological rep1


description:
10mM WT vs 50mM WT technical replicate 1 biological replicate 2
10mM_WTvs50mMWT_1b


title: HB101, exposed to C. elegans, biological rep3

description: Gene expression data from Escherchia coli HB101 exposed to C. elegans for 24 hours


title: HB101, exposed to C. elegans, biological rep2

source_name: Escherchia coli HB101 exposed to C. elegans for 24 hours


description:
10mM GS1a vs 50mM GS1a technical replicate 2 biological replicate 2
10mM_GS1avs50mMGS1a_2b

source_name: 50mM GS1a leaves

value: overexpressing a glutamine synthetase cytosolic pine (GS1a)

source_name: 10mM GS1a leaves


title: HB101, exposed to C. elegans, biological rep1


title: HB101, biological rep2

description: Gene expression data from Escherchia coli HB101

source_name: Escherchia coli HB101


description:
10mM GS1a vs 50mM GS1a technical replicate 1 biological replicate 2
10mM_GS1avs50mMGS1a_1b


title: HB101, biological rep3


title: mTORi 61

first: Joseph

middle: A.

last: Ludwig

state: Texas

department: Sarcoma Medical Oncology

institute: UT-MD-Anderson Cancer Center

description: Gene expression data from mTORi-treated EW5 xenograft

hyb_protocol: Amplified and biotinylated cRNAs were hybridized onto Affymetrix GeneChip Human Genome U133A 2.0 cartridge arrays, Washed, and Stained with kit following manufacturer’s instructions.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000 and the initial raw data were extracted using Affymetrix GeneChip Command Console-Expression software.

data_processing: The CEL files were quantified using Robust Multiarray Analysis (RMA) algorithm that borrows strength across arrays. Also, as part of the standard quality control (QC) analysis of gene expression profiling data, we first normalized the data using median centering. Then we used principal component analysis (PCA) to check if the batch effect exists. Feature-by-feature two-sample t-tests were used for comparisons between a treatment group and the control group. We also performed feature-by-feature one-way ANOVA followed by Tukey's test to do pair comparisons for all groups. The beta-uniform mixture (BUM) models were used to fit the resulting p-value distributions in order to adjust for multiple comparisons. The cutoff p-values and number of significant proteins were computed for several different false discovery rates (FDRs).  The biostatistical analyses comparing two groups in the current study were performed using an unpaired t-test with Gaussian distribution and followed with Welch’s correction. For multiple comparison testing we used one-way ANOVA testing with Geisser Greenhouse correction. Differences were considered significant for p<0.05.

label: Biotin

source_name: EW5 xenograft of Ewing Sarcoma

label_protocol: Labeling was performed using Affymetrix’s GeneChip®3’ IVT Express Kit following manufacturer’s instructions.

growth_protocol: Male non-obese diabetic (NOD)-SCID-IL-2Rgnull mice were used to generate EW5 explants (2 mm). Mice bearing subcutaneous tumors were randomized into treatment and control groups when their tumors reached a diameter of 6 mm

extract_protocol: Total RNA was extracted from EW5 Ewing sarcoma xenografts using the Qiagen miRNeasy Mini kit. RNA quality was assessed to have an RNA integrity number before amplification and labeling

treatment_protocol: Mice bearing tumors, when their tumors reached a diameter of 6 mm, they received MK-8669 (mTOR inhibitor, 5mg/kg per dose, once weekly), MK-0646 (IGF-1R inhibitor monoclonal antibody, 0.5mg IP twice weekly), or a placebo control (sterile buffer). Animals were treated either until their tumors reached 1500 mm3 in volume.

value: Human tumor (EW5 Ewing sarcoma xenograft)

tag: agent

value: mTORi


description:
10mM GS1a vs 50mM GS1a technical replicate 1 biological replicate 1
10mM_GS1avs50mMGS1a_1a


title: mTORi 64


title: mTORi 25


title: 50mM GS1a vs WT technical replicate 2 biological replicate 2

description:
Technical replicate 2 of 2. 50mM Nitrate
50mM_WTvsGS1a_2b

data_processing: Normalization and differential expression analysis of the data was done using limma R package (Smyth 2004). Normalization was carried out using quantile method and Bayes statistics were applied to determine the differential expression between the comparisons. Statistical significance was corrected for multiple testing using the Benjamini-Hochberg procedure. Genes were declared as differentially expressed with adjusted p-value < 0.05 and logFC > 1


description:
10mM GS1a vs 50mM GS1a technical replicate 2 biological replicate 1
10mM_GS1avs50mMGS1a_2a


title: mTORi 65


title: 50mM GS1a vs WT technical replicate 1 biological replicate 2

description:
Technical replicate 1 of 2. 50mM Nitrate
50mM_WTvsGS1a_1b


title: IGF-1Ri 20

description: Gene expression data from IGF-1Ri-treated EW5 xenograft


title: IGF-1Ri 21


title: 50mM GS1a vs WT technical replicate 1 biological replicate 1

description:
Technical replicate 1 of 2. 50mM Nitrate
50mM_WTvsGS1a_1a


title: Control 63

description: Gene expression data from untreated EW5 xenograft

value: control


title: 10mM GS1a vs WT technical replicate 1 biological replicate 1

description:
Technical replicate 1 of 2. 10mM Nitrate
10mM_WTvsGS1a_1a


title: IGF-1Ri 17


title: 10mM GS1a vs WT technical replicate 2 biological replicate 1

description:
Technical replicate 2 of 2. 10mM Nitrate
10mM_WTvsGS1a_2a


title: 50mM GS1a vs WT technical replicate 2 biological replicate 1

description:
Technical replicate 2 of 2. 50mM Nitrate
50mM_WTvsGS1a_2a


title: Control 59


title: 10mM GS1a vs WT technical replicate 2 biological replicate 2

description:
Technical replicate 2 of 2. 10mM Nitrate
10mM_WTvsGS1a_2b


title: Control 57


title: Control RV 2

city: Nashville

first: James

last: West

state: TN

address: 4200 E 9TH Ave, Box B133

department: Medicine

institute: Vanderbilt University

description: Control 2

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Obtained from patients at autopsy

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

tag: subject status

value: heart right ventricular wall


title: 10mM GS1a vs WT technical replicate 1 biological replicate 2

description:
Technical replicate 1 of 2. 10mM Nitrate
10mM_WTvsGS1a_1b

tag: genotype/variation


title: Control RV 1

description: Control 1


title: Ecell-miR181c

city: Tokyo

first: Naoomi

last: Tominaga

address: 5-1-1 Tsukiji, Chuo-ku

institute: National Cancer Center Research institute

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028520) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Macaca fascicularis

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

extract_protocol: Total RNA was extracted from cultured cells using the QIAzol reagent and the miRNeasy Mini Kit (Qiagen)

treatment_protocol: mRNA expression in brain endothelial cells was treated with negative control miRNA or miR-181c mimic and or with extracellular vesicles from MDA-MB-231-D3H1, MDA-MB-231-D3H2LN, BMD2a and BMD2b breast cancer cell lines.

value: brain

value: endothelial cells

value: miR-181c mimic


title: Ecell-NC

source_name: Ecell-NC

value: negative control miRNA


title: Ecell-B2aex

value: extracellular vesicles from B2a breast cancer cell line


title: Ecell-B2bex

value: extracellular vesicles from B2b breast cancer cell line


title: PAH with BMPR2 mutation 1

description: PPH

value: pulmonary arterial hypertension (PAH) with BMPR2 mutation


title: Idiopathic Dilated Cardiomyopathy 1

description: IDCC 1

value: idiopathic dilated cardiomyopathy (IDC)


title: PAH with BMPR2 mutation 2

description: SPH