title: Peripheral blood, 7471147089_R02C01

description: Population study sample.


title: Peripheral blood, 7471147088_R06C02

status: Public on Jan 22 2015

type: genomic

city: London

first: Benjamin

last: Lehne

address: Medicine, Norfolk Place, St Mary's Campus

department: Epidemiology and Biostatistics

country: United Kingdom

institute: Imperial College London

description: Population study sample.

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: Illumina HiScan using standard recommended Illumina scanner setting.

data_processing: Custom R scripts. Quantile normalisation of signal intensities.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Bisulfite conversion of genomic DNA from peripheral blood was performed using the EZ DNA methylation kit according to manufacturer's instructions (Zymo Research).

tag: tissue

value: peripheral blood

tag: dataset

value: population study

tag: gender

value: M

tag: age


title: Peripheral blood, 7471147088_R06C01

description: Population study sample.

value: F


title: Peripheral blood, 7471147088_R05C02

description: Population study sample.


title: Peripheral blood, 7471147092_R02C02

description: Population study sample.


title: Peripheral blood, 7471147088_R04C02

description: Population study sample.


title: Peripheral blood, 7471147088_R05C01

description: Population study sample.


title: Peripheral blood, 7471147089_R01C01

description: Population study sample.


title: Peripheral blood, 7471147088_R04C01

description: Population study sample.


title: Peripheral blood, 7471147088_R03C01

description: Population study sample.


title: Peripheral blood, 7471147088_R02C02

description: Population study sample.


title: Peripheral blood, 7471147090_R01C01

description: Population study sample.


title: Peripheral blood, 7471147088_R02C01

description: Population study sample.


title: Peripheral blood, 7471147087_R05C01

description: Population study sample.


title: Peripheral blood, 7471147089_R05C02

description: Population study sample.


title: Peripheral blood, 7471147087_R03C02

description: Population study sample.


title: Peripheral blood, 7471147088_R01C01

description: Population study sample.


title: Peripheral blood, 7471147087_R04C02

description: Population study sample.


title: Peripheral blood, 7471147087_R04C01

description: Population study sample.


title: Peripheral blood, 7471147087_R06C02

description: Population study sample.


title: Peripheral blood, 7471147115_R05C01

description: Population study sample.


title: Peripheral blood, 7471147087_R06C01

description: Population study sample.


title: Peripheral blood, 7471147087_R01C02

description: Population study sample.


title: Peripheral blood, 7471147087_R03C01

description: Population study sample.


title: Peripheral blood, 7471147087_R02C01

description: Population study sample.


title: Peripheral blood, 7471147085_R06C01

description: Population study sample.


title: Peripheral blood, 7471147087_R01C01

description: Population study sample.


title: Peripheral blood, 7471147085_R06C02

description: Population study sample.


title: Peripheral blood, 7471147085_R04C01

description: Population study sample.


title: Peripheral blood, 7471147087_R02C02

description: Population study sample.


title: Peripheral blood, 7471147085_R05C01

description: Population study sample.


title: Peripheral blood, 7471147085_R03C02

description: Population study sample.


title: Peripheral blood, 7471147085_R02C02

description: Population study sample.


title: Peripheral blood, 7471147085_R02C01

description: Population study sample.


title: Peripheral blood, 7471147088_R03C02

description: Population study sample.


title: Peripheral blood, 7471147085_R01C02

description: Population study sample.


title: Peripheral blood, 7471147085_R01C01

description: Population study sample.


title: Peripheral blood, 7471147083_R06C02

description: Population study sample.


title: Peripheral blood, 7471147083_R06C01

description: Population study sample.


title: Peripheral blood, 7471147083_R05C02

description: Population study sample.


title: Peripheral blood, 7471147088_R01C02

description: Population study sample.


title: Peripheral blood, 7471147083_R04C02

description: Population study sample.


title: Peripheral blood, 7471147083_R03C02

description: Population study sample.


title: Peripheral blood, 7471147083_R04C01

description: Population study sample.


title: Peripheral blood, 7471147083_R03C01

description: Population study sample.


title: Peripheral blood, 7471147083_R05C01

description: Population study sample.


title: Peripheral blood, 7471147083_R02C01

description: Population study sample.


title: Peripheral blood, 7471147083_R02C02

description: Population study sample.


title: Peripheral blood, 7471147083_R01C02

description: Population study sample.


title: Peripheral blood, 7471147081_R05C01

description: Population study sample.


title: Peripheral blood, 7471147081_R05C02

description: Population study sample.


title: Peripheral blood, 7471147081_R04C02

description: Population study sample.


title: Peripheral blood, 7471147081_R04C01

description: Population study sample.


title: Peripheral blood, 7471147081_R02C02

description: Population study sample.


title: Peripheral blood, 7471147085_R03C01

description: Population study sample.


title: Peripheral blood, 7471147083_R01C01

description: Population study sample.


title: Peripheral blood, 7471147081_R03C02

description: Population study sample.


title: Peripheral blood, 7471147081_R06C02

description: Population study sample.


title: Peripheral blood, 7471147081_R03C01

description: Population study sample.


title: Peripheral blood, 7471147085_R05C02

description: Population study sample.


title: Peripheral blood, 7471147079_R06C02

description: Population study sample.


title: Peripheral blood, 7471147079_R06C01

description: Population study sample.


title: Peripheral blood, 7471147079_R05C02

description: Population study sample.


title: Peripheral blood, 7471147079_R04C01

description: Population study sample.


title: Peripheral blood, 7471147079_R04C02

description: Population study sample.


title: Peripheral blood, 7471147079_R05C01

description: Population study sample.


title: Peripheral blood, 7471147081_R01C01

description: Population study sample.


title: Peripheral blood, 7471147079_R03C02

description: Population study sample.


title: Peripheral blood, 7471147079_R02C01

description: Population study sample.


title: Peripheral blood, 7471147079_R02C02

description: Population study sample.


title: Peripheral blood, 7471147079_R01C01

description: Population study sample.


title: Peripheral blood, 7471147078_R06C02

description: Population study sample.


title: Peripheral blood, 7471147078_R06C01

description: Population study sample.


title: Peripheral blood, 7471147079_R01C02

description: Population study sample.


title: Peripheral blood, 7471147078_R05C02

description: Population study sample.


title: Peripheral blood, 7471147078_R05C01

description: Population study sample.


title: Peripheral blood, 7471147081_R01C02

description: Population study sample.


title: Peripheral blood, 7471147078_R04C01

description: Population study sample.


title: Peripheral blood, 7471147078_R03C01

description: Population study sample.


title: Peripheral blood, 7471147078_R03C02

description: Population study sample.


title: Peripheral blood, 7471147078_R02C01

description: Population study sample.


title: Peripheral blood, 7471147078_R04C02

description: Population study sample.


title: Peripheral blood, 7471147077_R06C01

description: Population study sample.


title: Peripheral blood, 7471147077_R05C02

description: Population study sample.


title: Peripheral blood, 7471147078_R01C02

description: Population study sample.


title: Peripheral blood, 7471147077_R04C01

description: Population study sample.


title: Peripheral blood, 7471147077_R05C01

description: Population study sample.


title: Peripheral blood, 7471147077_R06C02

description: Population study sample.


title: Peripheral blood, 7471147077_R03C01

description: Population study sample.


title: Peripheral blood, 7471147077_R03C02

description: Population study sample.


title: Peripheral blood, 7471147077_R02C01

description: Population study sample.


title: Peripheral blood, 7471147079_R03C01

description: Population study sample.


title: Peripheral blood, 7471147077_R01C01

description: Population study sample.


title: Peripheral blood, 7471147077_R01C02

description: Population study sample.


title: Peripheral blood, 7471147075_R03C02

description: Population study sample.


title: Peripheral blood, 7471147075_R06C01

description: Population study sample.


title: Peripheral blood, 7471147075_R06C02

description: Population study sample.


title: Peripheral blood, 7471147075_R05C02

description: Population study sample.


title: Peripheral blood, 7471147075_R03C01

description: Population study sample.


title: Peripheral blood, 7471147075_R04C01

description: Population study sample.


title: Peripheral blood, 7471147075_R02C02

description: Population study sample.


title: Peripheral blood, 7471147075_R01C01

description: Population study sample.


title: Peripheral blood, 7471147074_R05C01

description: Population study sample.


title: Peripheral blood, 7471147078_R01C01

description: Population study sample.


title: Peripheral blood, 7471147074_R06C01

description: Population study sample.


title: Peripheral blood, 7471147078_R02C02

description: Population study sample.


title: Peripheral blood, 7471147074_R04C01

description: Population study sample.


title: Peripheral blood, 7471147075_R02C01

description: Population study sample.


title: Peripheral blood, 7471147074_R04C02

description: Population study sample.


title: Peripheral blood, 7471147074_R03C02

description: Population study sample.


title: Peripheral blood, 7471147074_R03C01

description: Population study sample.


title: Peripheral blood, 7471147074_R02C01

description: Population study sample.


title: Peripheral blood, 7471147077_R04C02

description: Population study sample.


title: Peripheral blood, 7471147072_R06C02

description: Population study sample.


title: Peripheral blood, 7471147077_R02C02

description: Population study sample.


title: Peripheral blood, 7471147074_R01C02

description: Population study sample.


title: Peripheral blood, 7471147074_R01C01

description: Population study sample.


title: Peripheral blood, 7471147072_R06C01

description: Population study sample.


title: Peripheral blood, 7471147072_R05C02

description: Population study sample.


title: Peripheral blood, 7471147072_R05C01

description: Population study sample.


title: Peripheral blood, 7471147072_R04C01

description: Population study sample.


title: Peripheral blood, 7471147072_R03C02

description: Population study sample.


title: Peripheral blood, 7471147072_R03C01

description: Population study sample.


title: Peripheral blood, 7471147072_R02C02

description: Population study sample.


title: Peripheral blood, 7471147072_R02C01

description: Population study sample.


title: Peripheral blood, 7471147072_R01C01

description: Population study sample.


title: Peripheral blood, 7471147071_R06C02

description: Population study sample.


title: Peripheral blood, 7471147074_R06C02

description: Population study sample.


title: Peripheral blood, 7471147071_R03C02

description: Population study sample.


title: Peripheral blood, 7471147071_R03C01

description: Population study sample.


title: Peripheral blood, 7471147071_R02C01

description: Population study sample.


title: Peripheral blood, 7471147071_R01C01

description: Population study sample.


title: Peripheral blood, 7471147070_R05C02

description: Population study sample.


title: Peripheral blood, 7471147070_R06C01

description: Population study sample.


title: Peripheral blood, 7471147070_R04C02

description: Population study sample.


title: Peripheral blood, 7471147070_R05C01

description: Population study sample.


title: Peripheral blood, 7471147070_R04C01

description: Population study sample.


title: Peripheral blood, 7471147070_R03C01

description: Population study sample.


title: Peripheral blood, 7471147070_R01C02

description: Population study sample.


title: Peripheral blood, 7471147070_R01C01

description: Population study sample.


title: Peripheral blood, 7471147070_R02C01

description: Population study sample.


title: Peripheral blood, 7471147070_R02C02

description: Population study sample.


title: Peripheral blood, 7471147070_R03C02

description: Population study sample.


title: Peripheral blood, 7471147069_R06C02

description: Population study sample.


title: Peripheral blood, 7471147069_R04C02

description: Population study sample.


title: Peripheral blood, 7471147069_R05C02

description: Population study sample.


title: Peripheral blood, 7471147069_R04C01

description: Population study sample.


title: Peripheral blood, 7471147069_R03C01

description: Population study sample.


title: Peripheral blood, 7471147069_R01C02

description: Population study sample.


title: Peripheral blood, 7471147069_R01C01

description: Population study sample.


title: Peripheral blood, 7471147071_R04C02

description: Population study sample.


title: Peripheral blood, 7471147069_R02C01

description: Population study sample.


title: Peripheral blood, 7471147068_R01C01

description: Population study sample.


title: Peripheral blood, 7471147068_R06C02

description: Population study sample.


title: Peripheral blood, 7471147068_R06C01

description: Population study sample.


title: Peripheral blood, 7471147071_R01C02

description: Population study sample.


title: Peripheral blood, 7471147068_R03C02

description: Population study sample.


title: Peripheral blood, 7471147070_R06C02

description: Population study sample.


title: Peripheral blood, 7471147068_R02C02

description: Population study sample.


title: Peripheral blood, 7471147068_R05C01

description: Population study sample.


title: Peripheral blood, 7471147068_R05C02

description: Population study sample.


title: Peripheral blood, 7471147067_R06C01

description: Population study sample.


title: Peripheral blood, 7471147068_R04C01

description: Population study sample.


title: Peripheral blood, 7471147067_R05C02

description: Population study sample.


title: Peripheral blood, 7471147067_R02C01

description: Population study sample.


title: Peripheral blood, 7471147068_R03C01

description: Population study sample.


title: Peripheral blood, 7471147068_R01C02

description: Population study sample.


title: Peripheral blood, 7471147067_R04C02

description: Population study sample.


title: Peripheral blood, 7471147067_R01C02

description: Population study sample.


title: Peripheral blood, 7471147067_R03C02

description: Population study sample.


title: Peripheral blood, 7471147067_R05C01

description: Population study sample.


title: Peripheral blood, 7471147067_R01C01

description: Population study sample.


title: Peripheral blood, 7471147067_R03C01

description: Population study sample.


title: Peripheral blood, 7471147065_R06C02

description: Population study sample.


title: Peripheral blood, 7471147065_R05C02

description: Population study sample.


title: Peripheral blood, 7471147065_R06C01

description: Population study sample.


title: Peripheral blood, 7471147065_R05C01

description: Population study sample.


title: Peripheral blood, 7471147065_R04C02

description: Population study sample.


title: Peripheral blood, 7471147068_R02C01

description: Population study sample.


title: Peripheral blood, 7471147065_R04C01

description: Population study sample.


title: Peripheral blood, 7471147067_R06C02

description: Population study sample.


title: Peripheral blood, 7471147065_R03C02

description: Population study sample.


title: Peripheral blood, 7471147065_R03C01

description: Population study sample.


title: Peripheral blood, 7471147065_R02C02

description: Population study sample.


title: Peripheral blood, 7471147067_R04C01

description: Population study sample.


title: Peripheral blood, 7471147065_R02C01

description: Population study sample.


title: Peripheral blood, 7471147064_R06C02

description: Population study sample.


title: Peripheral blood, 7471147065_R01C01

description: Population study sample.


title: Peripheral blood, 7471147065_R01C02

description: Population study sample.


title: Peripheral blood, 7471147064_R01C02

description: Population study sample.


title: Peripheral blood, 7471147064_R05C02

description: Population study sample.


title: Peripheral blood, 7471147064_R06C01

description: Population study sample.


title: Peripheral blood, 7471147064_R03C02

description: Population study sample.


title: Peripheral blood, 7471147064_R03C01

description: Population study sample.


title: Peripheral blood, 7471147064_R01C01

description: Population study sample.


title: Peripheral blood, 7471147064_R04C02

description: Population study sample.


title: Peripheral blood, 7471147064_R04C01

description: Population study sample.


title: Peripheral blood, 7471147064_R02C02

description: Population study sample.


title: Peripheral blood, 7471147062_R06C02

description: Population study sample.


title: Peripheral blood, 7471147062_R05C02

description: Population study sample.


title: Peripheral blood, 7471147062_R04C02

description: Population study sample.


title: Peripheral blood, 7471147062_R03C02

description: Population study sample.


title: Peripheral blood, 7471147062_R02C02

description: Population study sample.


title: Peripheral blood, 7471147062_R04C01

description: Population study sample.


title: Peripheral blood, 7471147062_R03C01

description: Population study sample.


title: Peripheral blood, 7471147062_R02C01

description: Population study sample.


title: Peripheral blood, 7471147062_R01C02

description: Population study sample.


title: Peripheral blood, 7471147062_R01C01

description: Population study sample.


title: Peripheral blood, 7471147064_R05C01

description: Population study sample.


title: Peripheral blood, 7471147061_R06C02

description: Population study sample.


title: Peripheral blood, 7471147061_R05C02

description: Population study sample.


title: Peripheral blood, 7471147061_R04C02

description: Population study sample.


title: Peripheral blood, 7471147061_R05C01

description: Population study sample.


title: Peripheral blood, 7471147061_R03C01

description: Population study sample.


title: Peripheral blood, 7471147061_R03C02

description: Population study sample.


title: Peripheral blood, 7471147061_R02C02

description: Population study sample.


title: Peripheral blood, 7471147064_R02C01

description: Population study sample.


title: Peripheral blood, 7471147062_R06C01

description: Population study sample.


title: Peripheral blood, 7471147061_R06C01

description: Population study sample.


title: Peripheral blood, 7471147059_R06C02

description: Population study sample.


title: Peripheral blood, 7471147061_R04C01

description: Population study sample.


title: Peripheral blood, 7471147061_R02C01

description: Population study sample.


title: Peripheral blood, 7471147061_R01C01

description: Population study sample.


title: Peripheral blood, 7471147059_R06C01

description: Population study sample.


title: Peripheral blood, 7471147062_R05C01

description: Population study sample.


title: Peripheral blood, 7471147059_R05C01

description: Population study sample.


title: Peripheral blood, 7471147061_R01C02

description: Population study sample.


title: Peripheral blood, 7471147059_R04C02

description: Population study sample.


title: Peripheral blood, 7471147059_R05C02

description: Population study sample.


title: Peripheral blood, 7471147059_R04C01

description: Population study sample.


title: Peripheral blood, 7471147059_R02C01

description: Population study sample.


title: Peripheral blood, 7471147059_R01C01

description: Population study sample.


title: Peripheral blood, 7471147059_R02C02

description: Population study sample.


title: Peripheral blood, 7471147059_R01C02

description: Population study sample.


title: Peripheral blood, 7471147059_R03C02

description: Population study sample.


title: Peripheral blood, 7471147057_R06C01

description: Population study sample.


title: Peripheral blood, 7471147058_R03C02

description: Population study sample.


title: Peripheral blood, 7471147058_R04C01

description: Population study sample.


title: Peripheral blood, 7471147057_R05C02

description: Population study sample.


title: Peripheral blood, 7471147057_R05C01

description: Population study sample.


title: Peripheral blood, 7471147057_R04C02

description: Population study sample.


title: Peripheral blood, 7471147057_R01C02

description: Population study sample.


title: Peripheral blood, 7471147057_R04C01

description: Population study sample.


title: Peripheral blood, 7471147057_R02C01

description: Population study sample.


title: Peripheral blood, 7471147058_R06C01

description: Population study sample.


title: Peripheral blood, 7471147055_R06C02

description: Population study sample.


title: Peripheral blood, 7471147057_R02C02

description: Population study sample.


title: Peripheral blood, 7471147055_R04C02

description: Population study sample.


title: Peripheral blood, 7471147055_R05C02

description: Population study sample.


title: Peripheral blood, 7471147055_R05C01

description: Population study sample.


title: Peripheral blood, 7471147055_R03C01

description: Population study sample.


title: Peripheral blood, 7471147055_R06C01

description: Population study sample.


title: Peripheral blood, 7471147055_R04C01

description: Population study sample.


title: Peripheral blood, 7471147055_R03C02

description: Population study sample.


title: Peripheral blood, 7471147055_R02C01

description: Population study sample.


title: Peripheral blood, 7471147059_R03C01

description: Population study sample.


title: Peripheral blood, 7471147055_R01C01

description: Population study sample.


title: Peripheral blood, 7471147055_R02C02

description: Population study sample.


title: Peripheral blood, 7471147055_R01C02

description: Population study sample.


title: Peripheral blood, 7471147049_R06C02

description: Population study sample.


title: Peripheral blood, 7471147049_R04C02

description: Population study sample.


title: Peripheral blood, 7471147049_R03C02

description: Population study sample.


title: Peripheral blood, 7471147049_R06C01

description: Population study sample.


title: Peripheral blood, 7471147049_R04C01

description: Population study sample.


title: Peripheral blood, 7471147057_R03C02

description: Population study sample.


title: Peripheral blood, 7471147049_R03C01

description: Population study sample.


title: Peripheral blood, 7471147049_R02C02

description: Population study sample.


title: Peripheral blood, 7471147049_R01C01

description: Population study sample.


title: Peripheral blood, 7471147047_R06C01

description: Population study sample.


title: Peripheral blood, 7471147047_R06C02

description: Population study sample.


title: Peripheral blood, 7471147049_R01C02

description: Population study sample.


title: Peripheral blood, 7471147047_R04C02

description: Population study sample.


title: Peripheral blood, 7471147047_R05C01

description: Population study sample.


title: Peripheral blood, 7471147047_R05C02

description: Population study sample.


title: Peripheral blood, 7471147047_R04C01

description: Population study sample.


title: Peripheral blood, 7471147047_R02C02

description: Population study sample.


title: Peripheral blood, 7471147047_R01C02

description: Population study sample.


title: Peripheral blood, 7471147047_R03C02

description: Population study sample.


title: Peripheral blood, 7471147047_R03C01

description: Population study sample.


title: Peripheral blood, 7471147041_R06C01

description: Population study sample.


title: Peripheral blood, 7471147041_R05C01

description: Population study sample.


title: Peripheral blood, 7471147041_R04C02

description: Population study sample.


title: Peripheral blood, 7471147041_R06C02

description: Population study sample.


title: Peripheral blood, 7471147047_R02C01

description: Population study sample.


title: Peripheral blood, 7471147041_R03C01

description: Population study sample.


title: Peripheral blood, 7471147041_R02C02

description: Population study sample.


title: Peripheral blood, 7471147041_R05C02

description: Population study sample.


title: Peripheral blood, 7471147041_R01C02

description: Population study sample.


title: Peripheral blood, 7471147041_R01C01

description: Population study sample.


title: Peripheral blood, 7471147040_R06C02

description: Population study sample.


title: Peripheral blood, 7471147040_R06C01

description: Population study sample.


title: Peripheral blood, 7471147041_R02C01

description: Population study sample.


title: Peripheral blood, 7471147049_R02C01

description: Population study sample.


title: Peripheral blood, 7471147040_R05C02

description: Population study sample.


title: Peripheral blood, 7471147040_R05C01

description: Population study sample.


title: Peripheral blood, 7471147040_R04C02

description: Population study sample.


title: Peripheral blood, 7471147040_R04C01

description: Population study sample.


title: Peripheral blood, 7471147040_R02C02

description: Population study sample.


title: Peripheral blood, 7471147040_R03C01

description: Population study sample.


title: Peripheral blood, 7471147040_R01C02

description: Population study sample.


title: Peripheral blood, 7471147040_R03C02

description: Population study sample.


title: Peripheral blood, 7471147040_R01C01

description: Population study sample.


title: Peripheral blood, 7471147040_R02C01

description: Population study sample.


title: Peripheral blood, 7471147036_R06C02

description: Population study sample.


title: Peripheral blood, 7471147036_R06C01

description: Population study sample.


title: Peripheral blood, 7471147041_R03C02

description: Population study sample.


title: Peripheral blood, 7471147036_R05C02

description: Population study sample.


title: Peripheral blood, 7471147036_R02C02

description: Population study sample.


title: Peripheral blood, 7471147036_R04C02

description: Population study sample.


title: Peripheral blood, 7471147034_R06C01

description: Population study sample.


title: Peripheral blood, 7471147034_R06C02

description: Population study sample.


title: Peripheral blood, 7471147036_R03C02

description: Population study sample.


title: Peripheral blood, 7471147036_R02C01

description: Population study sample.


title: Peripheral blood, 7471147036_R03C01

description: Population study sample.


title: Peripheral blood, 7471147034_R05C02

description: Population study sample.


title: Peripheral blood, 7471147036_R01C02

description: Population study sample.


title: Peripheral blood, 7471147034_R04C01

description: Population study sample.


title: Peripheral blood, 7471147034_R02C02

description: Population study sample.


title: Peripheral blood, 7471147034_R03C02

description: Population study sample.


title: Peripheral blood, 7471147034_R02C01

description: Population study sample.


title: Peripheral blood, 7471147034_R01C02

description: Population study sample.


title: Peripheral blood, 7471147034_R01C01

description: Population study sample.


title: Peripheral blood, 7471147030_R06C01

description: Population study sample.


title: Peripheral blood, 7471147036_R05C01

description: Population study sample.


title: Peripheral blood, 7471147030_R06C02

description: Population study sample.


title: Peripheral blood, 7471147030_R04C02

description: Population study sample.


title: Peripheral blood, 7471147030_R05C01

description: Population study sample.


title: Peripheral blood, 7471147030_R03C02

description: Population study sample.


title: Peripheral blood, 7471147036_R04C01

description: Population study sample.


title: Peripheral blood, 7471147030_R02C02

description: Population study sample.


title: Peripheral blood, 7471147030_R01C02

description: Population study sample.


title: Peripheral blood, 7471147034_R04C02

description: Population study sample.


title: Peripheral blood, 7471147034_R05C01

description: Population study sample.


title: Peripheral blood, 7471147027_R06C01

description: Population study sample.


title: Peripheral blood, 7471147027_R06C02

description: Population study sample.


title: Peripheral blood, 7471147027_R04C02

description: Population study sample.


title: Peripheral blood, 7471147030_R01C01

description: Population study sample.


title: Peripheral blood, 7471147027_R05C02

description: Population study sample.


title: Peripheral blood, 7471147027_R04C01

description: Population study sample.


title: Peripheral blood, 7471147027_R03C02

description: Population study sample.


title: Peripheral blood, 7471147027_R02C02

description: Population study sample.


title: Peripheral blood, 7471147027_R03C01

description: Population study sample.


title: Peripheral blood, 7471147030_R05C02

description: Population study sample.


title: Peripheral blood, 7471147027_R01C02

description: Population study sample.


title: Peripheral blood, 7471147027_R01C01

description: Population study sample.


title: Peripheral blood, 7471147027_R02C01

description: Population study sample.


title: Peripheral blood, 7471147025_R05C02

description: Population study sample.


title: Peripheral blood, 7471147025_R06C02

description: Population study sample.


title: Peripheral blood, 7471147030_R03C01

description: Population study sample.


title: Peripheral blood, 7471147030_R04C01

description: Population study sample.


title: Peripheral blood, 7471147025_R04C02

description: Population study sample.


title: Peripheral blood, 7471147025_R04C01

description: Population study sample.


title: Peripheral blood, 7471147025_R03C01

description: Population study sample.


title: Peripheral blood, 7471147025_R02C02

description: Population study sample.


title: Peripheral blood, 7471147025_R03C02

description: Population study sample.


title: Peripheral blood, 7471147025_R02C01

description: Population study sample.


title: Peripheral blood, 7471147025_R01C01

description: Population study sample.


title: Peripheral blood, 7471147025_R01C02

description: Population study sample.


title: Peripheral blood, 7471147024_R06C02

description: Population study sample.


title: Peripheral blood, 7471147024_R05C01

description: Population study sample.


title: Peripheral blood, 7471147024_R06C01

description: Population study sample.


title: Peripheral blood, 7471147024_R02C02

description: Population study sample.


title: Peripheral blood, 7471147024_R04C01

description: Population study sample.


title: Peripheral blood, 7471147024_R04C02

description: Population study sample.


title: Peripheral blood, 7471147024_R05C02

description: Population study sample.


title: Peripheral blood, 7471147024_R03C02

description: Population study sample.


title: Peripheral blood, 7471147025_R06C01

description: Population study sample.


title: Peripheral blood, 7471147012_R06C02

description: Population study sample.


title: Peripheral blood, 7471147012_R03C02

description: Population study sample.


title: Peripheral blood, 7471147012_R05C01

description: Population study sample.


title: Peripheral blood, 7471147024_R01C02

description: Population study sample.


title: Peripheral blood, 7471147012_R06C01

description: Population study sample.


title: Peripheral blood, 7471147012_R03C01

description: Population study sample.


title: Peripheral blood, 7471147012_R02C02

description: Population study sample.


title: Peripheral blood, 7471147012_R04C02

description: Population study sample.


title: Peripheral blood, 7471147012_R01C02

description: Population study sample.


title: Peripheral blood, 7471147012_R01C01

description: Population study sample.


title: Peripheral blood, 7471147006_R06C02

description: Population study sample.


title: Peripheral blood, 7471147012_R04C01

description: Population study sample.


title: Peripheral blood, 7471147006_R06C01

description: Population study sample.


title: Peripheral blood, 7471147006_R05C02

description: Population study sample.


title: Peripheral blood, 7471147012_R02C01

description: Population study sample.


title: Peripheral blood, 7471147024_R03C01

description: Population study sample.


title: Peripheral blood, 7471147006_R05C01

description: Population study sample.


title: Peripheral blood, 7471147006_R04C02

description: Population study sample.


title: Peripheral blood, 7471147024_R01C01

description: Population study sample.


title: Peripheral blood, 7471147006_R04C01

description: Population study sample.


title: Peripheral blood, 7471147006_R03C02

description: Population study sample.


title: Peripheral blood, 7471147006_R02C02

description: Population study sample.


title: Peripheral blood, 7471147006_R03C01

description: Population study sample.


title: Peripheral blood, 7471147006_R02C01

description: Population study sample.


title: Peripheral blood, 7471147012_R05C02

description: Population study sample.


title: Peripheral blood, 7471147004_R05C02

description: Population study sample.


title: Peripheral blood, 7471147006_R01C01

description: Population study sample.


title: Peripheral blood, 7471147004_R06C01

description: Population study sample.


title: Peripheral blood, 7471147004_R06C02

description: Population study sample.


title: Peripheral blood, 7471147004_R05C01

description: Population study sample.


title: Peripheral blood, 7471147004_R04C01

description: Population study sample.


title: Peripheral blood, 7471147004_R03C01

description: Population study sample.


title: Peripheral blood, 7471147004_R03C02

description: Population study sample.


title: Peripheral blood, 7471147004_R02C01

description: Population study sample.


title: Peripheral blood, 7471147003_R06C02

description: Population study sample.


title: Peripheral blood, 7471147004_R01C01

description: Population study sample.


title: Peripheral blood, 7471147003_R05C01

description: Population study sample.


title: Peripheral blood, 7471147003_R06C01

description: Population study sample.


title: Peripheral blood, 7471147003_R05C02

description: Population study sample.


title: Peripheral blood, 7471147003_R03C02

description: Population study sample.


title: Peripheral blood, 7471147003_R03C01

description: Population study sample.


title: Peripheral blood, 7471147003_R01C02

description: Population study sample.


title: Peripheral blood, 7471147006_R01C02

description: Population study sample.


title: Peripheral blood, 7471147002_R06C02

description: Population study sample.


title: Peripheral blood, 7471147002_R05C01

description: Population study sample.


title: Peripheral blood, 7471147002_R04C02

description: Population study sample.


title: Peripheral blood, 7471147002_R04C01

description: Population study sample.


title: Peripheral blood, 7471147003_R02C01

description: Population study sample.


title: Peripheral blood, 7471147003_R02C02

description: Population study sample.


title: Peripheral blood, 7471147002_R03C01

description: Population study sample.


title: Peripheral blood, 7471147002_R02C02

description: Population study sample.


title: Peripheral blood, 7471147004_R04C02

description: Population study sample.


title: Peripheral blood, 7471147002_R02C01

description: Population study sample.


title: Peripheral blood, 7786915157_R04C02

description: Technical replicate group 2, sample 33.

value: technical replication study


title: Peripheral blood, 7512560138_R01C01

description: Technical replicate group 2, sample 35.


title: Peripheral blood, 7512551008_R05C01

description: Technical replicate group 2, sample 36.


title: Peripheral blood, 7512551008_R04C02

description: Technical replicate group 2, sample 30.


title: Peripheral blood, 7786915157_R03C01

description: Technical replicate group 2, sample 32.


title: Peripheral blood, 7512560138_R06C01

description: Technical replicate group 2, sample 31.


title: Peripheral blood, 7471147003_R04C02

description: Population study sample.


title: Peripheral blood, 7512578059_R02C02

description: Technical replicate group 2, sample 34.


title: Peripheral blood, 7471147002_R01C02

description: Population study sample.


title: Peripheral blood, 7512560138_R04C01

description: Technical replicate group 2, sample 26.


title: Peripheral blood, 7786915157_R05C01

description: Technical replicate group 2, sample 25.


title: Peripheral blood, 7512578059_R05C02

description: Technical replicate group 2, sample 29.


title: Peripheral blood, 7786915157_R02C01

description: Technical replicate group 2, sample 27.


title: Peripheral blood, 7471147002_R03C02

description: Population study sample.


title: Peripheral blood, 7786915157_R05C02

description: Technical replicate group 2, sample 28.


title: Peripheral blood, 7512578059_R04C02

description: Technical replicate group 2, sample 18.


title: Peripheral blood, 7471147002_R05C02

description: Population study sample.


title: Peripheral blood, 7512560138_R02C01

description: Technical replicate group 2, sample 23.


title: Peripheral blood, 7512560138_R05C01

description: Technical replicate group 2, sample 24.


title: Peripheral blood, 7471147002_R01C01

description: Population study sample.


title: Peripheral blood, 7512551008_R05C02

description: Technical replicate group 2, sample 22.


title: Peripheral blood, 7512551008_R04C01

description: Technical replicate group 2, sample 21.


title: Peripheral blood, 7512551008_R02C02

description: Technical replicate group 2, sample 19.


title: Peripheral blood, 7786915157_R03C02

description: Technical replicate group 2, sample 17.


title: Peripheral blood, 7786915157_R02C02

description: Technical replicate group 2, sample 15.


title: Peripheral blood, 7786915157_R04C01

description: Technical replicate group 2, sample 16.


title: Peripheral blood, 7512551008_R02C01

description: Technical replicate group 2, sample 13.


title: Peripheral blood, 7512551008_R06C02

description: Technical replicate group 2, sample 14.


title: Peripheral blood, 7786915157_R06C02

description: Technical replicate group 2, sample 20.


title: Peripheral blood, 7512578059_R03C02

description: Technical replicate group 2, sample 5.


title: Peripheral blood, 7512551008_R03C02

description: Technical replicate group 2, sample 6.


title: Peripheral blood, 7512578059_R06C02

description: Technical replicate group 2, sample 10.


title: Peripheral blood, 7512560138_R03C01

description: Technical replicate group 2, sample 2.


title: Peripheral blood, 7512551008_R01C02

description: Technical replicate group 2, sample 1.


title: Peripheral blood, 7512551008_R06C01

description: Technical replicate group 2, sample 8.


title: Peripheral blood, 7786915157_R06C01

description: Technical replicate group 2, sample 7.


title: Peripheral blood, 7786915157_R01C02

description: Technical replicate group 2, sample 12.


title: Peripheral blood, 7786915075_R05C01

description: Technical replicate group 1, sample 35.


title: Peripheral blood, 7512551008_R03C01

description: Technical replicate group 2, sample 11.


title: Peripheral blood, 7786923067_R06C01

description: Technical replicate group 1, sample 31.

value: population study; technical replication study


title: Peripheral blood, 7786915105_R02C01

description: Technical replicate group 1, sample 29.


title: Peripheral blood, 7512578059_R01C02

description: Technical replicate group 2, sample 4.


title: Peripheral blood, 7512551008_R01C01

description: Technical replicate group 2, sample 3.


title: Peripheral blood, 7786915153_R05C01

description: Technical replicate group 1, sample 27.


title: Peripheral blood, 7471147134_R02C01

description: Technical replicate group 1, sample 26.


title: Peripheral blood, 7786915069_R03C01

description: Technical replicate group 1, sample 36.


title: Peripheral blood, 7786915048_R04C01

description: Technical replicate group 1, sample 25.


title: Peripheral blood, 7786923001_R06C01

description: Technical replicate group 1, sample 23.


title: Peripheral blood, 7471147081_R06C01

description: Technical replicate group 1, sample 21.


title: Peripheral blood, 7786923028_R03C01

description: Technical replicate group 1, sample 22.


title: Peripheral blood, 7786915116_R06C02

description: Technical replicate group 1, sample 34.


title: Peripheral blood, 7507875154_R05C01

description: Technical replicate group 1, sample 28.


title: Peripheral blood, 7786923077_R04C01

description: Technical replicate group 1, sample 30.


title: Peripheral blood, 7471147022_R02C02

description: Technical replicate group 1, sample 33.


title: Peripheral blood, 7786915047_R02C02

description: Technical replicate group 1, sample 32.


title: Peripheral blood, 7507875153_R03C02

description: Technical replicate group 1, sample 19.


title: Peripheral blood, 7471147069_R02C02

description: Technical replicate group 1, sample 17.


title: Peripheral blood, 7786923038_R03C02

description: Technical replicate group 1, sample 18.


title: Peripheral blood, 7786915157_R01C01

description: Technical replicate group 2, sample 9.


title: Peripheral blood, 7471147034_R03C01

description: Technical replicate group 1, sample 20.


title: Peripheral blood, 7786923066_R01C01

description: Technical replicate group 1, sample 10.


title: Peripheral blood, 7786915052_R01C01

description: Technical replicate group 1, sample 15.


title: Peripheral blood, 7786923028_R05C02

description: Technical replicate group 1, sample 8.


title: Peripheral blood, 7471147067_R02C02

description: Technical replicate group 1, sample 14.


title: Peripheral blood, 7471147089_R06C01

description: Technical replicate group 1, sample 24.


title: Peripheral blood, 7786923023_R02C01

description: Technical replicate group 1, sample 11.


title: Peripheral blood, 7796814020_R04C02

description: Technical replicate group 1, sample 13.


title: Peripheral blood, 7471147107_R05C02

description: Technical replicate group 1, sample 7.


title: Peripheral blood, 7471147030_R02C01

description: Population study sample.


title: Peripheral blood, 7512560087_R03C01

description: Technical replicate group 1, sample 9.


title: Peripheral blood, 7786923035_R01C01

description: Technical replicate group 1, sample 5.


title: Peripheral blood, 7786915035_R05C01

description: Technical replicate group 1, sample 4.


title: Peripheral blood, 7471147149_R06C01

description: Technical replicate group 1, sample 3.


title: Peripheral blood, 7786915135_R04C02

description: Technical replicate group 1, sample 2.


title: Peripheral blood, 7471147145_R06C01

description: Technical replicate group 1, sample 12.


title: Peripheral blood, 7786915023_R02C02

description: Technical replicate group 1, sample 1.


title: Peripheral blood, 7786923050_R03C01

description: Technical replicate group 1, sample 16.


title: Peripheral blood, 7471147072_R01C02

description: Technical replicate group 1, sample 6.


title: E3_HSCCCl4

status: Public on Dec 19 2014

type: RNA

city: New York

first: Robert

middle: F.

last: Schwabe

state: NY

address: 1150 St. Nicholas Ave.

department: Medicine- Division of Digestive Diseases

country: USA

institute: Columbia University

hyb_protocol: 10 μg of aRNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm as implemented in Bioconductor/R.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Hepatic stellate cells isolated from Balb/c mice treated with CCl4

label_protocol: 1000 ng RNA was amplified, biotin labeled and fragmented using the one cycle cDNA synthesis kit and one-cycle in vitro labeling kit.

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: RNA was isolated by column purification (Qiagen) and quantification by NanoDrop spectrophotometer.

treatment_protocol: Hepatic stellate cells were isolated from different groups of 8-10 week old male Balb/c mice using density centrifugation and subsequent depletion of F4/80 positive cells by MACs: Group 1: Quiescent HSCs were isolated from normal Balb/c mice and plated for 24h before lysis. Group 2: Activated hepatic stellate cells were isolated as above but cultured in media containing 10% fetal bovine serum for 5 days. Group 3: Hepatic stellate cells were  isolated as above and cultured in media containing 10% fetal bovine serum for 5 days in the presence of hepatic macrophages in a contact-independent manner using transwell inserts. Group4: Hepatic stellate cells were isolated from mice that had undergone ligating the common bile duct for 15 days  for the induction of fibrosis. After isolation, cells were plated for 24h. Group 5: Hepatic stellate cells were isolated from mice that had received 4 intraperitoneal injections of carbon tetrachloride (0.5 μl/g body weight) for the induction of fibrosis. After isolation, cells were plated for 24h.

value: male

tag: strain

value: Balb/c

value: liver stellate cells treated with CCl4


title: D2_HSCBDL

source_name: Hepatic stellate cells isolated from Balb/c mice subject to bile duct ligation

value: liver stellate cells derived from mice subject to bile duct ligation


title: C1_ActHSC+KC

source_name: Hepatic stellate cells isolated from Balb/c mice  activated for 5 days in plastic cell culture dishes in media containing 10% fetal bovine serum in the presence of Kupffer cells (contact-independent)

value: liver stellate cells co-cultured with Kupffer cells


title: E1_HSCCCl4


title: D1_HSCBDL


title: A3_QHSCX

source_name: Quiescent hepatic stellate cells isolated from Balb/c mice

value: liver stellate cells


title: A1_QHSC1


title: B1_ActHSC

source_name: Hepatic stellate cells isolated from Balb/c mice  activated for 5 days in plastic cell culture dishes in media containing 10% fetal bovine serum.


title: C2_ActHSC+KC


title: C3_ActHSC+KC


title: A5_QHSC5


title: B2_ActHSC


title: D3_HSCBDL


title: Patient 13C Non-Lesional Tissue Post-Treatment C

status: Public on Dec 04 2014

first: Mayte

last: Suarez-Farinas

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

institute: Mount SinaiSchool of Medicine

hyb_protocol: RNA was hybridized to HGU133 Plus 2.0 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor) and adjusted for batch effect (see publication)

source_name: human skin biopsy

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using miRNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

value: NL skin

tag: treatment

value: C Dupilumab 300 mg

tag: time

value: Post

tag: patient


title: Patient 16D Lesional Tissue Pre-Treatment D

value: LS skin

value: D Placebo

value: Pre


title: Patient 18D Lesional Tissue Pre-Treatment D


title: A4_QHSC4


title: A2_QHSC2


title: Patient 18D Lesional Tissue Post-Treatment D


title: Patient 15D Lesional Tissue Pre-Treatment D


title: Patient 17D Lesional Tissue Post-Treatment D


title: Patient 14C Lesional Tissue Pre-Treatment C


title: B3_ActHSC


title: Patient 14C Non-Lesional Tissue Pre-Treatment C


title: E2_HSCCCl4


title: Patient 14C Lesional Tissue Post-Treatment C


title: Patient 13C Lesional Tissue Post-Treatment C


title: Patient 14C Non-Lesional Tissue Post-Treatment C


title: Patient 13C Lesional Tissue Pre-Treatment C


title: Patient 9C Non-Lesional Tissue Post-Treatment C


title: Patient 13C Non-Lesional Tissue Pre-Treatment C


title: Patient 5B Lesional Tissue Post-Treatment B

value: B Dupilumab 150 mg


title: Patient 6B Lesional Tissue Post-Treatment B


title: Patient 11C Non-Lesional Tissue Pre-Treatment C


title: Patient 4B Non-Lesional Tissue Pre-Treatment B


title: Patient 11C Lesional Tissue Pre-Treatment C


title: Patient 9C Lesional Tissue Post-Treatment C


title: Patient 9C Non-Lesional Tissue Pre-Treatment C


title: Patient 4B Lesional Tissue Pre-Treatment B


title: Patient 1B Non-Lesional Tissue Post-Treatment B


title: Patient 12C Lesional Tissue Pre-Treatment C


title: Patient 6B Lesional Tissue Pre-Treatment B


title: Patient 9C Lesional Tissue Pre-Treatment C


title: Patient 3B Lesional Tissue Post-Treatment B


title: Patient 8C Lesional Tissue Pre-Treatment C


title: Patient 2B Lesional Tissue Post-Treatment B


title: Patient 1B Lesional Tissue Post-Treatment B


title: Patient 5B Lesional Tissue Pre-Treatment B


title: Patient 5B Non-Lesional Tissue Pre-Treatment B


title: Patient 7B Lesional Tissue Pre-Treatment B


title: Patient 5B Non-Lesional Tissue Post-Treatment B


title: Patient 4B Lesional Tissue Post-Treatment B


title: Patient 3B Lesional Tissue Pre-Treatment B


title: Patient 10C Lesional Tissue Post-Treatment C


title: Patient 1B Non-Lesional Tissue Pre-Treatment B


title: Hematopoietic_GFP+_rep1

status: Public on Nov 12 2014

city: Philadelphia

first: Nancy

middle: A

last: Speck

state: United States

address: 3451 Walnut St

department: Cell and Developmental Biology

institute: University of Pennsylvania

hyb_protocol: Labeled RNA was hybridized to the arrays overnight (17hrs) at 65C on a rotator.

scan_protocol: Arrays were scanned using Agilent Technologies Scanner G2505C according to manufacturer's recommendations.

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1-1010_Sep10 and Grid: 026655_D_F_20100123).
Probes were averaged on gene level, then genes were filtered using ANOVA and those with pvalue larger than 0.01 were excluded.

source_name: Ly6a-GFP+ hematopoietic cluster cells,lysed in TRIzol-LS,  homogenized by 70% ethanol, RNA was isolated using Qiagen RNeasy mini kit

label_protocol: Starting with 50ng of total RNA, Cy3 dye was coupled to cRNA made from the samples using Agilent's Low Input Quick Amp labeling kit.

growth_protocol: Tg(Ly6a-GFP) conceptuses were generated by crossing C57BL/6 x 129S1/SVImJ F1 females with Tg(Ly6a-GFP) males.

extract_protocol: RNA was split into 2 fractions and amplified by the Ovation® RNA-Seq System V2 (NuGEN)

treatment_protocol: A+U+V from 100 E10.5 Tg(Ly6a-GFP) embryos were dissected, and 30,000  Ly6a-GFP+ hematopoietic cluster cells (CD31+ VEC+ ESAM+ Kit+), 130,000 Ly6a-GFP- hematopoietic cluster cells, 70,000 Ly6a-GFP+ endothelial cells (CD31+ VEC+ ESAM+ Kit-), and 300,000 Ly6a-GFP- endothelial cells sorted into TRIzol-LS (Invitrogen). The cells were lysed in TRIzol-LS and the aqueous phase was collected after adding chloroform. The aqueous phase was homogenized by 70% ethanol. RNA was isolated using Qiagen RNeasy mini kit.

tag: cell type

value: Ly6a-GFP+ hematopoietic cluster cells


title: H9 SOX2

status: Public on Nov 05 2014

type: SRA

first: Raju

middle: S

last: Chaganti

address: 430 East, 67 Street, RRL-337,New York

department: Cell Biology

institute: MSKCC

description: SOX2 ChIPseq

library_source: genomic

data_processing:
Sequences were mapped to the human genome hg19 using ABI’s Corona Lite Plus genome mapping utility, allowing for up to four mismatches and retaining only unique matches.
We called peaks with MACS (Zhang, et al. 2008), using a band width of 200, model fold 5, and p-value cutoff of 1E-03 against IgG control
MACS identifies peaks on a per-window basis by comparing the number of tags in each genome window to the number of expected tags as calculated by a Poisson distribution and to the distribution of normalized per-window counts in IgG control
Candidate transcription-factor targets were identified based on transcription start site proximity (10Kb, 5Kb and 2Kb) to predicted peaks
Genome_build: HG19
Supplementary_files_format_and_content: text files contain macs output format

source_name: Embryonic Stem Cells_SOX2

extract_protocol:
Cells were sonicated using Covaris and then the TF-chromatin comples were isolated using magnetic beads linked to specific antibody
SOLiD System 2.0. Fragment Library Preparation protocol was based on size and concentration of ChIP-DNA

value: Embryonic Stem Cells

tag: cell line


title: Hematopoietic_GFP+_rep2


title: Endothelial_GFP+_rep2

source_name: Ly6a-GFP+ endothelial cells,lysed in TRIzol-LS,  homogenized by 70% ethanol,RNA was isolated using Qiagen RNeasy mini kit

value: Ly6a-GFP+ endothelial cells


title: Patient 2B Non-Lesional Tissue Pre-Treatment B


title: Hematopoietic_GFP-_rep1

source_name: Ly6a-GFP- hematopoietic cluster cells,lysed in TRIzol-LS,  homogenized by 70% ethanol, RNA was isolated using Qiagen RNeasy mini kit

value: Ly6a-GFP- hematopoietic cluster cells


title: H9 OCT4

description: OCT4 ChIPseq

source_name: Embryonic Stem Cells_OCT4


title: Hematopoietic_GFP-_rep2

value: male


title: H9 NANOG

description: NANOG ChIPseq

source_name: Embryonic Stem Cells_NANOG


title: Endothelial_GFP-_rep1

source_name: Ly6a-GFP- endothelial cells,lysed in TRIzol-LS,  homogenized by 70% ethanol,RNA was isolated using Qiagen RNeasy mini kit

value: Ly6a-GFP- endothelial cells


title: Endothelial_GFP+_rep1

source_name: Ly6a-GFP+ endothelial cells,lysed in TRIzol-LS,  homogenized by 70% ethanol, RNA was isolated using Qiagen RNeasy mini kit


title: VSL#3_BALBc_colon_mice4

status: Public on Oct 23 2014

city: Leiden

first: Rob

last: Mariman

address: Zernikedreef 9

country: Netherlands

institute: TNO

description: BALB/c mice

hyb_protocol: Hybridization and washing were performed according to the Illumina standard assay procedure.

scan_protocol: Scanning was performed on the IlluminaScanner (Illumina, Inc., San Diego, CA, U.S.A.)

data_processing:
Image analysis and extraction of raw and background subtracted expression data were performed with IlluminaBeadstudio v3 Gene Expression software using default settings.
GeneSpring GX 11.0 was used for quantile normalization of the probe-level, background subtracted expression values. After the normalization, unexpressed probes were removed from the further analyses. Because probes with a detection p-value <0.05 were all higher than 5, the latter value was considered as a cut-off value to eliminate unexpressed probes. All expression values below 5 (2.322 on log2 scale) were floored to 5. Differentially expressed probes were identified using the limma package of the R/Bioconductor project, applying linear models and moderated t-statistics that implement empirical Bayes regularization of standard errors

label_protocol: Biotinylated cRNA was prepared using the IlluminaTotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer’s specifications starting with 500 ng total RNA. Per sample, 750 ng cRNA was used to hybridize to the Sentrix MouseRef-8 BeadChips (Illumina, Inc., San Diego, CA, U.S.A.).

growth_protocol: Specific-pathogen-free 9-week old female C57BL/6 mice (Charles River, Maastricht, Netherlands) and female BALB/c mice (Janvier, St. Berthevin, France) were used in this study.

extract_protocol: Total RNA was isolated from frozen intestinal tissue using TRIzol reagent (Invitrogen, Breda, The Netherlands) according to the manufacturer's instructions. RNA was treated with DNAse and purified using Nucleospin RNAII Total RNA Isolation kit (Macherey-Nagel, Düren, Germany), according to the instructions of the manufacturer.

treatment_protocol: To study the effect of long-term probiotic administration, mice were gavaged with PBS or 3 x 108 CFU VSL#3 suspended in 200 μl PBS, 3 times a week, for a period of 4 weeks.

value: BALB/c

tag: tissue type

value: colonic tissue


title: VSL#3_BALBc_colon_mice3

description: BALB/c mice


title: Patient 1B Lesional Tissue Pre-Treatment B


title: Endothelial_GFP-_rep2

source_name: Ly6a-GFP- endothelial cells,lysed in TRIzol-LS,  homogenized by 70% ethanol, RNA was isolated using Qiagen RNeasy mini kit


title: VSL#3_BALBc_colon_mice5

description: BALB/c mice


title: VSL#3_BALBc_SI_mice3

description: BALB/c mice

value: small intestine tissue


title: VSL#3_BALBc_SI_mice2

description: BALB/c mice


title: VSL#3_BALBc_colon_mice1

description: BALB/c mice


title: VSL#3_BALBc_SI_mice4

description: BALB/c mice


title: VSL#3_BALBc_colon_mice2

description: BALB/c mice


title: VSL#3_BALBc_SI_mice1

description: BALB/c mice


title: VSL#3_BALBc_SI_mice5

description: BALB/c mice


title: PBS_C57BL6_SI_mice5

description: C57BL6 mice


title: PBS_C57BL6_SI_mice4

description: C57BL6 mice


title: PBS_C57BL6_colon_mice3

description: C57BL6 mice


title: PBS_C57BL6_SI_mice2

description: C57BL6 mice


title: PBS_C57BL6_SI_mice3

description: C57BL6 mice


title: PBS_C57BL6_colon_mice4

description: C57BL6 mice


title: PBS_C57BL6_colon_mice5

description: C57BL6 mice


title: PBS_C57BL6_SI_mice1

description: C57BL6 mice


title: PBS_C57BL6_colon_mice2

description: C57BL6 mice


title: VSL#3_C57BL6_colon_mice5

description: C57BL6 mice


title: VSL#3_C57BL6_SI_mice4

description: C57BL6 mice


title: PBS_C57BL6_colon_mice1

description: C57BL6 mice


title: VSL#3_C57BL6_colon_mice4

description: C57BL6 mice


title: PBS_BALBc_colon_mice5

description: BALB/c mice


title: PBS_BALBc_colon_mice4

description: BALB/c mice


title: PBS_BALBc_SI_mice4

description: BALB/c mice


title: VSL#3_C57BL6_SI_mice5

description: C57BL6 mice


title: VSL#3_C57BL6_colon_mice3

description: C57BL6 mice


title: VSL#3_C57BL6_SI_mice3

description: C57BL6 mice


title: VSL#3_C57BL6_SI_mice2

description: C57BL6 mice


title: VSL#3_C57BL6_colon_mice1

description: C57BL6 mice


title: VSL#3_C57BL6_colon_mice2

description: C57BL6 mice


title: PBS_BALBc_colon_mice3

description: BALB/c mice


title: PBS_BALBc_SI_mice5

description: BALB/c mice


title: PBS_BALBc_SI_mice3

description: BALB/c mice


title: VSL#3_C57BL6_SI_mice1

description: C57BL6 mice


title: PBS_BALBc_colon_mice2

description: BALB/c mice


title: Paired non-neoplastic tissue P260N

status: Public on Aug 31 2014

city: Prague 10

first: Pavel

last: Soucek

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

description: Control

data_processing:
Raw data were processed by REST2009 software according to Pfaffl et al Nucleic Acids Res. 2000;30: e36.
For the normalization it uses the average of four housekeeping genes: EIF2B1, MRPL19, IPO8, and UBB
Target gene signals normalized to housekeeping genes; 2^-ΔCt, where -ΔCt = -(Ct_Target − Ct_HKG)

label: FAM

source_name: Paired non-neoplastic tissue

label_protocol: cDNA was synthesized using 0.5 µg of total RNA by help of RevertAidTM First Strand cDNA Synthesis Kit with random hexamer primers according to manufacturer´s protocol (MBI Fermentas, Vilnius, Lithuania) and stored at -80 oC. qPCR was performed in RotorGene 6000 produced by Corbett Research (Sydney, Australia) with 45 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds. cDNA was preamplified using TaqMan PreAmp Master Mix (Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol: Total RNA was isolated from frozen tissues using Trizol reagent according to manufacturers protocol (Invitrogen, Carlsbad, CA, USA)

tag: age (years)

tag: menopause

tag: histology (1=idc, 0=other)

tag: grade

tag: size (mm)

tag: Stage

tag: pt

tag: pn

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)

tag: her2 (0=negative, 1= positive)

tag: neo-anthracycline

tag: neo-taxane

tag: response (0=sd/pd, 1=pr)

tag: relapse

tag: dfs (months)

value: Paired non-neoplastic tissue


title: Paired non-neoplastic tissue P249N

description: Control

tag: tissue


title: Paired non-neoplastic tissue P228N

description: Control

tag: age (years)


title: PBS_BALBc_SI_mice2

description: BALB/c mice

tag: strain

tag: tissue type


title: Paired non-neoplastic tissue P169N

description: Control

tag: menopause

tag: histology (1=idc, 0=other)

tag: grade


title: Paired non-neoplastic tissue P191N

description: Control

tag: size (mm)

tag: Stage

tag: pt


title: Paired non-neoplastic tissue P168N

description: Control

tag: pn

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)


title: Paired non-neoplastic tissue P185N

description: Control

tag: her2 (0=negative, 1= positive)

tag: neo-anthracycline

tag: neo-taxane


title: PBS_BALBc_colon_mice1

description: BALB/c mice


title: Cont 24h

status: Public on Sep 01 2014

city: Tokorozawa

first: Motoshi

last: Nagao

state: Saitama

address: 4-1 Namiki

department: Department of Rehabilitation for the Movement Functions

country: Japan

institute: Research Institute, National Rehabilitation Center for Persons with Disabilities

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Gene 1.0 ST array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Power Tool version 1.15.0 software, and obtained normalized intensity values.

source_name: Control virus-infected mouse E11.5 NPCs, cultured in the absence of FGF2 and EGF

label_protocol: The cRNA was amplified, labeled using GeneChip WT Terminal Labeling and Control Kit according to the manufacturer's instructions.

growth_protocol: NPCs derived from E11.5 mouse forebrains were maintained in the presence of FGF2 and EGF. After infection, the virus-infected NPCs were dissociated and seeded on poly-D-lysine -coated dishes, and then the cells were cultured for 1 day without  FGF2 and EGF.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: developmental stage

value: brain

tag: cell type

value: neural precursor cells

tag: infection

value: control retrovirus


title: PBS_BALBc_SI_mice1

description: BALB/c mice

tag: strain


title: Paired non-neoplastic tissue P162N

description: Control

tag: age (years)

tag: response (0=sd/pd, 1=pr)

tag: relapse

tag: dfs (months)

tag: tissue


title: Paired non-neoplastic tissue P178N

description: Control

tag: menopause

tag: histology (1=idc, 0=other)

tag: grade

tag: size (mm)

tag: Stage


title: Paired non-neoplastic tissue P156N

description: Control

tag: pt

tag: pn

tag: er (0=negative, 1= positive)

tag: pr (0=negative, 1= positive)

tag: her2 (0=negative, 1= positive)


title: Paired non-neoplastic tissue P135N

description: Control

tag: neo-anthracycline

tag: neo-taxane


title: Paired non-neoplastic tissue P155N

description: Control

tag: age (years)


title: Paired non-neoplastic tissue P144N

description: Control

tag: response (0=sd/pd, 1=pr)


title: Paired non-neoplastic tissue P131N

description: Control

tag: relapse


title: Paired non-neoplastic tissue P134N

description: Control

tag: dfs (months)


title: Paired non-neoplastic tissue P123N

description: Control

tag: tissue


title: Paired non-neoplastic tissue P133N

description: Control

tag: menopause


title: Paired non-neoplastic tissue P102N

description: Control

tag: histology (1=idc, 0=other)


title: Paired non-neoplastic tissue P109N

description: Control

tag: grade


title: Paired non-neoplastic tissue P114N

description: Control

tag: size (mm)


title: Paired non-neoplastic tissue P96N

description: Control

tag: Stage


title: Paired non-neoplastic tissue P95N

description: Control

tag: pt


title: Paired non-neoplastic tissue P167N

description: Control

tag: pn


title: Paired non-neoplastic tissue P85N

description: Control

tag: er (0=negative, 1= positive)


title: Paired non-neoplastic tissue P84N

description: Control

tag: pr (0=negative, 1= positive)


title: Paired non-neoplastic tissue P57N

description: Control

tag: her2 (0=negative, 1= positive)


title: Paired non-neoplastic tissue P43N

description: Control

tag: neo-anthracycline


title: Paired non-neoplastic tissue P143N

description: Control

tag: neo-taxane


title: Paired non-neoplastic tissue P15N

description: Control

tag: age (years)


title: Paired non-neoplastic tissue P13N

description: Control

tag: response (0=sd/pd, 1=pr)


title: Paired non-neoplastic tissue P8N

description: Control

tag: relapse


title: Paired non-neoplastic tissue P9N

description: Control

tag: dfs (months)


title: Paired non-neoplastic tissue P24N

description: Control

tag: tissue


title: Paired non-neoplastic tissue P32N

description: Control

tag: menopause


title: Paired non-neoplastic tissue P7N

description: Control

tag: histology (1=idc, 0=other)


title: Paired non-neoplastic tissue P117N

description: Control

tag: grade


title: Breast tumor P260T

description: Tumor

source_name: Breast tumor

value: post

tag: size (mm)

value: I

value: yes

value: no

value: Breast tumor


title: Paired non-neoplastic tissue P4N

description: Control

tag: Stage


title: Breast tumor P242T

description: Tumor

value: IIA

tag: pt


title: Breast tumor P253T

description: Tumor

value: pre

tag: pn


title: Paired non-neoplastic tissue P5N

description: Control

tag: er (0=negative, 1= positive)


title: Breast tumor P185T

description: Tumor

tag: pr (0=negative, 1= positive)


title: Breast tumor P249T

description: Tumor

value: unknown

tag: her2 (0=negative, 1= positive)


title: Breast tumor P228T

description: Tumor

tag: neo-anthracycline


title: Breast tumor P213T

description: Tumor

tag: neo-taxane


title: Breast tumor P186T

description: Tumor

tag: age (years)


title: Breast tumor P178T

description: Tumor

tag: response (0=sd/pd, 1=pr)


title: Breast tumor P170T

description: Tumor

value: IIB

tag: relapse


title: Breast tumor P223T

description: Tumor

value: IIC

tag: dfs (months)


title: Breast tumor P169T

description: Tumor

tag: tissue


title: Breast tumor P168T

description: Tumor

tag: menopause


title: Paired non-neoplastic tissue P3N

description: Control

tag: histology (1=idc, 0=other)


title: Breast tumor P167T

description: Tumor

tag: grade


title: Breast tumor P162T

description: Tumor

tag: size (mm)


title: Breast tumor P164T

description: Tumor

tag: Stage


title: Breast tumor P161T

description: Tumor

tag: pt


title: Breast tumor P144T

description: Tumor

tag: pn


title: Breast tumor P143T

description: Tumor

tag: er (0=negative, 1= positive)


title: Breast tumor P155T

description: Tumor

tag: pr (0=negative, 1= positive)


title: Breast tumor P157T

description: Tumor

tag: her2 (0=negative, 1= positive)


title: Breast tumor P141T

description: Tumor

tag: neo-anthracycline


title: Breast tumor P191T

description: Tumor

tag: neo-taxane


title: Paired non-neoplastic tissue P170N

description: Control

tag: age (years)


title: Breast tumor P134T

description: Tumor

value: III

tag: response (0=sd/pd, 1=pr)


title: Breast tumor P131T

description: Tumor

tag: relapse


title: Breast tumor P132T

description: Tumor

tag: dfs (months)


title: Breast tumor P133T

description: Tumor

tag: tissue


title: Breast tumor P135T

description: Tumor

tag: menopause


title: Breast tumor P123T

description: Tumor

tag: histology (1=idc, 0=other)


title: Breast tumor P120T

description: Tumor

tag: grade


title: Breast tumor P117T

description: Tumor

tag: size (mm)


title: Breast tumor P118T

description: Tumor

tag: Stage


title: Breast tumor P102T

description: Tumor

tag: pt


title: Breast tumor P109T

description: Tumor

tag: pn


title: Breast tumor P114T

description: Tumor

tag: er (0=negative, 1= positive)


title: Breast tumor P101T

description: Tumor

tag: pr (0=negative, 1= positive)


title: Breast tumor P156T

description: Tumor

tag: her2 (0=negative, 1= positive)


title: Breast tumor P95T

description: Tumor

tag: neo-anthracycline


title: Breast tumor P96T

description: Tumor

tag: neo-taxane


title: Breast tumor P97T

description: Tumor

tag: age (years)


title: Breast tumor P91T

description: Tumor

tag: response (0=sd/pd, 1=pr)


title: Breast tumor P85T

description: Tumor

tag: relapse


title: Breast tumor P84T

description: Tumor

tag: dfs (months)


title: Breast tumor P69T

description: Tumor

tag: tissue


title: Breast tumor P71T

description: Tumor

tag: menopause


title: Breast tumor P47T

description: Tumor

tag: histology (1=idc, 0=other)


title: Breast tumor P52T

description: Tumor

tag: grade


title: Breast tumor P57T

description: Tumor

tag: size (mm)


title: Breast tumor P45T

description: Tumor

tag: Stage


title: Breast tumor P55T

description: Tumor

tag: pt


title: Breast tumor P43T

description: Tumor

tag: pn


title: Breast tumor P122T

description: Tumor

tag: er (0=negative, 1= positive)


title: Breast tumor P24T

description: Tumor

tag: pr (0=negative, 1= positive)


title: Breast tumor P31T

description: Tumor

tag: her2 (0=negative, 1= positive)


title: Breast tumor P32T

description: Tumor

tag: neo-anthracycline


title: Breast tumor P15T

description: Tumor

tag: neo-taxane


title: Breast tumor P40T

description: Tumor

tag: age (years)


title: Breast tumor P13T

description: Tumor

tag: response (0=sd/pd, 1=pr)


title: Breast tumor P9T

description: Tumor

tag: relapse


title: Breast tumor P5T

description: Tumor

tag: dfs (months)


title: Breast tumor P3T

description: Tumor

tag: tissue


title: Breast tumor P4T

description: Tumor

tag: menopause


title: Breast tumor P7T

description: Tumor

tag: histology (1=idc, 0=other)


title: Breast tumor P67T

description: Tumor

tag: grade


title: Breast tumor P8T

description: Tumor

tag: size (mm)


title: H1975 cells, erlotinib 1 μM + quinacrine 3 μM, 12 h

status: Public on Jun 19 2014

city: Cleveland

first: George

last: Stark

state: OH

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

description: erlotinib 1 μM + quinacrine 3 μM, 12 h

hyb_protocol: Samples were hybridized using Affymetrix GeneTitan kit materials. Following fragmentation, samples were hybridized for 16 h at 45°C on Human Affymetrix Gene ST 2.1 array.

scan_protocol: Samples were scanned and digital images were archived using the Affymetrix GeneTitan MC automated system.

data_processing:
Raw CEL files were pre-processed using the Affymetrix Expression Console Software 1.30 with Robust Multi-array Average (RMA) normalization.
HuGene-2_1-st.pgf
HuGene-2_1-st.mps

source_name: NCI-H1975 human lung non-small cell adenocarcinoma cell line

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit from Affymetrix at the Gene Expression & Genotyping Core Facility at Case Comprehensive Cancer Center.

growth_protocol: Cells were maintained in DMEM medium supplemented with 5% fetal bovine serum. All cells were kept at 37°C in a humidified atmosphere with 5% CO2. After 2 or 3 passages, cells were plated at 50-70% confluency in 10 cm tissue culture dishes for treatment.

extract_protocol: RNA was isolated from cells using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 1 μM erlotinib, 3 μM or 5 μM quinacrine or a combination of both for 0, 6, 12, 24, or 48 h.

tag: treatment

value: erlotinib 1 μM + quinacrine 3 μM, 12 h

tag: cell line

value: NSCLC

tag: genotype/variation

value: mutant EGFR (L858R/T790M)


title: H1975 cells, quinacrine 3 μM, 12 h

description: quinacrine 3 μM, 12 h

value: quinacrine 3 μM, 12 h


title: H1975 cells, erlotinib 1 μM + quinacrine 3 μM, 24 h

description: erlotinib 1 μM + quinacrine 3 μM, 24 h

value: erlotinib 1 μM + quinacrine 3 μM, 24 h


title: H1975 cells, quinacrine 3 μM, 6 h

description: quinacrine 3 μM, 6 h

value: quinacrine 3 μM, 6 h


title: A549 cells, erlotinib 1 μM + quinacrine 5 μM, 12 h

description: erlotinib 1 μM + quinacrine 5 μM, 12 h

source_name: A549 human lung adenocarcinoma non-small cell epithelial cell line

value: erlotinib 1 μM + quinacrine 5 μM, 12 h

value: mutant KRAS (G61H), wildtype EGFR


title: H1975 cells, erlotinib 1 μM + quinacrine 3 μM, 48 h

description: erlotinib 1 μM + quinacrine 3 μM, 48 h

value: erlotinib 1 μM + quinacrine 3 μM, 48 h


title: H1975 cells, erlotinib 1 μM + quinacrine 3 μM, 6 h

description: erlotinib 1 μM + quinacrine 3 μM, 6 h

value: erlotinib 1 μM + quinacrine 3 μM, 6 h


title: H1975 cells, quinacrine 3 μM, 24 h

description: quinacrine 3 μM, 24 h

value: quinacrine 3 μM, 24 h


title: A549 cells, quinacrine 5 μM, 6 h

description: quinacrine 5 μM, 6 h

value: quinacrine 5 μM, 6 h

value: mutant KRAS (G12S), wildtype EGFR


title: H1975 cells, erlotinib 1 μM, 12 h

description: erlotinib 1 μM, 12 h

value: erlotinib 1 μM, 12 h


title: A549 cells, erlotinib 1 μM + quinacrine 5 μM, 24 h

description: erlotinib 1 μM + quinacrine 5 μM, 24 h

value: erlotinib 1 μM + quinacrine 5 μM, 24 h


title: A549 cells, erlotinib 1 μM, 12 h

description: erlotinib 1 μM, 12 h


title: A549 cells, quinacrine 5 μM, 24 h

description: quinacrine 5 μM, 24 h

value: quinacrine 5 μM, 24 h


title: H1975 cells, erlotinib 1 μM, 6 h

description: erlotinib 1 μM, 6 h

value: erlotinib 1 μM, 6 h


title: A549 cells, erlotinib 1 μM + quinacrine 5 μM, 48 h

description: erlotinib 1 μM + quinacrine 5 μM, 48 h

value: erlotinib 1 μM + quinacrine 5 μM, 48 h


title: H1975 cells, erlotinib 1 μM, 48 h

description: erlotinib 1 μM, 48 h

value: erlotinib 1 μM, 48 h

value: NSCLC


title: A549 cells, quinacrine 5 μM, 12 h

description: quinacrine 5 μM, 12 h

value: quinacrine 5 μM, 12 h


title: H1975 cells, erlotinib 1 μM, 24 h

description: erlotinib 1 μM, 24 h

value: erlotinib 1 μM, 24 h

value: mutant EGFR (L858R/T790M)


title: A549 cells, erlotinib 1 μM + quinacrine 5 μM, 6 h

description: erlotinib 1 μM + quinacrine 5 μM, 6 h

value: erlotinib 1 μM + quinacrine 5 μM, 6 h


title: A549 cells, erlotinib 1 μM, 24 h

description: erlotinib 1 μM, 24 h


title: A549 cells, erlotinib 1 μM, 48 h

description: erlotinib 1 μM, 48 h


title: Paired non-neoplastic tissue P118N

description: Control

tag: Stage

tag: pt

tag: pn

tag: er (0=negative, 1= positive)

value: Paired non-neoplastic tissue


title: caudate-HIVpositive_neurocognitiveabnormal_HIVE3-rep1

status: Public on Feb 18 2014

city: Omaha

first: Howard

last: Fox

state: Nebraska

address: 985800 Nebraska Medical Center - DRC 3008

department: Pharmacology and Experimental Neuroscience

institute: University of Nebraska Medical Center

description:
Hy3: 1_Exiqon_13994546_S01_Cropped.txt
Hy5: 0_Exiqon_13994546_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13

hyb_protocol: Exiqon used miRCURY™ LNA Array Power labeling kit allows highly efficient and uniform labeling of microRNAs with minimal sequence bias. Using Tecan hybridization stations the hybridization and washing steps are fully automated for excellent reproducibility.

scan_protocol: Arrays are scanned with highly sensitive equipment in ozone free environment to reduce day-to-day variation to a minimum. Image Analysis is then performed to quantify the signals on the arrays.

data_processing:
The data obtained is normalized using methods applicable to the performed experiment. Depending on the experimental setup and the size of the project customized data analysis is provided (including heat map/Unsupervised Hierarchical Clustering, PCA-plots etc based on TTests or ANOVA).
When calling of a particular miRNA failed on an array this is indicated by the acronym null in the row containing this miRNA and in the column corresponding to this array. The criteria for deciding that the calling of a miRNA had failed on a particular array, was that 3 or more of the 4 replicated measures of this miRNA were flagged (i.e. the signal is below background) by the image analysis software.

label_protocol: Mix: (1) CIP treated RNA sample, (2) Labeling buffer, (3) Hy3™ or Hy5™, (4) DMSO, (5) Enzyme

growth_protocol: Postmortem Human Brain Samples

extract_protocol: Trizol + column purification

value: caudate

tag: hiv

value: yes

tag: infection

value: HIV

tag: neurocognitive abnormal

tag: hive

source_name: caudate-pooled

value: all 17 samples pooled

tag: neurocognitive disorder


title: caudate-HIVpositive_neuroOK3-rep1

description:
Hy3: 1_Exiqon_13994548_S01_Cropped.txt
Hy5: 0_Exiqon_13994548_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13

tag: tissue

value: no


title: caudate-HIVpositive_neurocognitiveabnormal_HIVE1-rep1

description:
Hy3: 1_Exiqon_13994547_S01_Cropped.txt
Hy5: 0_Exiqon_13994547_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neurocognitiveabnormal4-rep1

description:
Hy3: 1_Exiqon_13994541_S01_Cropped.txt
Hy5: 0_Exiqon_13994541_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neurocognitiveabnormal_HIVE2-rep1

description:
Hy3: 1_Exiqon_13994545_S01_Cropped.txt
Hy5: 0_Exiqon_13994545_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neuroOK2-rep1

description:
Hy3: 1_Exiqon_13994535_S01_Cropped.txt
Hy5: 0_Exiqon_13994535_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-control2-rep1

description:
Hy3: 1_Exiqon_13994530_S01_Cropped.txt
Hy5: 0_Exiqon_13994530_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13

value: control


title: caudate-control4-rep1

description:
Hy3: 1_Exiqon_13994532_S01_Cropped.txt
Hy5: 0_Exiqon_13994532_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: A549 cells, untreated

description: untreated

value: untreated

value: mutant KRAS (G12S), wildtype EGFR


title: H1975 cells, untreated

description: untreated


title: A549 cells, erlotinib 1 μM, 6 h

description: erlotinib 1 μM, 6 h

value: erlotinib 1 μM, 6 h


title: RU-treated_unruptured follicle RU-UF3

status: Public on Feb 01 2014

city: Osaka

first: Kenjiro

last: Tsubota

address: 1-6, Kashima 2-chome

institute: Astellas Pharma

description: RU486-treated at 10:00, collected at 10:00 on the estrus day

hyb_protocol: Hybridization and following washing by fluidics were performed with hybridization, wash and stain kit(Affymetrix Inc.), in accordance with the manufacturer's instruction.

scan_protocol: Gene chip  was scanned using GeneChip scanner GCS3000 7G (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Scaling was not conducted. Signal intensity that was less than 1.0 was set as 1.0. 1st normalization was performed for the median of all probe sets(31099 probe sets) per chip and 2nd normalization was performed for the 1st normalized value per gene by Gene Spring 7.3(Agilent technology.). Statistical anlalysis(volcano plot analysis(welch t-test and 2 fold change)) and hierarchical analysis were performed by Gene Spring 7.3(Agilent technology.).

organism: Rattus norvegicus

source_name: ovarian follicle retrieved by LMD

label_protocol: In vitro transcription with IVT labeling kit(Affymetrix Inc.) generated multiple copies of biotin-labelled aRNA from the double-stranded cDNA templates.

growth_protocol: After 1-week of acclimatization, estrous phases of each animal was determined by vaginal smears for five consecutive days. During the study, animals were handled in accordance with Guidelines for Animal Experimentation issued by Astellas Pharma Inc., which is based on the guidelines for animal experimentation issued by the Japanese Association for Laboratory Animal Science.<br>The animals were sacrificed by exsanguination under anesthesia with ether at 10:00 a.m. on the proestrus day, 10:00 p.m. on the proestrus day, and 10:00 a.m. on the estrus day.

extract_protocol: The ovaries were removed and embedded in OCT (Tissue-Tek, Sakura Finetek, Torrance, CA), frozen in dry-ice-cold isopentan, and stored at -70°C until use. Frozen sections (8-micro-meter thick) were mounted on the membrane slides (MMI, Glatteburg, Zurich, Switzerland), and stained with HistogeneTM LCM frozen section staining kit (Arcturus Engineering, Mountain View, CA). Then, 15 follicles in each phase were retrieved by LMD system (CellCut Plus™, MMI). The collected follicle sections were lysed by the buffer RLT in the collection tube supplied in RNeasy Micro Kit (Qiagen, Hilden, Germany)

treatment_protocol: Animals were singly administered orally 4mg/kg of indomethacin (IM) at 16:00 or 100 mg/kg of RU486 (RU)  at 10:00 on the proestrus day, and sacrificed by exsanguination under anesthesia at 22:00 on the proestrus day (PeF: peri-ovulatory follicle), and 10:00 on the estrus day (PoF: post-ovulatory follicle).

tag: developmental stage

value: post-ovulatory follicle

tag: strain

value: Crl:CD(SD) rats

value: Ovarian follicle


title: caudate-HIVpositive_neurocognitiveabnormal3-rep1

description:
Hy3: 1_Exiqon_13994538_S01_Cropped.txt
Hy5: 0_Exiqon_13994538_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neurocognitiveabnormal6-rep1

description:
Hy3: 1_Exiqon_13994544_S01_Cropped.txt
Hy5: 0_Exiqon_13994544_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neurocognitiveabnormal1-rep1

description:
Hy3: 1_Exiqon_13994536_S01_Cropped.txt
Hy5: 0_Exiqon_13994536_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-control3-rep1

description:
Hy3: 1_Exiqon_13994531_S01_Cropped.txt
Hy5: 0_Exiqon_13994531_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neurocognitiveabnormal5-rep1

description:
Hy3: 1_Exiqon_13994542_S01_Cropped.txt
Hy5: 0_Exiqon_13994542_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neurocognitiveabnormal2-rep1

description:
Hy3: 1_Exiqon_13994537_S01_Cropped.txt
Hy5: 0_Exiqon_13994537_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-control5-rep1

description:
Hy3: 1_Exiqon_13994533_S01_Cropped.txt
Hy5: 0_Exiqon_13994533_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-control1-rep1

description:
Hy3: 1_Exiqon_13994529_S01_Cropped.txt
Hy5: 0_Exiqon_13994529_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: caudate-HIVpositive_neuroOK1-rep1

description:
Hy3: 1_Exiqon_13994534_S01_Cropped.txt
Hy5: 0_Exiqon_13994534_S01_Cropped.txt
the platform has recently been updated from miRCURY LNA microRNA Array, v.11.0 to miRBase v13


title: RU-treated_unruptured follicle RU-UF1

value: RU486-treated at 10:00, collected at 10:00 on the estrus day


title: aorta-20m-rep6

status: Public on Jan 14 2014

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

country: Germany

institute: University of Duesseldorf

hyb_protocol: After fragmentation labelled cRNA was hybridized to Agilent SurePrint G3 Mouse GE 8x60k Microarrays for 17 h at 65 °C

scan_protocol: Samples were scanned as described in the manufacturers protocol. Signal intensities on 20 bit tiff images were calculated by Feature Extraction software (FE, Vers. 10.7.1.1; Agilent Technologies).

data_processing: Data analyses were conducted with GeneSpring GX software (Vers. 12.5; Agilent Technologies). Probe signal intensities were quantile normalized across all samples to reduce inter-array variability (Bolstad et al., 2003). Input data pre-processing was concluded by baseline transformation to the median of all samples.

source_name: aorta, 20 months

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed on six replicates of each experimental condition (adult and old mice) according to the manufacturers protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA.

extract_protocol: The descending aorta was flushed thoroughly with ice-cold phosphate-buffered saline (PBS), through the left ventricle of the heart, cleaned of periadventitial fat and connective tissues, and snap-frozen in liquid nitrogen and stored at -80 °C. Extraction of total RNA from the tissue was followed with Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany). Total RNA from 6 individual mice of each group was treated with DNase I to remove residual genomic DNA. Total RNA preparations were checked for RNA integrity by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). All samples showed common high quality RNA Integrity Numbers (RIN 9.0-9.6) and RNA was quantified by photometric Nanodrop measurement.

treatment_protocol: Male C57BL/6 mice were obtained from Janvier (Saint Berthevin, France) and kept one week in the local animal house for acclimatization. Mice were aged 6 months and 20 months and water and standard rodent chow were fed ad libitum.

value: aorta

tag: gender

value: male

tag: age

value: 20 months


title: HUVEC CONTROL SI.2

status: Public on May 11 2013

city: New Haven

first: hyung

last: chun

state: CT

address: 300 George St Room 770H

department: Internal Medicine

institute: Yale University

hyb_protocol: Samples were hybridized onto beadchips according to gene expression profiling protocol from Illumina.

scan_protocol: The Illumina BeadArray Reader and BeadScan software were used to scan and extract raw intensity values.

data_processing: Background subtraction and quantile normalization were performed.

source_name: HUVEC

label_protocol: Samples were labeled according to gene expression profiling protocol from Illumina

growth_protocol: HUVECs grown in EGM-2 (Lonza)

extract_protocol: Qiagen miRNeasy per manufacturer's protocol

treatment_protocol: Transfected with siRNAs (Stealth siRNA, Invitrogen) for 72 hours

value: HUVEC

value: CONTROL


title: aorta-20m-rep5


title: aorta-20m-rep1


title: IM-treated_unruptured follicle IM-UF1

description: indomethacin-treated at 16:00, collected at 10:00 on the estrus day

tag: treatment


title: aorta-20m-rep4


title: aorta-20m-rep2


title: HUVEC CONTROL SI.1

tag: cell line


title: aorta-20m-rep3


title: IM-treated_unruptured follicle IM-UF2

value: indomethacin-treated at 16:00, collected at 10:00 on the estrus day


title: HUVEC APELIN/APJ SI.1

tag: genotype/variation

value: APELIN/APJ


title: RU-treated_unruptured follicle RU-UF2


title: IM-treated_unruptured follicle IM-UF3


title: HUVEC APELIN/APJ SI.2


title: Normal genomic DNA from sample 686

status: Public on Jan 21 2013

city: Shanghai

first: Yun

last: Liu

address: 130 Dong An Road

country: China

institute: Fudan University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: minfi, R

label: Cy3 and Cy5

source_name: PBL

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBLs using Qiagen DNeasy Kit according to standard instructions

tag: cell type

value: PBL

tag: disease state

value: Normal

tag: subject

value: f

tag: smoking status

value: never


title: Normal genomic DNA from sample 688

value: ex


title: Normal genomic DNA from sample 689


title: Normal genomic DNA from sample 684

value: current


title: Patient genomic DNA from sample 679

value: rheumatoid arthritis

value: Patient


title: Normal genomic DNA from sample 687


title: Normal genomic DNA from sample 685


title: T2N-DamID-Rep2

status: Public on Apr 08 2014

city: Geneva

first: Audrey

last: Letourneau

address: Rue Michel-Servet 1

department: Genetic Medicine and Development

country: Switzerland

institute: University of Geneva Medical School

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 50 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. The score was calculated as the log2 Dam-LaminB1: Dam ratio of the normalized data.

source_name: Dam-only DamID DNA from T2N fibroblasts

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: For the DamID: 1-2x10e5 cells were infected with lenti-virus expressing Dam or Dam-Lamin B1. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

tag: twin id

value: twin 2 (T2)

tag: twin condition

value: normal (N)

value: Primary fibroblasts

source_name: Dam-LaminB1 DamID DNA from T2N fibroblasts


title: Patient genomic DNA from sample 675


title: Normal genomic DNA from sample 670


title: Patient genomic DNA from sample 677


title: T1DS-DamID-Rep2

source_name: Dam-only DamID DNA from T1DS fibroblasts

value: twin 1 (T1)

value: Trisomy 21 (DS)

source_name: Dam-LaminB1 DamID DNA from T1DS fibroblasts


title: Patient genomic DNA from sample 672


title: Normal genomic DNA from sample 669


title: Patient genomic DNA from sample 680

value: occasional


title: Patient genomic DNA from sample 676


title: Normal genomic DNA from sample 671


title: Patient genomic DNA from sample 678


title: Normal genomic DNA from sample 666


title: Patient genomic DNA from sample 674


title: Normal genomic DNA from sample 682


title: Normal genomic DNA from sample 665


title: Patient genomic DNA from sample 681


title: T2N-DamID-Rep1


title: Normal genomic DNA from sample 664


title: Normal genomic DNA from sample 667


title: Normal genomic DNA from sample 683


title: Normal genomic DNA from sample 668


title: T1DS-DamID-Rep1


title: Patient genomic DNA from sample 673


title: Patient genomic DNA from sample 662


title: Patient genomic DNA from sample 661


title: Patient genomic DNA from sample 660


title: Patient genomic DNA from sample 657


title: Patient genomic DNA from sample 654


title: Patient genomic DNA from sample 651


title: Patient genomic DNA from sample 656


title: Patient genomic DNA from sample 659


title: Patient genomic DNA from sample 655


title: Patient genomic DNA from sample 643


title: Patient genomic DNA from sample 653


title: Patient genomic DNA from sample 641

value: m


title: Patient genomic DNA from sample 652


title: Patient genomic DNA from sample 648


title: Patient genomic DNA from sample 638


title: Patient genomic DNA from sample 645


title: Patient genomic DNA from sample 644


title: Patient genomic DNA from sample 658


title: Patient genomic DNA from sample 637


title: Patient genomic DNA from sample 636


title: Patient genomic DNA from sample 647


title: Patient genomic DNA from sample 642


title: Patient genomic DNA from sample 649


title: Patient genomic DNA from sample 646


title: Patient genomic DNA from sample 639


title: Patient genomic DNA from sample 635


title: Patient genomic DNA from sample 640


title: Patient genomic DNA from sample 634


title: Patient genomic DNA from sample 663


title: Patient genomic DNA from sample 631


title: Patient genomic DNA from sample 650


title: Patient genomic DNA from sample 633


title: Patient genomic DNA from sample 632


title: Patient genomic DNA from sample 630


title: Patient genomic DNA from sample 626


title: Patient genomic DNA from sample 627


title: Patient genomic DNA from sample 624


title: Patient genomic DNA from sample 619


title: Patient genomic DNA from sample 618


title: Normal genomic DNA from sample 607


title: Patient genomic DNA from sample 620


title: Normal genomic DNA from sample 608


title: Normal genomic DNA from sample 609


title: Patient genomic DNA from sample 615


title: Normal genomic DNA from sample 602


title: Normal genomic DNA from sample 610


title: Normal genomic DNA from sample 606


title: Patient genomic DNA from sample 622


title: Normal genomic DNA from sample 603


title: Patient genomic DNA from sample 625


title: Patient genomic DNA from sample 623


title: Patient genomic DNA from sample 628


title: Normal genomic DNA from sample 612


title: Normal genomic DNA from sample 601


title: Normal genomic DNA from sample 604


title: Normal genomic DNA from sample 605


title: Patient genomic DNA from sample 617


title: Normal genomic DNA from sample 613


title: Patient genomic DNA from sample 629


title: Patient genomic DNA from sample 616


title: Patient genomic DNA from sample 614


title: Normal genomic DNA from sample 600


title: Normal genomic DNA from sample 611


title: Patient genomic DNA from sample 621


title: Normal genomic DNA from sample 598


title: Normal genomic DNA from sample 599


title: Patient genomic DNA from sample 596


title: Patient genomic DNA from sample 594


title: Patient genomic DNA from sample 591


title: Patient genomic DNA from sample 593


title: Patient genomic DNA from sample 590


title: Patient genomic DNA from sample 588


title: Patient genomic DNA from sample 585


title: Normal genomic DNA from sample 578


title: Patient genomic DNA from sample 597


title: Patient genomic DNA from sample 586


title: Patient genomic DNA from sample 589


title: Patient genomic DNA from sample 573


title: Patient genomic DNA from sample 582


title: Normal genomic DNA from sample 576


title: Patient genomic DNA from sample 570


title: Normal genomic DNA from sample 579


title: Patient genomic DNA from sample 587


title: Patient genomic DNA from sample 568


title: Patient genomic DNA from sample 571


title: Normal genomic DNA from sample 575


title: Patient genomic DNA from sample 569


title: Patient genomic DNA from sample 583


title: Patient genomic DNA from sample 584


title: Normal genomic DNA from sample 577


title: Normal genomic DNA from sample 580


title: Patient genomic DNA from sample 592


title: Patient genomic DNA from sample 581


title: Patient genomic DNA from sample 595


title: Patient genomic DNA from sample 574


title: Patient genomic DNA from sample 564


title: Patient genomic DNA from sample 566


title: Patient genomic DNA from sample 562


title: Patient genomic DNA from sample 567


title: Patient genomic DNA from sample 563


title: Patient genomic DNA from sample 561


title: Patient genomic DNA from sample 555


title: Patient genomic DNA from sample 556


title: Patient genomic DNA from sample 559


title: Patient genomic DNA from sample 552


title: Patient genomic DNA from sample 560


title: Patient genomic DNA from sample 551


title: Patient genomic DNA from sample 545


title: Patient genomic DNA from sample 554


title: Patient genomic DNA from sample 553


title: Patient genomic DNA from sample 558


title: Patient genomic DNA from sample 547


title: Patient genomic DNA from sample 543


title: Patient genomic DNA from sample 544


title: Patient genomic DNA from sample 565


title: Patient genomic DNA from sample 548


title: Patient genomic DNA from sample 557


title: Patient genomic DNA from sample 542


title: Patient genomic DNA from sample 549


title: Patient genomic DNA from sample 550


title: Patient genomic DNA from sample 572


title: Patient genomic DNA from sample 540


title: Patient genomic DNA from sample 537


title: Patient genomic DNA from sample 535


title: Patient genomic DNA from sample 541


title: Patient genomic DNA from sample 539


title: Patient genomic DNA from sample 538


title: Patient genomic DNA from sample 533


title: Patient genomic DNA from sample 534


title: Patient genomic DNA from sample 546


title: Patient genomic DNA from sample 529


title: Normal genomic DNA from sample 523


title: Normal genomic DNA from sample 527


title: Patient genomic DNA from sample 531


title: Normal genomic DNA from sample 526


title: Normal genomic DNA from sample 525


title: Patient genomic DNA from sample 528