title: PP_AG_L1_R4

description:
90_PP_AG_L1_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.

value: 1st instar larvae (L1)


title: PP_AG_L2_R1

status: Public on Jan 30 2014

type: RNA

city: Las Vegas

first: Allen

middle: G.

last: Gibbs

state: Nevada

address: 4505 S Maryland Parkway

department: School of Life Sciences

country: USA

institute: University of Nevada

description:
91_PP_AG_L2_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.

hyb_protocol: Hybridizations with custom NimbleGen 12-plex microarrays were performed with a NimbleGen Hybridization System 4.

scan_protocol: Array scanning was performed with a GenePix 4000B scanner (Molecular Devices) and associated software at 532 nm, with photomultiplier gain settings that resulted in less than one in 105 normalized counts at saturation.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

molecule: total RNA

organism: Drosophila mojavensis

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen (Roche Diagnostics) One Color DNA Labeling kit.

growth_protocol: Bottle cultures were established at moderate larval densities to minimize nutritionally caused maternal/environmental effects from the vial cultures and maintained in an incubator programmed on a 14:10 LD photoperiod that cycled from 27° to 17° C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA). Invitrogen Superscript Double-Stranded cDNA Synthesis kits were used to synthesize double-stranded cDNA.  Each cDNA sample was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies).

tag: fly source

value: Punta Prieta 2008; PP08

tag: genotype

value: Wild-type

tag: origin

value: Punta Prieta, Baja California

tag: host diet

value: Agria (AG)

tag: life stage

value: 2nd instar larvae (L2)

tag: phenotype

value: normal


title: PP_AG_L1_R3

description:
89_PP_AG_L1_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.


title: PP_AG_L1_R1

description:
87_PP_AG_L1_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.


title: PP_AG_L1_R2

description:
88_PP_AG_L1_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.


title: 8647 HCC tumor

type: genomic

city: New York

first: Jing

last: Shen

address: 650 W. 168th St. Black Building Rm.1608

institute: Columbia University

description: DNA methylation in HCC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: HCC tumor

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted from 66 frozen tumor/adjacent tissues by standard proteinase K/RNase treatment and phenol/chloroform extraction.

tag: gender

value: Male

tag: tissue type

value: Liver

tag: diagnosis

value: hepatocellular carcinoma (HCC)


title: PP_AG_E6_R2

description:
84_PP_AG_E6_R2
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Agria cactus. Six hour old eggs were collected.

value: 6hr egg (E6)


title: PP_AG_E6_R4

description:
86_PP_AG_E6_R4
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Agria cactus. Six hour old eggs were collected.


title: PP_AG_E6_R1

description:
83_PP_AG_E6_R1
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Agria cactus. Six hour old eggs were collected.


title: PP_AG_E6_R3

description:
85_PP_AG_E6_R3
This sample is of wild-type Drosophila mojavensis originally from Punta Prieta, Baja California. Mothers of these eggs were raised on lab-media prepared from Agria cactus. Six hour old eggs were collected.


title: LB_OP_24D_R1

description:
82_LB_OP_24D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Twenty-four day old females were collected.

value: Las Bocas 2009:LB09

value: Las Bocas, Sonora

value: Organ pipe (OP)

value: 24 Day old adult (24D)


title: 8641 HCC tumor

description: DNA methylation in HCC


title: 8646 adjacent non-tumor tissue

description: DNA methylation in HCC

source_name: adjacent non-tumor tissue


title: 8645 HCC tumor

description: DNA methylation in HCC


title: 8643 HCC tumor

description: DNA methylation in HCC


title: LB_OP_18D_R1

description:
81_LB_OP_18D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Eighteen day old females were collected.

value: 18 Day old adult (18D)


title: 8640 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8637 HCC tumor

description: DNA methylation in HCC


title: LB_OP_14D_R2

description:
80_LB_OP_14D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Fourteen day old females were collected.

value: 14 Day old adult (14D)


title: LB_OP_14D_R1

description:
79_LB_OP_14D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Fourteen day old females were collected.


title: 8642 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_10D_R1

description:
77_LB_OP_10D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Ten day old females were collected.

value: 10 Day old adult (10D)


title: 8191 HCC tumor

description: DNA methylation in HCC


title: 8639 HCC tumor

description: DNA methylation in HCC


title: LB_OP_10D_R2

description:
78_LB_OP_10D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Ten day old females were collected.


title: 8190 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_6D_R1

description:
75_LB_OP_6D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Six day old females were collected.

value: 6 Day old adult (6D)


title: LB_OP_6D_R2

description:
76_LB_OP_6D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Six day old females were collected.

value: Wild-type


title: 8186 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8648 adjacent non-tumor tissue

description: DNA methylation in HCC

value: Female


title: 8649 HCC tumor

description: DNA methylation in HCC


title: 7976 HCC tumor

description: DNA methylation in HCC


title: LB_OP_3D_R1

description:
71_LB_OP_3D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.

value: 3 Day old adult (3D)


title: 7975 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7979 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 8188 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_3D_R4

description:
74_LB_OP_3D_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.


title: 8187 HCC tumor

description: DNA methylation in HCC


title: LB_OP_3D_R2

description:
72_LB_OP_3D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.


title: 7980 HCC tumor

description: DNA methylation in HCC


title: 7978 HCC tumor

description: DNA methylation in HCC


title: 7974 HCC tumor

description: DNA methylation in HCC


title: 8189 HCC tumor

description: DNA methylation in HCC


title: LB_OP_0D_R2

description:
68_LB_OP_0D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.

value: 0 Day old adult (0D)


title: LB_OP_0D_R4

description:
70_LB_OP_0D_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.

value: normal


title: 7972 HCC tumor

description: DNA methylation in HCC

value: Male


title: LB_OP_0D_R3

description:
69_LB_OP_0D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.


title: LB_OP_LP_R1

description:
66_LB_OP_LP_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Late stage pupae were collected.

value: Late pupal stage (LP)


title: LB_OP_0D_R1

description:
67_LB_OP_0D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ Pipe cactus. Zero day old females were collected.


title: LB_OP_EP_R3

description:
65_LB_OP_EP_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae were collected.

value: Early pupal stage (EP)


title: 8644 adjacent non-tumor tissue

description: DNA methylation in HCC

value: Liver

value: hepatocellular carcinoma (HCC)


title: LB_OP_EP_R2

description:
64_LB_OP_EP_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae were collected.

value: Las Bocas 2009:LB09

value: Las Bocas, Sonora


title: 7970 HCC tumor

description: DNA methylation in HCC


title: LB_OP_L3_R4

description:
62_LB_OP_L3_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Third instar larvae were collected.

value: Organ pipe (OP)

value: 3rd instar larvae (L3)


title: LB_OP_L3_R3

description:
61_LB_OP_L3_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Third instar larvae were collected.


title: 8638 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_EP_R1

description:
63_LB_OP_EP_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Organ pipe cactus. Early stage pupae were collected.


title: 7977 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_L3_R2

description:
60_LB_OP_L3_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Third instar larvae were collected.


title: LB_OP_3D_R3

description:
73_LB_OP_3D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Organ pipe cactus. Three day old females were collected.


title: LB_OP_L3_R1

description:
59_LB_OP_L3_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Third instar larvae were collected.


title: 7967 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_L2_R3

description:
57_LB_OP_L2_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae were collected.

value: 2nd instar larvae (L2)


title: LB_OP_L2_R4

description:
58_LB_OP_L2_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae were collected.


title: 8659 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_L2_R2

description:
56_LB_OP_L2_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae were collected.


title: LB_OP_L2_R1

description:
55_LB_OP_L2_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. Second instar larvae were collected.


title: 7971 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7966 HCC tumor

description: DNA methylation in HCC


title: 7964 HCC tumor

description: DNA methylation in HCC


title: 7973 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7965 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_L1_R4

description:
54_LB_OP_L1_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. First instar larvae were collected.

value: 1st instar larvae (L1)


title: 7968 HCC tumor

description: DNA methylation in HCC


title: 7969 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_L1_R2

description:
52_LB_OP_L1_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. First instar larvae were collected.


title: LB_OP_L1_R3

description:
53_LB_OP_L1_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. First instar larvae were collected.


title: 7959 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7953 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_L1_R1

description:
51_LB_OP_L1_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Organ pipe cactus. First instar larvae were collected.


title: 7960 HCC tumor

description: DNA methylation in HCC


title: 7957 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7963 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_OP_E6_R2

description:
48_LB_OP_E6_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.

value: 6hr egg (E6)


title: LB_OP_E6_R3

description:
49_LB_OP_E6_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.

value: Wild-type


title: 7948 HCC tumor

description: DNA methylation in HCC

value: Female


title: LB_OP_E6_R1

description:
47_LB_OP_E6_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.


title: 7954 HCC tumor

description: DNA methylation in HCC


title: 7951 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_24D_R2

description:
46_LB_AG_24D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Twenty-four day old females were collected.

value: Agria (AG)

value: 24 Day old adult (24D)


title: LB_AG_24D_R1

description:
45_LB_AG_24D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Twenty-four day old females were collected.

value: normal


title: 7952 HCC tumor

description: DNA methylation in HCC


title: 7958 HCC tumor

description: DNA methylation in HCC

value: Male


title: 7947 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 6091 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7946 HCC tumor

description: DNA methylation in HCC


title: LB_OP_E6_R4

description:
50_LB_OP_E6_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. Mothers of these eggs were raised on lab-media prepared from Organ pipe cactus. Six hour old eggs were collected.


title: LB_AG_14D_R3

description:
41_LB_AG_14D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Fourteen day old females were collected.

value: 14 Day old adult (14D)


title: LB_AG_14D_R2

description:
40_LB_AG_14D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Fourteen day old females were collected.


title: LB_AG_18D_R2

description:
43_LB_AG_18D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Eighteen day old females were collected.

value: 18 Day old adult (18D)


title: LB_AG_14D_R1

description:
39_LB_AG_14D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Fourteen day old females were collected.

value: 10 Day old adult (10D)


title: 6088 HCC tumor

description: DNA methylation in HCC

value: Liver

value: hepatocellular carcinoma (HCC)


title: 7681 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_10D_R4

description:
38_LB_AG_10D_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.

value: Las Bocas 2009:LB09

value: Las Bocas, Sonora


title: 7682 HCC tumor

description: DNA methylation in HCC


title: 6092 HCC tumor

description: DNA methylation in HCC


title: 7945 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_10D_R3

description:
37_LB_AG_10D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.


title: LB_AG_18D_R3

description:
44_LB_AG_18D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Eighteen day old females were collected.


title: LB_AG_10D_R2

description:
36_LB_AG_10D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.


title: LB_AG_6D_R3

description:
34_LB_AG_6D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.

value: 6 Day old adult (6D)


title: LB_AG_10D_R1

description:
35_LB_AG_10D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Ten day old females were collected.


title: 7673 HCC tumor

description: DNA methylation in HCC


title: LB_AG_18D_R1

description:
42_LB_AG_18D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Eighteen day old females were collected.


title: LB_AG_3D_R4

description:
31_LB_AG_3D_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Three day old females were collected.

value: 3 Day old adult (3D)


title: LB_AG_6D_R1

description:
32_LB_AG_6D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.


title: LB_AG_3D_R1

description:
28_LB_AG_3D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Three day old females were collected.


title: LB_AG_3D_R2

description:
29_LB_AG_3D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Three day old females were collected.


title: LB_AG_6D_R2

description:
33_LB_AG_6D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Six day old females were collected.


title: 7528 HCC tumor

description: DNA methylation in HCC


title: 7669 HCC tumor

description: DNA methylation in HCC


title: LB_AG_0D_R4

description:
27_LB_AG_0D_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.

value: 0 Day old adult (0D)


title: 7530 HCC tumor

description: DNA methylation in HCC


title: 7672 HCC tumor

description: DNA methylation in HCC


title: 7678 HCC tumor

description: DNA methylation in HCC


title: 7670 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7677 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7674 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_0D_R3

description:
26_LB_AG_0D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.


title: LB_AG_0D_R2

description:
25_LB_AG_0D_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.


title: 7529 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7671 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_0D_R1

description:
24_LB_AG_0D_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Zero day old females were collected.


title: LB_AG_LP_R2

description:
23_LB_AG_LP_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Late stage pupae were collected.

value: Late pupal stage (LP)


title: 6087 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7523 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7527 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7526 HCC tumor

description: DNA methylation in HCC


title: 7520 HCC tumor

description: DNA methylation in HCC


title: LB_AG_EP_R4

description:
21_LB_AG_EP_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Early stage pupae were collected.

value: Wild-type

value: Early pupal stage (EP)


title: LB_AG_LP_R1

description:
22_LB_AG_LP_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Late stage pupae were collected.

value: Agria (AG)


title: LB_AG_3D_R3

description:
30_LB_AG_3D_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These adult females were raised on lab-media prepared from Agria cactus. Three day old females were collected.


title: LB_AG_EP_R3

description:
20_LB_AG_EP_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Early stage pupae were collected.


title: 7525 adjacent non-tumor tissue

description: DNA methylation in HCC

value: Female


title: LB_AG_EP_R2

description:
19_LB_AG_EP_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Early stage pupae were collected.

value: normal


title: 7524 HCC tumor

description: DNA methylation in HCC

value: Male


title: LB_AG_EP_R1

description:
18_LB_AG_EP_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These pupae developed from larvae raised on lab-media prepared from Agria cactus. Early stage pupae were collected.


title: 7522 HCC tumor

description: DNA methylation in HCC


title: LB_AG_L3_R5

description:
17_LB_AG_L3_R5
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.

value: 3rd instar larvae (L3)


title: 7519 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 7521 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_L3_R4

description:
16_LB_AG_L3_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.


title: 7517 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_L3_R3

description:
15_LB_AG_L3_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.


title: 7518 HCC tumor

description: DNA methylation in HCC


title: LB_AG_L3_R2

description:
14_LB_AG_L3_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.


title: LB_AG_L3_R1

description:
13_LB_AG_L3_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Third instar larvae were collected.


title: 7515 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_L2_R2

description:
9_LB_AG_L2_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.

value: 2nd instar larvae (L2)


title: LB_AG_L2_R3

description:
10_LB_AG_L2_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.


title: LB_AG_L2_R4

description:
11_LB_AG_L2_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.


title: LB_AG_L1_R4

description:
7_LB_AG_L1_R4
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.

value: 1st instar larvae (L1)


title: 7512 HCC tumor

description: DNA methylation in HCC

value: Liver


title: 7516 HCC tumor

description: DNA methylation in HCC

value: hepatocellular carcinoma (HCC)


title: LB_AG_L1_R3

description:
6_LB_AG_L1_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.

value: Las Bocas 2009:LB09


title: LB_AG_L1_R2

description:
5_LB_AG_L1_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.

value: Las Bocas, Sonora


title: LB_AG_L2_R5

description:
12_LB_AG_L2_R5
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.


title: 6240 HCC tumor

description: DNA methylation in HCC


title: 6241 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_L1_R1

description:
4_LB_AG_L1_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora desert. These larvae were raised on lab-media prepared from Agria cactus. First instar larvae were collected.


title: 7514 HCC tumor

description: DNA methylation in HCC


title: LB_AG_E6_R2

description:
2_LB_AG_E6_R2
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. Mothers of these eggs were raised on lab-media prepared from Agria cactus. Six hour old eggs were collected.

value: 6hr egg (E6)


title: 6242 HCC tumor

description: DNA methylation in HCC


title: LB_AG_E6_R3

description:
3_LB_AG_E6_R3
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. Mothers of these eggs were raised on lab-media prepared from Agria cactus. Six hour old eggs were collected.


title: 7513 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 6239 adjacent non-tumor tissue

description: DNA methylation in HCC


title: LB_AG_E6_R1

description:
1_LB_AG_E6_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. Mothers of these eggs were raised on lab-media prepared from Agria cactus. Six hour old eggs were collected.


title: 6234 adjacent non-tumor tissue

description: DNA methylation in HCC


title: 6228 HCC tumor

description: DNA methylation in HCC


title: 6236 HCC tumor

description: DNA methylation in HCC


title: 6231 HCC tumor

description: DNA methylation in HCC


title: 6233 HCC tumor

description: DNA methylation in HCC


title: 6235 adjacent non-tumor tissue

description: DNA methylation in HCC


title: Vivo_morula rep3.2

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Slides were scanned using Agilent s High-Resolution C Scanner (Agilent Technologies, CA, USA) and features were extracted with the Agilent's Feature Extraction software (Agilent Technologies, CA, USA).

data_processing: Data were submitted to a simple background correction, a Loess within array normalization and a Quantile between array normalization.

organism: Bos taurus

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol:
flush out embryos from the reproductive tract
cultured in groups of 50 in four well dishes each containing 400 Î¼l CR1aa medium

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: sample type

tag: breed (cattle)

value: Simmental

tag: time of embryo collection

value: 6 dpi (days post-in-vivo insemination)

tag: blast staging method

value: Fixed Time

tag: reproductive status (cattle)

value: Heifer

source_name: InVivo

value: 7 dpi (days post-in-vivo insemination)

value: Morphological


title: LB_AG_L2_R1

description:
8_LB_AG_L2_R1
This sample is of wild-type Drosophila mojavensis originally from Las Bocas, Sonora. These larvae were raised on lab-media prepared from Agria cactus. Second instar larvae were collected.

value: Wild-type

value: Agria (AG)


title: Vivo_morula rep3


title: 6229 adjacent non-tumor tissue

description: DNA methylation in HCC

value: Male


title: Vivo_morula rep1


title: Vivo_morula rep1.2


title: genomic DNA from non-HIV lymphoma 20

city: Shinjuku

first: Akihiro

last: Matsunaga

state: Tokyo

department: Intractable Disease

country: Japan

institute: National Center for Global Health and Medicine

description:
SAMPLE 31
non-HIV lymphoma sample

hyb_protocol: All genomic DNA was ligated and then treated by sodium bisulfite. Bisulfite-converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan system (iScan control software v3.2.45) using standard recommended Illumina scanner setting.

data_processing:
Average beta values were normalized to internal array controls as implemented by GenomeStudio software (v2011.1) methylation module (v1.9.0).
File signal_intensities.txt: Unmethylated and methylated signal intensities normalized to internal controls.  Linked as supplementary file on Series record.
File RAW_data.txt: Outputted by GenomeStudio software without processing any normalization methods.  Linked as supplementary file on Series record.

source_name: non-HIV lymphoma 20

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed, paraffin-embedded (FFPE) and fresh-frozen tissues by standard procedure.

value: female

tag: age

tag: disease state

value: non-HIV lymphoma


title: Vivo_morula rep2


title: 6232 adjacent non-tumor tissue

description: DNA methylation in HCC


title: IVP rep3

source_name: IVP

value: 168 hpf (hours post-in-vitro fertilization)


title: 6094 HCC tumor

description: DNA methylation in HCC

value: Liver


title: 6230 HCC tumor

description: DNA methylation in HCC

value: hepatocellular carcinoma (HCC)


title: genomic DNA from non-HIV lymphoma 18

description:
SAMPLE 29
non-HIV lymphoma sample

source_name: non-HIV lymphoma 18


title: 7511 adjacent non-tumor tissue

description: DNA methylation in HCC

value: Female


title: IVP rep3.2


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample3

city: Leipzig

first: Animesh

last: Bhattacharya

state: Saxony

address: Johannisallee 30, MBFZ, Room no B-214

department: Dermatology

country: Germany

institute: University of Leipzig, Medical Faculty

description: 667 human miRNAs from miRBase version v.10

data_processing: The raw Ct values from the 7900HT Fast Real-Time PCR System were processed and analyzed using the Bioconductor package HTqPCR Version 1.12.0 (Dvinge and Bertone, 2009) in the statistical programming environment R. Rank invariant controls were chosen for ΔCt normalization. For the A plates of all samples the arithmetic mean Ct values of MammU6, RNU44, RNU48 were used for normalization, while in B plates the controls MammU6, RNU44, RNU48, RNU24, RNU43 and RNU6B (last three not present on plate A design) were used for normalization. For the relative quantification of miRNA expression a cut-off was set at a CT value of 40. Probes with Ct values of 40 or greater were considered as undetermined. Sample correlation (Pearson’s correlation) was assessed based on normalized Ct values in a heatmap using hierarchical clustering.

label: FAM

source_name: Distant cutaneous metastasis

label_protocol: 1µg of total RNA was reverse transcribed using the High Capacity cDNA reverse transcription kit (Applied Biosystems) and TaqMan® Micro-RNA Megaplex RT Human Pool Sets A & B. The arrays were performed according to the manufacturer’s instructions with an Applied Biosystems 7900HT thermocycler under the following conditions: 50oC for 2 min, 94.5oC for 10 min, followed by 40 cycles of 97oC for 30 sec and 59.7oC for 1 min. Raw data were exported using SDS Relative Quantification Software version 2.2.2 (Applied Biosystems) with automatic baseline and threshold settings.

extract_protocol: Laser microdissected patient tissue samples were subjected to total RNA extraction using the mirVana microRNA extraction kit (Ambion, Life Technologies, Darmstadt, Germany)

tag: tissue

value: Distant cutaneous metastasis


title: IVP rep2.2


title: genomic DNA from non-HIV lymphoma 19

description:
SAMPLE 30
non-HIV lymphoma sample

source_name: non-HIV lymphoma 19


title: 6093 adjacent non-tumor tissue

description: DNA methylation in HCC


title: Vivo_morula rep2.2


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample10


title: IVP rep2


title: 6090 HCC tumor

description: DNA methylation in HCC


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample5


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample2


title: 6089 adjacent non-tumor tissue

description: DNA methylation in HCC


title: genomic DNA from non-HIV lymphoma 17

description:
SAMPLE 28
non-HIV lymphoma sample

source_name: non-HIV lymphoma 17

value: male


title: IVP rep1

value: Simmental


title: genomic DNA from non-HIV lymphoma 13

description:
SAMPLE 24
non-HIV lymphoma sample

source_name: non-HIV lymphoma 13


title: IVP rep1.2


title: genomic DNA from non-HIV lymphoma 16

description:
SAMPLE 27
non-HIV lymphoma sample

source_name: non-HIV lymphoma 16


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample6


title: Vitro_morula rep3.2

value: 7 dpf (days post-in vitro fertilization)


title: Vitro_morula rep3


title: 6227 adjacent non-tumor tissue

description: DNA methylation in HCC


title: genomic DNA from non-HIV lymphoma 15

description:
SAMPLE 26
non-HIV lymphoma sample

source_name: non-HIV lymphoma 15


title: genomic DNA from non-HIV lymphoma 10

description:
SAMPLE 21
non-HIV lymphoma sample

source_name: non-HIV lymphoma 10


title: genomic DNA from non-HIV lymphoma 11

description: SAMPLE 22

source_name: non-HIV lymphoma 11


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample1


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample9


title: Vitro_morula rep2.2


title: genomic DNA from non-HIV lymphoma 12

description: SAMPLE 23

source_name: non-HIV lymphoma 12


title: Vitro_morula rep1.2


title: Cryopreserved patient material-lymph_node_metastasis_sample1

source_name: Lymph node metastasis

value: Lymph node metastasis


title: genomic DNA from non-HIV lymphoma 7

description:
SAMPLE 18
non-HIV lymphoma sample

source_name: non-HIV lymphoma 7


title: genomic DNA from non-HIV lymphoma 6

description:
SAMPLE 17
non-HIV lymphoma sample

source_name: non-HIV lymphoma 6


title: Vitro_morula rep2

value: Heifer


title: Cryopreserved patient material-lymph_node_metastasis_sample8


title: genomic DNA from non-HIV lymphoma 2

description:
SAMPLE 13
non-HIV lymphoma sample

source_name: non-HIV lymphoma 2


title: Cryopreserved patient material-distant_cutaneous_metastasis_sample4


title: Cryopreserved patient material-lymph_node_metastasis_sample7


title: genomic DNA from non-HIV lymphoma 8

description:
SAMPLE 19
non-HIV lymphoma sample

source_name: non-HIV lymphoma 8


title: genomic DNA from non-HIV lymphoma 14

description:
SAMPLE 25
non-HIV lymphoma sample

source_name: non-HIV lymphoma 14


title: genomic DNA from non-HIV lymphoma 1

description:
SAMPLE 12
non-HIV lymphoma sample

source_name: non-HIV lymphoma 1


title: Cryopreserved patient material-lymph_node_metastasis_sample9


title: AB-ref vs. AB-S19-KB-a

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using Agilent G2565BA scanner.

data_processing: Features were extracted using Imagene software from Biodiscovery. Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

label_protocol: robot amplification and labeling v1.0

extract_protocol: Add 1 ml Trizol per 5x 106 cells in suspension (1 ml trizol per 10 cm culture disk). RNeasy steps follow.

treatment_protocol: EBV-immoralized lymphoblast cell lines (LCLs) derived from either DBA patients or normal control individuals were selected: three lines carrying RPS19 mutations (two with splice site mutations, one with a small insertion leading to an early stop codon) or RPL11 mutations (two with a small insertion or deletion leading to an early stop codon, one with a splice site mutation). We performed sucrose density fractionations with the lysates from these cells along with three different normal control lines as follows: All steps of this protocol are performed at 4°C or on ice. Gradients of 17% to 50% sucrose (11ml) in gradient buffer (110mM KAc, 20mM MgAc and 10mM HEPES pH 7.6) were poured the evening before use. LCLs were lysed in 500µl polysome lysis buffer (gradient buffer containing 100mM KCl, 10mM MgCl, 0.1% NP-40, and freshly added 2mM DTT and 40U/ml RNAsin (Promega) using a Dounce tissue grinder (Wheaton). The samples were centrifuged at 1200g for 10 minutes to remove debris. Protein concentrations of each sample were calculated by Bradford analysis (Sigma), equalized using lysis buffer, and loaded onto the sucrose gradients. The gradients were ultracentrifuged for 2 hours at 120565g in an SW41 Ti rotor (Beckman-Coulter, US). The gradients were displaced into a UA6 absorbance reader (Teledyne ISCO) using a syringe pump (Brandel, US) containing 60% sucrose. Absorbance was recorded at an OD of 254nm. RNA was isolated from the polysomal peaks of the displaced sucrose gradients using the Trizol LS reagent (Invitrogen)

tag: cell type

value: mixed

value: universal human reference RNA (Stratagene)

tag: cell line

value: lymphoblasts


title: genomic DNA from non-HIV lymphoma 5

description:
SAMPLE 16
non-HIV lymphoma sample

source_name: non-HIV lymphoma 5


title: genomic DNA from HIV-associated lymphoma 10

description: SAMPLE 10

source_name: HIV-lymphoma 10

value: HIV-associated lymphoma


title: Cryopreserved patient material-lymph_node_metastasis_sample2


title: Vitro_morula rep1

source_name: InVivo

value: 7 dpi (days post-in-vivo insemination)

value: Morphological


title: Cryopreserved patient material-lymph_node_metastasis_sample5


title: AB-ref vs. AB-N-CC-a

value: N-CC


title: Cryopreserved patient material-lymph_node_metastasis_sample4


title: genomic DNA from HIV-associated lymphoma 8

description: SAMPLE 8

source_name: HIV-lymphoma 8


title: genomic DNA from HIV-associated lymphoma 4

description: SAMPLE 4

source_name: HIV-lymphoma 4


title: AB-ref vs. AB-S19-107-2-a


title: Cryopreserved patient material-lymph_node_metastasis_sample6


title: AB-ref vs. AB-L11-247-3-a


title: AB-ref vs. AB-N-AOB-a

value: N-AOB


title: genomic DNA from HIV-associated lymphoma 6

description: SAMPLE 6

source_name: HIV-lymphoma 6


title: genomic DNA from HIV-associated lymphoma 9

description: SAMPLE 9

source_name: HIV-lymphoma 9


title: AB-ref vs. AB-S19-120-3-a


title: genomic DNA from HIV-associated lymphoma 1

description: SAMPLE 1

source_name: HIV-lymphoma 1


title: AB-ref vs. AB-L11-231-3-a


title: genomic DNA from HIV-associated lymphoma 7

description: SAMPLE 7

source_name: HIV-lymphoma 7


title: Cryopreserved patient material-lymph_node_metastasis_sample3


title: Cryopreserved patient material-primary_malignant_melanoma_sample3

source_name: Primary melanoma

value: Primary melanoma


title: Cryopreserved patient material-primary_malignant_melanoma_sample6


title: genomic DNA from HIV-associated lymphoma 5

description: SAMPLE 5

source_name: HIV-lymphoma 5


title: genomic DNA from HIV-associated lymphoma 3

description: SAMPLE 3

source_name: HIV-lymphoma 3


title: genomic DNA from HIV-associated lymphoma 11

description: SAMPLE 11

source_name: HIV-lymphoma 11


title: genomic DNA from non-HIV lymphoma 4

description:
SAMPLE 15
non-HIV lymphoma sample

source_name: non-HIV lymphoma 4

value: non-HIV lymphoma


title: genomic DNA from non-HIV lymphoma 9

description:
SAMPLE 20
non-HIV lymphoma sample

source_name: non-HIV lymphoma 9


title: Cryopreserved patient material-primary_malignant_melanoma_sample7


title: Cryopreserved patient material-primary_malignant_melanoma_sample8


title: 3 ALMC1 S

city: Boston

first: Lakshmanan

middle: K

last: Iyer

state: MA

address: 136 Harrison Ave

department: Neuroscience

institute: Tufts University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: ALMC1 cells treated with si[IGLC]

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

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

treatment_protocol: Cells were treated with siRNA for light chain knockdown or control siRNA

value: myeloma


title: AB-S19-120-3-b vs. AB-ref


title: AB-N-CC-b vs. AB-ref


title: AB-S19-107-2-b vs. AB-ref


title: SK-Mel-147_Antagomir-miR-638-transfected_rep2

description: Replicate 2

scan_protocol: Arrays were scanned with an Illumina iScan microarray scanner. Bead level data preprocessing was done in Illumina GenomeStudio

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R. ANOVA was performed on the quantile normalized data of the distinctively treated cells. Differentially expressed genes were considered significant when adjusted p ≤ 0.01 (corrected for multiple testing by the Benjamini-Hochberg method). The genes which were both exclusively suppressed by miR-638 overexpression and de-repressed by miR-638 knockdown were considered for further validation. Finally, we reduced the number of candidates by considering only those genes with a total log10 fold change of 2 or more (sum of absolute fold changes). The data was processed and analyzed using the Bioconductor package lumi (Du et al., 2008) in the statistical programming environment R.

label: Biotin

source_name: SK-Mel-147 melanoma cells

label_protocol: Biotinylated cRNA were prepared with the TargetAmp™-Nano Labeling Kit for Illumina arrays

growth_protocol: SK-Mel-147 melanoma cells were cultured in growth medium containing Dulbecco's modified eagles medium(DMEM) containing 10% FCS and 1% L-glutamine with or without 1% Penicillin Streptomycin

extract_protocol: 48 hours post transfection, total RNA was extracted from the cells using miRVana microRNA isolation kit (Ambion, Life technologies, Darmstadt, germany)

treatment_protocol: SK-Mel-147 cells were cultured in complete growth medium (without antibiotics) and transfected with a non-targeting miRNA mimic or miR-638 mimic or miR-638 inhibitor mimic.

tag: treatment


title: Cryopreserved patient material-primary_malignant_melanoma_sample5


title: AB-S19-KB-b vs. AB-ref


title: AB-ref vs. AB-L11-70-3-a


title: AB-N2-b vs. AB-ref


title: 14 ALMC1 KD

source_name: ALMC1 cells treated with si[-]


title: 13 ALMC1 S


title: 4 ALMC1 KD


title: genomic DNA from HIV-associated lymphoma 2

description: SAMPLE 2

source_name: HIV-lymphoma 2


title: 1 ALMC1 S


title: genomic DNA from non-HIV lymphoma 3

description:
SAMPLE 14
non-HIV lymphoma sample

source_name: non-HIV lymphoma 3


title: Cryopreserved patient material-primary_malignant_melanoma_sample2


title: AB-N-AOB-b vs. AB-ref


title: Cryopreserved patient material-primary_malignant_melanoma_sample1


title: AB-ref vs. AB-N2-a


title: Cryopreserved patient material-primary_malignant_melanoma_sample4


title: SK-Mel-147_Antagomir-miR-638-transfected_rep1

description: Replicate 1


title: wheat Yumai 13 at 24, 48 hpi

city: Hangzhou

first: shaohui

last: Li

address: Yuhangtang road

country: China

institute: Zhejiang University

description: Gene expression date from wheat Yumai 13 at 24 and 48 h after powdery mildew inoculation.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Wheat Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the affymetrix scanner 3000 7G.The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of AGCC.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Triticum aestivum

source_name: Primary leaves from Yumai 13 at 24, 48 hpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Pregerminated seeds of susceptible wheat cultivar Yumai 13 and two horizontally resistant wheat cultivars HY and CYC were sown in the pots which were covered and placed in the greenhouse under 20℃/16℃ day/night with 70% relative humidity.

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

treatment_protocol: Seven-day-old wheat seedlings were inoculated at a density of approximately 200 conidia per mm2 of powdery mildew fungus Blumeria graminis f.sp. Tritici and sampled at 0, 24, 48 hpi.

tag: cultivar

value: Yumai 13

value: susceptible wheat cultivar

value: leaves

tag: time point


title: AB-L11-70-3-b vs. AB-ref


title: AB-L11-231-3-b vs. AB-ref


title: SK-Mel-147_miR-638-transfected_rep2

description: Replicate 2


title: wheat Yumai 13 at 0 hpi

description: Gene expression date from wheat Yumai 13 at 0 h after powdery mildew inoculation.

source_name: Primary leaves from Yumai 13 at 0 hpi

tag: phenotype

value: 0 h after powdery mildew inoculation


title: RPE cells treated with 250 ug/ml of cigarette smoke condensate, rep3

city: Baltimore

first: Marisol

middle: D

last: Cano

state: Maryland

address: 400 N Broadway

department: Ophthalmology

institute: Johns Hopkins University

description: CSE 250 3

hyb_protocol: Fragmented, biotinylated cDNA was hybridized to Human Exon 1.0 ST arrays for 17 hours at 45oC and 60rpm. The Affymetrix recommended signal amplifcation protocol for washing/staining of GeneChip ST arrays was performed in a FS450 automated fluidics station.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 7G scanner with autoloader.

data_processing:
Gene expression was analyzed using Partek® software (version 6.3 Copyright © 1993-2010, Partek Inc., St. Louis, MO). We performed GC pre-background adjustment, RMA background correction based on core-level probes annotated by Affymetrix. Quantile normalization was performed across all 9 microarrays for different conditions. The gene expression was summarized as mean value of all core-level exons of a gene. The genes with low expression (about 25% lowest expression level) over all conditions were removed from further analysis.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.mps

label_protocol: 2 ug total RNA was processed according to the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling assay manual, version 4.

growth_protocol: ARPE-19 cells were seeded at 100,000/cm2 and grown in Dulbecco's Modified Eagle medium/Hams F12 (DMEM/F12) with 15mM Hepes buffer and 10% fetal bovine serum (FBS) and 2mM L-glutamine solution at 37oC until confluent, and then grown in DMEM/F12 with 1% bovine serum albumin (BSA).

extract_protocol: Total RNA was extracted and purified with the Ambion RiboPure kit, according to the manufacturer's recommended protocol.

treatment_protocol: Cigarette smoke extract (CSE) was obtained from Murty Pharmaceuticals, Inc., Lexington, KY. CSE is 40mg/ml condensate, and 6% nicotine. According to the manufacturer, CSE is prepared by smoking University of Kentucky's 3R4F Standard Research Cigarettes on an FTC Smoke Machine. The smoke on the filter is calculated by the weight gain of the filter after smoking. The amount of DMSO is calculated that will dissolve a 4% (40mg/mL) solution. The extract was diluted in Dulbecco's Modified Eagle medium/Hams F12 (DMEM/F12).

value: retinal pigment epithelial (RPE) cells

value: cigarette smoke condensate

tag: treatment dosage

value: 250 ug/ml


title: wheat HY at 24, 48 hpi

description: Gene expression date from wheat HY at 24 and 48 h after powdery mildew inoculation.

source_name: Primary leaves from HY at 24, 48 hpi

value: HY

value: resistant wheat cultivar


title: RPE cells treated with 250 ug/ml of cigarette smoke condensate, rep2

description: CSE 250 2


title: SK-Mel-147_miR-638-transfected_rep1

description: Replicate 1


title: Control_Blood_4

city: Gainesville

first: Ignacio

middle: Alejandro

last: Rodriguez-Jorquera

state: Florida

address: Mowry Drive 471

department: Soil and Water Science

institute: University of Florida

hyb_protocol: Microarray hybridizations were performed according to the Agilent One-color microarray- (document no. G4140-90040 v6.5) using Cyanine 3 (Cy3) (Agilent, Palo Alto, CA).A final volume of 25 μl containing fragmented cRNA was added to the microarrays, and then hybridization proceeded for 17 h at 65 oC

scan_protocol: Agilent G2505B microarray scanner (same day). Data extraction was performed using Agilent Feature Extraction software (v9.5).

data_processing: Agilent Feature Extraction Software (v9.5) formed a composite of the scans and calculated parameters for Extended Dynamic Range. Data extraction was performed using Agilent Feature Extraction software. Background-subtracted raw expression data (gProcessedSignal) were imported into JMP Genomics v5 (SAS, Cary, NC). During import, data were log2-transformed and all control and non-uniform spots were removed prior to the final analysis. Raw intensity data for each microarray were normalized by LOAESS before performing ANOVA. Differentially regulated transcripts were identified using a one-way analysis of variance (false discovery rate [FDR] = 20%).

organism: Pimephales promelas

label_protocol: For blood samples, 25 ng of total RNA per sample was used to produce cDNA and 50 ng of RNA was used for liver samples. Each sample contained a specific activity >8.15 pmol Cy3/ug, and amounts were adjusted to a final mass of 600 ng for 8x15K microarray hybridizations.

growth_protocol: Reproductively mature pond-reared fathead minnow (FHM) were purchased from Andersen Minnow Farm (Lonoke, Arkansas) approximately 6 months before the exposures.

extract_protocol: Total RNA was extracted following the RNA STAT-60 reagent protocol (Tel-Test, 127 Friendswood, TX, USA).RNA was reconstituted in RNAsecure (Ambion), and DNase-treated with Turbo DNA-free (Ambion).The RNA quantity for microarray analysis was measured using the NanoDrop ND-1000 (Nanodrop Technologies, Wilmington, DE) and RNA quality was evaluated using the Agilent 2100 BioAnalyzer with the RNA 6000 Nanochip. RNA integrity values (RIN) range were 8.1 to 9.3 for blood samples and 7.5 to 9.4 for liver samples. Colum purification of DNAse treated RNA were performed. A fathead minnow oligonucleotide microarrays manufactured by Agilent (Palo Alto, CA) and designed in our laboratory (Agilent-019597 custom fathead minnow 60mer (8x15k)) was used in this study.

treatment_protocol: Liver tissue and whole blood was flash frozen using liquid nitrogen and stored at -80 °C until RNA extraction. Liver and blood were isolated from all males. The liver and blood from same individuals (four for each treatment) were used for RNA extraction.

tag: gender

value: male

tag: developmental stage

value: reproductively mature

tag: exposed to

value: none (control; 0 ug/L)

value: whole blood


title: wheat HY at 0 hpi

description: Gene expression date from wheat HY at 0 h after powdery mildew inoculation.

source_name: Primary leaves from HY at 0 hpi


title: AB-L11-247-3-b vs. AB-ref

value: lymphoblasts

value: mixed

tag: sample type

value: universal human reference RNA (Stratagene)


title: wheat CYC at 0 hpi

description: Gene expression date from wheat cultiar CYC at 0 h after powdery mildew inoculation.

source_name: Primary leaves from CYC at 0 hpi

value: CYC


title: RPE cells treated with 250 ug/ml of cigarette smoke condensate, rep1

description: CSE 250 1


title: non-HIV lymphoma 12-1

description: duplicate analysis of non-HIV lymphoma sample 12

hyb_protocol: All genomic DNA was subjected to sodium bisulfite conversion, labeled with fluorescent dyes, and hybridized to GoldenGate Methylation Cancer Panel I microarray.

scan_protocol: Arrays were imaged using BeadArray Reader scanner using standard recommended Illumina scanner setting.

data_processing: GenomeStudio (v2010.1) methylation module (v1.6.1) was used for dataset assembly. Data was not normalized as per manufacturer recommendation.

source_name: genomic DNA from non-HIV lymphoma

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed, paraffin-embedded (FFPE) by standard procedure.

value: female

tag: age (yrs)

value: non-HIV lymphoma


title: RPE cells treated with 100 ug/ml of cigarette smoke condensate, rep2

description: CSE 100 2

value: 100 ug/ml


title: High_Blood_3

value: high PFOS (25 ug/L)


title: NME-Post TGF-Rec-3

city: West Lafayette

first: Michael

last: Wendt

state: IN

address: 201 S. University St.

department: MCMP

institute: Purdue University

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The scanned dat files were converted to cel files using Affymetrix propriatary software Expression Console (EC). EC was also used to convert the cel files into spreadsheets of gene expression numbers using the RMA (Robust Multigene Analysis) feature of EC (RMA normalized data provided in sample table).  Raw data in logbase2 were converted into linear values and exported as a tab delimited text file along with appropriate annotations. Gene expression changes were defined as follows: The  group means were calculated for each gene.  Binary comparisons were generated  in which the group-mean ratio s were calculated for each gene. Raw data, group-means and group-mean ratios were imported into MS access data base manager. record were filtered for ratios >= 1.5 or <= 0.666666. Raw data (linear ) for each group were imported into BAMarray (Bayesian Analysis of Microarray data), a bootstrapping software  that uses z-values to confer statistical significance upon observed differences in the measurements.  Results for BAM analysis were imported into the same Access database and the BAM results cross-referenced to the group-mean ratios. Records that met both the group-mean ratio magnitude and BAM significance were deemed to be the differentially expressed genes (provided in the 'differentially_expressed.txt' series supplementary file)

organism: Mus musculus

source_name: NME-Post TGF-Recovery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical manual, 2001, Affymetrix)

growth_protocol: DMEM containing 10% FBS and 10mg/ml Insulin

extract_protocol: Quaigen RNAeasy

treatment_protocol: 5 ng/ml TGF-beta1 for 4 weeks added every 4 days, then exogenous TGF-beta1 was withdrawn and cells were cultured for an additional 4 weeks.

tag: cell line background

value: NMumG

value: normal murine mammary gland cells

tag: transformed by

value: overexpression of EGFR (NME)

tag: stimulated with

value: TGF-beta1 for 4 wks + recovery for 4 wks


title: non-HIV lymphoma 12-2

tag: disease state


title: wheat CYC at 24, 48 hpi

description: Gene expression date from wheat cultiar CYC at 24 and 48 h after powdery mildew inoculation.

source_name: Primary leaves from CYC at 24,48 hpi

value: resistant wheat cultivar

tag: tissue

value: leaves


title: Control_Blood_3

value: male

value: reproductively mature


title: NME-Post TGF-Rec-1

tag: cell type


title: non-HIV lymphoma 11-2

description: duplicate analysis of non-HIV lymphoma sample 11


title: NME-Post TGF-Rec-2


title: 2 ALMC1 KD

value: myeloma

tag: cell line


title: RPE cells treated with 100 ug/ml of cigarette smoke condensate, rep3

description: CSE 100 3

value: retinal pigment epithelial (RPE) cells

tag: treatment

value: cigarette smoke condensate


title: non-HIV lymphoma 11-1


title: non-HIV lymphoma 10-2

description: duplicate analysis of non-HIV lymphoma sample 10


title: RPE cells treated with vehicle control, rep3

description: Control 3

source_name: RPE cells treated with vehicle control

value: vehicle control


title: Low_Blood_4

value: low PFOS (0.5 ug/L)

value: whole blood


title: Control_Blood_2

value: none (control; 0 ug/L)


title: non-HIV lymphoma 10-1

value: non-HIV lymphoma


title: Mix_Blood_4

value: PFCs mixture


title: RPE cells treated with vehicle control, rep2

description: Control 2


title: RPE cells treated with vehicle control, rep1

description: Control 1


title: non-HIV lymphoma 9-2

description: duplicate analysis of non-HIV lymphoma sample 9

value: female


title: GFP Zfx ko 3

first: Stuart

last: Weisberg

state: NY

address: 650 W 168th Street

department: Pathology and Cell Biology

hyb_protocol: Biotinylated DNA probe was made according to the standard Affymetrix protocol

scan_protocol: Arrays were scanned according to the Affymetrix protocol

data_processing: Gene level RMA

source_name: Sorted Zfx ko myeloid progenitors overexpressing only GFP selectable marker

label_protocol: Used the Ambion WT labelling kit as per manufacturer's instructions using 200ng of starting total RNA

growth_protocol: Cells were cultured in RPMI 1640 with 20% FBS and the following cytokines: IL-3 (10 ng/mL), IL-6 (10 ng/mL), SCF (10 ng/mL)

treatment_protocol: Tamoxifen was administered via 5 mg daily gavage for three days.

tag: genotype/variation

value: Zfx fl/y CreER

value: infected with control retrovirus with GFP selectable marker


title: GFP Zfx wt 3

source_name: Sorted Zfx wt myeloid progenitors overexpressing only GFP selectable marker

value: Zfx wt/y CreER


title: non-HIV lymphoma 9-1


title: non-HIV lymphoma 8-2

description: duplicate analysis of non-HIV lymphoma sample 8


title: Control_Blood_1


title: Mix_Blood_3


title: Myc Zfx wt 3

source_name: Sorted Zfx wt myeloid progenitors overexpressing Myc using GFP selectable marker

value: infected with Myc expressing and control retrovirus with GFP selectable marker


title: patient21_B2_144h_2a

city: Basel

first: Zuzanna

last: Makowska

address: Hebelstrasse 20

department: Biomedicine

country: Switzerland

institute: University of Basel

hyb_protocol: The Hybridization, Wash and Stain Kit (Affymetrix) was used to hybridize all samples for 17 hours at 45°C in Affymetrix hybridization oven 645. The arrays were washed and stained on Fluidics station 450 using wash protocol FS450_0004 (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the arrays.

data_processing: Microarray data were preprocessed using standard RMA algorithm as implemented in the AFFY package of Bioconductor libraries of R statistical environment. Batch effects observed between the samples processed and hybridized at different times were corrected using the ComBat algorithm (Johnson et al, 2007, Biostatistics)

source_name: on-treatment liver biopsy (144h after pegIFNalpha-2a injection), chronic hepatitis C, patient 21

label_protocol: 1 ug of total RNA was reverse transcribed, amplified, labelled and fragmented with GeneChip 3'IVT Express Kit (Affymetrix) according to the manufacturer’s instructions.

extract_protocol: Total RNA was extracted from the liver samples using Qiazol reagent and miRNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction

treatment_protocol: All patients were recruited between March 2006 to April 2010 in the Hepatology Outpatient Clinic of the University Hospital Basel. Patients with CHC who underwent a biopsy for diagnostic purposes (B1) and gave written informed consent were screened for hepatic ISG expression. The 4-gene classifier (Dill et al, 2011, Hepatology) was used to assess the probability of sustained viral response (SVR). Patients with high probability of achieving SVR were asked to participate in the study, which included a second biopsy (B2) taken at a particular time point after the first therapeutic injection of pegIFNα. We included 3 patients for each of the following time points: 16, 48, 96 and 144 hours, and additionally, data of 6 patients from a previous study biopsied at 4 hours (Sarasin-Filipowicz et al, 2008, PNAS; GSE11190) were included in the analysis. The patients received 1.5 μg/kg body weight pegIFNα-2b (Essex Chemie, Switzerland). Weight-adjusted ribavirin treatment was initiated only after the second biopsy to avoid confounding effects. An additional 3 patients that were treated with 180µg of pegIFNα-2a (Roche, Switzerland) were included for the 144 hours time point. The study was approved by the Ethics Committee of Basel.

value: chronic hepatitis C

tag: patient

tag: time

value: B2 (144h after pegIFNalpha-2a injection)

value: liver biopsy


title: non-HIV lymphoma 7-2

description: duplicate analysis of non-HIV lymphoma sample 7

value: male


title: Myc Zfx ko 3

source_name: Sorted Zfx ko myeloid progenitors overexpressing Myc using GFP selectable marker


title: patient19_B2_144h_2a

source_name: on-treatment liver biopsy (144h after pegIFNalpha-2a injection), chronic hepatitis C, patient 19


title: patient18_B2_144h

source_name: on-treatment liver biopsy (144h after pegIFNalpha-2b injection), chronic hepatitis C, patient 18

value: B2 (144h after pegIFNalpha-2b injection)


title: Low_Blood_2

value: reproductively mature


title: Low_Blood_3


title: non-HIV lymphoma 8-1


title: non-HIV lymphoma 7-1


title: GFP Zfx ko 2


title: Mix_Blood_2


title: GFP Zfx wt 2


title: patient20_B2_144h_2a

source_name: on-treatment liver biopsy (144h after pegIFNalpha-2a injection), chronic hepatitis C, patient 20


title: patient17_B2_144h

source_name: on-treatment liver biopsy (144h after pegIFNalpha-2b injection), chronic hepatitis C, patient 17


title: non-HIV lymphoma 6-2

description: duplicate analysis of non-HIV lymphoma sample 6


title: Myc Zfx ko 2


title: Myc Zfx wt 2


title: RPE cells treated with 100 ug/ml of cigarette smoke condensate, rep1

description: CSE 100 1

value: retinal pigment epithelial (RPE) cells

value: cigarette smoke condensate

tag: treatment dosage

value: 100 ug/ml


title: patient16_B2_144h

source_name: on-treatment liver biopsy (144h after pegIFNalpha-2b injection), chronic hepatitis C, patient 16


title: non-HIV lymphoma 6-1

tag: gender


title: High_Blood_1

tag: developmental stage

value: high PFOS (25 ug/L)

value: whole blood


title: Low_Blood_1

tag: exposed to

value: low PFOS (0.5 ug/L)


title: patient15_B2_96h

source_name: on-treatment liver biopsy (96h after pegIFNalpha-2b injection), chronic hepatitis C, patient 15

value: B2 (96h after pegIFNalpha-2b injection)


title: non-HIV lymphoma 5-2

description: duplicate analysis of non-HIV lymphoma sample 5

value: non-HIV lymphoma


title: non-HIV lymphoma 5-1


title: non-HIV lymphoma 4-2

description: duplicate analysis of non-HIV lymphoma sample 4


title: Mix_Blood_1

value: PFCs mixture


title: Myc Zfx ko 1

value: Zfx fl/y CreER


title: non-HIV lymphoma 4-1


title: Low_Liver_10

value: Liver


title: patient14_B2_96h

source_name: on-treatment liver biopsy (96h after pegIFNalpha-2b injection), chronic hepatitis C, patient 14

value: chronic hepatitis C


title: Control_Liver_3

value: none (control; 0 ug/L)


title: 14846 - Tamoxifen

data_processing: Affymetrix Expression Console (1.1) was used for RMA normalization of all microarray data.

source_name: Sorted GFP+ T-ALL from Tamoxifen treated mouse

treatment_protocol: Leukemia cells were treated with Tamoxifen as they expanded in murine hosts in-vivo. Tamoxifen was administered via 5 mg daily gavage for three days.

value: Notch induced T-lymphoblastic leukemia (T-ALL)

value: ZFX null


title: patient12_B2_48h

source_name: on-treatment liver biopsy (48h after pegIFNalpha-2b injection), chronic hepatitis C, patient 12

value: B2 (48h after pegIFNalpha-2b injection)

value: liver biopsy


title: non-HIV lymphoma 3-2

description: duplicate analysis of non-HIV lymphoma sample 3

source_name: genomic DNA from non-HIV lymphoma

value: male


title: Mix_Liver_39

value: reproductively mature


title: GFP Zfx wt 1

value: Zfx wt/y CreER

value: infected with control retrovirus with GFP selectable marker


title: Myc Zfx wt 1

value: infected with Myc expressing and control retrovirus with GFP selectable marker


title: GFP Zfx ko 1


title: patient13_B2_96h

source_name: on-treatment liver biopsy (96h after pegIFNalpha-2b injection), chronic hepatitis C, patient 13


title: 14844 - Tamoxifen


title: patient10_B2_48h

source_name: on-treatment liver biopsy (48h after pegIFNalpha-2b injection), chronic hepatitis C, patient 10


title: non-HIV lymphoma 3-1


title: Low_Liver_11

value: low PFOS (0.5 ug/L)


title: Mix_Liver_38


title: patient11_B2_48h

source_name: on-treatment liver biopsy (48h after pegIFNalpha-2b injection), chronic hepatitis C, patient 11


title: patient9_B2_16h

source_name: on-treatment liver biopsy (16h after pegIFNalpha-2b injection), chronic hepatitis C, patient 9

value: B2 (16h after pegIFNalpha-2b injection)


title: Mother_healthy

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

description: Hybridized to Affymetrix SNP 6.2

hyb_protocol: According to standard manufacturer protocol (Affymetrix).

scan_protocol: The arrays were  washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G.

data_processing: Affymetrix GeneChip Command Console software was used for image processing and CEL files were processed by Affymetrix GTC using the BRLMM-P-Plus algorithm and regional GC correction configuration for Copy Number/LOH analysis. The HapMap270 file supplied by Affymetrix was used as the reference.

source_name: HH2A whole blood 3

extract_protocol: Genomic DNA was extracted from whole blood using the QIAgen DNA Blood Midi Kit. DNA quality and quantity were assessed using a Nanodrop Spectophotometer and Agilent BioAnalyzer.

value: blood

tag: relationship

value: Mother healthy

value: healthy


title: non-HIV lymphoma 2-2

description: duplicate analysis of non-HIV lymphoma sample 2

tag: age (yrs)

value: non-HIV lymphoma


title: patient8_B2_16h

source_name: on-treatment liver biopsy (16h after pegIFNalpha-2b injection), chronic hepatitis C, patient 8

value: chronic hepatitis C


title: non-HIV lymphoma 1-2

description: duplicate analysis of non-HIV lymphoma sample 1


title: non-HIV lymphoma 2-1


title: Control_Liver_5

value: none (control; 0 ug/L)

value: Liver


title: High_Blood_2

value: high PFOS (25 ug/L)

value: whole blood


title: High_Liver_28


title: 14846 - Veh

source_name: Sorted GFP+ T-ALL from Vehicle treated mouse

value: Notch induced T-lymphoblastic leukemia (T-ALL)

value: ZFX flox


title: Mix_Liver_34

value: male

value: reproductively mature

value: PFCs mixture


title: patient7_B2_16h

source_name: on-treatment liver biopsy (16h after pegIFNalpha-2b injection), chronic hepatitis C, patient 7

value: liver biopsy


title: Proband_affected

description: Hybridized to Affymetrix SNP 6.0

source_name: HH2A whole blood 1

label_protocol: According to standard manufacturer protocol (Affymetrix).

value: Proband affected

value: hemochromatosis type 2A


title: HIV lymphoma 9-2

description: duplicate analysis of HIV-assocaited lymphoma sample 9

source_name: genomic DNA from HIV-associated lymphoma

value: HIV-associated lymphoma


title: HIV lymphoma 9-1


title: patient21_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 21

value: control

value: B1 (before treatment)


title: non-HIV lymphoma 1-1

value: non-HIV lymphoma


title: High_Liver_25


title: 14844 - Veh


title: Father_healthy

description: Hybridized to Affymetrix SNP 6.1

source_name: HH2A whole blood 2

value: blood

value: Father healthy

value: healthy


title: Zfx wt MA9 cells + 4-OHT [10980]

source_name: c-Kit + MA9 AML Zfx wt

growth_protocol: Cells were grown at 37 degrees and 5% carbon dioxide in RPMI + 20% FBS with glutamine, non-essential amino acids, sodium pyruvate, penicillin/streptomycin additives plus IL-3, IL-6 at 10ng/mL and SCF at 20ng/mL

treatment_protocol: Cells were treated with 10nM 4-hydroxytamoxifen or ethanol vehicle

value: MLL-AF9 AML cell line 10980 (Zfx wt)

tag: treatment protocol

value: +OHT

value: wt


title: Mix_Liver_33

value: Liver


title: Zfx wt MA9 cells + Vehicle [10980]

value: vehicle


title: patient18_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 18

value: chronic hepatitis C


title: Low_Liver_15

value: male

value: reproductively mature

value: low PFOS (0.5 ug/L)


title: 14843 - Veh

value: Notch induced T-lymphoblastic leukemia (T-ALL)

value: ZFX flox


title: Zfx wt MA9 cells + 4-OHT [10977]

value: MLL-AF9 AML cell line 10977 (Zfx wt)


title: patient20_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 20

value: control

value: B1 (before treatment)

value: liver biopsy


title: HIV lymphoma 8-2

description: duplicate analysis of HIV-assocaited lymphoma sample 8

value: HIV-associated lymphoma


title: HIV lymphoma 8-1


title: Control_Liver_4

value: none (control; 0 ug/L)


title: High_Liver_27

value: high PFOS (25 ug/L)


title: HIV lymphoma 7-1

description: duplicate analysis of HIV-assocaited lymphoma sample 7


title: patient17_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 17


title: HIV lymphoma 6-2

description: duplicate analysis of HIV-assocaited lymphoma sample 6


title: patient16_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 16


title: patient15_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 15


title: HIV lymphoma 7-2


title: Zfx fl MA9 cells + Vehicle [10986]

source_name: c-Kit + MA9 AML Zfx fl

value: MLL-AF9 AML cell line 10986 (Zfx fl)

value: fl


title: Zfx fl MA9 cells + 4-OHT [10986]

source_name: c-Kit + MA9 AML Zfx KO

value: +OHT

value: cko


title: patient14_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 14

value: chronic hepatitis C


title: Zfx fl MA9 cells + 4-OHT [10950]

value: MLL-AF9 AML cell line 10950 (Zfx fl)


title: Zfx wt MA9 cells + Vehicle [10977]

value: vehicle

value: wt


title: High_Liver_31

value: male

value: reproductively mature

value: Liver


title: patient13_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 13

value: control


title: Zfx fl MA9 cells + Vehicle [10950]


title: Zfx fl MA9 cells + Vehicle [10949]

value: MLL-AF9 AML cell line 10949 (Zfx fl)


title: HIV lymphoma 5-2

description: duplicate analysis of HIV-assocaited lymphoma sample 5


title: patient11_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 11

value: B1 (before treatment)

value: liver biopsy


title: HIV lymphoma 6-1

value: HIV-associated lymphoma


title: patient12_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 12


title: rep2-Day7_Jack

city: Lexington

first: Sharyn

middle: E

last: Perry

state: KY

address: 1405 Veterans Dr.

department: Plant and Soil Sciences

institute: University of Kentucky

description: transcriptome data from explants of nontransgenic tissue placed onto D40 culture medium for 7 days,  replication 2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45°C on Arabidopsis ATH1 Genome Array in the Affymetrix GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner

data_processing: The data was scaled using the Affymetrix analysis software to a target intensity of 500.

organism: Glycine max

source_name: immature cotyledon explant cultured 7 days on D40 medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2007, Affymetrix).

growth_protocol: Greenhouse grown soybean plants were used to isolate immature embryos.

extract_protocol: Total RNA was performed using the RNeasy® plant mini kit (Qiagen) according to the manufacturer's instructions except that the extraction buffer contained 1.06% PEG.

treatment_protocol: Cotyledon explants from  4-5 mm developing soybean embryos were isolated and flash frozen for RNA isolation  (0 day timepoint) or placed onto D40 medium for 3 or 7 days and then flash frozen.

value: 7 d

value: immature cotyledon explant

tag: genotype

value: nontransgenic wild type


title: Zfx fl MA9 cells + 4-OHT [10949]

value: +OHT


title: rep2-Day7_35SGmAGL15

description: transcriptome data from explants of 35S:GmAGL15 tissue placed onto D40 culture medium for 7 days,  replication 2

value: overexpression of GmAGL15


title: HIV lymphoma 5-1


title: rep2-Day3_35SGmAGL15

description: transcriptome data from explants of 35S:GmAGL15 tissue placed onto D40 culture medium for 3 days,  replication 2

source_name: immature cotyledon explant cultured 3 days on D40 medium

value: 3 d


title: patient10_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 10

value: chronic hepatitis C


title: HIV lymphoma 4-1

description: duplicate analysis of HIV-assocaited lymphoma sample 4

source_name: genomic DNA from HIV-associated lymphoma


title: 14843 - Tamoxifen

source_name: Sorted GFP+ T-ALL from Tamoxifen treated mouse

value: Notch induced T-lymphoblastic leukemia (T-ALL)

value: ZFX null


title: patient9_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 9


title: HIV lymphoma 3-2

description: duplicate analysis of HIV-assocaited lymphoma sample 3

value: male


title: rep2-Day3-Jack

description: transcriptome data from explants of nontransgenic tissue placed onto D40 culture medium for 3 days,  replication 2


title: HIV lymphoma 4-2


title: AND1 SCL 14days EBs Rep 1

city: Granada

first: Pedro

middle: Jose

last: Real

state: Granada

address: Avda. Ilustracion 114

department: Molecular Oncology

country: Spain

institute: GENyO

description: Gene expression 14-day megakaryocytic differentiation Ebs

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65  °C) to Agilent Whole Human Genome Oligo Microarrays 6x60k V2 using Agilent’s recommended hybridization chamber and oven.  After hybridization, microarrays were washed 1 minute at room temperature with Agilent Gene Expression Wash Buffer 1 (Agilent Technologies) and 1 minute with 37 °C Agilent Gene Expression Wash Wash buffer 2 (Agilent Technologies), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner System.

data_processing: The scanned images were analyzed with Feature Extraction Software (FES) (Agilent Technologies). The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyed using the Rossetta Resolver gene expression data analysis system (Rosseta Biosoftware).

source_name: SCL-overexpressing AND1 14-day EBs

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Agilent Low Input Quick Amp Labeling kit (Agilent Technologies). cRNA yields and dye-incorporation were measured with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: hESCs were cultured over Matrigel (BD Bioscience)-coated T25 flasks in human feeder-conditioned medium that was supplemented with basic fibroblast growth factor (bFGF) (Miltenyi Biotec). Media changes were performed daily, and confluent cultures were split weekly using collagenase IV for 2-5 minutes (Invitrogen).

extract_protocol: Undifferentiated AND1 or 14 day-old EBs from AND1 EV and AND1 SCL were pulled down and total RNA was isolated using Trizol following manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer (NanoDrop Technologies) and quality was checked in the Agilent 2100 Bionalyzer platform (Agilent Technologies).

treatment_protocol: Megakaryocytic differentiation conditions were adapted from Lu SJ et al. Briefly, confluent, undifferentiated hESCs in a T-25 flask were treated with collagenase IV and scraped off of the Matrigel attachments. To form embryoid bodies (EBs), hESC clumps were transferred to ultra-low attachment plates (Corning, Lowell) in EB media without cytokines. The next day, the medium was changed to eliminate cell debris, and fresh EB medium supplemented with bone morphogenetic protein 4 (BMP4), vascular endothelial growth factor (VEGF) and bFGF (20 ng/mL) was added. From days 3 to 8, continuous EB medium changes containing BMP4, VEGF, bFGF, stem cell factor (SCF), thrombopoietin (THPO) and Fms-related tyrosine kinase 3 ligand (FLT3L) (were performed. From day 8 to 14, the cytokine cocktail-supplemented EB medium was simplified to THPO and SCF. All cytokines were purchased from PeproTech.

value: human embryonic stem cell


title: HIV lymphoma 3-1


title: rep2-Day0_Jack

description: transcriptome data from explants of nontransgenic tissue, no culture, replication 2

source_name: immature cotyledon explant, no culture

value: 0 d


title: AND1 SCL 14days EBs Rep 2

value: 14-day megakaryocytic differentiation Ebs


title: patient19_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 19

value: control


title: patient7_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 7

value: B1 (before treatment)


title: AND1 SCL undifferentiated hESCs Rep 2

description: Gene expression undifferentiated hESCs

source_name: SCL-overexpressing AND1 undifferentiated cell line

value: undifferentiated hESCs


title: AND1 EV 14days EBs Rep 2

source_name: AND1 EV 14-day EBs


title: rep1_Day3_35SGmAGL15

description: transcriptome data from explants of 35S:GmAGL15 tissue placed onto D40 culture medium for 3 days,  replication 1


title: AND1 EV 14days EBs Rep 1


title: AND1 SCL undifferentiated hESCs Rep 1

description: Gene expression undifferentiated hESCs


title: HIV-lymphoma 2-2

description: duplicate analysis of HIV-assocaited lymphoma sample 2

value: female

value: HIV-associated lymphoma


title: HIV lymphoma 2-1


title: patient8_B1

source_name: pretreatment liver biopsy, chronic hepatitis C, patient 8

value: liver biopsy


title: rep2-Day0_35SGmAGL15

description: transcriptome data from explants of 35S:GmAGL15 tissue, no culture, replication 2

value: immature cotyledon explant


title: rep1-Day7-Jack

description: transcriptome data from explants of nontransgenic tissue placed onto D40 culture medium for 7 days,  replication 1

value: 7 d

value: nontransgenic wild type


title: Low_Liver_13

value: reproductively mature

value: low PFOS (0.5 ug/L)

value: Liver


title: AND1 EV undifferentiated hESCs Rep 2

description: Gene expression undifferentiated hESCs

source_name: AND1 EV undifferentiated cell line


title: rep1-Day7_35SGmAGL15

description: transcriptome data from explants of 35S:GmAGL15 tissue placed onto D40 culture medium for 7 days,  replication 1

value: 6 d

value: overexpression of GmAGL15


title: 60h

city: Los Angeles

first: ANYOU

last: WANG

state: CA

address: Gonda BLDG

department: Human Genetics

institute: UCLA

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized following affy protocol

scan_protocol: GeneChips were scanned in stanford affy central

data_processing: The MAS5.0 data were generated with R.2.10.

source_name: coronary artery endothelial cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Endothelial Cell Basal Medium-2 was used to grow the cells to a confluence of ~80% and ~55%, respectively, for subsequent group 1 (0min, 5min, 25min, and 2H) and group 2 (24H and 60H) infections with C. pneumoniae

extract_protocol: RNA was purified using the RNeasy RNA purification kit (QIAGEN Inc. Valencia, CA).

treatment_protocol: The higher confluence and MOI for group 1 was used to ensure sufficient infection for a short period of C. pneumoniae growth for RNA extraction.  The lower confluence and MOI for group 2 allowed the cells to grow and for C. pneumoniae to infect these cells for the 24H and 60H time points

tag: infection

value: Chlamydophila pneumoniae

tag: time point


title: HIV-lymphoma 1-1

description: duplicate analysis of HIV-assocaited lymphoma sample 1

value: male

tag: disease state


title: rep1-Day3_Jack

description: transcriptome data from explants of nontransgenic tissue placed onto D40 culture medium for 3 days,  replication 1

value: 3 d

tag: tissue


title: 25min


title: AND1 EV undifferentiated hESCs Rep 1

description: Gene expression undifferentiated hESCs

value: human embryonic stem cell

tag: cell type


title: HIV-lymphoma 1-2


title: 24h


title: 2h


title: 24h Infection Replicate 1

status: Public on Jan 29 2014

city: Berlin

first: Carla

last: Winterling

address: Charitéplatz 1

institute: Max Planck Institute for Infection Biology

hyb_protocol: according to the supplier's protocol

scan_protocol: 5-μm resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies) with XDR extended range

data_processing: Raw microarray image data were analyzed with the Image Analysis/Feature Extraction software G2567AA v. A.10.5.1 (Agilent Technologies) using default settings

source_name: Uninfected Cells

label_protocol: RNA labeling was performed with the Low RNA Input Linear Amplification Kit PLUS (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer, and cRNA was subsequently labeled with Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: The A549 human lung epithelial cell line (CCL-185, ATCC-LGC) was grown in DMEM media (Invitrogen) supplemented with 4mM l-glutamine, 4mM sodium pyruvate and 10% fetal calf serum (FCS, Biochrom) at 37°C and 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: A549 cells were washed with PBS and then infected with viruses at MOI 1 in infection buffer (PBS supplemented with 0.2% bovine serum albumin) for 60 min at room temperature. Cells were incubated for the indicated time periods at 37 °C in DMEM supplemented with 0.2% bovine serum albumin, 4 mM l-glutamine and antibiotics.

tag: cell line

value: Human lung epithelial cells

source_name: Cells 24h infected with Influenza


title: rep1-Day0_Jack

description: transcriptome data from explants of nontransgenic tissue, no culture, replication 1

value: 0 d


title: 5min


title: 8h Infection Replicate 2

source_name: Cells 8h infected with Influenza


title: 8h Infection Replicate 1


title: 24h Infection Replicate 2


title: rep1-Day0-35SGmAGL15

description: transcriptome data from explants of 35S:GmAGL15 tissue, no culture, replication 1


title: RA-112 PB after/before  Methotrexate

city: Ibaraki

first: Norihiro

last: Nishimoto

state: Osaka

address: 7-7-20, Saito-Asagi

institute: Wakayama Medical University

hyb_protocol: The labeled aRNAs (mixture of Cy3 and Cy5) was hybridized onto microarray slide for 16 hours at 42ﾟC. Slides were washed in 2xSSC+0.1% SDS, 2xSSC, 1xSSC, and 0.1xSSC before air pressure drying and scanning.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a ScanArray Lite (PerkinElmer, Boston, MA) and signal values were calculated using DNASIS Array (Hitachi Software Engineering, Tokyo, Japan).

data_processing: Log2 ratios of Cy3 to Cy5 were calculated and normalized by the method of global ratio median normalization.

source_name: RA-112 PB after treatment

label_protocol: Total RNA was amplified. 5-(3-amino allyl)-UTP was incorporated to it using Amino Allyl MessageAmp aRNA Kit (Ambion, Austin, Texas). The amino allyl aRNA was further labeled by coupling reaction with NHS ester fluorescent dye, Cy3/Cy5.

extract_protocol: Peripheral blood was collected directly into PAXGene tubes (Qiagen, Valencia, CA). Total RNA was extracted using PAXGene Blood RNA Kit with the optimal on-column DNase digestion according to the manufacturer`s instructions.

tag: age (y)

value: rheumatoid arthritis

value: peripheral blood

tag: treatment

value: after methotrexate/MTX

source_name: RA-112 PB before treatment

value: before methotrexate/MTX


title: RA-111 PB after/before  Methotrexate

source_name: RA-111 PB after treatment

value: female

tag: patient

source_name: RA-111 PB before treatment


title: RA-108 PB after/before  Methotrexate

source_name: RA-108 PB after treatment

source_name: RA-108 PB before treatment


title: RA-108 PB before/after  Methotrexate


title: RA-112 PB before/after  Methotrexate


title: RA-107 PB before/after  Methotrexate

source_name: RA-107 PB before treatment

source_name: RA-107 PB after treatment


title: RA-110 PB before/after  Methotrexate

source_name: RA-110 PB before treatment

source_name: RA-110 PB after treatment


title: RA-111 PB before/after  Methotrexate


title: RA-109 PB after/before  Methotrexate

source_name: RA-109 PB after treatment

source_name: RA-109 PB before treatment


title: RA-104 PB after/before  Methotrexate

source_name: RA-104 PB after treatment

source_name: RA-104 PB before treatment


title: RA-105 PB before/after  Methotrexate

source_name: RA-105 PB before treatment

source_name: RA-105 PB after treatment


title: RA-103 PB after/before  Methotrexate

source_name: RA-103 PB after treatment

source_name: RA-103 PB before treatment


title: RA-110 PB after/before  Methotrexate


title: RA-109 PB before/after  Methotrexate


title: RA-107 PB after/before  Methotrexate


title: RA-105 PB after/before  Methotrexate


title: RA-106 PB before/after  Methotrexate

source_name: RA-106 PB before treatment

source_name: RA-106 PB after treatment


title: RA-104 PB before/after  Methotrexate


title: RA-106 PB after/before  Methotrexate


title: RA-99 PB after/before  Methotrexate

source_name: RA-99 PB after treatment

source_name: RA-99 PB before treatment


title: RA-99 PB before/after  Methotrexate


title: RA-98 PB after/before  Methotrexate

source_name: RA-98 PB after treatment

source_name: RA-98 PB before treatment


title: RA-100 PB after/before  Methotrexate

source_name: RA-100 PB after treatment

source_name: RA-100 PB before treatment


title: RA-100 PB before/after  Methotrexate


title: RA-102 PB before/after  Methotrexate

source_name: RA-102 PB before treatment

source_name: RA-102 PB after treatment


title: RA-102 PB after/before  Methotrexate


title: RA-101 PB after/before  Methotrexate

source_name: RA-101 PB after treatment

source_name: RA-101 PB before treatment


title: RA-103 PB before/after  Methotrexate


title: RA-101 PB before/after  Methotrexate


title: RA-97 PB after/before  Methotrexate

source_name: RA-97 PB after treatment

source_name: RA-97 PB before treatment


title: RA-97 PB before/after  Methotrexate


title: RA-98 PB before/after  Methotrexate


title: RA-96 PB before/after  Methotrexate

source_name: RA-96 PB before treatment

source_name: RA-96 PB after treatment


title: RA-94 PB before/after  Methotrexate

source_name: RA-94 PB before treatment

source_name: RA-94 PB after treatment


title: RA-96 PB after/before  Methotrexate


title: RA-89 PB before/after  Methotrexate

source_name: RA-89 PB before treatment

source_name: RA-89 PB after treatment


title: RA-95 PB before/after  Methotrexate

source_name: RA-95 PB before treatment

source_name: RA-95 PB after treatment


title: RA-94 PB after/before  Methotrexate


title: RA-95 PB after/before  Methotrexate


title: RA-93 PB before/after  Methotrexate

source_name: RA-93 PB before treatment

source_name: RA-93 PB after treatment


title: RA-90 PB before/after  Methotrexate

source_name: RA-90 PB before treatment

source_name: RA-90 PB after treatment


title: RA-89 PB after/before  Methotrexate


title: RA-93 PB after/before  Methotrexate


title: RA-91 PB after/before  Methotrexate

source_name: RA-91 PB after treatment

source_name: RA-91 PB before treatment


title: RA-92 PB before/after  Methotrexate

source_name: RA-92 PB before treatment

source_name: RA-92 PB after treatment


title: RA-90 PB after/before  Methotrexate


title: RA-88 PB after/before  Methotrexate

source_name: RA-88 PB after treatment

source_name: RA-88 PB before treatment


title: RA-87 PB before/after  Methotrexate

source_name: RA-87 PB before treatment

source_name: RA-87 PB after treatment


title: RA-86 PB before/after  Methotrexate

source_name: RA-86 PB before treatment

source_name: RA-86 PB after treatment


title: RA-91 PB before/after  Methotrexate


title: RA-87 PB after/before  Methotrexate


title: RA-92 PB after/before  Methotrexate


title: RA-88 PB before/after  Methotrexate


title: RA-84 PB before/after  Methotrexate

source_name: RA-84 PB before treatment

source_name: RA-84 PB after treatment


title: RA-85 PB before/after  Methotrexate

source_name: RA-85 PB before treatment

source_name: RA-85 PB after treatment


title: RA-83 PB before/after  Methotrexate

source_name: RA-83 PB before treatment

source_name: RA-83 PB after treatment


title: RA-83 PB after/before  Methotrexate


title: RA-84 PB after/before  Methotrexate


title: RA-86 PB after/before  Methotrexate


title: RA-82 PB after/before  Methotrexate

source_name: RA-82 PB after treatment

source_name: RA-82 PB before treatment


title: RA-85 PB after/before  Methotrexate


title: RA-80 PB before/after  Methotrexate

source_name: RA-80 PB before treatment

source_name: RA-80 PB after treatment


title: RA-80 PB after/before  Methotrexate


title: RA-82 PB before/after  Methotrexate


title: RA-81 PB before/after  Methotrexate

source_name: RA-81 PB before treatment

source_name: RA-81 PB after treatment