title: pbmc_population-based Illumina HT12v4_941


title: pbmc_population-based Illumina HT12v4_968

status: Public on Jun 29 2015

type: RNA

city: Leipzig

first: Holger

last: Kirsten

state: Saxony

address: Haertelstr. 16-18

department: IMISE

country: Germany

institute: University of Leipzig

description: population-based sample from Leipzig LIFE Heart Study

hyb_protocol: 750ng of cRNA were hybridized to Human HT-12 v4 Expression BeadChips (Illumina, San Diego, CA, USA) for 16 hours, stringency washed according to instructions of the manufacturer.

scan_protocol: The arrays were scanned on the Illumina HiScan instrument according to instructions of the manufacturer.

data_processing:
Raw data of all 47,323 probes was extracted by Illumina GenomeStudio, 47,308 probes could be successfully imputed in all samples. Data was further processed within R 2.13.1 / Bioconductor. 123 (4.9%) Individuals having an extreme number of expressed genes (<7,505 genes, defined as median ± 3 interquartile ranges (IQR) of the cohort’s values) were excluded. Transcripts that were not found to be expressed according to Illumina’s internal cut-off as implemented in Bioconductor package ‘lumi’ p = 0.05 in at least 5% of all samples were not further considered in the analysis. Expression values were quantile normalised and log2-transformed (PMID 20525181). For further outlier detection, we calculated the Euclidian distance between all individuals and an artificial individual having average expression levels of all transcripts. 69 (2.9%) of remaining individuals with a distance larger than median + 3 IQR were excluded. Furthermore, we defined for each individual a combined quantitative measure combining quality control features available for HT-12v4 (i.e. perfect-match and miss-match control probes, control probes present at different concentrations, mean of negative control probes, mean of house-keeping genes, Euclidian distances of expression values, number of expressed genes, mean signal strength of biotin-control-probes). We calculated Mahalanobis-distance between all individuals and an artificial individual having average values for these quality control features. 31 (1.3%) of remaining individuals with a distance larger than median + 3 IQR were excluded. Transcript levels were adjusted for known batch effects (Sentrix ID, i.e. the expression chip) using an empirical Bayes method as described (PMID: 16632515) and residualised for age, sex, monocyte counts and lymphocyte counts. Due to incomplete data 20 (0.9%) of the remaining individuals were excluded. A total of 612 expression probes still over-inflated following Bonferroni-correction were excluded. Additionally, we calculated principal components of the expression data and residualised for the first five principal components of expression data to account for unmeasured batch effects (PMID: 21829388). This initial preprocessing resulted in 28,295 expression probes corresponding to 15,217 genes available for 2,258 individuals. For 2,112 (93.5%) of these individuals, valid genotype data was available.
Please note that the 'non_normalized.txt'  includes 15 probes with missing data in some of the 2112 individuals. Missing data is indicated by NA, IDs of these 15 probes are ILMN_1880516, ILMN_1657128, ILMN_3288242, ILMN_1674878, ILMN_1740200, ILMN_1685079, ILMN_1784690, ILMN_2047480, ILMN_1657436, ILMN_3239173, ILMN_3247816, ILMN_1800488, ILMN_3246658, ILMN_3308225, ILMN_1869278.

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: 500 ng RNA per sample were ethanol precipitated with GlycoBlue (Invitrogen) as carrier and dissolved at a concentration of 50-300 ng/µl prior to probe synthesis. 250 ng of total RNA was reverse transcribed to cDNA (Target Amp labelling kit (Epicentre Biotechnologies, Madison, WI, USA and Superscript III, Life Technologies, Gaithersburg, MD, USA), which was further synthesized to cRNA by in vitro transcription (T7 RNA Polymerase and Target Amp labelling kit, Epicentre Biotechnologies, Madison, WI, USA). Subsequently, unincorporated nucleotides were removed using the RNeasy kit (QIAGEN, Hilden, Germany)

extract_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood samples using Cell Preparation Tubes (CPT, Becton Dickinson). Total RNA was extracted using TRIzol reagent (Invitrogen).

tag: gender

value: M

tag: age (yrs)

tag: lymphocytes

tag: monocytes

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)


title: pbmc_population-based Illumina HT12v4_943


title: pbmc_population-based Illumina HT12v4_930


title: pbmc_population-based Illumina HT12v4_935


title: pbmc_population-based Illumina HT12v4_928

value: F


title: pbmc_population-based Illumina HT12v4_929


title: pbmc_population-based Illumina HT12v4_926


title: pbmc_population-based Illumina HT12v4_940


title: pbmc_population-based Illumina HT12v4_925


title: pbmc_population-based Illumina HT12v4_934


title: pbmc_population-based Illumina HT12v4_932


title: pbmc_population-based Illumina HT12v4_933


title: pbmc_population-based Illumina HT12v4_931


title: pbmc_population-based Illumina HT12v4_927


title: pbmc_population-based Illumina HT12v4_937


title: pbmc_population-based Illumina HT12v4_923


title: pbmc_population-based Illumina HT12v4_936


title: pbmc_population-based Illumina HT12v4_920


title: pbmc_population-based Illumina HT12v4_919


title: pbmc_population-based Illumina HT12v4_922


title: pbmc_population-based Illumina HT12v4_921


title: pbmc_population-based Illumina HT12v4_924


title: pbmc_population-based Illumina HT12v4_918


title: pbmc_population-based Illumina HT12v4_917


title: pbmc_population-based Illumina HT12v4_911


title: pbmc_population-based Illumina HT12v4_912


title: pbmc_population-based Illumina HT12v4_914


title: pbmc_population-based Illumina HT12v4_913


title: pbmc_population-based Illumina HT12v4_910


title: pbmc_population-based Illumina HT12v4_915


title: pbmc_population-based Illumina HT12v4_909


title: pbmc_population-based Illumina HT12v4_916


title: pbmc_population-based Illumina HT12v4_908


title: pbmc_population-based Illumina HT12v4_906


title: pbmc_population-based Illumina HT12v4_903


title: pbmc_population-based Illumina HT12v4_898


title: pbmc_population-based Illumina HT12v4_895


title: pbmc_population-based Illumina HT12v4_899


title: pbmc_population-based Illumina HT12v4_902


title: pbmc_population-based Illumina HT12v4_894


title: pbmc_population-based Illumina HT12v4_905


title: pbmc_population-based Illumina HT12v4_907


title: pbmc_population-based Illumina HT12v4_893


title: pbmc_population-based Illumina HT12v4_901


title: pbmc_population-based Illumina HT12v4_897


title: pbmc_population-based Illumina HT12v4_891


title: pbmc_population-based Illumina HT12v4_892


title: pbmc_population-based Illumina HT12v4_896


title: pbmc_population-based Illumina HT12v4_904


title: pbmc_population-based Illumina HT12v4_900


title: pbmc_population-based Illumina HT12v4_889


title: pbmc_population-based Illumina HT12v4_887


title: pbmc_population-based Illumina HT12v4_885


title: pbmc_population-based Illumina HT12v4_876


title: pbmc_population-based Illumina HT12v4_880


title: pbmc_population-based Illumina HT12v4_884


title: pbmc_population-based Illumina HT12v4_886


title: pbmc_population-based Illumina HT12v4_868


title: pbmc_population-based Illumina HT12v4_872


title: pbmc_population-based Illumina HT12v4_878


title: pbmc_population-based Illumina HT12v4_870


title: pbmc_population-based Illumina HT12v4_875


title: pbmc_population-based Illumina HT12v4_890


title: pbmc_population-based Illumina HT12v4_883


title: pbmc_population-based Illumina HT12v4_879


title: pbmc_population-based Illumina HT12v4_873


title: pbmc_population-based Illumina HT12v4_874


title: pbmc_population-based Illumina HT12v4_877


title: pbmc_population-based Illumina HT12v4_863


title: pbmc_population-based Illumina HT12v4_881


title: pbmc_population-based Illumina HT12v4_865


title: pbmc_population-based Illumina HT12v4_882


title: pbmc_population-based Illumina HT12v4_867


title: pbmc_population-based Illumina HT12v4_871


title: pbmc_population-based Illumina HT12v4_864


title: pbmc_population-based Illumina HT12v4_869


title: pbmc_population-based Illumina HT12v4_862


title: pbmc_population-based Illumina HT12v4_860


title: pbmc_population-based Illumina HT12v4_866


title: pbmc_population-based Illumina HT12v4_861


title: pbmc_population-based Illumina HT12v4_859


title: pbmc_population-based Illumina HT12v4_851


title: pbmc_population-based Illumina HT12v4_853


title: pbmc_population-based Illumina HT12v4_849


title: pbmc_population-based Illumina HT12v4_857


title: pbmc_population-based Illumina HT12v4_858


title: pbmc_population-based Illumina HT12v4_840


title: pbmc_population-based Illumina HT12v4_842


title: pbmc_population-based Illumina HT12v4_855


title: pbmc_population-based Illumina HT12v4_852


title: pbmc_population-based Illumina HT12v4_850


title: pbmc_population-based Illumina HT12v4_938


title: pbmc_population-based Illumina HT12v4_844


title: pbmc_population-based Illumina HT12v4_848


title: pbmc_population-based Illumina HT12v4_856


title: pbmc_population-based Illumina HT12v4_841


title: pbmc_population-based Illumina HT12v4_854


title: pbmc_population-based Illumina HT12v4_846


title: pbmc_population-based Illumina HT12v4_839


title: pbmc_population-based Illumina HT12v4_843


title: pbmc_population-based Illumina HT12v4_845


title: pbmc_population-based Illumina HT12v4_838


title: pbmc_population-based Illumina HT12v4_836


title: pbmc_population-based Illumina HT12v4_835


title: pbmc_population-based Illumina HT12v4_833


title: pbmc_population-based Illumina HT12v4_847


title: pbmc_population-based Illumina HT12v4_834


title: pbmc_population-based Illumina HT12v4_837


title: pbmc_population-based Illumina HT12v4_832


title: pbmc_population-based Illumina HT12v4_829


title: pbmc_population-based Illumina HT12v4_831


title: pbmc_population-based Illumina HT12v4_827


title: pbmc_population-based Illumina HT12v4_825


title: pbmc_population-based Illumina HT12v4_819


title: pbmc_population-based Illumina HT12v4_818


title: pbmc_population-based Illumina HT12v4_828


title: pbmc_population-based Illumina HT12v4_820


title: pbmc_population-based Illumina HT12v4_823


title: pbmc_population-based Illumina HT12v4_816


title: pbmc_population-based Illumina HT12v4_814


title: pbmc_population-based Illumina HT12v4_824


title: pbmc_population-based Illumina HT12v4_817


title: pbmc_population-based Illumina HT12v4_812


title: pbmc_population-based Illumina HT12v4_813


title: pbmc_population-based Illumina HT12v4_815


title: pbmc_population-based Illumina HT12v4_811


title: pbmc_population-based Illumina HT12v4_821


title: pbmc_population-based Illumina HT12v4_808


title: pbmc_population-based Illumina HT12v4_807


title: pbmc_population-based Illumina HT12v4_809


title: pbmc_population-based Illumina HT12v4_822


title: pbmc_population-based Illumina HT12v4_888


title: pbmc_population-based Illumina HT12v4_826


title: pbmc_population-based Illumina HT12v4_806


title: pbmc_population-based Illumina HT12v4_805


title: pbmc_population-based Illumina HT12v4_804


title: pbmc_population-based Illumina HT12v4_803


title: pbmc_population-based Illumina HT12v4_801


title: pbmc_population-based Illumina HT12v4_802


title: pbmc_population-based Illumina HT12v4_810


title: pbmc_population-based Illumina HT12v4_797


title: pbmc_population-based Illumina HT12v4_800


title: pbmc_population-based Illumina HT12v4_799


title: pbmc_population-based Illumina HT12v4_798


title: pbmc_population-based Illumina HT12v4_792


title: pbmc_population-based Illumina HT12v4_788


title: pbmc_population-based Illumina HT12v4_794


title: pbmc_population-based Illumina HT12v4_790


title: pbmc_population-based Illumina HT12v4_791


title: pbmc_population-based Illumina HT12v4_795


title: pbmc_population-based Illumina HT12v4_830


title: pbmc_population-based Illumina HT12v4_784


title: pbmc_population-based Illumina HT12v4_787


title: pbmc_population-based Illumina HT12v4_786


title: pbmc_population-based Illumina HT12v4_779


title: pbmc_population-based Illumina HT12v4_780


title: pbmc_population-based Illumina HT12v4_796


title: pbmc_population-based Illumina HT12v4_777


title: pbmc_population-based Illumina HT12v4_782


title: pbmc_population-based Illumina HT12v4_793


title: pbmc_population-based Illumina HT12v4_785


title: pbmc_population-based Illumina HT12v4_775


title: pbmc_population-based Illumina HT12v4_776


title: pbmc_population-based Illumina HT12v4_781


title: pbmc_population-based Illumina HT12v4_778


title: pbmc_population-based Illumina HT12v4_774


title: pbmc_population-based Illumina HT12v4_789


title: pbmc_population-based Illumina HT12v4_783


title: pbmc_population-based Illumina HT12v4_770


title: pbmc_population-based Illumina HT12v4_771


title: pbmc_population-based Illumina HT12v4_773


title: pbmc_population-based Illumina HT12v4_767


title: pbmc_population-based Illumina HT12v4_769


title: pbmc_population-based Illumina HT12v4_772


title: pbmc_population-based Illumina HT12v4_763


title: pbmc_population-based Illumina HT12v4_762


title: pbmc_population-based Illumina HT12v4_757


title: pbmc_population-based Illumina HT12v4_755


title: pbmc_population-based Illumina HT12v4_754


title: pbmc_population-based Illumina HT12v4_761


title: pbmc_population-based Illumina HT12v4_765


title: pbmc_population-based Illumina HT12v4_760


title: pbmc_population-based Illumina HT12v4_752


title: pbmc_population-based Illumina HT12v4_745


title: pbmc_population-based Illumina HT12v4_758


title: pbmc_population-based Illumina HT12v4_749


title: pbmc_population-based Illumina HT12v4_743


title: pbmc_population-based Illumina HT12v4_751


title: pbmc_population-based Illumina HT12v4_768


title: pbmc_population-based Illumina HT12v4_766


title: pbmc_population-based Illumina HT12v4_747


title: pbmc_population-based Illumina HT12v4_746


title: pbmc_population-based Illumina HT12v4_753


title: pbmc_population-based Illumina HT12v4_750


title: pbmc_population-based Illumina HT12v4_739


title: pbmc_population-based Illumina HT12v4_741


title: pbmc_population-based Illumina HT12v4_756


title: pbmc_population-based Illumina HT12v4_764


title: pbmc_population-based Illumina HT12v4_738


title: pbmc_population-based Illumina HT12v4_759


title: pbmc_population-based Illumina HT12v4_736


title: pbmc_population-based Illumina HT12v4_732


title: pbmc_population-based Illumina HT12v4_742


title: pbmc_population-based Illumina HT12v4_740


title: pbmc_population-based Illumina HT12v4_744


title: pbmc_population-based Illumina HT12v4_734


title: pbmc_population-based Illumina HT12v4_748


title: pbmc_population-based Illumina HT12v4_735


title: pbmc_population-based Illumina HT12v4_731


title: pbmc_population-based Illumina HT12v4_733


title: pbmc_population-based Illumina HT12v4_737


title: pbmc_population-based Illumina HT12v4_730


title: pbmc_population-based Illumina HT12v4_729


title: pbmc_population-based Illumina HT12v4_723


title: pbmc_population-based Illumina HT12v4_728


title: pbmc_population-based Illumina HT12v4_726


title: pbmc_population-based Illumina HT12v4_727


title: pbmc_population-based Illumina HT12v4_716


title: pbmc_population-based Illumina HT12v4_724


title: pbmc_population-based Illumina HT12v4_718


title: pbmc_population-based Illumina HT12v4_715


title: pbmc_population-based Illumina HT12v4_717


title: pbmc_population-based Illumina HT12v4_721


title: pbmc_population-based Illumina HT12v4_719


title: pbmc_population-based Illumina HT12v4_722


title: pbmc_population-based Illumina HT12v4_712


title: pbmc_population-based Illumina HT12v4_711


title: pbmc_population-based Illumina HT12v4_710


title: pbmc_population-based Illumina HT12v4_708


title: pbmc_population-based Illumina HT12v4_725


title: pbmc_population-based Illumina HT12v4_720


title: pbmc_population-based Illumina HT12v4_714


title: pbmc_population-based Illumina HT12v4_706


title: pbmc_population-based Illumina HT12v4_707


title: pbmc_population-based Illumina HT12v4_709


title: pbmc_population-based Illumina HT12v4_704


title: pbmc_population-based Illumina HT12v4_705


title: pbmc_population-based Illumina HT12v4_701


title: pbmc_population-based Illumina HT12v4_700


title: pbmc_population-based Illumina HT12v4_713


title: pbmc_population-based Illumina HT12v4_703


title: pbmc_population-based Illumina HT12v4_702


title: pbmc_population-based Illumina HT12v4_698


title: pbmc_population-based Illumina HT12v4_699


title: pbmc_population-based Illumina HT12v4_697


title: pbmc_population-based Illumina HT12v4_694


title: pbmc_population-based Illumina HT12v4_695


title: pbmc_population-based Illumina HT12v4_693


title: pbmc_population-based Illumina HT12v4_690


title: pbmc_population-based Illumina HT12v4_687


title: pbmc_population-based Illumina HT12v4_696


title: pbmc_population-based Illumina HT12v4_691


title: pbmc_population-based Illumina HT12v4_688


title: pbmc_population-based Illumina HT12v4_683


title: pbmc_population-based Illumina HT12v4_692


title: pbmc_population-based Illumina HT12v4_680


title: pbmc_population-based Illumina HT12v4_675


title: pbmc_population-based Illumina HT12v4_679


title: pbmc_population-based Illumina HT12v4_676


title: pbmc_population-based Illumina HT12v4_677


title: pbmc_population-based Illumina HT12v4_681


title: pbmc_population-based Illumina HT12v4_685


title: pbmc_population-based Illumina HT12v4_682


title: pbmc_population-based Illumina HT12v4_684


title: pbmc_population-based Illumina HT12v4_689


title: pbmc_population-based Illumina HT12v4_686


title: pbmc_population-based Illumina HT12v4_674


title: pbmc_population-based Illumina HT12v4_673


title: pbmc_population-based Illumina HT12v4_671


title: pbmc_population-based Illumina HT12v4_670


title: pbmc_population-based Illumina HT12v4_678


title: pbmc_population-based Illumina HT12v4_672


title: pbmc_population-based Illumina HT12v4_669


title: pbmc_population-based Illumina HT12v4_668


title: pbmc_population-based Illumina HT12v4_665


title: pbmc_population-based Illumina HT12v4_664


title: pbmc_population-based Illumina HT12v4_667


title: pbmc_population-based Illumina HT12v4_663


title: pbmc_population-based Illumina HT12v4_658


title: pbmc_population-based Illumina HT12v4_652


title: pbmc_population-based Illumina HT12v4_656


title: pbmc_population-based Illumina HT12v4_660


title: pbmc_population-based Illumina HT12v4_653


title: pbmc_population-based Illumina HT12v4_662


title: pbmc_population-based Illumina HT12v4_657


title: pbmc_population-based Illumina HT12v4_655


title: pbmc_population-based Illumina HT12v4_661


title: pbmc_population-based Illumina HT12v4_654


title: pbmc_population-based Illumina HT12v4_666


title: pbmc_population-based Illumina HT12v4_651


title: pbmc_population-based Illumina HT12v4_659


title: pbmc_population-based Illumina HT12v4_649


title: pbmc_population-based Illumina HT12v4_644


title: pbmc_population-based Illumina HT12v4_645


title: pbmc_population-based Illumina HT12v4_648


title: pbmc_population-based Illumina HT12v4_637


title: pbmc_population-based Illumina HT12v4_646


title: pbmc_population-based Illumina HT12v4_641


title: pbmc_population-based Illumina HT12v4_647


title: pbmc_population-based Illumina HT12v4_639


title: pbmc_population-based Illumina HT12v4_638


title: pbmc_population-based Illumina HT12v4_640


title: pbmc_population-based Illumina HT12v4_650


title: pbmc_population-based Illumina HT12v4_636


title: pbmc_population-based Illumina HT12v4_635


title: pbmc_population-based Illumina HT12v4_642


title: pbmc_population-based Illumina HT12v4_643


title: pbmc_population-based Illumina HT12v4_633


title: pbmc_population-based Illumina HT12v4_632


title: pbmc_population-based Illumina HT12v4_634


title: pbmc_population-based Illumina HT12v4_626


title: pbmc_population-based Illumina HT12v4_630


title: pbmc_population-based Illumina HT12v4_629


title: pbmc_population-based Illumina HT12v4_627


title: pbmc_population-based Illumina HT12v4_631


title: pbmc_population-based Illumina HT12v4_628


title: pbmc_population-based Illumina HT12v4_622


title: pbmc_population-based Illumina HT12v4_625


title: pbmc_population-based Illumina HT12v4_623


title: pbmc_population-based Illumina HT12v4_621


title: pbmc_population-based Illumina HT12v4_624


title: pbmc_population-based Illumina HT12v4_618


title: pbmc_population-based Illumina HT12v4_619


title: pbmc_population-based Illumina HT12v4_617


title: pbmc_population-based Illumina HT12v4_620


title: pbmc_population-based Illumina HT12v4_616


title: pbmc_population-based Illumina HT12v4_605


title: pbmc_population-based Illumina HT12v4_596


title: pbmc_population-based Illumina HT12v4_610


title: pbmc_population-based Illumina HT12v4_611


title: pbmc_population-based Illumina HT12v4_607


title: pbmc_population-based Illumina HT12v4_612


title: pbmc_population-based Illumina HT12v4_614


title: pbmc_population-based Illumina HT12v4_597


title: pbmc_population-based Illumina HT12v4_591


title: pbmc_population-based Illumina HT12v4_602


title: pbmc_population-based Illumina HT12v4_592


title: pbmc_population-based Illumina HT12v4_595


title: pbmc_population-based Illumina HT12v4_598


title: pbmc_population-based Illumina HT12v4_601


title: pbmc_population-based Illumina HT12v4_588


title: pbmc_population-based Illumina HT12v4_599


title: pbmc_population-based Illumina HT12v4_615


title: pbmc_population-based Illumina HT12v4_600


title: pbmc_population-based Illumina HT12v4_603


title: pbmc_population-based Illumina HT12v4_608


title: pbmc_population-based Illumina HT12v4_590


title: pbmc_population-based Illumina HT12v4_609


title: pbmc_population-based Illumina HT12v4_606


title: pbmc_population-based Illumina HT12v4_613


title: pbmc_population-based Illumina HT12v4_594


title: pbmc_population-based Illumina HT12v4_604


title: pbmc_population-based Illumina HT12v4_593


title: pbmc_population-based Illumina HT12v4_589


title: pbmc_population-based Illumina HT12v4_586


title: pbmc_population-based Illumina HT12v4_578


title: pbmc_population-based Illumina HT12v4_582


title: pbmc_population-based Illumina HT12v4_585


title: pbmc_population-based Illumina HT12v4_583


title: pbmc_population-based Illumina HT12v4_580


title: pbmc_population-based Illumina HT12v4_575


title: pbmc_population-based Illumina HT12v4_571


title: pbmc_population-based Illumina HT12v4_569


title: pbmc_population-based Illumina HT12v4_573


title: pbmc_population-based Illumina HT12v4_572


title: pbmc_population-based Illumina HT12v4_581


title: pbmc_population-based Illumina HT12v4_566


title: pbmc_population-based Illumina HT12v4_567


title: pbmc_population-based Illumina HT12v4_563


title: pbmc_population-based Illumina HT12v4_574


title: pbmc_population-based Illumina HT12v4_576


title: pbmc_population-based Illumina HT12v4_579


title: pbmc_population-based Illumina HT12v4_587


title: pbmc_population-based Illumina HT12v4_564


title: pbmc_population-based Illumina HT12v4_577


title: pbmc_population-based Illumina HT12v4_568


title: pbmc_population-based Illumina HT12v4_562


title: pbmc_population-based Illumina HT12v4_561


title: pbmc_population-based Illumina HT12v4_565


title: pbmc_population-based Illumina HT12v4_560


title: pbmc_population-based Illumina HT12v4_559


title: pbmc_population-based Illumina HT12v4_555


title: pbmc_population-based Illumina HT12v4_557


title: pbmc_population-based Illumina HT12v4_553


title: pbmc_population-based Illumina HT12v4_550


title: pbmc_population-based Illumina HT12v4_554


title: pbmc_population-based Illumina HT12v4_556


title: pbmc_population-based Illumina HT12v4_552


title: pbmc_population-based Illumina HT12v4_549


title: pbmc_population-based Illumina HT12v4_584


title: pbmc_population-based Illumina HT12v4_538


title: pbmc_population-based Illumina HT12v4_558


title: pbmc_population-based Illumina HT12v4_545


title: pbmc_population-based Illumina HT12v4_539


title: pbmc_population-based Illumina HT12v4_542


title: pbmc_population-based Illumina HT12v4_544


title: pbmc_population-based Illumina HT12v4_543


title: pbmc_population-based Illumina HT12v4_535


title: pbmc_population-based Illumina HT12v4_533


title: pbmc_population-based Illumina HT12v4_546


title: pbmc_population-based Illumina HT12v4_551


title: pbmc_population-based Illumina HT12v4_548


title: pbmc_population-based Illumina HT12v4_540


title: pbmc_population-based Illumina HT12v4_547


title: pbmc_population-based Illumina HT12v4_541


title: pbmc_population-based Illumina HT12v4_536


title: pbmc_population-based Illumina HT12v4_531


title: pbmc_population-based Illumina HT12v4_530


title: pbmc_population-based Illumina HT12v4_534


title: pbmc_population-based Illumina HT12v4_537


title: pbmc_population-based Illumina HT12v4_532


title: pbmc_population-based Illumina HT12v4_527


title: pbmc_population-based Illumina HT12v4_526


title: pbmc_population-based Illumina HT12v4_524


title: pbmc_population-based Illumina HT12v4_523


title: pbmc_population-based Illumina HT12v4_525


title: pbmc_population-based Illumina HT12v4_528


title: pbmc_population-based Illumina HT12v4_521


title: pbmc_population-based Illumina HT12v4_520


title: pbmc_population-based Illumina HT12v4_529


title: pbmc_population-based Illumina HT12v4_519


title: pbmc_population-based Illumina HT12v4_522


title: pbmc_population-based Illumina HT12v4_512


title: pbmc_population-based Illumina HT12v4_508


title: pbmc_population-based Illumina HT12v4_517


title: pbmc_population-based Illumina HT12v4_518


title: pbmc_population-based Illumina HT12v4_514


title: pbmc_population-based Illumina HT12v4_515


title: pbmc_population-based Illumina HT12v4_501


title: pbmc_population-based Illumina HT12v4_509


title: pbmc_population-based Illumina HT12v4_506


title: pbmc_population-based Illumina HT12v4_511


title: pbmc_population-based Illumina HT12v4_500


title: pbmc_population-based Illumina HT12v4_513


title: pbmc_population-based Illumina HT12v4_510


title: pbmc_population-based Illumina HT12v4_494


title: pbmc_population-based Illumina HT12v4_503


title: pbmc_population-based Illumina HT12v4_495


title: pbmc_population-based Illumina HT12v4_502


title: pbmc_population-based Illumina HT12v4_498


title: pbmc_population-based Illumina HT12v4_496


title: pbmc_population-based Illumina HT12v4_505


title: pbmc_population-based Illumina HT12v4_497


title: pbmc_population-based Illumina HT12v4_504


title: pbmc_population-based Illumina HT12v4_570


title: pbmc_population-based Illumina HT12v4_499


title: pbmc_population-based Illumina HT12v4_492


title: pbmc_population-based Illumina HT12v4_507


title: pbmc_population-based Illumina HT12v4_490


title: pbmc_population-based Illumina HT12v4_489


title: pbmc_population-based Illumina HT12v4_491


title: pbmc_population-based Illumina HT12v4_493


title: pbmc_population-based Illumina HT12v4_487


title: pbmc_population-based Illumina HT12v4_486


title: pbmc_population-based Illumina HT12v4_483


title: pbmc_population-based Illumina HT12v4_480


title: pbmc_population-based Illumina HT12v4_516


title: pbmc_population-based Illumina HT12v4_479


title: pbmc_population-based Illumina HT12v4_474


title: pbmc_population-based Illumina HT12v4_484


title: pbmc_population-based Illumina HT12v4_469


title: pbmc_population-based Illumina HT12v4_476


title: pbmc_population-based Illumina HT12v4_472


title: pbmc_population-based Illumina HT12v4_481


title: pbmc_population-based Illumina HT12v4_478


title: pbmc_population-based Illumina HT12v4_485


title: pbmc_population-based Illumina HT12v4_470


title: pbmc_population-based Illumina HT12v4_477


title: pbmc_population-based Illumina HT12v4_488


title: pbmc_population-based Illumina HT12v4_466


title: pbmc_population-based Illumina HT12v4_467


title: pbmc_population-based Illumina HT12v4_482


title: pbmc_population-based Illumina HT12v4_473


title: pbmc_population-based Illumina HT12v4_471


title: pbmc_population-based Illumina HT12v4_475


title: pbmc_population-based Illumina HT12v4_463


title: pbmc_population-based Illumina HT12v4_465


title: pbmc_population-based Illumina HT12v4_461


title: pbmc_population-based Illumina HT12v4_468


title: pbmc_population-based Illumina HT12v4_460


title: pbmc_population-based Illumina HT12v4_464


title: pbmc_population-based Illumina HT12v4_457


title: pbmc_population-based Illumina HT12v4_456


title: pbmc_population-based Illumina HT12v4_454


title: pbmc_population-based Illumina HT12v4_452


title: pbmc_population-based Illumina HT12v4_458


title: pbmc_population-based Illumina HT12v4_455


title: pbmc_population-based Illumina HT12v4_453


title: pbmc_population-based Illumina HT12v4_448


title: pbmc_population-based Illumina HT12v4_462


title: pbmc_population-based Illumina HT12v4_450


title: pbmc_population-based Illumina HT12v4_447


title: pbmc_population-based Illumina HT12v4_445


title: pbmc_population-based Illumina HT12v4_451


title: pbmc_population-based Illumina HT12v4_446


title: pbmc_population-based Illumina HT12v4_443


title: pbmc_population-based Illumina HT12v4_442


title: pbmc_population-based Illumina HT12v4_440


title: pbmc_population-based Illumina HT12v4_439


title: pbmc_population-based Illumina HT12v4_449


title: pbmc_population-based Illumina HT12v4_444


title: pbmc_population-based Illumina HT12v4_459


title: pbmc_population-based Illumina HT12v4_435


title: pbmc_population-based Illumina HT12v4_434


title: pbmc_population-based Illumina HT12v4_441


title: pbmc_population-based Illumina HT12v4_438


title: pbmc_population-based Illumina HT12v4_437


title: pbmc_population-based Illumina HT12v4_432


title: pbmc_population-based Illumina HT12v4_428


title: pbmc_population-based Illumina HT12v4_429


title: pbmc_population-based Illumina HT12v4_424


title: pbmc_population-based Illumina HT12v4_422


title: pbmc_population-based Illumina HT12v4_425


title: pbmc_population-based Illumina HT12v4_427


title: pbmc_population-based Illumina HT12v4_421


title: pbmc_population-based Illumina HT12v4_419


title: pbmc_population-based Illumina HT12v4_418


title: pbmc_population-based Illumina HT12v4_436


title: pbmc_population-based Illumina HT12v4_417


title: pbmc_population-based Illumina HT12v4_412


title: pbmc_population-based Illumina HT12v4_430


title: pbmc_population-based Illumina HT12v4_413


title: pbmc_population-based Illumina HT12v4_416


title: pbmc_population-based Illumina HT12v4_420


title: pbmc_population-based Illumina HT12v4_423


title: pbmc_population-based Illumina HT12v4_414


title: pbmc_population-based Illumina HT12v4_431


title: pbmc_population-based Illumina HT12v4_410


title: pbmc_population-based Illumina HT12v4_415


title: pbmc_population-based Illumina HT12v4_433


title: pbmc_population-based Illumina HT12v4_411


title: pbmc_population-based Illumina HT12v4_405


title: pbmc_population-based Illumina HT12v4_409


title: pbmc_population-based Illumina HT12v4_406


title: pbmc_population-based Illumina HT12v4_407


title: pbmc_population-based Illumina HT12v4_408


title: pbmc_population-based Illumina HT12v4_402


title: pbmc_population-based Illumina HT12v4_404


title: pbmc_population-based Illumina HT12v4_397


title: pbmc_population-based Illumina HT12v4_395


title: pbmc_population-based Illumina HT12v4_400


title: pbmc_population-based Illumina HT12v4_396


title: pbmc_population-based Illumina HT12v4_398


title: pbmc_population-based Illumina HT12v4_393


title: pbmc_population-based Illumina HT12v4_401


title: pbmc_population-based Illumina HT12v4_390


title: pbmc_population-based Illumina HT12v4_403


title: pbmc_population-based Illumina HT12v4_387


title: pbmc_population-based Illumina HT12v4_426


title: pbmc_population-based Illumina HT12v4_392


title: pbmc_population-based Illumina HT12v4_389


title: pbmc_population-based Illumina HT12v4_391


title: pbmc_population-based Illumina HT12v4_394


title: pbmc_population-based Illumina HT12v4_388


title: pbmc_population-based Illumina HT12v4_383


title: pbmc_population-based Illumina HT12v4_399


title: pbmc_population-based Illumina HT12v4_386


title: pbmc_population-based Illumina HT12v4_385


title: pbmc_population-based Illumina HT12v4_382


title: pbmc_population-based Illumina HT12v4_381


title: pbmc_population-based Illumina HT12v4_380


title: pbmc_population-based Illumina HT12v4_378


title: pbmc_population-based Illumina HT12v4_377


title: pbmc_population-based Illumina HT12v4_374


title: pbmc_population-based Illumina HT12v4_376


title: pbmc_population-based Illumina HT12v4_384


title: pbmc_population-based Illumina HT12v4_375


title: pbmc_population-based Illumina HT12v4_379


title: pbmc_population-based Illumina HT12v4_370


title: pbmc_population-based Illumina HT12v4_369


title: pbmc_population-based Illumina HT12v4_367


title: pbmc_population-based Illumina HT12v4_371


title: pbmc_population-based Illumina HT12v4_368


title: pbmc_population-based Illumina HT12v4_366


title: pbmc_population-based Illumina HT12v4_362


title: pbmc_population-based Illumina HT12v4_373


title: pbmc_population-based Illumina HT12v4_365


title: pbmc_population-based Illumina HT12v4_353


title: pbmc_population-based Illumina HT12v4_355


title: pbmc_population-based Illumina HT12v4_361


title: pbmc_population-based Illumina HT12v4_356


title: pbmc_population-based Illumina HT12v4_364


title: pbmc_population-based Illumina HT12v4_358


title: pbmc_population-based Illumina HT12v4_359


title: pbmc_population-based Illumina HT12v4_354


title: pbmc_population-based Illumina HT12v4_360


title: pbmc_population-based Illumina HT12v4_352


title: pbmc_population-based Illumina HT12v4_357


title: pbmc_population-based Illumina HT12v4_348


title: pbmc_population-based Illumina HT12v4_345


title: pbmc_population-based Illumina HT12v4_344


title: pbmc_population-based Illumina HT12v4_349


title: pbmc_population-based Illumina HT12v4_346


title: pbmc_population-based Illumina HT12v4_351


title: pbmc_population-based Illumina HT12v4_350


title: pbmc_population-based Illumina HT12v4_347


title: pbmc_population-based Illumina HT12v4_338


title: pbmc_population-based Illumina HT12v4_342


title: pbmc_population-based Illumina HT12v4_341


title: pbmc_population-based Illumina HT12v4_339


title: pbmc_population-based Illumina HT12v4_340


title: pbmc_population-based Illumina HT12v4_336


title: pbmc_population-based Illumina HT12v4_337


title: pbmc_population-based Illumina HT12v4_334


title: pbmc_population-based Illumina HT12v4_327


title: pbmc_population-based Illumina HT12v4_343


title: pbmc_population-based Illumina HT12v4_333


title: pbmc_population-based Illumina HT12v4_331


title: pbmc_population-based Illumina HT12v4_330


title: pbmc_population-based Illumina HT12v4_332


title: pbmc_population-based Illumina HT12v4_326


title: pbmc_population-based Illumina HT12v4_329


title: pbmc_population-based Illumina HT12v4_320


title: pbmc_population-based Illumina HT12v4_323


title: pbmc_population-based Illumina HT12v4_319


title: pbmc_population-based Illumina HT12v4_317


title: pbmc_population-based Illumina HT12v4_318


title: pbmc_population-based Illumina HT12v4_322


title: pbmc_population-based Illumina HT12v4_363


title: pbmc_population-based Illumina HT12v4_325


title: pbmc_population-based Illumina HT12v4_311


title: pbmc_population-based Illumina HT12v4_324


title: pbmc_population-based Illumina HT12v4_313


title: pbmc_population-based Illumina HT12v4_316


title: pbmc_population-based Illumina HT12v4_309


title: pbmc_population-based Illumina HT12v4_310


title: pbmc_population-based Illumina HT12v4_312


title: pbmc_population-based Illumina HT12v4_314


title: pbmc_population-based Illumina HT12v4_305


title: pbmc_population-based Illumina HT12v4_302


title: pbmc_population-based Illumina HT12v4_306


title: pbmc_population-based Illumina HT12v4_307


title: pbmc_population-based Illumina HT12v4_304


title: pbmc_population-based Illumina HT12v4_303


title: pbmc_population-based Illumina HT12v4_328


title: pbmc_population-based Illumina HT12v4_301


title: pbmc_population-based Illumina HT12v4_295


title: pbmc_population-based Illumina HT12v4_293


title: pbmc_population-based Illumina HT12v4_315


title: pbmc_population-based Illumina HT12v4_296


title: pbmc_population-based Illumina HT12v4_297


title: pbmc_population-based Illumina HT12v4_298


title: pbmc_population-based Illumina HT12v4_299


title: pbmc_population-based Illumina HT12v4_292


title: pbmc_population-based Illumina HT12v4_300


title: pbmc_population-based Illumina HT12v4_291


title: pbmc_population-based Illumina HT12v4_290


title: pbmc_population-based Illumina HT12v4_294


title: pbmc_population-based Illumina HT12v4_372


title: pbmc_population-based Illumina HT12v4_289


title: pbmc_population-based Illumina HT12v4_321


title: pbmc_population-based Illumina HT12v4_281


title: pbmc_population-based Illumina HT12v4_286


title: pbmc_population-based Illumina HT12v4_283


title: pbmc_population-based Illumina HT12v4_277


title: pbmc_population-based Illumina HT12v4_285


title: pbmc_population-based Illumina HT12v4_287


title: pbmc_population-based Illumina HT12v4_280


title: pbmc_population-based Illumina HT12v4_282


title: pbmc_population-based Illumina HT12v4_278


title: pbmc_population-based Illumina HT12v4_279


title: pbmc_population-based Illumina HT12v4_284


title: pbmc_population-based Illumina HT12v4_288


title: pbmc_population-based Illumina HT12v4_276


title: pbmc_population-based Illumina HT12v4_272


title: pbmc_population-based Illumina HT12v4_275


title: pbmc_population-based Illumina HT12v4_274


title: pbmc_population-based Illumina HT12v4_269


title: pbmc_population-based Illumina HT12v4_268


title: pbmc_population-based Illumina HT12v4_273


title: pbmc_population-based Illumina HT12v4_262


title: pbmc_population-based Illumina HT12v4_271


title: pbmc_population-based Illumina HT12v4_264


title: pbmc_population-based Illumina HT12v4_265


title: pbmc_population-based Illumina HT12v4_267


title: pbmc_population-based Illumina HT12v4_270


title: pbmc_population-based Illumina HT12v4_263


title: pbmc_population-based Illumina HT12v4_259


title: pbmc_population-based Illumina HT12v4_261


title: pbmc_population-based Illumina HT12v4_266


title: pbmc_population-based Illumina HT12v4_255


title: pbmc_population-based Illumina HT12v4_257


title: pbmc_population-based Illumina HT12v4_251


title: pbmc_population-based Illumina HT12v4_260


title: pbmc_population-based Illumina HT12v4_254


title: pbmc_population-based Illumina HT12v4_246


title: pbmc_population-based Illumina HT12v4_258


title: pbmc_population-based Illumina HT12v4_249


title: pbmc_population-based Illumina HT12v4_253


title: pbmc_population-based Illumina HT12v4_308


title: pbmc_population-based Illumina HT12v4_250


title: pbmc_population-based Illumina HT12v4_256


title: pbmc_population-based Illumina HT12v4_247


title: pbmc_population-based Illumina HT12v4_252


title: pbmc_population-based Illumina HT12v4_244


title: pbmc_population-based Illumina HT12v4_241


title: pbmc_population-based Illumina HT12v4_243


title: pbmc_population-based Illumina HT12v4_248


title: pbmc_population-based Illumina HT12v4_236


title: pbmc_population-based Illumina HT12v4_238


title: pbmc_population-based Illumina HT12v4_335


title: pbmc_population-based Illumina HT12v4_245


title: pbmc_population-based Illumina HT12v4_235


title: pbmc_population-based Illumina HT12v4_239


title: pbmc_population-based Illumina HT12v4_242


title: pbmc_population-based Illumina HT12v4_234


title: pbmc_population-based Illumina HT12v4_233


title: pbmc_population-based Illumina HT12v4_240


title: pbmc_population-based Illumina HT12v4_232


title: pbmc_population-based Illumina HT12v4_237


title: pbmc_population-based Illumina HT12v4_228


title: pbmc_population-based Illumina HT12v4_223


title: pbmc_population-based Illumina HT12v4_220


title: pbmc_population-based Illumina HT12v4_230


title: pbmc_population-based Illumina HT12v4_224


title: pbmc_population-based Illumina HT12v4_218


title: pbmc_population-based Illumina HT12v4_219


title: pbmc_population-based Illumina HT12v4_221


title: pbmc_population-based Illumina HT12v4_216


title: pbmc_population-based Illumina HT12v4_229


title: pbmc_population-based Illumina HT12v4_211


title: pbmc_population-based Illumina HT12v4_225


title: pbmc_population-based Illumina HT12v4_210


title: pbmc_population-based Illumina HT12v4_213


title: pbmc_population-based Illumina HT12v4_231


title: pbmc_population-based Illumina HT12v4_222


title: pbmc_population-based Illumina HT12v4_227


title: pbmc_population-based Illumina HT12v4_226


title: pbmc_population-based Illumina HT12v4_212


title: pbmc_population-based Illumina HT12v4_215


title: pbmc_population-based Illumina HT12v4_214


title: pbmc_population-based Illumina HT12v4_205


title: pbmc_population-based Illumina HT12v4_208


title: pbmc_population-based Illumina HT12v4_203


title: pbmc_population-based Illumina HT12v4_202


title: pbmc_population-based Illumina HT12v4_209


title: pbmc_population-based Illumina HT12v4_207


title: pbmc_population-based Illumina HT12v4_206


title: pbmc_population-based Illumina HT12v4_204


title: pbmc_population-based Illumina HT12v4_201


title: pbmc_population-based Illumina HT12v4_198


title: pbmc_population-based Illumina HT12v4_196


title: pbmc_population-based Illumina HT12v4_186


title: pbmc_population-based Illumina HT12v4_192


title: pbmc_population-based Illumina HT12v4_187


title: pbmc_population-based Illumina HT12v4_200


title: pbmc_population-based Illumina HT12v4_199


title: pbmc_population-based Illumina HT12v4_197


title: pbmc_population-based Illumina HT12v4_188


title: pbmc_population-based Illumina HT12v4_191


title: pbmc_population-based Illumina HT12v4_193


title: pbmc_population-based Illumina HT12v4_190


title: pbmc_population-based Illumina HT12v4_194


title: pbmc_population-based Illumina HT12v4_195


title: pbmc_population-based Illumina HT12v4_185


title: pbmc_population-based Illumina HT12v4_183


title: pbmc_population-based Illumina HT12v4_182


title: pbmc_population-based Illumina HT12v4_184


title: pbmc_population-based Illumina HT12v4_181


title: pbmc_population-based Illumina HT12v4_179


title: pbmc_population-based Illumina HT12v4_175


title: pbmc_population-based Illumina HT12v4_189


title: pbmc_population-based Illumina HT12v4_177


title: pbmc_population-based Illumina HT12v4_173


title: pbmc_population-based Illumina HT12v4_168


title: pbmc_population-based Illumina HT12v4_171


title: pbmc_population-based Illumina HT12v4_169


title: pbmc_population-based Illumina HT12v4_170


title: pbmc_population-based Illumina HT12v4_178


title: pbmc_population-based Illumina HT12v4_176


title: pbmc_population-based Illumina HT12v4_180


title: pbmc_population-based Illumina HT12v4_174


title: pbmc_population-based Illumina HT12v4_172


title: pbmc_population-based Illumina HT12v4_167


title: pbmc_population-based Illumina HT12v4_159


title: pbmc_population-based Illumina HT12v4_154


title: pbmc_population-based Illumina HT12v4_155


title: pbmc_population-based Illumina HT12v4_217


title: pbmc_population-based Illumina HT12v4_156


title: pbmc_population-based Illumina HT12v4_165


title: pbmc_population-based Illumina HT12v4_164


title: pbmc_population-based Illumina HT12v4_157


title: pbmc_population-based Illumina HT12v4_160


title: pbmc_population-based Illumina HT12v4_158


title: pbmc_population-based Illumina HT12v4_162


title: pbmc_population-based Illumina HT12v4_163


title: pbmc_population-based Illumina HT12v4_161


title: pbmc_population-based Illumina HT12v4_166


title: pbmc_population-based Illumina HT12v4_151


title: pbmc_population-based Illumina HT12v4_153


title: pbmc_population-based Illumina HT12v4_149


title: pbmc_population-based Illumina HT12v4_150


title: pbmc_population-based Illumina HT12v4_148


title: pbmc_population-based Illumina HT12v4_146


title: pbmc_population-based Illumina HT12v4_140


title: pbmc_population-based Illumina HT12v4_144


title: pbmc_population-based Illumina HT12v4_141


title: pbmc_population-based Illumina HT12v4_147


title: pbmc_population-based Illumina HT12v4_152


title: pbmc_population-based Illumina HT12v4_145


title: pbmc_population-based Illumina HT12v4_142


title: pbmc_population-based Illumina HT12v4_143


title: pbmc_population-based Illumina HT12v4_139


title: pbmc_population-based Illumina HT12v4_137


title: pbmc_population-based Illumina HT12v4_133


title: pbmc_population-based Illumina HT12v4_136


title: pbmc_population-based Illumina HT12v4_138


title: pbmc_population-based Illumina HT12v4_134


title: pbmc_population-based Illumina HT12v4_132


title: pbmc_population-based Illumina HT12v4_135


title: pbmc_population-based Illumina HT12v4_125


title: pbmc_population-based Illumina HT12v4_129


title: pbmc_population-based Illumina HT12v4_131


title: pbmc_population-based Illumina HT12v4_130


title: pbmc_population-based Illumina HT12v4_126


title: pbmc_population-based Illumina HT12v4_117


title: pbmc_population-based Illumina HT12v4_123


title: pbmc_population-based Illumina HT12v4_121


title: pbmc_population-based Illumina HT12v4_122


title: pbmc_population-based Illumina HT12v4_119


title: pbmc_population-based Illumina HT12v4_110


title: pbmc_population-based Illumina HT12v4_115


title: pbmc_population-based Illumina HT12v4_120


title: pbmc_population-based Illumina HT12v4_127


title: pbmc_population-based Illumina HT12v4_114


title: pbmc_population-based Illumina HT12v4_124


title: pbmc_population-based Illumina HT12v4_108


title: pbmc_population-based Illumina HT12v4_109


title: pbmc_population-based Illumina HT12v4_113


title: pbmc_population-based Illumina HT12v4_111


title: pbmc_population-based Illumina HT12v4_112


title: pbmc_population-based Illumina HT12v4_118


title: pbmc_population-based Illumina HT12v4_128


title: pbmc_population-based Illumina HT12v4_116


title: pbmc_population-based Illumina HT12v4_106


title: pbmc_population-based Illumina HT12v4_107


title: pbmc_population-based Illumina HT12v4_105


title: pbmc_population-based Illumina HT12v4_103


title: pbmc_population-based Illumina HT12v4_98


title: pbmc_population-based Illumina HT12v4_99


title: pbmc_population-based Illumina HT12v4_102


title: pbmc_population-based Illumina HT12v4_104


title: pbmc_population-based Illumina HT12v4_96


title: pbmc_population-based Illumina HT12v4_91


title: pbmc_population-based Illumina HT12v4_86


title: pbmc_population-based Illumina HT12v4_97


title: pbmc_population-based Illumina HT12v4_85


title: pbmc_population-based Illumina HT12v4_89


title: pbmc_population-based Illumina HT12v4_95


title: pbmc_population-based Illumina HT12v4_92


title: pbmc_population-based Illumina HT12v4_90


title: pbmc_population-based Illumina HT12v4_93


title: pbmc_population-based Illumina HT12v4_94


title: pbmc_population-based Illumina HT12v4_79


title: pbmc_population-based Illumina HT12v4_80


title: pbmc_population-based Illumina HT12v4_83


title: pbmc_population-based Illumina HT12v4_88


title: pbmc_population-based Illumina HT12v4_101


title: pbmc_population-based Illumina HT12v4_82


title: pbmc_population-based Illumina HT12v4_84


title: pbmc_population-based Illumina HT12v4_100


title: pbmc_population-based Illumina HT12v4_78


title: pbmc_population-based Illumina HT12v4_77


title: pbmc_population-based Illumina HT12v4_74


title: pbmc_population-based Illumina HT12v4_81


title: pbmc_population-based Illumina HT12v4_75


title: pbmc_population-based Illumina HT12v4_76


title: pbmc_population-based Illumina HT12v4_87


title: pbmc_population-based Illumina HT12v4_71


title: pbmc_population-based Illumina HT12v4_73


title: pbmc_population-based Illumina HT12v4_60


title: pbmc_population-based Illumina HT12v4_67


title: pbmc_population-based Illumina HT12v4_68


title: pbmc_population-based Illumina HT12v4_66


title: pbmc_population-based Illumina HT12v4_72


title: pbmc_population-based Illumina HT12v4_61


title: pbmc_population-based Illumina HT12v4_64


title: pbmc_population-based Illumina HT12v4_52


title: pbmc_population-based Illumina HT12v4_65


title: pbmc_population-based Illumina HT12v4_56


title: pbmc_population-based Illumina HT12v4_62


title: pbmc_population-based Illumina HT12v4_58


title: pbmc_population-based Illumina HT12v4_70


title: pbmc_population-based Illumina HT12v4_53


title: pbmc_population-based Illumina HT12v4_59


title: pbmc_population-based Illumina HT12v4_45


title: pbmc_population-based Illumina HT12v4_63


title: pbmc_population-based Illumina HT12v4_54


title: pbmc_population-based Illumina HT12v4_50


title: pbmc_population-based Illumina HT12v4_49


title: pbmc_population-based Illumina HT12v4_46


title: pbmc_population-based Illumina HT12v4_48


title: pbmc_population-based Illumina HT12v4_51


title: pbmc_population-based Illumina HT12v4_55


title: pbmc_population-based Illumina HT12v4_57


title: pbmc_population-based Illumina HT12v4_69


title: pbmc_population-based Illumina HT12v4_47


title: pbmc_population-based Illumina HT12v4_44


title: pbmc_population-based Illumina HT12v4_39


title: pbmc_population-based Illumina HT12v4_38


title: pbmc_population-based Illumina HT12v4_42


title: pbmc_population-based Illumina HT12v4_40


title: pbmc_population-based Illumina HT12v4_31


title: pbmc_population-based Illumina HT12v4_41


title: pbmc_population-based Illumina HT12v4_34


title: pbmc_population-based Illumina HT12v4_43


title: pbmc_population-based Illumina HT12v4_35


title: pbmc_population-based Illumina HT12v4_32


title: pbmc_population-based Illumina HT12v4_37


title: pbmc_population-based Illumina HT12v4_30


title: pbmc_population-based Illumina HT12v4_28


title: pbmc_population-based Illumina HT12v4_36


title: pbmc_population-based Illumina HT12v4_29


title: pbmc_population-based Illumina HT12v4_27


title: pbmc_population-based Illumina HT12v4_33


title: E21 fetal lung, mother fed 200 mM acetate in drinking water, biological rep4

city: Clayton

first: Charles

last: Mackay

state: VIC

address: Wellington st

country: Australia

institute: Monash University

description: Gene expression data from fetal lung E21  Mother fed with 200 mM in drinking water

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

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

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

organism: Mus musculus

source_name: E21 fetal lung mother on 200 mM acetate in drinking water

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

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

treatment_protocol: Whole lung, unmanipulated, was dissected from E21 fetal mice. The mothers of these mice had been fed either high fibre diet, or acetate in drinking water, or normal chow.

tag: tissue

value: E21 fetal lung

tag: strain

tag: age

value: E21 fetal tissue from mothers approx 10 weeks of age

tag: diet

value: 200 mM acetate in drinking water


title: E21 fetal lung, mother fed 200 mM acetate in drinking water, biological rep3


title: E21 fetal lung, mother fed 200 mM acetate in drinking water, biological rep2


title: pbmc_population-based Illumina HT12v4_25


title: E21 fetal lung, mother fed normal chow, biological rep4

description: Gene expression data from fetal lung E21  Mother fed normal chow

source_name: E21 fetal lung mother on normal chow

value: normal chow


title: E21 fetal lung, mother fed 200 mM acetate in drinking water, biological rep1


title: pbmc_population-based Illumina HT12v4_24


title: E21 fetal lung, mother fed high fibre diet, biological rep3

description: Gene expression data from fetal lung E21  Mother fed high fibre diet

source_name: E21 fetal lung mother on high fibre diet

value: high fibre diet


title: pbmc_population-based Illumina HT12v4_26


title: pbmc_population-based Illumina HT12v4_19


title: pbmc_population-based Illumina HT12v4_22


title: pbmc_population-based Illumina HT12v4_21


title: E21 fetal lung, mother fed high fibre diet, biological rep2


title: E21 fetal lung, mother fed high fibre diet, biological rep4


title: pbmc_population-based Illumina HT12v4_23


title: E21 fetal lung, mother fed normal chow, biological rep3


title: E21 fetal lung, mother fed high fibre diet, biological rep1


title: E21 fetal lung, mother fed normal chow, biological rep2


title: pbmc_population-based Illumina HT12v4_18


title: pbmc_population-based Illumina HT12v4_4


title: E21 fetal lung, mother fed normal chow, biological rep1


title: pbmc_population-based Illumina HT12v4_17


title: pbmc_population-based Illumina HT12v4_11


title: pbmc_population-based Illumina HT12v4_6


title: pbmc_population-based Illumina HT12v4_15


title: pbmc_population-based Illumina HT12v4_13


title: pbmc_population-based Illumina HT12v4_16


title: pbmc_population-based Illumina HT12v4_5


title: pbmc_population-based Illumina HT12v4_10


title: pbmc_population-based Illumina HT12v4_7


title: pbmc_population-based Illumina HT12v4_8


title: M2

type: genomic

city: Beijing

first: Huimin

last: Kang

state: Beijing

address: Beijing

country: China

institute: China Agriculture University

description: 1M probes in total

hyb_protocol: according to the productor's instruction.

data_processing:
Raw data was normalized (algorithm: LOWESS) using Feature Extraction software 10.7 (Agilent technologies). Then Agilent Genomic Workbench Standard Edition 6.5 software (Agilent Technologies) was used to perform the statistical analysis for CNV interval detection.
The Aberration Detection Method 2 algorithm (ADM2), with threshold of 6, bin of 10, and a centralization threshold of 6, was used to identify genomic variation given the log2 ratio of fluorescent signals between test and reference DNA samples.  Additonally, we applied a relatively stringent post-analysis filter: 5 probes, 0.5 log ratio, to ignore small, spurious, or low-quality aberrations.

molecule: genomic DNA

organism: Sus scrofa

source_name: ear tissue

label_protocol: Test DNA and reference DNA samples were independently labeled with either Cy3 or Cy5 dyes.

extract_protocol: Genomic DNA for each individuals was extracted from the ear tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany).

tag: breed

value: Min pig

value: female

value: ear

source_name: reference sample

value: Duroc


title: W1

description: 1M probes in total

scan_protocol: according to the productor's instruction.

value: Daweizi pig


title: pbmc_population-based Illumina HT12v4_12


title: pbmc_population-based Illumina HT12v4_9


title: DN5

description: 1M probes in total

value: Diannan small-ear pig


title: A1

description: 1M probes in total

value: wild pig


title: R2

description: 1M probes in total

value: Rongchang pig

value: male


title: C57BL/6J-WT2

city: St. Louis

first: Joseph

middle: D

last: Planer

state: Missouri

address: 4444 Forest Park Ave

department: Pathology

country: USA

institute: Washington University School of Medicine

description: Sample name: 15383

hyb_protocol: Standard Affymetrix protocols were used for hybridization of the cDNA targets to each B. thetaiotaomicron GeneChip

scan_protocol: Standard Affymetrix protocols were used

data_processing:
Arrays were normalized in dChip2006, using Model-based expression filtered on B. thetaiotaomicron probes, with Mismatch probe background subtraction based on medial quantiles and a running median smoothing method.
After normalization of the data, model-based expression values were generated (PM-MM model). Signals from spike-in control transcripts and oligo-B2 (Affymetrix) were used to assess the quality of target preparation and target hybridization, respectively.

organism: Bacteroides thetaiotaomicron

source_name: C57BL/6J WT mouse replicate 2

label_protocol: The cDNA product was isolated (QiaQuick Spin columns; Qiagen), fragmented by treatment with DNase I (Amersham Biosciences), and biotinylated (BioArray Terminal Labeling Kit, Enzo).

growth_protocol: 260.8 hybridoma cells were grown in DMEM supplemented with penicillin (100 units/mL) and streptomycin (100µg/mL) until they were 50-75% confluent and subsequently washed three times in pyrogen-free saline. Cells were introduced into the gnotobiotic isolators in a way that preserved sterility and then injected subcutaneously on the dorsum of germ-free 6-8 week-old male C57BL/6J Rag1-/- recipients (2x10^6 cells/mouse). Ten days after implantation, each mouse with a palpable subcutaneous hybridoma was colonized with a single gavage of 10^8 CFU of B. thetaiotaomicron.

extract_protocol: Cecal contents were flash frozen in liquid nitrogen immediately after their harvest from each mouse in each treatment group (n=4 mice/group with hybridoma backpacks and controls). An aliquot (~200 mg) was thawed in 2-3 volumes of RNAProtect (Qiagen), centrifuged (3,000 x g for 10 min), and 500µL of 200mM NaCl/20 mM EDTA was added to the resulting pellet together with 200µL of 20% SDS and 500µL phenol:chloroform:isoamyl alcohol (125:24:1; pH 4.5; Ambion). Acid-washed silica beads (Sigma; 212-300µm diameter; 250mg) were added to the mixture and bacteria were lysed (Mini-Beadbeater; Biospec; ‘high’ setting for 5 min at room temperature). Following centrifugation (13,000 x g for 3 min at 4˚C), the sample was re-extracted in phenol:chloroform:isoamyl alcohol, precipitated with 60µL of 3M sodium acetate (pH 5.2) plus 600µL of cold isopropanol. RNA was purified (RNEasy kit; Qiagen). Residual genomic DNA was subsequently removed by treatment with DNAfree (Ambion).

treatment_protocol: Mice were sacrificed 10 d following colonization and cecal contents were recovered.

tag: monocolonized host

value: C57BL/6J WT mouse

value: cecal contents of monocolonized mouse


title: Z5

description: 1M probes in total

value: Tibetan pig


title: MS8

description: 1M probes in total

value: Meishan pig


title: pbmc_population-based Illumina HT12v4_14

value: M

value: peripheral blood mononuclear cells (PBMCs)


title: MS7

description: 1M probes in total


title: C3

description: 1M probes in total

value: Landrace


title: Y2

description: 1M probes in total

value: Yorkshire


title: Z2

description: 1M probes in total


title: DN1

description: 1M probes in total


title: pbmc_population-based Illumina HT12v4_20

value: F


title: pbmc_population-based Illumina HT12v4_1


title: Rag-3

description: Sample name: 15379

source_name: Rag1-/- mouse replicate 3

value: Rag1-/- mouse


title: Ecoli_AUGnsrR_rep3

status: Public on Jun 27 2015

city: Richardson

first: Stephen

last: Spiro

state: TX

address: 800 West Campbell Road

department: Molecular and Cell Biology

institute: University of Texas at Dallas

description: This sample is of Escherichia coli MG1655 K-12 containing a modified nsrR (AUGnsrR). It is the third of three AUGnsrR strain biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al., 2003, Biostatistics 4:249), quantile normalization (Bolstad et al., 2003, Bioinformatics 19:185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli MG1655 K-12 AUGnsrR

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: The cultures were grown aerobically at 37ºC in L broth to mid-exponential phase (OD650nm = ~0.6).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and the RNAprotect reagent (Qiagen). Contaminating DNA was removed by on-column DNase digestion by the RNase-Free DNase Set (Qiagen), and RNA purity was checked by UV absorbance and by agarose gel electrophoresis.

tag: genotype

value: nsrR deletion, leu::AUGnsrR-kan


title: Ecoli_WTnsrR_rep1

description: This sample is of Escherichia coli MG1655 K-12 containing a wild-type nsrR (GUGnsrR). It is the first of three WT strain biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli MG1655 K-12 wild-type nsrR

value: nsrR deletion, leu::GUGnsrR-kan


title: BP-4

description: Sample name: 15374

source_name: Rag1-/- 260.8 backpack  mouse replicate 4

value: Rag1-/- 260.8 backpack mouse


title: Ecoli_AUGnsrR_rep1

description: This sample is of Escherichia coli MG1655 K-12 containing a modified nsrR (AUGnsrR). It is the first of three AUGnsrR strain biological replicates used in this experiment, each from separate cultures.


title: Rag-1

description: Sample name: 15377

source_name: Rag1-/- mouse replicate 1


title: Rag-2

description: Sample name: 15378

source_name: Rag1-/- mouse replicate 2


title: Ecoli_AUGnsrR_rep2

description: This sample is of Escherichia coli MG1655 K-12 containing a modified nsrR (AUGnsrR). It is the second of three AUGnsrR strain biological replicates used in this experiment, each from separate cultures.


title: Ecoli_WTnsrR_rep2

description: This sample is of Escherichia coli MG1655 K-12 containing a wild-type nsrR (GUGnsrR). It is the second of three WT strain biological replicates used in this experiment, each from separate cultures.


title: Rag-4

description: Sample name: 15380

source_name: Rag1-/- mouse replicate 4


title: Ecoli_dnsrR_rep3

description: This sample is of Escherichia coli MG1655 K-12 lacking the nsrR gene. It is the third of three mutant strain biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli MG1655 K-12 nsrR-deletion

value: nsrR deletion, leu::kan


title: Ecoli_WTnsrR_rep3

description: This sample is of Escherichia coli MG1655 K-12 containing a wild-type nsrR (GUGnsrR). It is the third of three WT strain biological replicates used in this experiment, each from separate cultures.


title: BP-2

description: Sample name: 15372

source_name: Rag1-/- 260.8 backpack mouse replicate 2


title: Ecoli_dnsrR_rep2

description: This sample is of Escherichia coli MG1655 K-12 lacking the nsrR gene. It is the second of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: C57BL/6J-WT4

description: Sample name: 15385

source_name: C57BL/6J WT mouse replicate 4


title: pbmc_population-based Illumina HT12v4_3


title: C57BL/6J-WT3

description: Sample name: 15384

source_name: C57BL/6J WT mouse replicate 3


title: BP-1

description: Sample name: 15371

source_name: Rag1-/- 260.8 backpack mouse replicate 1


title: Ecoli_dnsrR_rep1

description: This sample is of Escherichia coli MG1655 K-12 lacking the nsrR gene. It is the first of three mutant strain biological replicates used in this experiment, each from separate cultures.


title: Psoriasis Patient 1 Doublets

city: Cleveland

first: Jackelyn

middle: B

last: Golden

state: Ohio

address: 2109 Adelbert Rd

department: Dermatology

institute: Case Western Reserve University

description: Test

data_processing:
RT-PCR data was uploaded to the SA Biosciences RT2 Profiler PR Array Data Analysis site, where all samples were normalized to the housekeeping gene HPRT1. Each individual patient's singlet monocytes served as the comparator for the test conditions of doublet monocytes and adhered monocytes. The exported document from the software contained raw  CT values, normalized CT values, and their corresponding fold changes.
SA Biosciences RT2 Profiler PR Array Data Online Analysis computed normalized signal based on housekeeping genes, fold changes calculated from ratios of doublet monocytes compared to singlet monocytes or adhered monocytes compared to singlet monocytes using the following equation: =IF(value>1,value,(1/value)*-1).

label: SYBR Green

source_name: Human Peripheral Blood, Sorted Classical Monocyte Aggregates

label_protocol: cDNA was generated using the RT2 First Strand Kit (SA Biosciences, Valencia, CA). cDNA was combined with RT2 SYBR Green Mastermix and dispensed into a PCR Array for Human Extracellular Matrix & Adhesion Molecules (Qiagen) with a 384 (4 x 96) E, G format. The plates were run on an ABI 7900HT machine via the associated protocol on the SA Biosciences website [One hold, 10 minutes at 95C] [40 cycles of 15 seconds at 95C, 1 minutes at 60C]

growth_protocol: Primary cells (PBMCs) were isolated from 5 controls and 5 psoriasis patients using Ficoll-Paque centrifugation, washed, and red blood cells were lysed using ACK (Invitrogen, Carlsbad, CA);

extract_protocol: RNA was extracted from flow-sorted cells using the QIAGEN RNeasy Minikit in combination with the QIAGEN QIAshredder kit per the manufacturer's protocol.

treatment_protocol: PBMCs were immediately stained for surface markers, CD14 and CD16, for 20 minutes on ice. The PBMCs were then sorted for classical monocytes based on CD14 and CD16 co-expression.

value: Peripheral Blood Monocytes

tag: disease

value: Psoriasis

value: Male

tag: race

value: African American

value: blood


title: Psoriasis Patient 1 Singlets

description: Control

source_name: Human Peripheral Blood, Sorted Classical Monocytes


title: Healthy Control 5 Adhered

description: Test

source_name: Human Peripheral Blood, Sorted Classical Monocytes, Adhered to Plastic 4 hours

value: Caucasian


title: Healthy Control 4 Singlets

description: Control


title: Healthy Control 5 Doublets

description: Test


title: Healthy Control 4 Doublets

description: Test


title: Healthy Control 4 Adhered

description: Test


title: Healthy Control 5 Singlets

description: Control


title: Healthy Control 3 Adhered

description: Test

value: Female


title: Healthy Control 3 Doublets

description: Test


title: C57BL/6J-WT1

description: Sample name: 15382

source_name: C57BL/6J WT mouse replicate 1

value: C57BL/6J WT mouse

value: cecal contents of monocolonized mouse


title: pbmc_population-based Illumina HT12v4_2

value: M

value: peripheral blood mononuclear cells (PBMCs)


title: Healthy Control 2 Adhered

description: Test


title: Healthy Control 2 Doublets

description: Test


title: Healthy Control 1 Adhered

description: Test


title: Healthy Control 2 Singlets

description: Control


title: Healthy Control 1 Doublets

description: Test


title: Healthy Control 1 Singlets

description: Control


title: Psoriasis Patient 5 Adhered

description: Test


title: n-H1 OCT4:GFP, rep1

city: Leiden

first: Nannan

last: He

address: Einthovenweg 20

country: Netherlands

institute: Leiden University Medical Center

description:
9374343064_R03C01
hESC line H1 OCT4:GFP from WiCell.

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: DNA methylation data was corrected for background and color bias and the data was quantile normalized using lumi. Probes were discarded if they had a low bead count (< 3), high detection P value (> 0.01), or a low success rate (< 95%).

source_name: H1 OCT4:GFP hESC, naive

label_protocol: According to Illumina protocol.

extract_protocol: Chloroform/isoamyl alcohol protocol.

tag: cell line

value: H1 OCT4:GFP

value: human embryonic stem cells (hESCs)

tag: cell state

value: naïve


title: Healthy Control 3 Singlets

description: Control


title: n-UGent11-2, rep2

description:
9374343064_R02C01
In-house derived hESC line UGent11-2.

source_name: UGent11-2 hESC, naive


title: Psoriasis Patient 5 Doublets

description: Test


title: Psoriasis Patient 5 Singlets

description: Control


title: Psoriasis Patient 4 Doublets

description: Test


title: Psoriasis Patient 4 Adhered

description: Test


title: n-H1 OCT4:GFP, rep2

description:
9374343064_R04C01
hESC line H1 OCT4:GFP from WiCell.


title: UGent11-2

description:
9374343064_R05C01
In-house derived hESC line UGent11-2.

source_name: UGent11-2 hESC, primed

value: primed


title: Psoriasis Patient 3 Adhered

description: Test


title: Psoriasis Patient 3 Doublets

description: Test


title: Psoriasis Patient 2 Singlets

description: Control


title: Psoriasis Patient 3 Singlets

description: Control


title: Psoriasis Patient 4 Singlets

description: Control


title: Psoriasis Patient 2 Adhered

description: Test


title: H1 OCT4:GFP

description:
9374343064_R06C01
hESC line H1 OCT4:GFP from WiCell.

source_name: H1 OCT4:GFP hESC, primed


title: BP-3

description: Sample name: 15373

source_name: Rag1-/- 260.8 backpack mouse replicate 3

value: Rag1-/- 260.8 backpack mouse


title: n-UGent11-2, rep1

description:
9374343064_R01C01
In-house derived hESC line UGent11-2.


title: Treatment with 3'-demethoxy-6-O-demethylisoguaiacin

city: Monterrey

first: Aldo

middle: Francisco

last: Clemente soto

state: Nuevo Leon

address: Vicente Guerrero

department: Farmacia

country: Mexico

institute: UNIVERSIDAD AUTONOMA DE NUEVO LEÓN

description:
Analysis used log phase culture for comparison to log phase culture exposed to specific concentration of 3'-demethoxy-6-O-demethylisoguaiacin.
Meticillin-resistant Staphylococcus aureus
mRNA

hyb_protocol: Labeled cDNAs were hybridized on whole genome DNA chip of S. aureus MRSA252 (CAT-30K from MYcroarray) using SSPE 6X, formamide 10%, 0.01 mg/mL acetylated BSA, Tween 20 0.01%, control oligo 1%. Then a dynamic hybridization was performed in a hybridization Chamber (G2534A from Agilent) covered with gasket slide (G2534‐60002 from Agilent) during 24h at 42°C. Array then washed thrice employing SSPE 1X and one washed SSPE 0.25X.

scan_protocol: Array scanned using a GenePix 4000B scanner and Array-Pro Analyzer V.4.1.5.48 software from Media Cybernetics.

data_processing:
Scans were saved as TIFF images and quantified.
Data were then normalized and analyzed with genArise software (genArise-methodology.pdf; PMIDs 12454644 and 12707371 were used to develop genArise). Values that were equal to or lower than control, or from chip duplicates that were not congruent, were removed. Z-scores were calculated for each gene, which identify differentially expressed genes.

organism: Staphylococcus aureus subsp. aureus MRSA252

source_name: Log phase culture exposed to 3'-Demethoxy-6-O-Demethylisoguaiacin during one hour

label_protocol: Labeled cDNAs were obtained after cDNA synthesis by incorporation of Cy3 and Cy5 Dyes using Amino Allyl cDNA Labeling (AM1705 from Ambion) and Amersham CyDye Post-Labeling Reactive Dye Packs.

growth_protocol: Two Erlenmeyer flasks with 100 mL of Mueller-Hinton broth each were inoculated with MRSA and the turbidity was adjusted at 0.5 MacFarland’s standard (1.5 x 10^8 CFU). Both flasks were incubated for 4 h to achieve logarithmic phase.

extract_protocol: Total RNA of each bacterial pellet was isolated and purified with the RiboPure-Bacteria kit (AM1925 from Ambion) according to the manufacturer's protocol, including a DNase digestion step. To obtain the mRNA from each total RNA (10 μg), the MICROBExpress kit (AM1905 from Ambion) was used according to the manufacturer's protocol.

treatment_protocol: Drug treatment was conducted by adding 3'-demethoxy-6-O-demethylisoguaiacin to one of the cultures to achieve a final concentration of 12.5 μg/ml. Untreated control bacteria was grown under identical conditions to treated bacteria, with the exception that no drug was added. Both flasks were incubated 1 h during drug treatment.

value: ATCC BAA-44

tag: growth phase

value: log

tag: treatment

source_name: Log phase culture without exposure to 3'-Demethoxy-6-O-Demethylisoguaiacin


title: Il1b KO sipnal cord, biological rep4

city: Québec

first: Steve

last: Lacroix

state: Québec

address: 2705, boul. Laurier

department: Médecine moléculaire

country: Canada

institute: Centre de recherche du Centre hospitalier universitaire (CHU) de Québec - CHUL

hyb_protocol: Five µg of fragmented single-stranded cDNA was hybridized for 16 hours at 45°C with constant rotation on a GeneChip® Mouse Gene 1.0 ST Array (Affymetrix). After hybridization, were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol FS450_0007).

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Images were extracted with the GeneChip Operating Software (Affymetrix GCOS v1.4). Quality control of microarrays was performed using the AffyQCReport software. Background subtraction and normalization of probe set intensities was performed using the method of Robust Multiarray Analysis (RMA). Data analysis was performed using the AffylmGUI Graphical User Interface for the LIMMA microarray package (Wettenhall et al., 2006), and Partek Genomics Suite (Partek Incorporated)

source_name: Il1b KO lesioned spinal cord, 24 hours after injury

label_protocol: Two hundred nanograms of total RNA was labeled using the Ambion® WT Expression Kit protocol, as described by the manufacturer (Affymetrix, Santa Clara, CA). The quality of total RNA, cDNA synthesis, cRNA amplification, and cDNA fragmentation was monitored by microcapillary electrophoresis (Bioanalyzer 2100, Agilent Technologies).

extract_protocol: Spinal cord segments of 6 mm-long centered over the lesion were rapidly dissected, frozen in liquid nitrogen, and stored at -80°C until RNA extraction. Total RNA was isolated by TRI Reagent and purified with the GenElute mammalian total RNA miniprep kit (Sigma-Aldrich Canada Ltd.).

treatment_protocol: Spinal cord contusion of 50 kdyn was performed using the Infinite Horizon SCI device (Precision Systems & Instrumentation).

tag: background strain

tag: genotype/variation

value: Il1b KO

value: 8-12 weeks

value: Spinal cord


title: Il1a KO sipnal cord, biological rep3

source_name: Il1a KO lesioned spinal cord, 24 hours after injury

value: Il1a KO


title: Il1b KO sipnal cord, biological rep1


title: Il1b KO sipnal cord, biological rep3


title: E18.5 cortex rep3

city: London

first: Justyna

last: Nitarska

address: Gower Street

department: MRC Laboratory for Molecular Cell Biology

country: United Kingdom

institute: University College London

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Signal intensities were quantile normalized using the Bioconductor package lumi

source_name: embryonic cortex

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit, followed by DNase I treatment with Turbo DNA free kit (Ambion) in accordance with the protocol. Quality control was performed with Agilent Bioanalyser.

tag: developmental stage

value: embryonic cortex


title: Il1b KO sipnal cord, biological rep2


title: C57BL/6 sipnal cord, biological rep3

source_name: C57BL/6 lesioned spinal cord, 24 hours after injury

value: wild type


title: C57BL/6 sipnal cord, biological rep2


title: E18.5 cortex rep1


title: E18.5 cortex rep2


title: Il1a KO sipnal cord, biological rep2


title: Il1a KO sipnal cord, biological rep4


title: E18.5 cortex rep4


title: Wild-type

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

country: Japan

institute: National Center for Global Health and Medicine

description: Gene expression in wild-type Treg cells

hyb_protocol: 480 ng of Cy3-labelled 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 manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarray Ver2.0 (4x44k) Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°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 (G2539A) using one color scan setting for 4x44k array slides ( Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with GeneSpring GX Ver.11.0 (Agilent) using default parameters (protocol GE1_1010_sep10 and Grid: 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Wild-type Treg cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 600 ng RNA using the Low Input Quick Amp labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNA-iso (Takara, Japan) following the manufacturer's recommendations. Extracted total RNA was further purified using RNAeasy-micro kit.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Treg cells from wild-type or Nr4a-TKO mice were sorted, and directly lysed with RNA-iso total RNA extraction solution (Takara, Japan).

value: 5 week old

tag: cell type

value: regulatory T cells


title: C57BL/6 sipnal cord, biological rep1

tag: tissue


title: Psoriasis Patient 2 Doublets

description: Test

value: Peripheral Blood Monocytes

value: Psoriasis

tag: gender

value: Male

value: Caucasian

value: blood


title: C57BL/6 sipnal cord, biological rep4

tag: age


title: Il1a KO sipnal cord, biological rep1


title: E15.5 cortex rep4


title: E15.5 cortex rep2


title: E12.5 cortex rep4


title: E12.5 cortex rep1


title: E12.5 cortex rep3


title: A549 cells, 25μmol/L dihydroberberine plus 2μmol/L sunitinib, 48 h

status: Public on Jun 26 2015

city: Xi’an

first: Yanmin

last: Zhang

address: No. 76, Yanta West Street, #54

department: School of Pharmacy

institute: Xi’an Jiaotong University

description: Gene expression after 25μmol/L dihydroberberine plus 2μmol/L sunitinib for 48hr

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

scan_protocol: Arrays were scanned by Affymetrix GeneChip® Scanner 3000 (Cat#00-00213, Affymetrix, Santa Clara, CA, US).

data_processing: Command Console Software (Affymetrix, Santa Clara, CA, US) was used to control the scanner and summarize probe cell intensity data (CEL file generation) with default settings. Then raw data were normalized by Expression Console.

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

growth_protocol: Human lung cancer cell line A549 was cultured in RPMI-1640 supplemented with 10 % FBS and  incubated at 37 °C in a 5 % CO2 atmosphere.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Exponentially growing A549 cell was plated to the 6-well plate and cultivated for 24 h. Then 25μmol/L dihydroberberine, 2μmol/L sunitinib, 25μmol/L dihydroberberine plus 2μmol/L sunitinib were added to the 6-well plate. After 48 h, total RNA was extracted using TRIZOL Reagent.


title: Nr4a-deficient

description: Gene expression in Nr4a-deficient Treg cells

source_name: Nr4a-deficient Treg cells


title: E15.5 cortex rep3


title: E15.5 cortex rep1


title: A549 cells, sunitinib, 2μmol/L, 48 h

description: Gene expression after sunitinib treated at 2μmol/L for 48hr

source_name: A549 cells, sunitinib, 2μmol/L, 48 h

value: sunitinib treated at 2μmol/L for 48hr


title: E12.5 cortex rep2


title: Optic Nerve Crush 2

city: Perth

first: Kim

middle: Warwick

last: Carter

state: Western Australia

address: 100 Roberts Road, Subiaco

institute: Telethon Kids Institute

hyb_protocol: Agilent Zebrafish 4x44K V3 GE array (one-colour labeling, hybridization and scanning) was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia), according to the manufacturer’s (Agilent) instructions.

data_processing: Processing of the array data included background correction using a normal-exponential convolution model {Ritchie et al , 2007} and quantile normalisation  {Yang et al 2003}, with Limma {Smyth et al, 2004} used for differential expression analysis.

organism: Danio rerio

source_name: Right retinae tissue after crush

extract_protocol: Total RNA from pooled tissue was extracted using Trizol reagent (Life Technologies) according to manufacturer’s instructions.  Column-purified with miRNeasy kits (Qiagen)

tag: tissue type

value: retinae


title: Optic Nerve Crush 1

scan_protocol: Agilent Zebrafish 4x44K V3 GE array (one-colour labeling, hybridization and scanning) was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia), according to the manufacturer’s (Agilent) instructions.


title: Optic Nerve Crush 3

label_protocol: Agilent Zebrafish 4x44K V3 GE array (one-colour labeling, hybridization and scanning) was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Australia), according to the manufacturer’s (Agilent) instructions.


title: Control 3

source_name: Unoperated right retinae tissue


title: Optic Nerve Crush 4


title: Control 1


title: Control 2


title: Control 4


title: MCF7_LASPKD_biological_rep1

city: Nashville

first: Dayanidhi

last: Raman

state: TN

address: PRB436, 23rd Ave S @ Pierce

department: Cancer Biology

institute: Vanderbilt Universirty

description: Grown on Matrigel

hyb_protocol: Biotinylated reaction products were added to Hybridization mix and targets (final  ~25ng/ul) were hybridized in the hybridization cocktail for a total of 2.5ug of fragmented target.  The targets are heat denatured, centrifuged, and hybridized overnight to Human Gene 1.0 ST exon array, stained, washed and scanned.

scan_protocol: Affymetrix 7G plus  scanner using AGCC v. 3.2.4

data_processing: Analyzed on Affymetrix Expression Console v. 1.2 using a RMA normalization algorithm producing log base 2 results that forms the value for comparisons or for calcualting fold change.

label: Biotin-Streptavidin-Phycoerythrin

source_name: MCF7-LASP-KD cells

label_protocol: Ambion kit was used to synthesize the first and second strand RNA. IVT reactions were done overnight, purified and quantified. cRNA products from the overnight IVT reactions were purifed. Quantitated cRNA was used : random primer heat denaturation, 2nd cycle cDNA synthesis and cRNA hydrolysis with RNase H; cDNA was purified, fragmented and TdT-labeled with biotin.

growth_protocol: MCF cells (Non-silencing and LASP-1 knock down) were cultured on growth factor reduced Matrigel for 3 days to form spheroids.

extract_protocol: Total RNA was quantitated from MCF7 spheroids using the QuBit RNA assay and were run on the Agilent Bioanalyzer.

treatment_protocol: Not applicable

value: Luminal breast cells


title: MCF7_LASPKD_biological_rep4

description: Grown on Matrigel


title: MCF7_NS_biological_rep4

description: Grown on Matrigel

source_name: MCF7 cells


title: MCF7_LASPKD_biological_rep2

description: Grown on Matrigel


title: A549 cells, dihydroberberine, 25μmol/L, 48 h

description: Gene expression after dihydroberberine treated at  25μmol/L for 48hr

source_name: A549 cells, dihydroberberine, 25 mol/L, 48 h


title: E18 Ctx total 18A

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets. The concordance between the SECT and the normal salivary core transcriptome (NSCT) was evaluated assuming hypergeometric distributions.

source_name: Cortex

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Timed pregnant dams were collected at the times indicated.  Mice were wild-type CD-1 from Charles River.

extract_protocol: Total cellular RNA was made from frozen tissue samples using standard Trizol protocols.

treatment_protocol: There were no specific treatments of the animals prior to collection.


title: C57BL6 LIVER S1 (9996338116_F)

city: Singapore

first: Walter

last: Stunkel

address: 30 Medical Drive

department: Growth Development Metabolism

country: Singapore

institute: Singapore Institute for Clinical Sciences

description: Liver sox6_kd-S1 replicate

data_processing: Background subtraction was performed in GenomeStudio then data was exported. Probes were filtered for detection p-value <0.05 and NBEADS>3 in R. Data was then loaded into Arraystudio version 6 (Omicsoft). All expression values were log2 transformed and quantile normalised (lumi/R-bioconductor).

source_name: Liver

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

growth_protocol: All animal procedures were performed according to the Institutional Animal Care and Use Committee of the Agency for Science, Technology and Research (A*STAR) of Singapore. All mice were male, of the C57BL/6J genetic background and housed in a 12-hour light-dark cycle with access ad libitum to water and a NCD (Harlan 2018 Teklab Global 18% Protein Rodent Diet).

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

treatment_protocol: Mice were injected intraperitoneal with either SOX6 specific or control antisense oligonucleotides and effects of the treatment studied after 48h.

tag: strain

value: sox6 knockdown

value: Liver


title: MCF7_LASPKD_biological_rep3

description: Grown on Matrigel


title: E13 Ctx total 13A


title: MCF7_NS_biological_rep3

description: Grown on Matrigel


title: E18 Ctx total 18B


title: E13 Ctx total 13B


title: E15 Ctx total 15A


title: MCF7_NS_biological_rep1

description: Grown on Matrigel


title: A549 cells, 48 h

description: Gene expression in the absence of dihydroberberine or sunitinib

source_name: A549 cells, 48 h


title: E15 Ctx total 15B


title: MCF7_NS_biological_rep2

description: Grown on Matrigel


title: MPH45M

city: Tallahassee

first: Jonathan

last: Dennis

state: Florida

address: 319 Stadium Drive

department: Biological Science

institute: Florida State University

hyb_protocol: The labeled DNA was precipitated with 2 volumes ethanol and .3 M sodium acetate, and hybridized according to manufacturer's protocols. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on a Nimblegen scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan CGH arrays.

source_name: Jurkat Clone E6-1 cells_Mononucleosomal Protected DNA_45min_postMPH

label_protocol: 1 µg of mononucleosomally protected and genomic DNA was directly labeled by Klenow (Nimblegen) random priming with Cy3 and Cy5 7-mers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). The mononucleosome protected DNA sample was labeled with a fluorescently labeled Cy3 primer, whereas the reference, total bare genomic, untreated DNA was labeled with a fluorescently labeled Cy5 primer. The labeled DNA was then hybridized to a 12-plex, custom designed, NimbleGen HD2 microarray. Each sub-array on the slide probes for 2 kb flanking 856 cancer and immunity, transcription-start sites (TSSs). The labeled mononucleosomal DNA binds to these probes and reveals nucleosome protected regions on the genome when analyzed by a microarray scanner.

growth_protocol: Jurkat Clone E6-1 (ATCC® TIB-152™) cells are grown in RPMI 1640, 10% FBS, 30 mg/mL gentamicin media in 15-cm diameter, sterile, polystyrene plates.

extract_protocol: The chromatin was harvested by cross-linking with the addition of 10% methanol-free formaldehyde. After 10 minutes of formaldehyde incubation, the cross-linking reaction was quenched with 2.5M glycine. The samples were aliquotted into 15-mL conicals and centrifuged at 1000 RPM (714.29 g) for 5 minutes. Nuclei pellets were resuspended in 1 mL of Nucleus Isolation Buffer (0.3 M sucrose, 2 mM MgOAc2, 1 mM CaCl2, 1% Nonidet P-40, 10 mM Hepes, pH 7.8). 250 μL aliquots of the resuspended cells were transferred to 1.5-mL centrifuge tubes. Each aliquot was digested by a different concentration of MNase. The concentrations were made by titrating MNase to 10 U/ml, 5 U/ml, 2.5 U/ml, and 1.25 U/ml in MNase cleavage buffer (4 mM CaCl2, 25 mM KCl, 4 mM MgCl2, 12.5% glycerol, 50 mM HEPES, pH 7.8). One volume of the MNase titrations was added for 5 minutes at 37°C. MNase activity was stopped with 50mM EDTA. MNase-digested nuclei were then treated with proteinase K to a final concentration of 0.2 μg/μl for 45 minutes at 55°C.  20% sodium dodecyl sulfate (SDS) was added to a final concentration of 1% to denature proteins in the samples. The cross-links were reversed by overnight incubation at 65°C. DNA was extracted from the samples with phenol-chloroform, precipitated with alcohol, and dissolved in TE (10 mM Tris-Cl. pH 8.0, 0.1 mM EDTA). Following DNA extraction, the digested, purified samples were resolved in a 2% agarose gel buffered with 1x sodium borate buffer. Mononucleosomally protected DNA (~150 bp) was isolated by excision of the specific sample’s band, and the DNA was purified by freeze-and-squeeze.

treatment_protocol: Cells were plated at 0.5 x10^6 cells/mL and grown to a density of 2x10^7 cells/mL before being treated with 2mM MPH. After treatment, cells were harvested at 15-, 45- and 240-minute time points post MPH stimulus.

value: Jurkat Clone E6-1

source_name: Jurkat Clone E6-1_Bare Genomic DNA


title: jacks-00113: KT49

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: lung tumor

value: lung tumor

tag: Sex

value: male

value: F1 129svJae X C57/BL25

tag: phenotype

value: lung cancer

value: lung

value: Jacks lab/MIT CCR

value: adenocarcinoma

tag: histology

value: columnar


title: MPH15M

source_name: Jurkat Clone E6-1 cells_Mononucleosomal Protected DNA_15min_postMPH

label_protocol: 1 µg of mononucleosomally protected and genomic DNA was directly labeled by Klenow (Nimblegen) random priming with Cy3 and Cy5 7-mers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).  The mononucleosome protected DNA sample was labeled with a fluorescently labeled Cy3 primer, whereas the reference, total bare genomic, untreated DNA was labeled with a fluorescently labeled Cy5 primer. The labeled DNA was then hybridized to a 12-plex, custom designed, NimbleGen HD2 microarray. Each sub-array on the slide probes for 2 kb flanking 856 cancer and immunity, transcription-start sites (TSSs). The labeled mononucleosomal DNA binds to these probes and reveals nucleosome protected regions on the genome when analyzed by a microarray scanner.


title: C57BL6 LIVER C1 (9996338116_D)

description: Liver control-C1 replicate

value: control


title: E11 Ctx total 11B


title: jacks-00113: normal3

scan_protocol: See mage-tab files linked to series entry for additional details

source_name: normal lung

value: normal lung

tag: genotype

value: F1 129svJae X C57/BL46


title: jacks-00113: KT112

data_processing: See mage-tab files linked to series entry for additional details

value: female

value: F1 129svJae X C57/BL33


title: U1A

source_name: Jurkat Clone E6-1 cells_Mononucleosomal Protected DNA_0min_postMPH

tag: cell line


title: E11 Ctx total 11A


title: C57BL6 LIVER S1 (9996338116_C)

description: Liver sox6_kd-S1 replicate


title: MPH4H

source_name: Jurkat Clone E6-1 cells_Mononucleosomal Protected DNA_240min_postMPH


title: jacks-00113: KT78

label_protocol: See mage-tab files linked to series entry for additional details

value: F1 129svJae X C57/BL35


title: jacks-00113: KT88

extract_protocol: See mage-tab files linked to series entry for additional details

value: F1 129svJae X C57/BL40


title: C57BL6 LIVER C2 (9996338116_B)

description: Liver control-C2 replicate

value: Liver


title: jacks-00113: normal4

value: F1 129svJae X C57/BL47


title: jacks-00113: KT102

value: lung tumor

value: F1 129svJae X C57/BL42


title: jacks-00113: KT90

value: male

value: F1 129svJae X C57/BL41


title: jacks-00113: KT86

value: F1 129svJae X C57/BL39

value: lung cancer

value: lung


title: C57BL6 LIVER S2 (9996338109_C)

description: Liver sox6_kd

value: sox6 knockdown


title: C57BL6 EWAT S1 (9996338109_A)

description: EWAT sox6_kd-S1 replicate

source_name: Epididymal White Adipose Tissue

value: EWAT


title: jacks-00113: KT77

value: F1 129svJae X C57/BL34

value: Jacks lab/MIT CCR

value: adenocarcinoma


title: jacks-00113: KT111

value: female

value: F1 129svJae X C57/BL43


title: jacks-00113: KT50

value: F1 129svJae X C57/BL27


title: C57BL6 EWAT C3 (9996338116_A)

description: EWAT control

value: control


title: C57BL6 EWAT S2 (9996338109_D)

description: EWAT sox6_kd


title: C57BL6 EWAT C1 (9996338109_E)

description: EWAT control-C1 replicate


title: C57BL6 EWAT S3 (9986350041_E)

description: EWAT sox6_kd


title: C57BL6 LIVER C3 (9996338109_F)

description: Liver control-C3 replicate

value: Liver


title: C57BL6 EWAT C1 (9996338109_B)

description: EWAT control-C1 replicate


title: C57BL6 LIVER S4 (9986350041_F)

description: Liver sox6_kd-S4 replicate


title: jacks-00113: KT99

value: lung tumor

value: F1 129svJae X C57/BL32


title: C57BL6 LIVER C2 (9986350041_C)

description: Liver control-C2 replicate


title: jacks-00113: KT83

value: male

value: F1 129svJae X C57/BL37


title: Psoriasis Patient 1 Adhered

description: Test

source_name: Human Peripheral Blood, Sorted Classical Monocytes, Adhered to Plastic 4 hours

value: Peripheral Blood Monocytes

tag: disease

value: Psoriasis

value: Male

tag: race

value: African American

value: blood


title: jacks-00113: KT85

value: F1 129svJae X C57/BL38

value: lung cancer

value: lung


title: C57BL6 EWAT C2 (9986350041_D)

description: EWAT control

tag: treatment

value: EWAT


title: jacks-00113: normal16

value: normal lung

value: female

value: F1 129svJae X C57/BL59

value: Jacks lab/MIT CCR

value: adenocarcinoma


title: C57BL6 LIVER C4 (9986350036_F)

description: Liver control-C4 replicate

value: control

value: Liver


title: C57BL6 LIVER S4 (9986350041_B)

description: Liver sox6_kd-S4 replicate

value: sox6 knockdown


title: jacks-00113: normal14

value: F1 129svJae X C57/BL57


title: C57BL6 LIVER C3 (9986350041_A)

description: Liver control-C3 replicate


title: MDA-Bone-Un_NS_biological_rep1

description: Grown on Matrigel

source_name: MDA-Bone-Un-NS cells

label_protocol: Ambion kit was used to synthesize the first and second strand RNA. IVT reactions were done overnight, cRNA productswas purified and quantified. Quantitated cRNA was used : random primer heat denaturation, 2nd cycle cDNA synthesis and cRNA hydrolysis with RNase H; cDNA was purified, fragmented and TdT-labeled with biotinylated nucleotides.

growth_protocol: MDA-MB-231S and MDA-Bone-Un breast cancer cells (Non-silencing and LASP-1 knock down) were cultured on growth factor reduced Matrigel for 3 days to form stellate clusters.

extract_protocol: Total RNA from MDA-MB-231S and MDA-Bone-Un stellate clusters was quantitated using the QuBit RNA assay and were run on the Agilent Bioanalyzer.

value: MDA-Bone-Un

value: Basal-like breast cells


title: jacks-00113: KT80

value: lung tumor

value: male

value: F1 129svJae X C57/BL36