title: 100550_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100545_peripheral_CD14 [methylation]

status: Public on Nov 24 2014

type: genomic

city: Winston-Salem

first: Yongmei

last: Liu

state: NC

address: Medical Center Blvd.

country: USA

institute: Wake Forest School of Medicine

description: human peripheral CD14+ cells

hyb_protocol: The resuspended samples were hybridized on HumanMethylation 450 BeadChips at 48°C for 16 h.

scan_protocol: Illumina HiScan reader

data_processing: Bead-level methylation data were summarized in GenomeStudio.  Because a two-channel system and both Infinium I and II assays were used, normalization was performed in several steps using the lumi package (27). We first adjusted for color bias using “smooth quantile normalization”. Next, the data were background adjusted by subtracting the median intensity value of the negative control probes.  Lastly, data were normalized across all samples by standard quantile normalization applied to the bead-type intensities and combined across Infinium I and II assays and both colors.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: CD14+ cell

label_protocol: The Illumina HumanMethylation450 BeadChip and HiScan reader were used to perform the epigenome-wide methylation analysis. The EZ-96 DNA MethylationTM Kit (Zymo Research, Orange, CA) was used for bisulfate conversation with 1ug of input DNA (at 45 ul). 4 ul of bisulfite-converted DNA were used for DNA methylation assays, following the Illumina Infinium HD Methylation protocol. This consisted of a whole genome amplification step followed by enzymatic end-point fragmentation, precipitation, and resuspension.

growth_protocol: Not applicable

extract_protocol: Blood was initially collected in sodium heparin-containing Vacutainer CPTTM cell separation tubes (Becton Dickinson, Rutherford, NJ) to separate peripheral blood mononuclear cells from other elements within 2 hours from blood draw. Subsequently, monocytes were isolated with the anti-CD14 coated magnetic beads, respectively, using AutoMACs automated magnetic separation unit (Miltenyi Biotec, Bergisch Gladbach, Germany).  DNA and RNA were isolated from samples simultaneously using the AllPrep DNA/RNA Mini Kit (Qiagen, Inc., Hilden, Germany).

treatment_protocol: Not applicable

tag: ChIP

tag: well

tag: age

tag: racegendersite

tag: bcell

tag: tcell

tag: nkcell

tag: neutro

tag: plaque

tag: cac


title: 100546_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100556_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100543_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100542_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100013_peripheral_CD14

type: RNA

description: human peripheral CD14+ cells

hyb_protocol: 700 ng of biotinylated cRNA was hybridized to a BeadChip at 580C for 16-17 hours.

scan_protocol: Illumina Bead Array Reader

data_processing:
Data corrected for local background were obtained from Illumina’s proprietary software GenomeStudio. QC analyses and bead type summarization (average bead signal for each type after outlier removal) were performed using the beadarray package (25). Detection P-values were computed using the negative controls on the array. The neqc function of the limma (26) package was used to perform a normal-exponential convolution model analysis to estimate non-negative signal, quantile normalization using all probes (gene and control, detected and not detected) and samples, addition of a recommended (small) offset, log2 transformation, and elimination of control probe data from the normalized expression matrix.
sample data table cotains quantile normalized values - neqc function of the limma package was used to perform a normal-exponential convolution model analysis to estimate the quantile normalization using all probes/samples

label: biotin

molecule: total RNA

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit (Ambion/Applied Biosystems, DaeMStadt, Germany) was used for reverse transcription, and amplification with 500 ng of input total RNA (at 11ul).

value: K


title: 100539_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100538_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100016_peripheral_CD14

description: human peripheral CD14+ cells

value: B


title: 100005_peripheral_CD14

description: human peripheral CD14+ cells


title: 100002_peripheral_CD14

description: human peripheral CD14+ cells

value: A


title: 100007_peripheral_CD14

description: human peripheral CD14+ cells

value: F


title: 100541_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100006_peripheral_CD14

description: human peripheral CD14+ cells

value: E


title: 100552_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100537_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100004_peripheral_CD14

description: human peripheral CD14+ cells


title: 100003_peripheral_CD14

description: human peripheral CD14+ cells

value: C


title: 100009_peripheral_CD14

description: human peripheral CD14+ cells

value: L


title: 100008_peripheral_CD14

description: human peripheral CD14+ cells


title: 100540_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100534_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100535_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100533_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100532_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100536_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100526_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100531_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100528_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100524_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100525_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100516_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100517_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100520_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100522_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100518_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100519_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100523_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100514_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100521_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100513_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100529_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100512_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100515_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100510_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100506_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100001_peripheral_CD14

description: human peripheral CD14+ cells

value: I


title: 100509_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100508_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100507_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100527_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100511_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100504_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100503_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100505_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100502_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100501_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100530_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100576_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100498_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100495_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100494_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100499_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100496_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100492_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100488_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100491_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100482_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100493_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100489_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100484_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100485_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100480_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100487_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100486_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100490_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100481_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100477_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100483_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100478_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100476_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100475_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100474_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100500_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100497_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100472_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100471_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100469_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100479_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100467_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100462_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100466_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100461_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100468_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100456_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100465_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100460_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100458_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100459_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100446_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100450_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100448_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100452_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100451_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100444_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100455_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100445_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100442_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100443_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100441_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100470_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100440_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100447_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100435_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100439_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100433_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100426_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100432_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100437_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100430_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100438_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100464_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100422_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100425_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100421_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100428_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100420_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100457_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100423_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100436_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100419_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100417_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100418_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100415_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100416_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100427_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100434_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100413_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100431_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100414_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100424_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100412_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100411_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100408_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100410_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100407_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100404_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100406_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100403_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100544_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100396_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100400_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100398_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100395_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100402_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100401_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100394_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100391_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100392_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100393_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100390_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100389_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100383_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100384_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100385_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100388_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100386_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100387_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100409_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100378_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100375_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100377_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100381_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100379_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100547_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100376_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100374_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100373_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100371_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100372_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100370_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100367_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100366_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100368_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100369_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100361_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100365_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100363_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100362_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100364_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100360_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100359_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100357_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100351_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100352_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100356_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100355_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100358_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100354_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100349_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100338_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100340_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100347_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100342_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100348_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100346_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100345_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100337_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100341_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100339_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100344_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100326_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100319_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100318_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100322_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100328_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100333_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100334_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100320_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100323_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100332_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100327_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100331_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100343_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100324_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100335_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100330_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100336_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100316_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100315_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100314_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100313_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100317_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100312_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100310_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100306_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100307_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100311_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100308_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100287_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100304_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100288_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100300_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100302_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100303_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100305_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100298_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100294_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100293_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100299_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100296_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100292_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100291_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100321_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100329_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100309_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100297_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100282_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100280_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100284_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100281_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100279_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100271_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100270_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100273_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100272_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100265_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100278_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100266_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100277_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100301_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100269_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100268_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100275_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100263_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100260_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100261_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100259_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100256_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100255_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100262_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100285_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100274_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100254_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100252_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100251_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100250_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100286_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100257_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100246_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100248_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100244_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100243_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100238_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100241_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100249_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100240_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100234_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100231_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100232_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100235_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100230_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100237_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100253_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100229_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100225_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100267_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100226_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100247_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100245_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100224_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100221_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100242_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100222_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100236_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100219_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100220_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100218_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100217_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100216_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100214_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100215_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100228_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100209_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100211_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100210_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100212_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100207_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100213_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100227_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100204_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100203_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100202_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100205_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100201_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100206_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100197_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100198_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100194_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100196_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100195_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100200_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100208_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100189_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100185_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100187_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100192_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100199_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100178_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100184_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100177_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100191_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100183_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100190_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100179_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100173_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100170_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100176_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100174_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100180_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100175_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100171_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100193_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100169_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100167_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100164_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100166_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100168_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100181_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100162_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100163_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100160_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100165_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100158_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100157_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100159_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100155_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100154_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100153_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100156_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100146_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100145_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100150_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100144_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100147_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100148_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100139_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100138_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100140_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100141_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100143_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100134_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100135_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100182_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100142_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100133_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100161_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100132_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100136_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100128_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100131_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100137_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100127_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100151_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100126_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100152_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100130_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100124_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100119_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100116_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100117_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100121_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100122_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100113_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100114_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100110_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100111_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100112_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100109_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100105_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100125_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100104_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100103_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100097_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100099_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100100_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100095_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100098_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100101_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100093_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100096_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100102_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100223_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100115_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100089_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100086_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100088_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100090_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100091_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100087_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100085_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100094_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100107_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100083_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100084_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100082_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100080_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100079_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100078_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100081_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100073_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100077_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100092_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100070_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100071_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100061_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100065_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100066_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100064_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100060_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100058_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100054_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100051_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100057_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100050_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100056_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100049_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100046_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100048_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100043_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100045_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100076_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100042_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100044_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100039_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100038_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100040_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100041_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100074_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100037_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100036_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100027_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100033_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100031_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100028_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100035_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100032_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100026_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100023_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100024_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100029_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100021_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100055_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100016_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100022_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100018_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100017_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100019_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100025_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100007_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100013_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100014_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100008_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100012_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100015_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100005_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100006_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100011_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100030_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100004_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100003_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100002_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100001_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100010_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: 100009_peripheral_CD14 [methylation]

description: human peripheral CD14+ cells


title: H67

status: Public on Aug 01 2014

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: standard Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

source_name: dysplastic nevus

label_protocol: Affymetrix double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

tag: tissue

value: dysplastic nevus

tag: amplification

value: Double

tag: material

value: sliced section


title: H69


title: H15

source_name: common nevus

value: common nevus


title: H17


title: H59


title: H19


title: H21


title: H18


title: H60


title: H23


title: mole-1


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6572

status: Public on Oct 15 2013

city: New Haven

first: JOSE

middle: DAVID

last: HERAZO MAYA

state: CT

address: 300 Cedar Street

department: Medicine

institute: Yale University

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6572

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA High Resolution Microarray Scanner (G2505C US45102918) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 μm, Tiff 20 bit, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (GE1_107_Sep09 and Grid: 014850_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities. Gene expression data was normalized to the geometric mean of all the IPF samples and controls using cyclic loess, for the normalization and statistical analysis we used the average gene expression values of the replicated probes, the number of probes after the average and normalization process was 29807.

source_name: Peripheral blood mononuclear cells, blood draw, 30 minutes interval

label_protocol: Labeling reactions were performed for each sample using Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color (5184-3523, Agilent Technologies, Santa Clara, CA). Briefly, with a starting concentration of 400 nanograms of total RNA, an initial cDNA strand was synthesized using a oligo(dT)24 primer containing a T7 RNA polymerase, this cDNA was then used as a template to generate Cy3 labeled cRNA by a reverse transcriptase enzyme. After the cRNA was obtained a purification step was performed using RNeasy Mini Kit (74104, Qiagen, Valencia, CA) followed by measurement of the yield and specific activity of each sample

extract_protocol:
10 ml of blood was drawn by venipuncture in each participant and collected in a cell preparation tube (CPT) followed by centrifugation at 1500 g for 30 minutes at room temperature. After plasma removal, the cell layer was transferred into a 15 ml conical tube and 5 ml of RNase free PBS was added, the contents were mixed by turning upside down followed by centrifugation at 300 g for 15 minutes. Once the supernatant was removed, the PBS washing step previously described was repeated using 10 ml of PBS, with centrifugation for 10 minutes. After the PBMC isolation was completed, 1 ml of QIAzol (79306, Qiagen, Valencia, CA) was added to each sample and they were snap frozen in -80 celsius.
Total RNA was extracted and purified using the miRNeasy Mini Kit (217004, Qiagen, Valencia, CA) under fully automated sample preparation by the assistance of the QIAcube device (9001292, Qiagen, Valencia CA) following the manufacturer’s protocol.After extraction, total RNA yield and quality were evaluated using NanoDrop at 260 nm and the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

tag: cell type

value: Peripheral blood mononuclear cells (PBMC)

tag: disease status

value: control

tag: gender

value: Female

tag: survival status

value: not applicable

tag: time to survival

value: not aplicable


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6561

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6561

value: Male


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6564

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6564


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6431

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6431


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL5656

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 5656


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6493

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6493


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6573

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6573


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6565

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6565


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6567

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6567


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6589

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6589


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL5644

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 5644


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6543

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6543


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL5642

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 5642


title: mole-2


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6580

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6580


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL5646

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 5646


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL5641

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 5641


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6432

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6432


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL6581

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 6581


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_CTRL5639

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
CTRL 5639


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0101

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0101

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x GEx Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried immediately.

value: idiopathic pulmonary fibrosis (IPF)

tag: outcome

tag: time to outcome

value: 1.350 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0094

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0094

tag: age

value: 1.624 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0085

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0085

value: 1.912 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0102

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0102

value: 1.312 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0098

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0098

value: 0.208 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0095

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0095

value: 1.558 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0088

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0088

value: 0.323 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0083

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0083

value: 1.980 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0087

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0087

value: 1.849 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0078

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0078

value: 1.273 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0089

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0089

value: Peripheral blood mononuclear cells (PBMC)

value: 1.641 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0093

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0093

value: Female

value: 1.731 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0080

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0080

value: 2.076 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0097

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0097

value: Male

value: 1.471 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0069

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0069

value: idiopathic pulmonary fibrosis (IPF)

value: 2.564 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0071

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0071

value: 0.679 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0086

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0086

value: 1.865 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0076

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0076

tag: years to outcome


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0066

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0066

value: 1.189 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0081

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0081

value: 2.057 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0070

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0070

value: 2.336 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0074

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0074

value: 1.616 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0091

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0091

value: 1.123 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0077

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0077

value: 2.315 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0068

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0068

value: Peripheral blood mononuclear cells (PBMC)

value: 2.602 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0075

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0075


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0072

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0072

value: Female

value: 2.487 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0073

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0073

value: 0.684 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0079

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0079

value: Male

value: 1.808 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0067

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0067

value: idiopathic pulmonary fibrosis (IPF)

value: 0.646 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0063

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0063

value: 0.520 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0062

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0062

value: 2.386 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0061

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0061

value: 0.917 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0046

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0046

value: 2.958 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0056

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0056

value: 2.2 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0050

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0050

value: 0.150 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0064

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0064

value: 0.958 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0055

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0055

value: 0.073 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0059

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0059

value: Peripheral blood mononuclear cells (PBMC)

tag: time to outcomel

value: 0.594 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0048

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0048

value: 0.350 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0045

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0045

value: 1.930 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0054

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0054


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0047

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0047

value: Female

value: 3.553 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0041

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0041

value: Male

value: 3.594 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0044

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0044

value: idiopathic pulmonary fibrosis (IPF)

value: 3.241 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0037

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0037

value: 3.802 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0042

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0042

value: 0.013 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0052

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0052

value: 3.495 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0038

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0038

value: 3.564 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0034

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0034

value: 1.167 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0030

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0030

value: 2.632 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0029

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0029

value: 3.536 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0036

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0036

value: Peripheral blood mononuclear cells (PBMC)

value: 3.810 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0031

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0031

value: 0.120 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0024

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0024

value: 1.372 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0026

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0026

value: Female

value: 3.158 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0018

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0018

value: Male


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0025

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0025

value: 2.268 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0013

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0013

value: idiopathic pulmonary fibrosis (IPF)

value: 3.887 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0022

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0022

value: 4.032 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0021

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0021

value: 0.484 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0017

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0017

value: 1.180 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0008

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0008


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0007

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0007

value: 0.183 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0033

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0033

value: 0.2 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0011

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0011

value: 3.433 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0027

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0027

value: 1.956 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0002

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0002

value: Peripheral blood mononuclear cells (PBMC)

value: 0.052 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0004

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0004

value: 4.186 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0020

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0020

value: 1.561 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0023

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0023

value: 0.649 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0019

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0019

value: 3.586 years


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0012

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0012

value: Female


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0010

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0010

value: Male

value: 0.684 years


title: HapMap DNase Seq GM19239

status: Public on Jan 26 2012

type: SRA

city: Chicago

first: Jacob

middle: F

last: Degner

state: IL

department: Human Genetics

institute: University of Chicago

description: DNase-Seq

library_source: genomic

data_processing: Raw data from GAII are provided for each individual.  We also provide BED file format data for each individual for the top 5% of the genome in terms of total sensitivity.  This data was mapped to hg18 using a custom read-mapping algorithm which we describe in detail in the associated publication.  Measures of DNase sensitivity were quantile normalized within each individual to a standard normal distribution.  Each individual was corrected for GC bias and the top 4 principle components were removed from the data (See manuscript).

source_name: lymphoblastoid cell line

growth_protocol: 37o in RPMI

extract_protocol: Dnase seq protocol (provided as supplementary file linked to GSE31388)

value: lymphoblastoid cell line

tag: population

value: YRI

tag: ethnicity

value: YORUBA

tag: country of origin

value: NIGERIA


title: HapMap DNase Seq GM19225

description: DNase-Seq


title: HapMap DNase Seq GM19238

description: DNase-Seq


title: HapMap DNase Seq GM19257

description: DNase-Seq


title: HapMap DNase Seq GM19223

description: DNase-Seq


title: HapMap DNase Seq GM19222

description: DNase-Seq


title: HapMap DNase Seq GM19210

description: DNase-Seq


title: HapMap DNase Seq GM19207

description: DNase-Seq


title: HapMap DNase Seq GM19209

description: DNase-Seq


title: HapMap DNase Seq GM19206

description: DNase-Seq


title: HapMap DNase Seq GM19201

description: DNase-Seq


title: HapMap DNase Seq GM19192

description: DNase-Seq


title: HapMap DNase Seq GM19203

description: DNase-Seq


title: HapMap DNase Seq GM19200

description: DNase-Seq


title: HapMap DNase Seq GM19193

description: DNase-Seq


title: HapMap DNase Seq GM19171

description: DNase-Seq


title: HapMap DNase Seq GM19160

description: DNase-Seq


title: HapMap DNase Seq GM19143

description: DNase-Seq


title: HapMap DNase Seq GM19141

description: DNase-Seq


title: HapMap DNase Seq GM19138

description: DNase-Seq


title: HapMap DNase Seq GM19131

description: DNase-Seq


title: HapMap DNase Seq GM19152

description: DNase-Seq


title: HapMap DNase Seq GM19130

description: DNase-Seq


title: HapMap DNase Seq GM19147

description: DNase-Seq


title: HapMap DNase Seq GM19119

description: DNase-Seq


title: HapMap DNase Seq GM19144

description: DNase-Seq


title: HapMap DNase Seq GM19204

description: DNase-Seq


title: HapMap DNase Seq GM19137

description: DNase-Seq


title: HapMap DNase Seq GM19127

description: DNase-Seq


title: HapMap DNase Seq GM19116

description: DNase-Seq


title: HapMap DNase Seq GM19114

description: DNase-Seq


title: HapMap DNase Seq GM19101

description: DNase-Seq


title: HapMap DNase Seq GM19098

description: DNase-Seq


title: HapMap DNase Seq GM19159

description: DNase-Seq


title: HapMap DNase Seq GM19093

description: DNase-Seq


title: HapMap DNase Seq GM19190

description: DNase-Seq


title: HapMap DNase Seq GM19140

description: DNase-Seq


title: HapMap DNase Seq GM19092

description: DNase-Seq


title: HapMap DNase Seq GM18916

description: DNase-Seq


title: HapMap DNase Seq GM19153

description: DNase-Seq


title: HapMap DNase Seq GM18913

description: DNase-Seq


title: HapMap DNase Seq GM18912

description: DNase-Seq


title: HapMap DNase Seq GM18909

description: DNase-Seq


title: HapMap DNase Seq GM18870

description: DNase-Seq


title: HapMap DNase Seq GM18907

description: DNase-Seq


title: HapMap DNase Seq GM18862

description: DNase-Seq


title: HapMap DNase Seq GM18856

description: DNase-Seq


title: HapMap DNase Seq GM19099

description: DNase-Seq


title: HapMap DNase Seq GM18859

description: DNase-Seq


title: HapMap DNase Seq GM18522

description: DNase-Seq


title: HapMap DNase Seq GM18852

description: DNase-Seq


title: HapMap DNase Seq GM18853

description: DNase-Seq


title: HapMap DNase Seq GM18861

description: DNase-Seq


title: HapMap DNase Seq GM18519

description: DNase-Seq


title: HapMap DNase Seq GM18520

description: DNase-Seq


title: HapMap DNase Seq GM18517

description: DNase-Seq


title: HapMap DNase Seq GM18511

description: DNase-Seq


title: HapMap DNase Seq GM18507

description: DNase-Seq


title: HapMap DNase Seq GM18508

description: DNase-Seq


title: HapMap DNase Seq GM18510

description: DNase-Seq


title: HapMap DNase Seq GM18505

description: DNase-Seq


title: HapMap DNase Seq GM18516

description: DNase-Seq


title: HapMap DNase Seq GM18504

description: DNase-Seq


title: HapMap DNase Seq GM18501

description: DNase-Seq


title: HapMap DNase Seq GM18502

description: DNase-Seq


title: HapMap DNase Seq GM18486

description: DNase-Seq


title: HapMap DNase Seq GM18498

description: DNase-Seq


title: HapMap DNase Seq GM18855

description: DNase-Seq


title: HapMap DNase Seq GM18499

description: DNase-Seq


title: HapMap DNase Seq GM18858

description: DNase-Seq


title: H3K27me3

status: Public on May 06 2008

city: Boston

first: Jonghwan

last: Kim

state: MA

address: 1 Blackfan circle Karp-7

institute: HMS/CHB

description:
antibodyChIP
3meH3K27_1.CEL
3meH3K27_2.CEL
3meH3K27_3.CEL
Input_J1_1.CEL
Input_J1_2.CEL
Input_J1_3.CEL

hyb_protocol: According to standard Affymetrix protocols.

data_processing: MAT (Johnson et al., 2006) was used to process the raw CEL files. The following settings; Bandwith = 300, MaxGap = 300, MinProbe = 10 were used. Initially BAR and BED files were generated by using Mm_PromPR_v02-1_NCBIv33.bpmap and genomic coordinates in BED files were converted to new coordinates based on mouse genome assembly mm8.

organism: Mus musculus

source_name: antibody H3K27me3 ChIP DNA from ES cells (3 repeats)

label_protocol: Each ChIP was amplified using ligation-mediated PCR (LM-PCR). Labeling was according to standard Affymetrix protocols.

growth_protocol: Normal J1 ES growth condition

extract_protocol: For biotin-mediated ChIP, approximately, 5 × 107 mES cells expressing both BirA and biotinylated proteins were used. Briefly, cells were cross-linked by addition of final 1% formaldehyde for 7 min at room temperature. Cross-linking was terminated by adding final 125 mM glycine and cells were washed with cold phosphate-buffered saline (PBS) containing PMSF, scraped off the plates, collected by centrifugation and washed again. Collected cell pellet was resuspended in SDS ChIP buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl pH 8.1, 150 mM NaCl, and protease inhibitors). Cells were sonicated and fragmented DNA was visualized on an agarose gel (average size 0.5-1 kb). The sample was centrifuged at 12000 rpm at 4°C for 10 min and supernatant was collected. Sample was pre-cleared with protein A beads at 4°C for 1 hr and incubated with streptavidin beads (Dynabeads® MyOne™ Streptavidin T1) at 4°C overnight. For reference sample, J1 ES cells expressing BirA enzyme without biotinylated protein were used. Immunoprecipitated complexes were successively washed with buffer I (2% SDS), buffer II (0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA, 50 mM HEPES pH 7.5, 500 mM NaCl), buffer III (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-Cl pH 8.1) and TE buffer (10 mM Tris-Cl pH 7.5, 1 mM EDTA). All washes were for 8 min at room temperature. SDS elution buffer was added and incubated at 65°C overnight to reverse crosslink protein-DNA complexes. The sample was treated with RNase A and Proteinase K, extracted with phenol:chloroform and precipitated. The pellet was resuspended in 25μl of water.

tag: J1 ES cells

source_name: Input DNA from normal J1 ES cells (3 repeats)

tag: Reference for antibodyChIP


title: H3K4me3

description:
antibodyChIP
3meH3K4_1.CEL
3meH3K4_2.CEL
3meH3K4_3.CEL
Input_J1_1.CEL
Input_J1_2.CEL
Input_J1_3.CEL

scan_protocol: According to standard Affymetrix protocols.

source_name: antibody H3K4me3 ChIP DNA from ES cells (3 repeats)


title: abMyc

description:
antibodyChIP
abMyc_1.CEL
abMyc_2.CEL
abMyc_3.CEL
Input_J1_1.CEL
Input_J1_2.CEL
Input_J1_3.CEL

source_name: antibody Myc ChIP DNA from ES cells (3 repeats)


title: Peripheral blood mononuclear cells_30 minutes interval_replicate 1_GAP0057

description:
Gene expression microarrays of peripheral blood mononuclear cells obtained at blood draw date
GAP0057

value: idiopathic pulmonary fibrosis (IPF)

value: 2.013 years


title: J1BirA

description:
Reference for bioChIP
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL
Input_BirAJ1_1.CEL
Input_BirAJ1_2.CEL
Input_BirAJ1_3.CEL
Input_BirAJ1_4.CEL

source_name: Mock biotin ChIP DNA from ES cells expression BirA (4 repeats)

source_name: Input DNA from ES cells expressing BirA (4 repeats)

tag: Input for BirA expressing J1 ES cells


title: bioSox2

description:
bioChIP
bSox2_1.CEL
bSox2_2.CEL
bSox2_3.CEL
bSox2_4.CEL
bSox2_5.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioSox2 ChIP DNA from ES cells (5 repeats)

tag: Reference for bioChIP


title: bioZfp281

description:
bioChIP
bZfp281_1.CEL
bZfp281_2.CEL
bZfp281_3.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioZfp281 ChIP DNA from ES cells (3 repeats)


title: abNanog

description:
antibodyChIP
abNanog_1.CEL
abNanog_2.CEL
abNanog_3.CEL
Input_J1_1.CEL
Input_J1_2.CEL
Input_J1_3.CEL

source_name: antibody Nanog ChIP DNA from ES cells (3 repeats)


title: bioKlf4

description:
bioChIP
bKlf4_1.CEL
bKlf4_2.CEL
bKlf4_3.CEL
bKlf4_4.CEL
bKlf4_5.CEL
bKlf4_6.CEL
bKlf4_7.CEL
bKlf4_8.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioKlf4 ChIP DNA from ES cells (8 repeats)


title: bioMyc

description:
bioChIP
bMyc_1.CEL
bMyc_2.CEL
bMyc_3.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioMyc ChIP DNA from ES cells (3 repeats)


title: bioRex1

description:
bioChIP
bRex1_1.CEL
bRex1_2.CEL
bRex1_3.CEL
bRex1_4.CEL
bRex1_5.CEL
bRex1_6.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioRex1 ChIP DNA from ES cells (6 repeats)


title: bioNac1

description:
bioChIP
bNac1_1.CEL
bNac1_2.CEL
bNac1_3.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioNac1 ChIP DNA from ES cells (3 repeats)


title: bioNanog

description:
bioChIP
bNanog_1.CEL
bNanog_2.CEL
bNanog_3.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioNanog ChIP DNA from ES cells (3 repeats)


title: bioDax1

description:
bioChIP
bDax1_1.CEL
bDax1_2.CEL
bDax1_3.CEL
bDax1_4.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioDax1 ChIP DNA from ES cells (4 repeats)


title: bioOct4

description:
bioChIP
bOct4_1.CEL
bOct4_2.CEL
bOct4_3.CEL
BirA_1.CEL
BirA_2.CEL
BirA_3.CEL
BirA_4.CEL

source_name: bioOct4 ChIP DNA from ES cells (3 repeats)


title: L3Trachea_InfectionEcc2141_technicalreplicate2

status: Public on May 11 2009

city: Kiel

first: Christina

last: Wagner

address: Am Botanischen Garten 1-9

department: Zoophysiology

country: Germany

institute: Zoological Institute

description: nothing left

hyb_protocol: No blocking: Hybridisation of labeled cRNA in DigEasy hyb (Roche) overnight at 42°C in hyb chambers. Washing: 2x15 min 1xSSC and 0.1% Triton-X-100 at 60°C 2x15 min 0.1xSSC and 0.1% Triton-X-100 at 37°C 1x30 sec 0.1xSSC 1x10 sec water

scan_protocol: digitalisation of the fluorescence intensities was carried out using the GenePix 4000B scanner. scanner release: 10 µm laser power: 100%

data_processing: for spot finding and generating preliminary result files the raw scanned image files were analysed using the GenePixPro version 6.0 whereas data normalisation (sub-grid), quality assurance and control, filtering and clustering were carried out with GeneTraffic (Iobion).

organism: Drosophila melanogaster

label_protocol: Two-step method used to generate labeled aacRNA. In the first step amino-allyl UTPs are incorporated during cRNA synthesis. Subsequently, monofunctional forms of Cy3 dyes are reacted with the amino-allyl cRNA

growth_protocol: Approximately 200 second instar larvae were placed in a 2-ml microfuge tube containing 200 µl of concentrated bacterial pellet (OD=200) from an overnight culture and 400 µl of crushed banana. The tube was incubated at room temperature for 30 min. The mixture were transferred to a standard corn-meal fly medium and incubated at 29°C.

extract_protocol:
RNA was extracted from 20 pairs of trachea using the manufacture protocoll of Macharay and Nagel, NucleoSpin Kit II.
cDNA was synthesised from RNA using Superscript III-Kit from Invitrogen and amplified by the CapFinder strategy.
cRNA was synthesised from the amplified DNA using the Ambion's MEGAscript High Yield Transcription Kit.

treatment_protocol: Infection of second instar larvae with Ecc 2141. Infection were perfomed with the reporter strain YW DD1 in order to visualize the immune reaction after the Ecc2141 infection.

tag: Strain

value: YW DD1

tag: Stage

value: third instar larva infected by Ecc2141

tag: Age

value: 10 days

tag: Tissue

value: trachea

label_protocol: Two-step method used to generate labeled aacRNA. In the first step amino-allyl UTPs are incorporated during cRNA synthesis. Subsequently, monofunctional forms of Cy5 dyes are reacted with the amino-allyl cRNA.

growth_protocol: Approximately 200 second instar larvae were placed in a 2-ml microfuge tube containing 200 µl of 1xPBS and 400 µl of crushed banana. The tube was incubated at room temperature for 30 min. The mixture were transferred to a standard corn-meal fly medium and incubated at 29°C.

treatment_protocol: Incubation of second instar larvae with 1xPBS.

value: third instar larva non-infected


title: L3Trachea_InfectionEcc2141_technicalreplicate1

description: nothing left


title: L3Trachea_InfectionEcc2141_biologicalreplicate1

description: nothing left


title: L3Trachea_InfectionEcc2141_biologicalreplicate2

description: nothing left