title: 382546A07_B73_R2_T1

source_name: B73, above ground seedling tissue

value: Stiff-stalk


title: 382546A06_M162W_R2_T1

status: Public on Apr 01 2012

type: RNA

city: Saint Paul

first: Nathan

middle: M

last: Springer

state: MN

address: 1445 Gortner Ave

department: Plant Biology

country: USA

institute: University of Minnesota

hyb_protocol: Per sample, ~20μg of Cy3- or Cy5-labeled RNAs were hybridized for 16-20 hours at 42°C using the NimbleGen Hybridization System.  Post hybridization, slides were washed (NimbleGen Wash Buffer Kit) and dried for two minutes by centrifugation.

scan_protocol: Slides were immediately scanned using the GenePix 4000B Scanner (Molecular Devices, Sunnyvale, CA) according to the array manufacturer protocol.

data_processing: Array images and data were processed using NimbleScan software.  Briefly, images from each slide were separated into 12 subarrays and aligned to a grid to extract signal intensity for each feature on the array.  Experimental integrity was verified by evaluation of the signal intensities of the sample tracking control features for each subarray.  In addition, metrics reports were produced for each array to report the signal uniformity across the array and the intensity of known empty features, random probes and experimental probes.  Signal-to-noise ratios were estimated by dividing the average signal intensity of the experimental gene probes (signal) by the average signal intensity of the random sequence control probes (noise).  Only slides with a signal-to-noise ratio ≤ 2 were retained. NimbleScan was used to generate RMA-normalized (Irizarry et al. 2003) gene expression values from the spatially-corrected probe signal intensities on a per probe and per gene basis.  Normalized gene expression values across multiple replications (technical or biological) of the same genotype were averaged, when possible. Comparisons of the distributions of signal intensity for the random sequence controls to the experimental gene probes on each array (Figure SM2) were used to determine a reasonable signal threshold for positive expression across all slides.  The plots demonstrate that in most cases, the random sequence control log2 signal intensity is ≤ 10 suggesting that signals above that threshold are true signal.  Hence, genes with average probe log2 signals of  >10 in at least three arrays were retained as expressed (N=19,792 expressed genes).  Since genetic polymorphisms could contribute to differences in hybridization between transcripts from some genotypes and probes developed based on the B73 reference sequence we further filtered the probeset based on a previous comparative genomic hybridization dataset developed using many of the same genotypes and the same array platform (Swanson-Wagner et al., 2010).  Any probes that exhibit substantially reduced CGH values for at least three genotypes (26,937 probes) were removed resulting in a set of 46,167 probes that detect expression of 18,242 genes with one to four probes per gene.   This dataset of N=18,242 expressed genes detected by probes without substantial evidence for polymorphisms was used for all analyses.

molecule: total RNA

organism: Zea mays

source_name: M162W, above ground seedling tissue

label_protocol: Purified RNAs (10ug per sample) were reverse transcribed and labeled according to the array manufacturer protocol (NimbleGen Arrays User’s Guide: Gene Expression Analysis v3.2).

growth_protocol: Maize seeds were grown in a greenhouse with 50% field soil and 50% Metromix with a 16hour light and 8 hour dark treatment

extract_protocol: RNAs were isolated using the commercial TRIzol (Invitrogen, Carlsbad, CA; cat# 15596026) from above-ground tissue.  RNAs were purified by Lithium Chloride treatment followed by 3M sodium acetate (0.1 vol) and 95% ethanol (2.5 vol) precipitation.

treatment_protocol: No treatments

tag: pooling type

value: pooled multiple seedlings

tag: genotype

tag: classification


title: 382546A03_Ky21_R2_T1

source_name: Ky21, above ground seedling tissue


title: surgical resection HC5

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Gene expression data from combined hepatocellular-cholangiocarcinoma

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix expression console was used to check the scaned data and RMA on R programm  was used as the normalisation method.

label: biotin

organism: Homo sapiens

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was extracted from clinical and pathologic records from patient in agreement with French laws and ethical guidelines related to the protection of the patient

tag: tissue type

tag: gender

value: male


title: 382544A12_A680_Ind_T1

source_name: A680, above ground seedling tissue

value: single seedling


title: surgical resection HC14


title: 382544A11_I.A. 36-5_Ind_T1

organism: Zea mays subsp. parviglumis

source_name: I.A. 36, above ground seedling tissue

value: IA 36


title: surgical resection HC11


title: surgical resection HC12


title: surgical resection HC13

value: female


title: surgical resection HC10


title: 382546A11_Oh7B_R2_T1

source_name: Oh7B, above ground seedling tissue

value: Non-stiff stalk


title: 382544A06_W22_Ind_T1

source_name: W22, above ground seedling tissue


title: 382544A09_PHG47_Ind_T1

source_name: PHG47, above ground seedling tissue

value: ex-PVP


title: surgical resection HC7


title: 382546A05_TIL1_R2_T1

source_name: TIL 1, above ground seedling tissue

value: TIL 1


title: 382544A07_I.A. 29-3_Ind_T1

source_name: I.A. 29, above ground seedling tissue

value: IA 29


title: 382199A10_B73-3_Ind_T2


title: surgical resection HC4


title: surgical resection C1

description: Gene expression data from primary liver cancer cholangiocarcinoma

source_name: intrahepatic cholangiocarcinoma

value: intrahepatic cholangiocarcinoma


title: surgical resection HC3


title: surgical resection C2


title: 382544A08_I.A. 36-3_Ind_T1


title: surgical resection C3


title: surgical resection H5

description: Gene expression data from primary liver cancer

source_name: hepatocellular carcinoma

value: hepatocellular carcinoma


title: surgical resection H6


title: 382544A04_PHG35_Ind_T1

source_name: PHG35, above ground seedling tissue


title: 382199A03_B73-1_Ind_T1


title: surgical resection HC2


title: surgical resection H2


title: Induced pluripotent cells  [iPS_III6]

city: Stanford

first: Leng

last: Han

state: CA

address: 265 Campus Dr

institute: Stanford University

description: Gene expression data from iPSC

hyb_protocol: Hybridization were followed standard Affymetrix protocol in Affymetrix GeneChip Hybridization Oven 640

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

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

source_name: iPSC for patient III-6

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

growth_protocol: Matrigel coated culture dishes and mTeSR

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

tag: cell type

value: iPS cells

tag: disease state

value: Hypertrophic cardiomyopathy


title: surgical resection H4


title: surgical resection HC1


title: 382199A01_Mo17-1_Ind_T2

source_name: Mo17, above ground seedling tissue


title: 382544A03_I.A. 36-2_Ind_T1


title: 382128A12_CML277_R2_T1

source_name: CML277, above ground seedling tissue

value: Tropical


title: 382544A01_I.A. 31-5_Ind_T1

source_name: I.A. 31, above ground seedling tissue

value: IA 31


title: surgical resection H7


title: surgical resection H3


title: 382199A11_Mo17-4_Ind_T1


title: Induced pluripotent cells  [iPS_III5]

description: Gene expression data from iPSC

source_name: iPSC for patient III-5


title: surgical resection H1


title: Induced pluripotent cells  [iPS_III4]

description: Gene expression data from iPSC

source_name: iPSC for patient III-4


title: 382199A05_Mo17-3_Ind_T1


title: 382199A06_B73-2_Ind_T2

source_name: B73, above ground seedling tissue


title: 382199A04_Mo17-2_Ind_T1


title: 382128A11_NC358_R2_T1

source_name: NC358, above ground seedling tissue


title: Induced pluripotent cells  [iPS_II1]

description: Gene expression data from iPSC

source_name: iPSC for patient II-1


title: Induced pluripotent cells  [iPS_III7]

description: Gene expression data from iPSC

source_name: iPSC for patient III-7


title: 382128A06_CML322_R2_T1

source_name: CML322, above ground seedling tissue


title: Induced pluripotent cells  [iPS_III3]

description: Gene expression data from iPSC

source_name: iPSC for patient III-3


title: human embyonic stem cells

description: Gene expression data from human embyonic stem cells.

source_name: human embyonic stem cells

value: Stem cells

value: Normal


title: 382116A12_PHG84_Ind_T1

source_name: PHG84, above ground seedling tissue


title: 382128A08_Hp301_R2_T1

source_name: Hp301, above ground seedling tissue

value: pooled multiple seedlings

value: mixed


title: 382128A09_TIL17_R2_T1

source_name: TIL 17, above ground seedling tissue

value: TIL 17


title: Induced pluripotent cells  [iPS_III2]

description: Gene expression data from iPSC

source_name: iPSC for patient III-2


title: Induced pluripotent cells  [iPS_II2]

description: Gene expression data from iPSC

source_name: iPSC for patient II-2


title: rho0 cell, technical rep 5

city: Daejeon

first: Seungwoo

last: Hwang

address: 52 Eoeun-dong Yuseong-gu

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

description:
Gene expression data from rho0 cell
rho0-5

hyb_protocol: The prepared targets were hybridized to GeneChip Human Gene 1.0 ST Array (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using Scanner 3000 7G (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions.

data_processing: The CEL files were imported to Affymetrix Expression Console software and normalized by RMA (Robust Multi-chip Average) method and log2 transformed.

source_name: rho0 cell

label_protocol: Targets were prepared by using the GeneChip Whole Transcript Sense Target Labeling Assay (Affymetrix, Santa Clara, CA).

growth_protocol: The rho0 cell was obtained after long-term exposure of osteoscarcoma cell line to ethidium bromide (50ng/ml) and was grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 100 mg/ml 5-bromodeoxyuridine (BrdU), 50 ug/ml uridine, and 10% fetal bovine serum (FBS).

extract_protocol: Isolation of total RNA from cells was performed using Rneasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

treatment_protocol: Cybrid clones from three mtDNA haplogroups were generated as follows. Platelets from twelve persons from three mtDNA haplogroups were separated from whole blood by centrifugation and fusion was carried out by mixing rho0 cells with platelets in a 1:1 ratio and then centrifuging at 1,500g for 15 miniutes. DMEM was removed and the cells were resuspended in 0.8 ml of 50% (v/v) polyethylene glycol (Signam-Aldrich). Sixty seconds after fusion, the cells were resuspended in DMEM and left to recover at 37 degree Celcius for 45 minutes. 24 fours after fusion, the medium was replaced with DMEM lacking uridine to select against unfused cells.

value: rho0 cell

tag: mtdna haplogroup


title: 382128A10_Ki11_R2_T1

source_name: Ki11, above ground seedling tissue


title: 382116A10_I.A. 29-2_Ind_T1

source_name: I.A. 29, above ground seedling tissue

value: single seedling


title: 382199A02_B73-4_Ind_T1

value: Stiff-stalk


title: 382128A03_Oh43_R2_T1

source_name: Oh43, above ground seedling tissue

value: Non-stiff stalk


title: 382116A11_PHZ51_Ind_T1

source_name: PHZ51, above ground seedling tissue

value: ex-PVP


title: Induced pluripotent cells  [iPS_III1]

description: Gene expression data from iPSC

source_name: iPSC for patient III-1


title: rho0 cell, technical rep 6

description:
Gene expression data from rho0 cell
rho0-6


title: rho0 cell, technical rep 1

description:
Gene expression data from rho0 cell
rho0-1


title: rho0 cell, technical rep 3

description:
Gene expression data from rho0 cell
rho0-3


title: Cybrid from haplogroup N9a, biological rep 4, technical rep 4

description:
Gene expression data from cybrid clone N9a-4
N9a-4-4

source_name: Cybrid clone with mtDNA from person 4 in haplogroup N9a

value: Cybrid clone

tag: mtdna from

value: person 4


title: rho0 cell, technical rep 4

description:
Gene expression data from rho0 cell
rho0-4


title: 382128A04_CML52_R2_T1

source_name: CML52, above ground seedling tissue


title: 382116A08_PHJ40_Ind_T1

source_name: PHJ40, above ground seedling tissue


title: Cybrid from haplogroup N9a, biological rep 3, technical rep 4

description:
Gene expression data from cybrid clone N9a-3
N9a-3-4

source_name: Cybrid clone with mtDNA from person 3 in haplogroup N9a

value: person 3


title: 382116A07_I.A. 36-1_Ind_T1

source_name: I.A. 36, above ground seedling tissue

value: IA 36


title: Cybrid from haplogroup N9a, biological rep 4, technical rep 1

description:
Gene expression data from cybrid clone N9a-4
N9a-4-1


title: 382128A02_Tx303_R2_T2

source_name: Tx303, above ground seedling tissue


title: rho0 cell, technical rep 2

description:
Gene expression data from rho0 cell
rho0-2


title: Cybrid from haplogroup N9a, biological rep 4, technical rep 2

description:
Gene expression data from cybrid clone N9a-4
N9a-4-2


title: 382116A02_Wf9_Ind_T1

source_name: Wf9, above ground seedling tissue


title: Cybrid from haplogroup N9a, biological rep 3, technical rep 2

description:
Gene expression data from cybrid clone N9a-3
N9a-3-2


title: 382116A03_I.A. 29-1_Ind_T1

value: IA 29


title: 382110A12_I.A. 31-3_Ind_T2

source_name: I.A. 31, above ground seedling tissue


title: Cybrid from haplogroup N9a, biological rep 3, technical rep 3

description:
Gene expression data from cybrid clone N9a-3
N9a-3-3


title: 382116A01_I.A. 31-1_Ind_T1


title: Cybrid from haplogroup N9a, biological rep 2, technical rep 3

description:
Gene expression data from cybrid clone N9a-2
N9a-2-3

source_name: Cybrid clone with mtDNA from person 2 in haplogroup N9a

value: person 2


title: 382116A05_I205_Ind_T1

source_name: I205, above ground seedling tissue


title: Cybrid from haplogroup N9a, biological rep 3, technical rep 1

description:
Gene expression data from cybrid clone N9a-3
N9a-3-1


title: 382110A11_PHG39_Ind_T1

source_name: PHG39, above ground seedling tissue


title: Cybrid from haplogroup N9a, biological rep 2, technical rep 4

description:
Gene expression data from cybrid clone N9a-2
N9a-2-4


title: 382110A09_I.A. 36-6_Ind_T1


title: Cybrid from haplogroup N9a, biological rep 4, technical rep 3

description:
Gene expression data from cybrid clone N9a-4
N9a-4-3


title: Cybrid from haplogroup N9a, biological rep 2, technical rep 2

description:
Gene expression data from cybrid clone N9a-2
N9a-2-2


title: Cybrid from haplogroup N9a, biological rep 2, technical rep 1

description:
Gene expression data from cybrid clone N9a-2
N9a-2-1


title: 382110A06_I.A. 29-5_Ind_T1


title: Cybrid from haplogroup N9a, biological rep 1, technical rep 2

description:
Gene expression data from cybrid clone N9a-1
N9a-1-2

source_name: Cybrid clone with mtDNA from person 1 in haplogroup N9a

value: person 1


title: Cybrid from haplogroup N9a, biological rep 1, technical rep 1

description:
Gene expression data from cybrid clone N9a-1
N9a-1-1


title: 382110A07_I.A. 29-6_Ind_T1


title: 382110A08_LH1_Ind_T1

source_name: LH1, above ground seedling tissue


title: 382110A10_LH82_Ind_T1

source_name: LH82, above ground seedling tissue


title: 382110A04_I.A. 31-6_Ind_T1

value: IA 31


title: 382110A03_B84_Ind_T1

source_name: B84, above ground seedling tissue


title: Cybrid from haplogroup F, biological rep 5, technical rep 4

description:
Gene expression data from cybrid clone F-5
F-5-4

source_name: Cybrid clone with mtDNA from person 5 in haplogroup F

value: person 5

value: F


title: 382076A12_Tzi8_R1_T1

source_name: Tzi8, above ground seedling tissue

value: pooled multiple seedlings


title: 382110A02_B79_Ind_T1

source_name: B79, above ground seedling tissue


title: Cybrid from haplogroup N9a, biological rep 1, technical rep 4

description:
Gene expression data from cybrid clone N9a-1
N9a-1-4


title: 382076A10_M162W_R1_T1

source_name: M162W, above ground seedling tissue


title: Cybrid from haplogroup N9a, biological rep 1, technical rep 3

description:
Gene expression data from cybrid clone N9a-1
N9a-1-3


title: Cybrid from haplogroup F, biological rep 5, technical rep 1

description:
Gene expression data from cybrid clone F-5
F-5-1


title: Cybrid from haplogroup F, biological rep 4, technical rep 3

description:
Gene expression data from cybrid clone F-4
F-4-3

source_name: Cybrid clone with mtDNA from person 4 in haplogroup F


title: Cybrid from haplogroup F, biological rep 5, technical rep 3

description:
Gene expression data from cybrid clone F-5
F-5-3


title: 382076A09_P39_R1_T1

source_name: P39, above ground seedling tissue

value: mixed


title: Cybrid from haplogroup F, biological rep 4, technical rep 2

description:
Gene expression data from cybrid clone F-4
F-4-2


title: 382076A04_Mo18W_R1_T1

source_name: Mo18W, above ground seedling tissue


title: Cybrid from haplogroup F, biological rep 3, technical rep 4

description:
Gene expression data from cybrid clone F-3
F-3-4

source_name: Cybrid clone with mtDNA from person 3 in haplogroup F


title: 382076A05_TIL11_R1_T1

source_name: TIL11, above ground seedling tissue


title: Cybrid from haplogroup F, biological rep 4, technical rep 1

description:
Gene expression data from cybrid clone F-4
F-4-1


title: Cybrid from haplogroup F, biological rep 5, technical rep 2

description:
Gene expression data from cybrid clone F-5
F-5-2


title: 382076A11_M37W_R1_T1

source_name: M37W, above ground seedling tissue

value: Tropical


title: Cybrid from haplogroup F, biological rep 3, technical rep 2

description:
Gene expression data from cybrid clone F-3
F-3-2


title: Cybrid from haplogroup F, biological rep 3, technical rep 3

description:
Gene expression data from cybrid clone F-3
F-3-3


title: Cybrid from haplogroup F, biological rep 3, technical rep 1

description:
Gene expression data from cybrid clone F-3
F-3-1


title: 382076A03_TIL1_R1_T1

source_name: TIL1, above ground seedling tissue


title: 382076A07_Tx303_R1_T1

source_name: Tx303, above ground seedling tissue


title: 382076A02_B97_R1_T1

source_name: B97, above ground seedling tissue


title: 382076A01_B73_R1_T1

source_name: B73, above ground seedling tissue


title: 382116A09_I.A. 31-4_Ind_T1

source_name: I.A. 31, above ground seedling tissue

value: single seedling


title: 382076A08_Ki3_R1_T1

source_name: Ki3, above ground seedling tissue


title: 382116A04_I.A. 31-2_Ind_T1


title: Cybrid from haplogroup F, biological rep 2, technical rep 3

description:
Gene expression data from cybrid clone F-2
F-2-3

source_name: Cybrid clone with mtDNA from person 2 in haplogroup F


title: 382068A12_B73-2_Ind_T1

value: Stiff-stalk


title: 382068A11_Mo17-1_Ind_T1

source_name: Mo17, above ground seedling tissue

value: Non-stiff stalk


title: Cybrid from haplogroup F, biological rep 2, technical rep 1

description:
Gene expression data from cybrid clone F-2
F-2-1


title: Cybrid from haplogroup F, biological rep 2, technical rep 2

description:
Gene expression data from cybrid clone F-2
F-2-2


title: 382068A09_B73-3_Ind_T1


title: 382068A08_CML333_R1_T1

source_name: CML333, above ground seedling tissue


title: Cybrid from haplogroup F, biological rep 1, technical rep 2

description:
Gene expression data from cybrid clone F-1
F-1-2

source_name: Cybrid clone with mtDNA from person 1 in haplogroup F


title: 382128A05_TIL14_R2_T1

source_name: TIL 14, above ground seedling tissue

value: TIL 14


title: Cybrid from haplogroup F, biological rep 1, technical rep 3

description:
Gene expression data from cybrid clone F-1
F-1-3

value: Cybrid clone


title: Cybrid from haplogroup F, biological rep 1, technical rep 1

description:
Gene expression data from cybrid clone F-1
F-1-1


title: 382068A05_TIL14_R1_T1

source_name: TIL14, above ground seedling tissue


title: 382068A10_B73_R1_T3


title: Cybrid from haplogroup F, biological rep 1, technical rep 4

description:
Gene expression data from cybrid clone F-1
F-1-4


title: 382046A10_Tzi8_R2_T1

source_name: Tzi8, above ground seedling tissue


title: Fibroblast

description: Gene expression data from firboblast

source_name: Human fibroblast

value: Fibroblast cells

value: Normal


title: 382068A06_Mo17_R1_T1


title: 382046A09_TIL11_R2_T1

source_name: TIL 11, above ground seedling tissue

value: TIL 11


title: Cybrid from haplogroup D5, biological rep 3, technical rep 2

description:
Gene expression data from cybrid clone D5-3
D5-3-2

source_name: Cybrid clone with mtDNA from person 3 in haplogroup D5

value: person 3


title: Cybrid from haplogroup D5, biological rep 2, technical rep 3

description:
Gene expression data from cybrid clone D5-2
D5-2-3

source_name: Cybrid clone with mtDNA from person 2 in haplogroup D5

value: person 2


title: Cybrid from haplogroup D5, biological rep 3, technical rep 1

description:
Gene expression data from cybrid clone D5-3
D5-3-1


title: 382068A03_CML277_R1_T1

source_name: CML277, above ground seedling tissue


title: 382046A07_TIL15_R2_T1

source_name: TIL 15, above ground seedling tissue

value: TIL 15


title: Cybrid from haplogroup D5, biological rep 3, technical rep 4

description:
Gene expression data from cybrid clone D5-3
D5-3-4


title: Cybrid from haplogroup D5, biological rep 3, technical rep 3

description:
Gene expression data from cybrid clone D5-3
D5-3-3


title: 382068A02_CML247_R1_T1

source_name: CML247, above ground seedling tissue


title: Cybrid from haplogroup D5, biological rep 2, technical rep 1

description:
Gene expression data from cybrid clone D5-2
D5-2-1


title: Cybrid from haplogroup D5, biological rep 2, technical rep 4

description:
Gene expression data from cybrid clone D5-2
D5-2-4


title: Cybrid from haplogroup D5, biological rep 2, technical rep 2

description:
Gene expression data from cybrid clone D5-2
D5-2-2


title: 382068A01_CML103_R1_T1

source_name: CML103, above ground seedling tissue


title: 382046A04_TIL6_R2_T1

source_name: TIL 6, above ground seedling tissue

value: TIL 6


title: 382046A06_Mo18W_R2_T1

source_name: Mo18W, above ground seedling tissue


title: Cybrid from haplogroup D5, biological rep 1, technical rep 3

description:
Gene expression data from cybrid clone D5-1
D5-1-3

source_name: Cybrid clone with mtDNA from person 1 in haplogroup D5

value: person 1


title: 382046A03_CML103_R2_T1


title: Cybrid from haplogroup D5, biological rep 1, technical rep 4

description:
Gene expression data from cybrid clone D5-1
D5-1-4


title: 382046A05_TIL9_R2_T1

source_name: TIL 9, above ground seedling tissue

value: TIL 9


title: Cybrid from haplogroup D5, biological rep 1, technical rep 1

description:
Gene expression data from cybrid clone D5-1
D5-1-1


title: 382040A11_Ki11_R1_T1

source_name: Ki11, above ground seedling tissue

value: pooled multiple seedlings


title: Cybrid from haplogroup D5, biological rep 1, technical rep 2

description:
Gene expression data from cybrid clone D5-1
D5-1-2


title: 382040A10_TIL17_R1_T1

source_name: TIL17, above ground seedling tissue


title: 382040A08_NC358_R1_T1

source_name: NC358, above ground seedling tissue


title: 382046A02_CML247_R2_T1


title: 382110A01_I.A. 29-4_Ind_T1

source_name: I.A. 29, above ground seedling tissue

value: IA 29


title: 382040A09_TIL9_R1_T1

source_name: TIL9, above ground seedling tissue


title: 382040A05_CML322_R1_T1

source_name: CML322, above ground seedling tissue


title: 382040A04_TIL15_R1_T1

source_name: TIL15, above ground seedling tissue


title: Cybrid from haplogroup F, biological rep 4, technical rep 4

description:
Gene expression data from cybrid clone F-4
F-4-4

source_name: Cybrid clone with mtDNA from person 4 in haplogroup F

value: person 4

value: F


title: 382040A03_CML228_R1_T1

source_name: CML228, above ground seedling tissue


title: 382040A07_CML52_R1_T1

source_name: CML52, above ground seedling tissue


title: Cybrid from haplogroup F, biological rep 2, technical rep 4

description:
Gene expression data from cybrid clone F-2
F-2-4

source_name: Cybrid clone with mtDNA from person 2 in haplogroup F


title: PAO66711 (delta cbrB) strain_B [LB]

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

hyb_protocol: Affymetrix P. aeruginosa GeneChip arrays were hybridized with 11 microgramme of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues and each time points separately.

organism: Pseudomonas aeruginosa

source_name: Bacterial RNA

label_protocol: The synthesis of cRNA was performed using the GeneChip® One-Cycle cDNA Synthesis according to the manufacturer' protocol (Affymetrix, Santa Clara, CA, USA). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (www.affymetrix.com).

growth_protocol: PAO1 wild type strain and PAO6673 (delta crc), PAO66711 (delta cbrB), PAO6679 (delta crcZ) strains were grown in LB medium to an OD600 of 1.6 Total RNA treated with RNA protect bacteria reagent® (Qiagen) was purified.

extract_protocol: RNA purification was performed by the hot phenol method as described (Leoni et al, 1996). Briefly, the cell pellets of 10 ml culture were mixed with pre-heated (65°C) 2.5 ml lysis buffer (2% sodium dodecyl sulfate, 30 mM Na-acetate and 3 mM EDTA, pH 5.5) and 5 ml phenol (pH 5.5). The mixture was vigorously shaken for 8 min and incubated for 5 min on ice and then centrifuged at 4°C for 15 min at 5000 rpm. Total RNA was obtained by phenol chloroform extraction and precipitated with ethanol and Na-acetate (pH 5.5). To eliminate DNA contamination the total RNA was treated with 40 U of DNAse I (Roche) followed by phenol-chloroform extraction and ethanol precipitation. The quality of the RNA was determined on MOPS-formaldehyde agarose-gels (Sambrook and Russel, 2001).

tag: strain

tag: genotype/variation

value: delta cbrB

tag: medium

value: LB


title: 382046A08_B97_R2_T1

source_name: B97, above ground seedling tissue


title: PAO66711 (delta cbrB) strain_A [LB]


title: PAO6679 (delta crcZ) strain_A [LB]

value: delta crcZ


title: PAO6679 (delta crcZ) strain_B [LB]


title: PAO6673 (delta crc) strain_B [LB]

value: delta crc


title: PAO1 wild type strain_B [LB]

organism: Pseudomonas aeruginosa PAO1

value: wild type


title: PAO6673 (delta crc) strain_A [LB]


title: PAO1 wild type strain_A [LB]


title: Tumor 1841

type: genomic

city: New York

first: Luc

middle: GT

last: Morris

state: NY

address: 1275 York Avenue

institute: Memorial Sloan-Kettering Cancer Center

hyb_protocol: Labelled DNA-Cy5 hybridized together with matching labelled-Cy3 reference for 40 hrs at 65C on SurePrint G3 Human CGH Microarray Kit, 1x1M Array.

scan_protocol: Agilent Chips were washed and Scanned according to the standard Agilent protocol using the High Resolution Agilent Scanner.

data_processing: Feature Extraction Software v10.9.3 (Agilent)

molecule: genomic DNA

source_name: tumor

label_protocol: Genomic DNA were fragmented and labelled Cy5 and Cy3 according to the standard Agilent protocol from 1-3ug total DNA.

extract_protocol: DNA was extracted using the Qiagen blood and tissue kit

treatment_protocol: Tumors were collected at the time of surgical resection and snap frozen in liquid nitrogen. Tumor and normal tissue were histologically confirmed. Frozen slides were microdissected to enrich tumor content to >70%.

tag: tissue

value: oral cavity squamous cell carcinoma

source_name: Human genomic DNA

tag: reference

value: Human Genomic DNA (Roche catalog. 11691112001)


title: Tumor 1637


title: PAO6679 (delta crcZ) strain_B [BSM]

growth_protocol: PAO1 wild type strain and PAO6673 (delta crc), PAO66711 (delta cbrB), PAO6679 (delta crcZ) strains were grown in BSM medium amended with 40mM succinate to an OD600 of 1.6 Total RNA treated with RNA protect bacteria reagent® (Qiagen) was purified.

value: BSM medium amended with 40mM succinate


title: Tumor 583


title: Tumor 1690


title: PAO6679 (delta crcZ) strain_A [BSM]


title: Tumor 1825


title: Tumor 1775


title: PAO66711 (delta cbrB) strain_B [BSM]


title: PB_7067

city: salamanca

first: Maria

middle: Eugenia

last: Sarasquete

state: salamanca

address: Paseo San Vicente 58-182

department: Hematology

country: Spain

institute: Hospital Universitario de Salamanca

description: Hybridized to Affymetrix 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000 7G and AGCC

data_processing: The complete dataset was analyzed by visual inspection using the Genotyping Console 4.0 (Affymetrix) and Chromosome Analysis Suite (ChAS) software (Affymetrix).

source_name: Peripheral blood patient

label_protocol: According to manufacturer’s instructions

extract_protocol: DNA from purified bone marrow plasma cells was extracted using commercially available kits (Allprep kit,Qiagen, Valencia, CA)

value: Peripheral blood


title: PAO66711 (delta cbrB) strain_A [BSM]


title: Tumor 1798


title: PAO6673 (delta crc) strain_A [BSM]


title: Tumor 886


title: PAO6673 (delta crc) strain_B [BSM]


title: PB_1485

description: Hybridized to Affymetrix 6.0


title: Tumor 408


title: Tumor 600


title: Tumor 1157


title: PB_3713

description: Hybridized to Affymetrix 6.0


title: Tumor 350


title: PAO1 wild type strain_A [BSM]


title: PB_1343

description: Hybridized to Affymetrix 6.0


title: MM_1148

description: Hybridized to Affymetrix 6.0

source_name: Bone Marrow MM patient

value: Bone Marrow MM


title: PAO1 wild type strain_B [BSM]


title: Tumor 399


title: PB_6842

description: Hybridized to Affymetrix 6.0


title: PB_6412

description: Hybridized to Affymetrix 6.0


title: NRP2

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: The data were analyzed with Partek GS 6.4 software (St. Louis, MO) using GCRMA normalization algorithm

source_name: PC3 prostate cancer cells

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

growth_protocol: cells were cultured at 37οC in RPMI 1640 with L-glutamine (Invitrogen, Carlsbad, California) media with 10% fetal bovine serum (Invitrogen) and supplemented with penicillin/streptomycin (Invitrogen).

extract_protocol: Qiagen RNA extraction kit used according to the manufacturer's protocol

treatment_protocol: Cells were transfected with SmartPool cocktail siRNA for NRP-2 (Santa Cruz Biotechnology), VEGF-C, LAMP-2, (Dharmacon RNA Technologies, Chicago, IL), using DharmaFECT 1-4 (Dharmacon RNA Technologies). siRNA transfection was allowed to proceed 72 h before collection of whole-cell extract or total RNA.

tag: cell line

value: transfected with siRNA for NRP-2


title: PB_4305

description: Hybridized to Affymetrix 6.0


title: NRP1


title: Tumor 290


title: PB_3955

description: Hybridized to Affymetrix 6.0


title: VC1

value: transfected with siRNA for VEGF-C


title: PB_391

description: Hybridized to Affymetrix 6.0


title: SCR1

value: treated with scrambled siRNA.


title: SCR2


title: VC2


title: Tumor 288


title: MM1S, CGS-21680 and low dose dexamethasone treated, biological rep2

city: Cambridge

first: Winnie

middle: F

last: Tam

state: MA

address: 245 First Street

department: Oncology

institute: Zalicus, Inc

description:
MM1S cells treated with 12.5nM CGS-21680 and 25nM dexamethasone for 6 hours
Greenstein S et al., Exp Hematol 31:271

hyb_protocol: The fragmented cRNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a mircroarray chip overnight at 45oC.  The chips are transferred to a fluidics intrument that performs washes to remove cRNA that has not hybridized to its complementary oligonucleotide probe.  The bound cRNA is then fluorescently labeled using phycoerythrin-conjugated stretavidin (SAPE); additonal fluors are then added using biotinlyated anti-streptavidin antibody and additional SAPE. The fluidics station used is GeneChip Fluidics Station 450

scan_protocol: The scanner used is Affymetrix GeneChip Scanner 3000, 7G

data_processing: The data were analyzed with Gene Pattern module ExpressionFileCreater using GCRMA method, quantile normalization, background correction and median scaling.

label_protocol: RNA is converted into cDNA using a T7 promoter-tailed oligo-dT primer in the synthesis of the first cDNA strand; second strand cDNA synthesis is then carried out.  The double-stranded cDNA is used as the template in an in vitro transcription (IVT) reaction catalyzed by T7 polymerase and containign biotinylated CTP ad UTP in addition to the four unmodified ribonucleoside triphosphates.

growth_protocol: MM1S cells were maintained in RPMI-1640 +10% Fetal bovine serum at 37oC, 5% CO2 incubator

extract_protocol: Total RNA was extracted with Qiagen miniprep kit according to the manufacturer's instruction.

treatment_protocol: MM1S cells were treated with the compounds as indicated for 6 hours prior to the RNA isolation

value: Multiple myeloma cell line


title: MM1S, salmeterol and low dose dexamethasone treated, biological rep2

description:
MM1S cells treated with 1nM salmeterol and 25nM dexamethasone for 6 hours
Greenstein S et al., Exp Hematol 31:271


title: MM1S, CGS-21680 treated, biological rep2

description:
MM1S cells treated with 12.5nM CGS-21680 for 6 hours
Greenstein S et al., Exp Hematol 31:271


title: PB_2162

description: Hybridized to Affymetrix 6.0


title: MM_1137

description: Hybridized to Affymetrix 6.0


title: Tumor 230


title: MM1S, low dose dexomethasone treated, biological rep2

description:
MM1S cells treated with25nM dexamethasone for 6 hours
Greenstein S et al., Exp Hematol 31:271


title: MM1S, high dose dexomethasone treated, biological rep2

description:
MM1S cells treated with 2µM dexamethasone for 6 hours
Greenstein S et al., Exp Hematol 31:271


title: MM_1142

description: Hybridized to Affymetrix 6.0


title: MM1S, salmeterol treated, biological rep2

description:
MM1S cells treated with 1nM Salmeterol for 6 hours
Greenstein S et al., Exp Hematol 31:271


title: MM1S, untreated, biological rep2

description:
untreated MM1S
Greenstein S et al., Exp Hematol 31:271

source_name: untreated MM1S


title: MM1S, CGS-21680 and low dose dexamethasone treated, biological rep1

source_name: MM1S cells treated with 12.5nM CGS-21680 and 25nM dexamethasone for 6 hours


title: Tumor 335


title: MM1S, salmeterol and low dose dexamethasone treated, biological rep1

source_name: MM1S cells treated with 1nM salmeterol and 25nM dexamethasone for 6 hours


title: MM_1134

description: Hybridized to Affymetrix 6.0


title: Tumor 92


title: MM_1117

description: Hybridized to Affymetrix 6.0


title: MM1S, high dose dexomethasone treated, biological rep1

source_name: MM1S cells treated with 2µM dexamethasone for 6 hours


title: MM1S, low dose dexomethasone treated, biological rep1

source_name: MM1S cells treated with25nM dexamethasone for 6 hours


title: MM_1111

description: Hybridized to Affymetrix 6.0


title: MM1S, salmeterol treated, biological rep1

source_name: MM1S cells treated with 1nM Salmeterol for 6 hours


title: Preterm labour control villous tree_JK1

city: Toronto

first: Brian

middle: Joseph

last: Cox

state: Ontario

address: 1 King's College Circle, Rm 3360

department: Physiology

country: Canada

institute: University of Toronto

description: gene expression data

hyb_protocol: as per Affymetrics protocols

scan_protocol: as per Affymetrics protocols

data_processing: processed in Expression console using the PLIER method to normalize samples and generate intensity values

source_name: Preterm labour control villous tree

label_protocol: as per Affymetrics protocols

growth_protocol: “Normal term” placentas were collected following an uncomplicated delivery of an appropriately grown infant at greater than 37 weeks gestational age (n=3). “Normal preterm” placentas were collected from appropriately grown preterm pregnancies being delivered for obstetrical indications between 24 and 34 weeks gestational age, excluding chorioamnionitis (n=3). “Severe IUGR” preterm placentas were collected from patients with birth weight <10th percentile with absent/reversed end-diastolic flow velocities (A/REDFV) in the umbilical artery Doppler and  delivery for obstetrical indications between 24 -34 weeks gestational age (n=6). Placental biopsies were sampled from fresh placenta, immediately following delivery. Biopsies were taken from the distal maternal side of the placenta, and included approximately two-thirds of the placental depth (Figure 1 A). This technique was used to preferentially sample the terminal villi / microvasculature, rather than the larger vessels closer to the proximal (fetal) surface of the placenta. The placental samples chosen were clear of obvious infarction or calcification.

extract_protocol: RNA was extracted immediately from either the term placenta or the isolated PlMEC using Trizol according to the manufacturer’s instructions (Invitrogen). The RNA was further purified and concentrated before microarray using a mini-elute RNA extraction kit (Qiagen, Missisauga, ON, Canada), designed to remove genomic DNA effectively.

treatment_protocol: The placental biopsies (totaling 50 g) were then processed immediately for endothelial cell isolation and subsequent RNA extraction. The placental biopsies were washed with HBSS without Calcium and Magnesium (-/-) to remove excess blood and minced using sterile scalpel blades. The minced tissue was washed again with HBSS-/- and collected for digestion in 0.25%Trypsin, 20g.ml DNase 1, 250mM Hepes, 0.5M MgSO4 (Sigma, St Louis, MO, USA) in HBSS-/- for 30m at 37ºC tissue (Figure 1B). Tissue was collected using a 200m filter and the remaining tissue subjected to a second trypsin digestion to remove the trophoblast (37ºC for 20 minutes). After the second trypsin digestion, finely branched microvessels are visible (Figure 1C). The tissue was collected using a 200m filter and then further digested with 1mg/ml Collagenase II, 0.1mg/ml DNase1, 2mM L-Glutamine, (Sigma) 0.1% Normocin (Cedarlane, Burlington, Ontario, CA) in RPMI (Invitrogen, Burlington, Ontario, CA) at 37 ºC for 30 minutes, separating the microvessels into a single cell suspension. Blood cells were removed from the suspension by gradient separation with Ficoll (GE Healthcare, Mississauga, ON, CA). Cell viability was confirmed using Trypan blue exclusion. Tocosylated magnetic Dynabeads (Invitrogen) labeled with Human Endothelial Antigen (HEA) lectin (Sigma), were prepared as described in [20] and incubated with the cell suspension for 20min at 4ºC to positively select for intact endothelial cells. Selected cells were collected by applying the solution to a magnet and washed 5 times in HBSS-/-, 2% FBS.

tag: pathology

value: PTL


title: MM1S, untreated, biological rep1


title: MM1S, CGS-21680  treated, biological rep1

source_name: MM1S cells treated with 12.5nM CGS-21680 for 6 hours


title: Tumor 1805


title: MM_1105

description: Hybridized to Affymetrix 6.0


title: Tumor 70


title: Tumor 38


title: Preterm labour control endothelial cells_S09

description: gene expression data

tag: collection date

tag: maternal age (yrs)

tag: gravidity

tag: parity

tag: indication for delivery

value: IOL for other fetal indications:Yes

tag: chronic htn (diagnosed <20 weeks or pre-pregnancy)

value: No

tag: other medical issues

value: GDM on insulin, smoking, fetal anomalies (cardiac and renal)

tag: new or superimposed preeclampsia

tag: max sbp

tag: max dbp

tag: proteinuria (max values)

tag: thrombocytes (x10^9/l) (range)

tag: alt (u/l) (range)

tag: creatinine (um) (range)

tag: smoker

value: Yes; chronic smoker throughout pregnancy (>1/2 pack/day) and marijuana use (1-5x/day) through first trimester

tag: pre-pregnancy bmi

tag: afi (cm) (closest to delivery)

value: Normal (@ 31w)

tag: umbilical art dopper (closest to delivery)

value: No data

tag: other dopplers (closest to delivery)

tag: bpp (closest to delivery)

tag: nst (closest to delivery)

value: FHR stable (Dec 11'06)

tag: c-section (y/n)

tag: gestational age at delivery

tag: birthweight (g)

tag: birthweight percentile

value: 10th to 50th

tag: placental weight (g) fresh (before biopsies)

tag: placental weight (g) in path

tag: path placental weight percentile

value: Male

tag: apgars

tag: distal villous hypoplasia

value: Yes (foci)

tag: other

value: Wt < 10th, undercoiled cord, partial circumarginate insertion of membranes


title: Tumor 1764

tag: tissue

value: oral cavity squamous cell carcinoma

tag: reference

value: Human Genomic DNA (Roche catalog. 11691112001)


title: Tumor 1736


title: MM_1104

description: Hybridized to Affymetrix 6.0

tag: cell type

value: Bone Marrow MM


title: Preterm labour control endothelial cells_S07

description: gene expression data

tag: pathology

tag: collection date

tag: maternal age (yrs)

tag: gravidity

tag: parity

tag: indication for delivery

value: Sontaneous Preterm Labour:Yes

tag: chronic htn (diagnosed <20 weeks or pre-pregnancy)

tag: other medical issues

value: Endometriosus (stage I, diagnosed at 21 years of age)

tag: new or superimposed preeclampsia

tag: max sbp

tag: max dbp

tag: proteinuria (max values)

tag: thrombocytes (x10^9/l) (range)

tag: alt (u/l) (range)

tag: creatinine (um) (range)

tag: smoker

tag: pre-pregnancy bmi

tag: afi (cm) (closest to delivery)

tag: umbilical art dopper (closest to delivery)

value: 50th to 90th

tag: gender

value: Yes

value: Overcoiled cord, focal villous hypoplasia


title: IUGR endothelial cells_S06

description: gene expression data

source_name: IUGR endothelial cells

tag: pathology

value: IUGR

tag: collection date

tag: maternal age (yrs)

tag: gravidity

value: Severe Preeclampsia:Yes

value: Non-reasuring fetal testing:Yes

value: Elevated triglycerides, hyperprolactinemia and GBS bacteriuria

value: Superimposed

value: No

value: AEDV (and intermittent REDV on one side)

tag: other dopplers (closest to delivery)

value: Deep A wave (ductus venosus) and cerebral redistribution noted

tag: bpp (closest to delivery)

tag: nst (closest to delivery)

value: (NRFHR)*

tag: c-section (y/n)

tag: gestational age at delivery

tag: birthweight (g)

tag: birthweight percentile

value: 5th to 10th

tag: placental weight (g) fresh (before biopsies)

tag: placental weight (g) in path

tag: path placental weight percentile

tag: apgars

tag: advanced villous maturity

tag: decidual vasculopathy

tag: other

value: Laminar necrosis of decidua parietalis


title: Tumor 39

tag: tissue

value: oral cavity squamous cell carcinoma

tag: reference

value: Human Genomic DNA (Roche catalog. 11691112001)


title: MM_1100

description: Hybridized to Affymetrix 6.0

tag: cell type

value: Bone Marrow MM


title: IUGR endothelial cells_S08

description: gene expression data

tag: pathology

tag: collection date

tag: maternal age (yrs)

tag: gravidity

tag: parity

tag: indication for delivery

tag: chronic htn (diagnosed <20 weeks or pre-pregnancy)

tag: new or superimposed preeclampsia

tag: max sbp

tag: max dbp

tag: proteinuria (max values)

tag: thrombocytes (x10^9/l) (range)

tag: alt (u/l) (range)

tag: creatinine (um) (range)

tag: smoker

tag: pre-pregnancy bmi

tag: afi (cm) (closest to delivery)

tag: umbilical art dopper (closest to delivery)

value: REDF

tag: other dopplers (closest to delivery)

value: MCA PI 1.44-1.69, MCA PSV 55.3-62.6, fetal redistribution noted

value: NRFHR (repeated decels noted)

value: 10th to 50th

value: 10th to 25th

tag: gender

value: Male

tag: distal villous hypoplasia


title: IUGR endothelial cells_S04

description: gene expression data

tag: pathology

value: IUGR

tag: collection date

tag: maternal age (yrs)

tag: gravidity

tag: parity

value: Non-reasuring fetal testing:Yes

value: Yes

tag: other medical issues

value: Hearing impaired, and polydipsia

value: No proteinuria

value: Trace only

value: REDF (intermittent)

value: Deep A wave (ductus venosus), redistributed MCA

tag: bpp (closest to delivery)

tag: nst (closest to delivery)

value: NRFHR

tag: c-section (y/n)

tag: gestational age at delivery

tag: birthweight (g)

tag: birthweight percentile

tag: placental weight (g) fresh (before biopsies)

tag: placental weight (g) in path

tag: path placental weight percentile

value: Female

tag: apgars

tag: other

value: Multifocal infarction


title: MM_1093

description: Hybridized to Affymetrix 6.0

tag: cell type

value: Bone Marrow MM


title: IUGR endothelial cells_S03

description: gene expression data

tag: pathology

tag: collection date

tag: indication for delivery

value: Severe Preeclampsia:Yes

tag: chronic htn (diagnosed <20 weeks or pre-pregnancy)

value: No

tag: new or superimposed preeclampsia

value: New

tag: max sbp

tag: max dbp

tag: proteinuria (max values)

tag: thrombocytes (x10^9/l) (range)

tag: alt (u/l) (range)

tag: creatinine (um) (range)

tag: smoker

tag: pre-pregnancy bmi

tag: afi (cm) (closest to delivery)

tag: umbilical art dopper (closest to delivery)

tag: other dopplers (closest to delivery)

value: Normal uterine artery and ductus venosus Dopplers. MCA PI range 1.1-1.8

value: (NRFHR)*

value: 3rd to 5th

tag: gender

tag: distal villous hypoplasia

tag: fetal thrombotic vasculopathy

value: Circummarginate insertion of membranes, velamentous insertion of the umbilical cord


title: larva workers of Solenopsis richteri from colony 17.1, sample no. H

city: San Michele all'Adige

first: Lino

last: Ometto

state: Trento

address: Via Mach 1

department: Department of Biodiversity and Molecular Ecology

country: Italy

institute: Fondazione Edmund Mach

hyb_protocol: The combined Cy3- and Cy5-labeled probes were purified using the Qiaquick PCR Purification Kit (QIAGEN) and eluted in 82ul of elution buffer. We finally added 16.5ul of 20x standard saline citrate (SSC), 3.0ul of yeast transfer RNA (10 lg/ll), 1.8ul of polyA cDNA (2ug/ul; Sigma), and 1.8ul of 10% sodium dodecyl sulfate (SDS), then denatured this reaction mix at 95 °C for 45 s and hybridized to the microarray slides at 64 °C overnight (18–22 h). Excess probe was removed by washing the slides at room temperature twice for 5 min in a 2x SSC/0.1% SDS solution, twice for 1 min in a 0.2x SSC solution, 1 min in a 0.1x SSC solution, and twice for 5 min in a 0.1x SSC/0.1% Triton solution.

scan_protocol: slides were scanned using an Agilent Technologies Scanner

data_processing: signal intensities for each spot were extracted (low-quality spots were flagged and removed prior to analyses) using GenePix software. We used the software package limma to perform adaptive background correction, within-array print-tip loess normalization and between-array normalization of the intensities

organism: Solenopsis invicta

source_name: Solenopsis invicta common reference

label_protocol: Total RNA was amplified (Ambion MessageAmp II kit) and then an ~6ug aliquot of this amplified RNA was mixed with 2ul of random 9mers (2ug/ul), 0.5ul of Alien mRNA Spike mix (Stratagene), and water for a final volume of 17.9ul. The mix was incubated for 10 min at 70 °C, then held for 5 min on ice. Reverse transcription was performed for 2 h at 50 °C after adding 6ul of 5 first-strand buffer, 3ul of 0.1 M dithiothreitol, 0.6ul of 50X aminoallyl-deoxynucleotide triphosphate mix (25 mM deoxyadenosine triphosphate, 25 mM deoxycytidine triphosphate, 25 mM deoxyguanosine triphosphate, 15 mM deoxythymidine triphosphate, and 10 mM aminoallyl-deoxyuridine triphosphate), 0.5ul of RNAse inhibitor (15 U/ll, Invitrogen), and 2ul of SuperScript III reverse transcriptase (200 U/ml, Invitrogen). The residual RNA was hydrolyzed by adding 15ul of 0.1 M NaOH and incubating for 10 min at 70 °C. Subsequently, the pH was returned to neutrality by the addition of 15ul of 0.1 M HCl. The purification of the aminoallyl-labeled cDNA and the coupling to Cy3 or Cy5 dyes (GE Healthcare, Little Chalfont, UK) were done using a modified Qiaquick PCR Purification Kit (QIAGEN) protocol.

growth_protocol: All colonies were collected in the field between 2005 and 2007 and later returned to the laboratory and maintained in a rearing room under standard conditions (see Jouvenaz et al. 1977, The Florida Entomologist 60:275-279).

extract_protocol: ach pooled sample was promptly snap-frozen in liquid nitrogen in tubes containing 1 g of 1.4-mm ceramic beads (Quackenbush) and then homogenized in Trizol (Invitrogen) using a Retsch bead shaker. Both RNA and DNA were extracted according to the manufacturer’s protocol.

tag: caste

value: Mix of workers, queens and males

tag: developmental stage

value: Mix of adults, pupae and larvae

organism: Solenopsis richteri

source_name: larva workers of Solenopsis richteri

value: workers

value: larva


title: Tumor 1450

tag: tissue

value: oral cavity squamous cell carcinoma

tag: reference

value: Human Genomic DNA (Roche catalog. 11691112001)


title: larva workers of Solenopsis richteri from colony 6.2, sample no. H


title: Tumor 1626


title: larva workers of Solenopsis richteri from colony 15.1, sample no. H


title: MM_1094

description: Hybridized to Affymetrix 6.0

tag: cell type


title: IUGR endothelial cells_S05

description: gene expression data

tag: pathology

value: IUGR

tag: collection date

tag: maternal age (yrs)

tag: gravidity

tag: parity

tag: indication for delivery

value: Non-reasuring fetal testing:Yes

tag: chronic htn (diagnosed <20 weeks or pre-pregnancy)

value: Yes

tag: other medical issues

value: Increased cholesterol

tag: new or superimposed preeclampsia

value: Superimposed

tag: max sbp

tag: max dbp

tag: proteinuria (max values)

value: AEDF

value: Bilateral abnormal uterine artery Dopplers, and fetal cerebral redistribution noted (abnormal MCA). Normal DV.

tag: bpp (closest to delivery)

tag: nst (closest to delivery)

value: Non-reactive results on Nov 2,3 2006

tag: c-section (y/n)

tag: gestational age at delivery

tag: birthweight (g)

tag: birthweight percentile

tag: placental weight (g) fresh (before biopsies)

tag: placental weight (g) in path

tag: path placental weight percentile

value: Male

tag: apgars

value: Yes (focal)

tag: advanced villous maturity

tag: decidual vasculopathy

tag: other

value: Multifocal infarction, chronic deciduitis


title: Tumor 1517

tag: tissue

tag: reference


title: IUGR endothelial cells_S02

description: gene expression data

tag: pathology

tag: collection date

tag: maternal age (yrs)

tag: gravidity

tag: parity

tag: indication for delivery

value: Severe Preeclampsia:Mild-moderate

tag: chronic htn (diagnosed <20 weeks or pre-pregnancy)

value: No

tag: new or superimposed preeclampsia

value: New

tag: max sbp

tag: max dbp

tag: thrombocytes (x10^9/l) (range)

tag: alt (u/l) (range)

tag: creatinine (um) (range)

tag: smoker

tag: pre-pregnancy bmi

tag: afi (cm) (closest to delivery)

value: Normal (@ 28w)

tag: umbilical art dopper (closest to delivery)

value: REDF

tag: other dopplers (closest to delivery)

value: Bilateral abnormal uterine artery Dopplers, and fetal cerebral redistribtion  noted (abnormal MCA)

value: (NRFHR)*

value: No data

tag: gender

tag: excess perivillous fibrin desposition

value: Yes (5% of parenchyma)

tag: distal villous hypoplasia

value: Laminar necrosis of decidua parietalis


title: Preterm labour control endothelial cells_S01

description: gene expression data

tag: pathology

value: PTL

tag: collection date

tag: maternal age (yrs)

tag: gravidity

tag: parity

value: Sontaneous Preterm Labour:Yes

tag: other medical issues

value: Random glucose measurement on Oct 20 2006 was 16.5 mM

tag: proteinuria (max values)

tag: bpp (closest to delivery)

tag: nst (closest to delivery)

tag: c-section (y/n)

tag: gestational age at delivery

tag: birthweight (g)

tag: birthweight percentile

tag: placental weight (g) fresh (before biopsies)

tag: placental weight (g) in path

tag: path placental weight percentile

value: 10 to 25th

tag: apgars

tag: other

value: Laminar necrosis of decidua capsilaris, foci of intravillous hemorrhage


title: MM_1070

description: Hybridized to Affymetrix 6.0

tag: cell type

value: Bone Marrow MM


title: larva workers of Solenopsis richteri from colony 11.1, sample no. H

tag: caste

value: Mix of workers, queens and males

tag: developmental stage

value: Mix of adults, pupae and larvae

value: workers

value: larva


title: larva workers of Solenopsis richteri from colony 33.2, sample no. E


title: MM_1089

description: Hybridized to Affymetrix 6.0


title: MM_1069

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta from colony 31.1, sample no. H

source_name: larva workers of Solenopsis invicta


title: larva workers of Solenopsis richteri from colony 30.2, sample no. E


title: MM_1081

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta from colony 25.1, sample no. H


title: Tumor 1720

source_name: tumor

tag: tissue

value: oral cavity squamous cell carcinoma

tag: reference

value: Human Genomic DNA (Roche catalog. 11691112001)


title: larva workers of Solenopsis invicta from colony 15.1, sample no. H


title: Tumor 1339

source_name: Human genomic DNA


title: MM_1062

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta from colony 12.1, sample no. H


title: Tumor 1421


title: MM_1054

description: Hybridized to Affymetrix 6.0


title: MM_1049

description: Hybridized to Affymetrix 6.0


title: MM_1048

description: Hybridized to Affymetrix 6.0


title: Tumor 414


title: larva workers of Solenopsis invicta from colony 3.1, sample no. E


title: MM_1051

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta from colony 2.1, sample no. E


title: MM_1042

description: Hybridized to Affymetrix 6.0


title: MM_1041

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 119

city: Bethesda

first: Dinah

last: Singer

state: Maryland

address: 9000 Rockville Pike

department: Experimental Immunology Branch

institute: National Cancer Institute

description:
m119
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

hyb_protocol: Microarrays were hybridized overnight with 5 ug biotin-labelled ss-DNA, and washed in fluidics station wash protocol: FS450_0001.

scan_protocol: GeneChip scanner 3000 7G was used.

data_processing: Exon array data were analyzed with Affymetrix Expression Console SoftwareTM (version 1.1). The Robust Multi-array Analysis (RMA) algorithm was used for gene intensity analysis. Only genes in the “core” set, which represents RefSeq and full-length GenBank mRNAs, were included in the analysis.

organism: Mus musculus

source_name: embryonic fibroblasts, Taf7(+/+)-2, infected, 72 hrs

label_protocol: Labeling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual.

growth_protocol: The MEFs are grown in DMEM with 10% Fetal Calf Serum, Hepes 20mM, and gentamycin.

extract_protocol: Total RNA is extracted using shredders and the Qiagen RNeasy mini kit. Their quality was assayed before using for hybridization.

tag: background strain

value: C57/BL6 and 129 mix

value: mouse embryonic fibroblast (MEF)

tag: genotype

tag: mscv cre-gfp retroviral infection

value: yes

tag: time recovery (hour)


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 112

description:
m112
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-2, infected, 48 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 113

description:
m113
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-2, uninfected, 72 hrs

value: no


title: MM_957

description: Hybridized to Affymetrix 6.0

source_name: Bone Marrow MM patient


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 115

description:
m115
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: MM_944

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 9.1, sample no. H

organism: Solenopsis invicta x Solenopsis richteri


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 110

description:
m110
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 121

description:
m121
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 111

description:
m111
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 13.1, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 120

description:
m120
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 106

description:
m106
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-2, uninfected, 48 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 114

description:
m114
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: MM_956

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 107

description:
m107
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-2, infected, 48 hrs


title: MM_896

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 105

description:
m105
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: MM_919

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 104

description:
m104
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 14.2, sample no. H


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 11.1, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 103

description:
m103
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-2, uninfected, 48 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 108

description:
m108
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: MM_893

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 17.2, sample no. E


title: MM_880

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 17.1, sample no. 9


title: larva workers of Solenopsis richteri from colony 19.1a, sample no. H


title: MM_856

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis richteri from colony 17.1a, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 102

description:
m102
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: larva workers of Solenopsis richteri from colony 33.1a, sample no. E


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 101

description:
m101
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 53

description:
m53
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-1, infected, 72 hrs


title: MM_842

description: Hybridized to Affymetrix 6.0


title: MM_813

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis richteri from colony 30.1e, sample no. E


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 51

description:
m51
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-1, infected, 72 hrs


title: larva workers of Solenopsis invicta from colony 31.1d, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 54

description:
m54
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 47

description:
m47
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-1, uninfected, 72 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 50

description:
m50
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 48

description:
m48
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 44

description:
m44
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-1, uninfected, 72 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 49

description:
m49
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 46

description:
m46
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: MM_687

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta from colony 25.2a, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 41

description:
m41
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-1, infected, 48 hrs


title: SMM_1403

description: Hybridized to Affymetrix 6.0

source_name: Bone Marrow SMM patient

value: Bone Marrow SMM


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 43

description:
m43
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: SMM_1415

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta from colony 24.1c, sample no. H

source_name: Solenopsis invicta common reference


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 40

description:
m40
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 45

description:
m45
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: SMM_1398

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 39

description:
m39
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-1, infected, 48 hrs


title: larva workers of Solenopsis invicta from colony 3.2a_, sample no. 1

source_name: larva workers of Solenopsis invicta


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 36

description:
m36
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-1, uninfected, 48 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 52

description:
m52
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: SMM_1384

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 42

description:
m42
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: SMM_1377

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 37

description:
m37
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: larva workers of Solenopsis invicta from colony 3.1d_, sample no. 1


title: MM_797

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 9.1e_, sample no. 7


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 35

description:
m35
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: larva workers of Solenopsis invicta from colony 15.1e, sample no. H


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 14.1c, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 34

description:
m34
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: SMM_1495

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 38

description:
m38
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 32

description:
m32
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-1, uninfected, 48 hrs


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 13.1a, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 33

description:
m33
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: SMM_1360

description: Hybridized to Affymetrix 6.0


title: SMM_1365

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 24

description:
m24
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-1, infected, 24 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 31

description:
m31
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 22

description:
m22
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 20

description:
m20
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-2, infected, 24 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 23

description:
m23
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 11.1a, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 21

description:
m21
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 18

description:
m18
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-2, infected, 24 hrs


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 4.1d_, sample no. 1


title: SMM_1340

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 17.2d, sample no. E


title: SMM_1336

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 17

description:
m17
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: larva workers of Solenopsis richteri from colony 19.1d, sample no. H

source_name: larva workers of Solenopsis richteri


title: SMM_1329

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 15

description:
m15
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-1, infected, 24 hrs


title: SMM_1306

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis richteri from colony 30.1a, sample no. E


title: SMM_1331

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 19

description:
m19
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: 13635387

city: Nouzilly

first: Joel

last: Gautron

address: UR83 Recherches avicoles

institute: INRA

description: Liver of female chicken (hen 38 weeks old and pullet 10 weeks old).

hyb_protocol: Samples were hybridized at 42°C for 16 h using the Slide-Booster (Olympus Advalytix, Germany), and PRONTO buffer (Corning, Life Sciences).

scan_protocol: Microarray slides were scanned at 532 nm for Alexa® 555 and 635 nm for Alexa® 647 using a GenePix 4000B microarray scanner (Axon Molecular Devices, Sunnyvale, CA, USA).

data_processing: GenePix Pro 6.0 software was used to acquire the fluorescent images, align the spots, quantify their intensity and finally export GenePix report (GPR) files containing spot intensity raw data. The profiling of differentially expressed genes was determined using Anapuce package (http://www.inapg.fr/ens_rech/maths/outil.html). Spot intensities were calculated using the median value that was logarithm transformed (log2). A normalization consisting of global locally-weighted regression (LOWESS) was applied on the overall intensity log ratio to remove the bias due to fluorescence incorporation. A block effect was also corrected by subtracting the median value of the block. We performed statistical tests using VarMixt model assuming various group of variance for all genes. P-values were adjusted by a Benjamini-Hochberg (BH) multiple testing procedure, taking into account that all tests were simultaneous.

label: Alexa 555

organism: Gallus gallus

label_protocol: Thirty micrograms of total RNA were used for labeling the cDNA with Alexa 555 or 647 fluorophores using Superscript indirect cDNA labeling system.

extract_protocol: Total RNA was extract from liver using Macherey Nagel Nucleospin RNA-L kit according to the recommendation of the fabricant.

treatment_protocol: Liver was collected and immediately frozen in liquid N2, then kept at -80°C until total RNA extraction.

tag: Stage

value: sexually immature (10 weeks)

tag: collected date

tag: tissue weigth

tag: extraction date

tag: rna

tag: total rna

tag: ratio 28s/18s

tag: foi (dye/1000 bases)

tag: labeled cdna

label: Alexa 647

value: sexually mature (38 weeks)


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 13

description:
m13
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

tag: cell type


title: SMM_1280

description: Hybridized to Affymetrix 6.0


title: 13635305


title: 13635308


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 16

description:
m16
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: larva workers of Solenopsis invicta from colony 25.1a, sample no. H

tag: caste

tag: developmental stage


title: larva workers of Solenopsis invicta from colony 31.1a, sample no. H


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 14

description:
m14
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: larva workers of Solenopsis invicta from colony 12.1a, sample no. H


title: 13635303


title: day 4 post-exposure to S. mansoni (10) 13653202-D4-10

city: Albuquerque

first: Michelle

middle: A.

last: Forys

state: NM

address: MSC03 2020, 1 University of New Mexico

department: Biology

institute: University of New Mexico

description:
day 4 post-exposure to S. mansoni (10)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

hyb_protocol: Purified Cy3 and Cy5 labeled products were then pooled, ethanol precipitated, resuspended in 45 µL hybridization buffer (40 % formamide, 5x Denhardt’s, 5x SSC, 1 mM sodium pyrophosphate, 50 mM Tris (pH 7.4) and 0.1 % SDS) and incubated at 95°C for 5 min followed by 50°C for 5 min. Arrays were pre-hybridized for 26 h at 42°C in hybridization buffer prior to hybridization with labeled probes. Labeled cDNA was hybridized overnight at 42°C.

scan_protocol: Microarray slides were scanned with a GenePix® 4000B scanner (Axon Instruments) with GenePix® Pro 6.0 (Axon Instruments) software using a modified protocol as described by Aragon and colleagues.

data_processing: A preloaded grid was used to align and identify array spots. Alignment diameter minimum and maximums were set at 50% and 200%, respectively. Nearest negative control spots were selected for background subtraction. Acuity version 4.0 (Axon Instruments) software was used in array analyses and arrays were normalized using a ratio of medians to Myosin essential light chain. SAM was used to determine significantly differentially regulated genes with a cut of 1-fold and a 5% false detection rate.

organism: Biomphalaria glabrata

source_name: Biomphalaria glabrata injected with GFP specific DSiRNA oligos and 2 hours later exposed to S. mansoni miracidia

label_protocol: Complementary DNA was synthesized, amplified, labeled and hybridized using the modified SMART (Clontech) cDNA labeling protocol described by Petalidis and colleagues. Briefly, 300 ng total RNA were mixed with 3 µL of 10 μM 3′ SMART CDS primer IIA (5′-AAGCAGTGGTATCAACGCAGAGTACT30VN-3′) and 3 µL 10 μM template switching primer (5′-d(AAGCAGTGGTATCAACGCAGAGTACGC)r(GGG)-3′) and brought to a final volume of 15 µL with RNase free dH2O. The template switching primer is a DNA:RNA hybrid where the last 3 bases are RNA. The reaction was then incubated at 72°C for 2 min and then placed on ice. Six microliters of 5x first-strand buffer (Clontech), 3 µL DTT (20 mM), 3 µL dNTPs (10 mM), and 3 µL and PowerScriptTM reverse transcriptase (Clontech) were then added to the reaction and the mixture incubated at 42°C for 1.0 h to generate first strand cDNA. Second-strand cDNA was then amplified by mixing 15 µL of the first-strand cDNA reaction with 57 µL dH2O, 10 µL 10x PCR buffer II (Applied Biosystems), 10 µL 25 mM MgCl2, 2 µL 10 mM dNTPs, 4 µL 10 μM 5’ PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) and 2 µl AmpliTaq® (40 U/µL). Amplification conditions were 95°C for 1 min for one cycle followed by 95°C for 5 s, 65°C for 5 s, and 68°C for 6 min for 15 cycles. Second strand cDNA was then purified using a QIAquick® PCR Purification Kit (Qiagen), quantified using a NanoDrop® ND-1000 spectrophotometer and labeled with Cy3/Cy5 d-CTPs (GE Healthcare-Amersham) using BioPrime® DNA Labeling System (Invitrogen). For labeling, 200 ng of second-strand cDNA suspended in 21 µL dH2O was mixed with 20 μL of 2.5x random primer reaction buffer (Invitrogen) and incubated at 95°C for 5 min, then placed on ice. While on ice, 2 µL dH2O, 5 μL low-C dNTP mix (5 mM dATP, 5 mM dGTP, 5 mM dTTP, 2 mM dCTP), 1 µL Cy3 or Cy5 dCTP and 1 μL Klenow enzyme (40 U/µL; Invitrogen) were mixed and incubated at 37°C for 2.0 h. The labeling reaction was stopped by adding 5 μL stop buffer (Invitrogen). For all experiments, reference samples were labeled with Cy3 and experimental samples with Cy5. Cy3 and Cy5 labeled probes were purified separately using an AutoSeqTM G-50 Dye Terminator Removal Kit (GE Healthcare) and labeling efficiency quantified using a NanoDrop® ND-1000 spectrophotometer.

growth_protocol: Snails and trematodes used in this study were maintained at the University of New Mexico

extract_protocol: Total RNA was extracted using Trizol and the RNA mini kit from Ambion with an on-column DNAse procedure as described in the manual.

treatment_protocol: B. glabrata snails were injected with a 10ul cocktail containing 200ng of DSiRNA oligos specific to either FREP3 or GFP. Two hours later, the snails were placed in well plates with artificial spring water and exposed to 30 S. mansoni miricidia for 24 hours on day 0. After 24 hours, they were placed into aquaria for the remainder of the experiment. On day 2 and 4 post-exposure, ten snails from each group were collected for analysis using the snail array. Other controls in this experiment include uninjected BS-90's and M-line snails both exposed to S. mansoni miracidia at the same time as the other two groups, but these were not examined using the microarray.

tag: strain

tag: experimental variable

value: injected with GFP specific DSiRNA oligos and exposed to S. mansoni miracidia 2 hours later

source_name: Biomphalaria glabrata injected with FREP3 specific DSiRNA oligos and 2 hours later exposed to S. mansoni miracidia

value: Injected with FREP3 specific DSiRNA oligos and two hours later exposed to S. mansoni miracidia


title: SMM_1313

description: Hybridized to Affymetrix 6.0


title: 13635301


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 9

description:
m9
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-2, uninfected, 24 hrs

tag: background strain

tag: genotype


title: 13635300

value: 67 µg


title: larva workers of Solenopsis invicta from colony 2.2a_, sample no. 1


title: 13635311

value: 42 µg


title: 13635293

value: 53 µg


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 13.2d, sample no. H

value: Mix of workers, queens and males

value: Mix of adults, pupae and larvae


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 7

description:
m7
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

tag: mscv cre-gfp retroviral infection

tag: time recovery (hour)


title: day 4 post-exposure to S. mansoni (9) 13653202-D4-9

description:
day 4 post-exposure to S. mansoni (9)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: MCF7 Six1 clone 3 biological rep 2

city: Aurora

first: Heide

last: Ford

state: CO

address: 12800 E 19th Ave RC1 North, Room 5102

department: OB/Gyn

institute: University of Colorado at Denver

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45C on Affymetrix HT Human Genome U133A Array.

scan_protocol: standard Affymetrix protocol

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

source_name: MCF7 mammary carcinoma Six1 overexpressing clone, orthotopic tumor

growth_protocol: Cells were orthotopically injected in to the mammary gland of NOD/Scid mice and the resulting tumors allowed to grow to 2 cm^3

extract_protocol: Trizol extraction according to the manufacturer's instructions

tag: cell line

tag: tissue

value: xenograft tumor

tag: genotype/variation

value: Six1 expressing clone


title: SMM_1268

description: Hybridized to Affymetrix 6.0


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 10

description:
m10
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-1, uninfected, 24 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 3

description:
m3
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

source_name: embryonic fibroblasts, Taf7(+/+)-1, uninfected, 24 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 6

description:
m6
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

source_name: embryonic fibroblasts, Taf7f/f-2, uninfected, 24 hrs


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 8

description:
m8
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: SMM_1221

description: Hybridized to Affymetrix 6.0

source_name: Bone Marrow SMM patient


title: SMM_1259

description: Hybridized to Affymetrix 6.0


title: MCF7 Control clone 2 biological rep 1

source_name: MCF7 mammary carcinoma control clone, orthotopic tumor

value: control clone


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 1

description:
m1
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.

value: C57/BL6 and 129 mix


title: day 4 post-exposure to S. mansoni (7) 13653384-D4-7

description:
day 4 post-exposure to S. mansoni (7)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: day 4 post-exposure to S. mansoni (8) 13653384-D4-8

description:
day 4 post-exposure to S. mansoni (8)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: SMM_1241

description: Hybridized to Affymetrix 6.0


title: larva workers of Solenopsis invicta X Solenopsis richteri hybrid from colony 17.1b, sample no. E

value: workers

value: larva

source_name: Solenopsis invicta common reference


title: day 4 post-exposure to S. mansoni (6) 13653035-D4-6

description:
day 4 post-exposure to S. mansoni (6)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: MCF7 Six1 clone 1 biological rep 1


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 12

description:
m12
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.

value: mouse embryonic fibroblast (MEF)

value: no


title: pupa workers of Solenopsis richteri from colony 33, sample no. 2

source_name: pupa workers of Solenopsis richteri

value: pupa


title: pupa workers of Solenopsis richteri from colony 30, sample no. 1


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 11

description:
m11
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 2

description:
m2
Taf7(+/+)-1 and Taf7(+/+)-2 represent 2 different wild-type MEF cell lines.


title: day 4 post-exposure to S. mansoni (5) 13653035-D4-5

description:
day 4 post-exposure to S. mansoni (5)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 5

description:
m5
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: day 4 post-exposure to S. mansoni (4) 13653036-D4-4

description:
day 4 post-exposure to S. mansoni (4)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: MCF7 Control clone 1 biological rep 1


title: MCF7 Six1 clone 3 biological rep 1


title: TAF7 Depletion in Mouse Embryonic Fibroblasts, sample 4

description:
m4
Taf7f/f-1 and Taf7f/f-2 represent 2 different MEF cell lines.


title: MGUS_1708

description: Hybridized to Affymetrix 6.0

source_name: Bone Marrow MGUS patient

value: Bone Marrow MGUS


title: pupa workers of Solenopsis richteri from colony 17, sample no. 1


title: day 4 post-exposure to S. mansoni (3) 13653036-D4-3

description:
day 4 post-exposure to S. mansoni (3)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

value: injected with GFP specific DSiRNA oligos and exposed to S. mansoni miracidia 2 hours later


title: MCF7 Control clone 1 biological rep 2


title: NORMAL 23S

city: PHILADELPHIA

first: Adam

last: Ertel

state: PA

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

hyb_protocol: The resultant fragmented and labeled cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Hybridization was run for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640.  Following hybridization, the array was washed and stained on the GeneChip® Fluidics Station 450.

scan_protocol: Arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip® Scanner 3000

data_processing:
Raw intensity files from the Affymetrix Human Exon 1.0 ST GeneChip arrays were processed using Affymetrix Expression Console version 1.1.   Gene-level expression measurements were computed using the iterPLIER algorithm on the “core” probesets and exported with annotation release 32, dated June 23rd, 2011.
HuGene-1_0-st-v1.r4.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: NORMAL 23S

label_protocol: Amplified single-stranded cDNA was fragmented and labeled using the Encore™ cDNA Biotin Module. The enzymatically and chemically fragmented product (50-100 nt) was labeled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented cDNA.

extract_protocol: Neoplastic epithelial cells and tumor stroma were laser capture microdissected using Leica LCM system (Leica Microsystems, Germany).  Total RNA was extracted using Qiagen microRNA kit.

tag: tissue compartment

value: stroma

tag: phenotype

value: normal

tag: subject

value: NORMAL 23


title: pupa workers of Solenopsis richteri from colony 6, sample no. 1


title: pupa workers of Solenopsis richteri from colony 11, sample no. 1


title: NORMAL 23E

source_name: NORMAL 23E

value: epithelium


title: SMM_1216

description: Hybridized to Affymetrix 6.0

value: Bone Marrow SMM


title: day 4 post-exposure to S. mansoni (1) 13653038-D4-1

description:
day 4 post-exposure to S. mansoni (1)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

value: Injected with FREP3 specific DSiRNA oligos and two hours later exposed to S. mansoni miracidia


title: NORMAL 22S

source_name: NORMAL 22S

value: NORMAL 22


title: MGUS_1694

description: Hybridized to Affymetrix 6.0


title: day 2 post-exposure to S. mansoni (10) 13653386-D2-10

description:
day 2 post-exposure to S. mansoni (10)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: NORMAL 22E

source_name: NORMAL 22E


title: NORMAL 21S

source_name: NORMAL 21S

value: NORMAL 21


title: day 2 post-exposure to S. mansoni (9) 13653386-D2-9

description:
day 2 post-exposure to S. mansoni (9)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

source_name: Biomphalaria glabrata injected with GFP specific DSiRNA oligos and 2 hours later exposed to S. mansoni miracidia


title: day 2 post-exposure to S. mansoni (8) 13653383-D2-8

description:
day 2 post-exposure to S. mansoni (8)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

source_name: Biomphalaria glabrata injected with FREP3 specific DSiRNA oligos and 2 hours later exposed to S. mansoni miracidia


title: pupa queens of Solenopsis richteri from colony 33, sample no. 2

source_name: pupa queens of Solenopsis richteri

value: queens

value: Mix of workers, queens and males

value: Mix of adults, pupae and larvae


title: pupa queens of Solenopsis richteri from colony 30, sample no. 1


title: NORMAL 21E

source_name: NORMAL 21E


title: pupa queens of Solenopsis richteri from colony 19, sample no. 1


title: day 4 post-exposure to S. mansoni (2) 13653038-D4-2

description:
day 4 post-exposure to S. mansoni (2)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: day 2 post-exposure to S. mansoni (7) 13653383-D2-7

description:
day 2 post-exposure to S. mansoni (7)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: IDC 20S

source_name: IDC 20S

value: invasive breast cancer

value: IDC 20


title: pupa queens of Solenopsis richteri from colony 15, sample no. 1


title: pupa queens of Solenopsis richteri from colony 17, sample no. 1


title: MGUS_1702

description: Hybridized to Affymetrix 6.0


title: IDC 20E

source_name: IDC 20E


title: IDC 19S

source_name: IDC 19S

value: IDC 19


title: MGUS_1559

description: Hybridized to Affymetrix 6.0


title: pupa males of Solenopsis richteri from colony 33, sample no. 1

source_name: pupa males of Solenopsis richteri

value: males

value: pupa


title: day 2 post-exposure to S. mansoni (5) 13653201-D2-5

description:
day 2 post-exposure to S. mansoni (5)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

value: injected with GFP specific DSiRNA oligos and exposed to S. mansoni miracidia 2 hours later


title: pupa males of Solenopsis richteri from colony 30, sample no. 1


title: IDC 19E

source_name: IDC 19E


title: day 2 post-exposure to S. mansoni (4) 13653037-D2-4

description:
day 2 post-exposure to S. mansoni (4)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: effect of GC-fed after SDS treatment rep4

city: Yokohama

first: Ritsuro

last: Ideta

address: 2-12-1 Fukuura, Kanazawa-ku

department: Functional Food Research & Development Center

country: Japan

institute: Shiseido Research Center

description: Biological replicate 4 of 4. 14 days after feeding with Gccontaine/non-GC diet, 2days after the begging of SDS treatment, treated two times

hyb_protocol: Two labeled cDNA samples, one from GC-fed mouse and the other from control-fed mouse were combined. For each hybridization, 825 ng of labeled cRNAs were mixed, fragmented, and hybridized at 65°C for 17 hours to an Agilent 4x44K Whole Mouse Genome Microarray (Agilent 14868) in Agilent's G2545A hybridization oven.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing:
Feature extraction software version 9.1.3.1 (Agilent Technologies) was used to assess fluorescent hybridization signals and to normalize signals using linear regression and a Lowess curve-fit technique.
Genespring (Agilent) was used further data processing. Feature extraction software version 9.1.3.1 (Agilent Technologies) was used to assess fluorescent hybridization signals and to normalize signals using linear regression and a Lowess curve-fit technique.Flagged signals were eliminated. Since some genes have multiple probes on the Agilent platform, gene-level expression values were calculated by using the "Gene-level experiment" function in Genespring. Expression values below 200 were floored to 200. Processed signal values of GC-fed mice were divided by processed signal values of references, and these values were used as expression ratio data. Log base 2 of expression ratio (log ratio) was used for further analysis. Grubb's method was used to eliminate outliers.

source_name: two times SDS treated, dorsal skin of GC-fed mouse

label_protocol: 500 ng of total RNA was reverse-transcribed to double-stranded cDNA using a poly dT-T7 promoter primer and MMLV-RT enzyme. cDNA products were used as templates for in vitro transcription to generate fluorescent cRNA using T7 RNA polymerase and Cy5-labeled or Cy3-labeled CTP. Labeled cRNAs were purified using QIAGEN RNeasy mini spin columns and eluted in nuclease-free water. cRNA quantity and cyanine incorporation were determined using a Nanodrop ND-1000 with Bioanalyzer.

growth_protocol: 5 weeks old male HR-1 mice were fed with GC-containing / non-containing AIN-93G (Oriental Yeast, Tokyo, Japan) rodent diet for 14 days.

extract_protocol: Total RNA extracted using Isogen. They were further purified using a RNeasy Fibrous Tissue Mini Kit (QIAGEN, Valencia, CA) following manufacturer's instructions.

treatment_protocol: The dorsal skin on the right side of each mouse was treated with 10% SDS for five minutes daily for two days.

value: skin

tag: age

value: 5 weeks

tag: gender

value: male

source_name: two times SDS treated, dorsal skin of control-fed mouse


title: MGUS_1611

description: Hybridized to Affymetrix 6.0

source_name: Bone Marrow MGUS patient

tag: cell type

value: Bone Marrow MGUS


title: DCIS 18S

source_name: DCIS 18S

value: stroma

value: ductal carcinoma in situ

value: DCIS 18


title: pupa males of Solenopsis richteri from colony 17, sample no. 1

source_name: Solenopsis invicta common reference

tag: caste


title: pupa males of Solenopsis richteri from colony 19, sample no. 1

tag: developmental stage


title: day 2 post-exposure to S. mansoni (3) 13653037-D2-3

description:
day 2 post-exposure to S. mansoni (3)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

tag: strain

value: Injected with FREP3 specific DSiRNA oligos and two hours later exposed to S. mansoni miracidia


title: effect of GC-fed after SDS treatment rep3

description: Biological replicate 3 of 4. 14 days after feeding with Gccontaine/non-GC diet, 2days after the begging of SDS treatment, treated two times


title: pupa workers of Solenopsis richteri from colony 15, sample no. 1

source_name: pupa workers of Solenopsis richteri

value: workers


title: day 2 post-exposure to S. mansoni (2) 13653059-D2-2

description:
day 2 post-exposure to S. mansoni (2)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.

tag: experimental variable


title: pupa workers of Solenopsis invicta from colony 31, sample no. 1

source_name: pupa workers of Solenopsis invicta

value: Mix of workers, queens and males


title: effect of GC-fed after SDS treatment rep2

description: Biological replicate 2 of 4. 14 days after feeding with Gccontaine/non-GC diet, 2days after the begging of SDS treatment, treated two times


title: effect of GC-fed after SDS treatment rep1

description: Biological replicate 1 of 4. 14 days after feeding with Gccontaine/non-GC diet, 2days after the begging of SDS treatment, treated two times

data_processing:
Feature extraction software version 9.1.3.1 (Agilent Technologies) was used to assess fluorescent hybridization signals and to normalize signals using linear regression and a Lowess curve-fit technique.
Processed signal values of GC-fed mice were divided by processed signal values of references, and these values were used as expression ratio data. Log base 2 of expression ratio (log ratio) was used for further analysis. Grubb's method was used to eliminate outliers.


title: day 2 post-exposure to S. mansoni (1) 13653059-D2-1

description:
day 2 post-exposure to S. mansoni (1)
Each array was probed with total RNA converted to cDNA of one Cy3 labeled GFP knock-down snail and one Cy5 labeled FREP3 knock-down snail from the same time point. There are ten from each time point (2dpe and 4dpe) for each treatment type.


title: IDC 17E

source_name: IDC 17E

value: epithelium

value: IDC 17


title: IDC 17S

source_name: IDC 17S

value: invasive breast cancer