title: WhiteSpruce_29B14_29C03_bark

description: cross29, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repC

value: tree 03


title: Cord blood leukocyte_Child of normal mother_Sample 13

status: Public on Jan 01 2011

type: RNA

city: Chicago

first: Jinhee

last: Kim

state: IL

address: 676 North St. Clair Street Arkes Suite 2330

department: Infectious Disease

country: USA

institute: Northwestern University

description: column in raw data file: NMC_13

hyb_protocol: Illumina's BeadArray protocol

scan_protocol: Illumina's BeadArray protocol and BeadStudio (Gene expression Module)

data_processing: Raw data was log2 transformed and median-centered using JMP Genomics 4.0 (SAS Institute, Cary NC).

molecule: total RNA

organism: Homo sapiens

source_name: Cord blood leukocytes, Child from a normal-weight mother

label_protocol: cDNA and cRNA labeling and amplification were all performed using a single kit : Ambion's Illumina TotalPrep RNA Aamplification kit.

extract_protocol: Total RNA was extracted from leukocyte samples using Ambion's Leukolocks kit. Quality control was performed using Agilent's Bioanalyzer.

tag: life stage

value: newborn baby

tag: tissue

value: umbilical cord blood

tag: cell type

value: leukocytes

tag: rna integrity score


title: Cord blood leukocyte_Child of normal mother_Sample 18

description: column in raw data file: NMC_18


title: WhiteSpruce_29B18_29A01_bark

city: Vancouver

first: Ilga

last: Porth

address: 2424 Main Mall

country: Canada

institute: University of British Columbia

description: cross29, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repA

hyb_protocol: Hybridizations were performed using the Genisphere Array350 kit (Genisphere, Hatfield, USA) following manufacturer's instructions. Following pooling of the appropriate Cy3 and Cy5 cDNAs, samples were precipitated with linear acrylamide and resuspended in 17.7 μL nuclease-free water. A 27.3 μL hybridisation mixture containing 22.5 μL 2xSDS buffer, 4 μL LNA d(T) blocker, 2 μg sheared salmon testes DNA (Invitrogen) and 0.3 μL of Cy5-labeled GFP cDNA (Cy5-dUTP and Ready-To-Go labeling beads, Amersham Pharmacia Biotech) was added to the cDNA probe. Immediately prior to use, arrays were pre-washed 2x in 0.1% SDS at room temperature for 5 min each, followed by two washes in MilliQ-H2O for 2 min each, 3 min at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat denatured at 80ºC for 10 min, then maintained at 65ºC prior to adding to a microarray slide heated to 55ºC, covered with a 22 x 60 x 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 60ºC. Arrays were washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, then three washes of 5 min in 2x SSC at room temperature, and three washes of 5 min in 0.2x SSC at room temperature, and dried by centrifugation. The Cy3 and Cy5 3DNA capture reagent (Genisphere) were then hybridized to the bound cDNA on the microarray in a 45 μL volume consisting of 22.5 μL 2x SDS buffer, 17.5 μL nuclease-free water, 2.5 μL Cy3 capture reagent and 2.5 μL Cy5 capture reagent. The 3DNA capture reagent is bound to its complementary cDNA capture sequence on the Cy3 or Cy5 oligo d(T) primers. The second hybridization was performed for 3 h at 60ºC, then washed and dried as before.

scan_protocol: Fluorescent images of hybridized arrays were acquired by using ScanArray Express (PerkinElmer, Foster City, USA). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively. All scans were performed at the same laser power (90%), but with the photomultiplier tube settings for the two channels adjusted such that the ratio of the mean signal intensities was ~1, and the percentage of saturated array elements was < 0.5% but > 0%, while minimizing background fluorescence. Fluorescent intensity data were extracted by using the ImaGene 6.0 software (Biodiscovery, El Segundo, USA).

data_processing: After quantification of the signal intensities in each array the local background was subtracted for each subgrid. Data were normalized to compensate for non-linearity of intensity distributions using the variance stabilizing normalization method (Huber, et al. 2002). A linear model was fit to the normalized intensities in the Cy3 and Cy5 channels to account for technical effects within the experiment (gene-specific ‘dye’ effect, replicate ‘block’, microarray fabrication ‘batch’, experimenter ‘person’ are all fixed effects). All statistical analyses were done using the R statistical package (www.r-project.org/). The residuals were used in the subsequent QTL analysis.

organism: Picea engelmannii x Picea glauca

label_protocol: 40 micrograms total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen) and oligo d(T18) primers with a 5' unique sequence overhang specific to either the Cy3 or Cy5 labeling reactions. The RNA strand of the resulting cDNA:RNA hybrid was hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: Trees were planted in 1995 and grown in the field in a complete randomized block design. Experimental spruce populations originated from a controlled-cross progeny trial that had been established in 1995 at Kalamalka Research Station in Vernon, BC, Canada {{Alfaro, 2004}). The respective sires and dams had been selected from individuals previously ranked for weevil-resistance in open-pollinated progeny tests conducted in north central BC in the late 1980’s ({Kiss, 1991}). Out of twenty crosses segregating for the resistance phenotype ({Alfaro, 2004}), we selected four families from the trial based on two important criteria: clear intermediate weevil resistance and shared parentage.

extract_protocol: Total RNA was isolated according to procedures described in Kolosova et al. (2004) Biotechniques 36: 821-824. Total RNA was quantified and quality checked by NanoDrop ND-1000 Spectrophotometer and agarose gel. RNA was also evaluated for integrity using the Agilent 2100 Bioanalyzer

treatment_protocol: During the seasonal onset of weevil attack, on May 16 to May 18, 2006, unaffected terminal leaders were cut , bark/phloem tissue detached from the cambium was harvested, immediately flash frozen in liquid nitrogen.

tag: origin

value: Twelve year old trees from a weevil screening trial

tag: cross

tag: replicate

value: B

tag: specimen

value: tree 18

value: from the leader of each tree, bark with attached phloem and cambium

tag: collection dates

tag: biomaterial provider

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: A

value: tree 01


title: WhiteSpruce_29B09_29C06_bark

value: tree 09

value: C

value: tree 06


title: WhiteSpruce_29B07_29A03_bark

value: tree 07


title: Cord blood leukocyte_Child of normal mother_Sample 14

description:
column in raw data file: NMC_14
pair with NMM_10


title: Cord blood leukocyte_Child of normal mother_Sample 10

description: column in raw data file: NMC_10


title: WhiteSpruce_29B10_29A02_bark

value: tree 10

value: tree 02


title: Cord blood leukocyte_Child of normal mother_Sample 12

description:
column in raw data file: NMC_12
pair with NMM_2


title: WhiteSpruce_29B01_29A20_bark

value: tree 20


title: Cord blood leukocyte_Child of normal mother_Sample 9

description:
column in raw data file: NMC_9
pair with NMM_4

value: newborn baby


title: Cord blood leukocyte_Child of normal mother_Sample 8

description:
column in raw data file: NMC_8
pair with NMM_7

value: umbilical cord blood


title: Cord blood leukocyte_Child of normal mother_Sample 11

description: column in raw data file: NMC_11

value: leukocytes


title: Cord blood leukocyte_Child of obese mother, Sample 9

description:
column in raw data file: OBC_9
pair with OBM_2

source_name: Cord blood leukocytes, Child from a obese mother


title: Cord blood leukocyte_Child of normal mother_Sample 6

description: column in raw data file: NMC_6


title: WhiteSpruce_29B05_29A07_bark

value: Twelve year old trees from a weevil screening trial

value: tree 05


title: WhiteSpruce_29B06_29A25_bark

value: B

value: tree 25


title: Cord blood leukocyte_Child of normal mother_Sample 5

description: column in raw data file: NMC_5


title: WhiteSpruce_29A24_29C10_bark

description: cross29, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repC

value: tree 24

value: from the leader of each tree, bark with attached phloem and cambium

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests


title: Cord blood leukocyte_Child of normal mother_Sample 3

description: column in raw data file: NMC_3


title: WhiteSpruce_29A21_29B20_bark

description: cross29, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repB

value: A

value: tree 21


title: Cord blood leukocyte_Child of gestational mother_Sample 8

description: column in raw data file: GSC_8

source_name: Cord blood leukocytes, newborn child from a gestational diabetic mother


title: Cord blood leukocyte_Child of normal mother_Sample 1

description:
column in raw data file: NMC_1
pair with NMM_8


title: WhiteSpruce_29A17_29B17_bark

value: tree 17


title: WhiteSpruce_29A06_29B08_bark

value: tree 06

value: tree 08


title: WhiteSpruce_29A11_29C01_bark

value: tree 11

value: C

value: tree 01


title: WhiteSpruce_29A19_29B16_bark

value: tree 19

value: tree 16


title: Cord blood leukocyte_Child of gestational mother_Sample 7

description: column in raw data file: GSC_7

value: newborn baby

value: umbilical cord blood

value: leukocytes


title: WhiteSpruce_29A22_29B23_bark

value: Twelve year old trees from a weevil screening trial

value: tree 22

value: B

value: tree 23


title: Cord blood leukocyte_Child of normal mother_Sample 2

description: column in raw data file: NMC_2


title: Cord blood leukocyte_Child of obese mother, Sample 8

description:
column in raw data file: OBC_8
pair with OBM_6


title: Cord blood leukocyte_Child of gestational mother_Sample 6

description:
column in raw data file: GSC_6
pair with GSM_1


title: Cord blood leukocyte_Child of gestational mother_Sample 5

description: column in raw data file: GSC_5


title: WhiteSpruce_32A02_32C23_bark

description: cross32, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repC

value: A

value: tree 02

value: from the leader of each tree, bark with attached phloem and cambium

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests


title: WhiteSpruce_29A08_29C23_bark

value: tree 08


title: WhiteSpruce_27C19_27A24_bark

description: cross27, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repA

value: tree 24


title: Cord blood leukocyte_Child of normal mother_Sample 7

description:
column in raw data file: NMC_7
pair with NMM_5


title: WhiteSpruce_29A16_29B04_bark

value: tree 04


title: Cord blood leukocyte_Child of gestational mother_Sample 3

description: column in raw data file: GSC_3


title: Cord blood leukocyte_Child of gestational mother_Sample 4

description: column in raw data file: GSC_4


title: WhiteSpruce_27C16_27A11_bark

value: C

value: tree 11


title: WhiteSpruce_27B15_27C13_bark

description: cross27, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repC

value: tree 15

value: tree 13


title: WhiteSpruce_27C04_27A23_bark


title: WhiteSpruce_27B18_27A22_bark

description: cross27, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repA

value: tree 18


title: WhiteSpruce_27B16_27C02_bark

value: tree 16


title: WhiteSpruce_27C08_27B20_bark

description: cross27, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repB

value: Twelve year old trees from a weevil screening trial

value: tree 20


title: Peripheral blood leukocyte_city, Sample 24

description: column in raw data file: BN79_L

source_name: Peripheral blood leukocyte, City

tag: gender

value: MAL

tag: weight

tag: height

tag: age

tag: bmi

tag: batch effect

value: PA

tag: life style

value: city


title: Peripheral blood leukocyte_suburban, Sample 76

description: column in raw data file: BN79_K

source_name: Peripheral blood leukocyte, Suburban

value: suburban


title: Peripheral blood leukocyte_suburban, Sample 74

description: column in raw data file: BN79_I


title: WhiteSpruce_29A05_29B12_bark

value: A

value: tree 05

value: from the leader of each tree, bark with attached phloem and cambium

value: B

value: tree 12


title: WhiteSpruce_27C03_27B12_bark

value: C

value: tree 03

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests


title: WhiteSpruce_27B13_27A10_bark

value: tree 13

value: tree 10


title: Cord blood leukocyte_Child of gestational mother_Sample 1

description: column in raw data file: GSC_1

tag: life stage

value: newborn baby

value: umbilical cord blood

value: leukocytes


title: Peripheral blood leukocyte_suburban, Sample 75

description: column in raw data file: BN79_J

value: FEM


title: WhiteSpruce_27C12_27B09_bark

value: Twelve year old trees from a weevil screening trial

tag: tissue

value: tree 09


title: WhiteSpruce_27B08_27C10_bark

value: tree 08


title: Peripheral blood leukocyte_city, Sample 22

description: column in raw data file: BN79_E

value: PA

value: city


title: Cord blood leukocyte_Child of gestational mother_Sample 2

description:
column in raw data file: GSC_2
pair with GSM_2

tag: cell type


title: Peripheral blood leukocyte_suburban, Sample 73

description: column in raw data file: BN79_H

tag: rna integrity score

value: suburban


title: Cord blood leukocyte_Child of normal mother_Sample 4

description: column in raw data file: NMC_4


title: Peripheral blood leukocyte_city, Sample 23

description: column in raw data file: BN79_F


title: WhiteSpruce_27B07_27A16_bark

tag: origin

value: B

value: tree 07

value: from the leader of each tree, bark with attached phloem and cambium

value: A

value: tree 16


title: WhiteSpruce_27A25_27B01_bark

description: cross27, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repB

tag: cross

value: tree 25

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: tree 01


title: WhiteSpruce_27A17_27B25_bark

tag: replicate

value: tree 17


title: Peripheral blood leukocyte_suburban, Sample 71

description: column in raw data file: BN79_C


title: Peripheral blood leukocyte_city, Sample 21

description: column in raw data file: BN79_B


title: WhiteSpruce_27A14_27C23_bark

description: cross27, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repC

tag: specimen

value: tree 14

value: C

value: tree 23


title: Peripheral blood leukocyte_suburban, Sample 68

description: column in raw data file: BN69_K

value: FEM


title: Peripheral blood leukocyte_suburban, Sample 64

description: column in raw data file: BN69_G


title: Peripheral blood leukocyte_suburban, Sample 72

description: column in raw data file: BN79_D

value: MAL


title: Peripheral blood leukocyte_suburban, Sample 70

description: column in raw data file: BN79_A

value: PA


title: Peripheral blood leukocyte_city, Sample 20

description: column in raw data file: BN69_D

value: city


title: Peripheral blood leukocyte_suburban, Sample 69

description: column in raw data file: BN69_L

value: suburban


title: WhiteSpruce_26C21_26B18_bark

description: cross26, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repB

value: Twelve year old trees from a weevil screening trial

value: tree 21

tag: collection dates

value: B

value: tree 18


title: WhiteSpruce_27A08_27C18_bark

value: A

value: tree 08

value: from the leader of each tree, bark with attached phloem and cambium

tag: biomaterial provider


title: Peripheral blood leukocyte_suburban, Sample 63

description: column in raw data file: BN69_F

tag: gender


title: Peripheral blood leukocyte_suburban, Sample 67

description: column in raw data file: BN69_J

tag: weight


title: Peripheral blood leukocyte_suburban, Sample 62

description: column in raw data file: BN69_E

tag: height


title: WhiteSpruce_26C18_26A17_bark

description: cross26, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repC-repA

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests


title: WhiteSpruce_26C22_26B14_bark

value: tree 22


title: WhiteSpruce_26C19_26B06_bark

value: tree 19

value: tree 06


title: Peripheral blood leukocyte_suburban, Sample 65

description: column in raw data file: BN69_H

tag: age


title: WhiteSpruce_26C08_26A08_bark

value: C


title: WhiteSpruce_27A01_27B03_bark

value: tree 01

value: tree 03


title: Peripheral blood leukocyte_suburban, Sample 66

description: column in raw data file: BN69_I

value: FEM

tag: bmi

value: PA


title: WhiteSpruce_26C04_26B13_bark

value: tree 04

value: tree 13


title: WhiteSpruce_26C02_26A09_bark

value: Twelve year old trees from a weevil screening trial

value: tree 02

value: tree 09


title: WhiteSpruce_26C20_26A21_bark

value: tree 20

value: A

value: tree 21


title: WhiteSpruce_27A18_27C07_bark

value: tree 18

value: from the leader of each tree, bark with attached phloem and cambium

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: tree 07


title: Peripheral blood leukocyte_suburban, Sample 61

description: column in raw data file: BN69_C

value: MAL

tag: batch effect

value: suburban


title: Peripheral blood leukocyte_city, Sample 19

description: column in raw data file: BN69_B

tag: life style

value: city


title: WhiteSpruce_26B20_26A12_bark

description: cross26, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repA

value: B

value: tree 12


title: WhiteSpruce_26B23_26C13_bark

description: cross26, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repB-repC

value: tree 23

value: C


title: Peripheral blood leukocyte_city, Sample 18

description: column in raw data file: BN69_A

value: FEM

value: PA


title: WhiteSpruce_26B24_26C12_bark

value: Twelve year old trees from a weevil screening trial

value: tree 24


title: Peripheral blood leukocyte_city, Sample 17

description: column in raw data file: BN44_L

value: PB


title: WhiteSpruce_26B17_26A11_bark

value: tree 17

value: A

value: tree 11


title: Peripheral blood leukocyte_suburban, Sample 60

description: column in raw data file: BN44_K


title: Peripheral blood leukocyte_city, Sample 16

description: column in raw data file: BN44_J


title: Mixture Replicate 1

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

hyb_protocol: 300 ng sample and 300 ng ref combined with blocking agent and fragmented; 2x GEx HI-RPM hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After 17 hr hybridization, slides were washed sequentially in wash 1, wash 2, and stabilization & drying solution.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing: Agilent GeneSpring Software (v GX10): threshold set to 1.0, no baseline transformation, LOWESS normalization.

organism: Pimephales promelas

source_name: fathead minnow brain tissue treated with a mixture of all three

label_protocol: 900 ng aliquot per microarray; Agilent's Quick-AMP 2-color labeling kit and 2-color spike-in kit

extract_protocol: Total RNA extracted by Thomas lab; DNase-treated

tag: sample type

value: Pooled sample containing equal amounts (1 mg) of total RNA from 3 individual animals

tag: sex

value: Mixed males, females, and indeterminate

value: Brain

source_name: Reference

value: pooled sample of control (untreated) liver, brain and gonad, M and F


title: Mixture Replicate 2

tag: tissue


title: Peripheral blood leukocyte_city, Sample 14

description: column in raw data file: BN44_C

value: MAL

tag: rna integrity score

value: city


title: Peripheral blood leukocyte_suburban, Sample 57

description: column in raw data file: BN44_E

value: suburban


title: Peripheral blood leukocyte_suburban, Sample 55

description: column in raw data file: BN44_B


title: WhiteSpruce_26B10_26C16_bark

tag: origin

value: B

value: tree 10

value: from the leader of each tree, bark with attached phloem and cambium

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: tree 16


title: Peripheral blood leukocyte_suburban, Sample 59

description: column in raw data file: BN44_I

value: FEM


title: WhiteSpruce_26A24_26C17_bark

description: cross26, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repC

value: Twelve year old trees from a weevil screening trial

tag: cross

value: tree 24

value: C


title: WhiteSpruce_26B16_26C07_bark

tag: replicate

value: tree 07


title: WhiteSpruce_26A25_26C05_bark

value: A

tag: specimen

value: tree 25

value: tree 05


title: Carbamazepinereplicate 3

source_name: fathead minnow brain tissue treated with carbamazepine

value: Pooled sample containing equal amounts (1 mg) of total RNA from 3 individual animals

value: Mixed males, females, and indeterminate

value: Brain

value: pooled sample of control (untreated) liver, brain and gonad, M and F


title: WhiteSpruce_26B15_26A05_bark

value: B

value: tree 15

tag: collection dates


title: WhiteSpruce_26B09_26A02_bark

value: tree 09

value: from the leader of each tree, bark with attached phloem and cambium

tag: biomaterial provider

value: tree 02


title: Peripheral blood leukocyte_city, Sample 15

description: column in raw data file: BN44_F

tag: gender

value: MAL

value: PB

value: city


title: Venlafaxine Replicate 2

source_name: fathead minnow brain tissue treated with venlafaxine


title: Peripheral blood leukocyte_suburban, Sample 56

description: column in raw data file: BN44_D

value: FEM

value: suburban


title: WhiteSpruce_26A23_26B02_bark

description: cross26, bark/phloem tissue, untreated, harvested at onset of weevil activity, biological replicate, hybs between repA-repB

value: Twelve year old trees from a weevil screening trial

value: A

value: tree 23

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests


title: WhiteSpruce_26A19_26B11_bark

value: tree 19

value: tree 11


title: Peripheral blood leukocyte_suburban, Sample 58

description: column in raw data file: BN44_H

tag: weight


title: Peripheral blood leukocyte_suburban, Sample 54

description: column in raw data file: BN44_A

tag: height


title: Alcohol only

source_name: fathead minnow brain tissue treated with alcohol only

value: Pooled sample containing equal amounts (1 mg) of total RNA from 3 individual animals

value: Mixed males, females, and indeterminate

value: Brain

value: pooled sample of control (untreated) liver, brain and gonad, M and F


title: Control Replicate 2

source_name: fathead minnow brain tissue not treated


title: Control Replicate 1


title: Fluoxetine Replicate 3

source_name: fathead minnow brain tissue treated with fluoxetine


title: WhiteSpruce_26A13_26B12_bark

value: tree 13

value: from the leader of each tree, bark with attached phloem and cambium

value: B

value: tree 12


title: PFOS_6

city: Zeist

first: MJ

last: van Erk

address: PO Box 360

country: Netherlands

institute: TNO Quality of Life

description: gene expression data of ApoE3L.CETP mice liver samples

hyb_protocol: Briefly, fragmented cRNA was mixed with spiked controls and hybridized with murine GeneChip® 430 2.0 arrays. The hybridization, probe array washing and staining, and washing procedures were executed as described in the Affymetrix protocols

scan_protocol: Probe arrays were scanned with a Hewlett-Packard Gene Array Scanner (ServiceXS, Leiden, The Netherlands).

data_processing:
Raw signal intensities (from CEL-files) were normalized using the GCRMA algorithm (gc-rma slow). For annotation of probes and summarization of signals from probes representing one gene the custom MNBI CDF-file was used (based on EntrezGene, version 11.0.2; GPL10288) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/cdfreadme.htm).
gcRMA slow normalized data, log2 transformed. Genes were filtered for expression above 5 in 3 or more samples (dataset including 6 arrays from fenofibrate treatment (GSM530353-358), GSE21211), resulting in a set of 11587 genes that was used for further analysis.

label: biotin

organism: Mus musculus

source_name: ApoE3L.CETP mice liver

label_protocol: The Affymetrix 3’ IVT-Express labeling Kit (#901229) and the protocols optimized by Affymetrix were used to synthesize Biotin-labeled cRNA (from 100 ng of total RNA) for microarray hybridization. For the hybridization 15 μg cRNA was used for further fragmentation and finally 10 μg for the hybridizations. The quality of intermediate products (that is, biotin-labeled cRNA and fragmented cRNA) was again checked.

extract_protocol: Total RNA was extracted from individual livers using RNA-Bee (Bio-Connect, Huissen, The Netherlands) and glass beads according to the manufacturer's instructions. The RNA was further purified using the nucleospin RNA II kit (Machery-Nagel, Düren, Germany) according to the manufacturer's instructions. The integrity of each RNA sample obtained was examined by Agilent Lab-on-a-chip technology using a RNA 6000 Nano LabChip kit and a Bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands).

treatment_protocol: Male E3L.CETP mice were fed a cholesterol-rich Western-type diet for 4-6 weeks. Mice were randomized and fed the same diet without (time-matched control group) or with different PFAS (0.03% PFBS, 0.006% PFHxS or 0.003% PFOS) for another 4 weeks. Livers were isolated for hepatic lipid analysis and hepatic gene expression analysis using an Affymetrix technology platform and Affymetrix GeneChip® mouse genome 430 2.0 arrays

tag: diet group

value: PFOS

value: liver

value: male

tag: background strain

tag: mouse model


title: Carbamazepine replicate 2


title: Carbamazepine replicate 1


title: Afp_fetal liver_rep5

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Normalisation with GenePix Pro 6.0: Ratio based normalized data in each image so that the mean of ratio of means of all of the features is equal to 1. The VALUE column contains the log2 ratio of the result file after normalisation

source_name: Mouse ID: L9

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

value: female

tag: age

source_name: AFP wild type pool liver (Mouse IDs: W7, W9, Y2, Y6)

tag: mouse ids


title: WhiteSpruce_26A04_26B08_bark

value: Twelve year old trees from a weevil screening trial

value: A

value: tree 04

value: tree 08


title: Peripheral blood leukocyte_city, Sample 13

description: column in raw data file: BN33_K

value: FEM

tag: bmi

tag: batch effect

value: PA

tag: life style

value: city


title: Mixture Replicate 3

tag: sample type

value: Pooled sample containing equal amounts (1 mg) of total RNA from 3 individual animals

tag: sex

value: Mixed males, females, and indeterminate

tag: tissue

value: Brain


title: PFOS_2


title: PFOS_3


title: PFOS_4


title: Peripheral blood leukocyte_suburban, Sample 53

description: column in raw data file: BN33_L

tag: rna integrity score

value: suburban


title: PFOS_5


title: Venlafaxine  Replicate 1

value: pooled sample of control (untreated) liver, brain and gonad, M and F


title: WhiteSpruce_26A01_26C06_bark

tag: origin

tag: cross

tag: replicate

tag: specimen

value: tree 01

value: from the leader of each tree, bark with attached phloem and cambium

tag: collection dates

value: Seed collected from controlled crosses between individuals ranked in open-pollinated progeny tests

value: C

value: tree 06


title: WhiteSpruce_26A18_26C11_bark

value: Twelve year old trees from a weevil screening trial

value: tree 18

tag: biomaterial provider

value: tree 11


title: Fluoxetine Replicate 2


title: Peripheral blood leukocyte_suburban, Sample 52

description: column in raw data file: BN33_I

tag: gender


title: Afp_fetal liver_rep4

source_name: Mouse ID: L11

value: female


title: Peripheral blood leukocyte_city, Sample 11

description: column in raw data file: BN33_H

value: MAL

tag: weight

tag: height


title: Peripheral blood leukocyte_suburban, Sample 51

description: column in raw data file: BN33_F

tag: age

value: PA


title: Peripheral blood leukocyte_city, Sample 10

description: column in raw data file: BN33_G

tag: bmi

value: city


title: Afp_fetal liver_rep6

source_name: Mouse ID: L1

tag: mouse ids


title: Control Replicate 3

value: Pooled sample containing equal amounts (1 mg) of total RNA from 3 individual animals


title: Peripheral blood leukocyte_city, Sample 12

description: column in raw data file: BN33_J

value: FEM

tag: batch effect

tag: life style


title: Afp_fetal liver_rep1

source_name: Mouse ID: K2

value: male


title: Venlafaxine Replicate 3

tag: sample type

tag: sex

value: Mixed males, females, and indeterminate

value: Brain


title: PFOS_1

tag: diet group

value: PFOS

tag: tissue

value: liver

tag: background strain

tag: mouse model


title: PFHxS_6

value: PFHxS


title: Afp_fetal liver_rep3

source_name: Mouse ID: L14


title: Afp_fetal liver_rep2

source_name: Mouse ID: K6


title: Peripheral blood leukocyte_suburban, Sample 50

description: column in raw data file: BN33_E

tag: rna integrity score

value: suburban


title: Fluoxetine Replicate 1

value: pooled sample of control (untreated) liver, brain and gonad, M and F


title: tef1:lae1 mutant 2 on lactose_rep2

city: Vienna

first: Christian

middle: P.

last: Kubicek

address: Getreidemarkt 9

country: Austria

institute: TU Vienna

description:
SAMPLE 8
58978202_532

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

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

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

organism: Trichoderma reesei

source_name: T. reesei growing on lactose for 28 hrs

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

growth_protocol: Trichoderma reesei strains QM9414 (ATCC 26921) and the lae1 deleted strain were grown in 1 l Erlenmeyerflasks flasks on a rotary shaker (250 rpm) at 30 C in the medium described by Seiboth et al. (2004) [Mol Microbiol 51:1015-25] with lactose as a carbon source at a final concentration of 10 g l-1.

extract_protocol: Total RNAs were extracted using TRIzol® reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), according to the manufacturer's instructions, and then purified using the RNeasy MinElute Cleanup Kit (Qiagen, Hilden, Germany). The RNA quality and quantity were determined using a Nanodrop spectrophotometer.

treatment_protocol: Mycelia from both stages were freeze-dried and ground in liquid nitrogen using a mortar and pestle. For each of the two experimental conditions, five independent replicates of mycelium were mixed.

tag: strain

value: tef1:lae1 overexpression mutant 2

tag: growth protocol

value: grown on lactose


title: PFHxS_3

tag: gender


title: tef1:lae1 mutant 1 on lactose_rep2

description:
SAMPLE 6
58978102_532

value: tef1:lae1 overexpression mutant 1


title: tef1:lae1 mutant 2 on lactose_rep1

description:
SAMPLE 7
58978002_532


title: PFHxS_1


title: PFHxS_4


title: tef1:lae1 mutant 1 on lactose_rep1

description:
SAMPLE 5
56936402_532


title: Afp liver adult rep11

value: 17 weeks


title: Peripheral blood leukocyte_suburban, Sample 47

description: column in raw data file: BN33_A

source_name: Peripheral blood leukocyte, Suburban


title: Afp liver adult rep9


title: Afp liver adult rep10


title: PFHxS_5


title: PFHxS_2


title: PFBS_6

value: PFBS


title: Peripheral blood leukocyte_suburban, Sample 49

description: column in raw data file: BN33_D

tag: weight

value: PA


title: Peripheral blood leukocyte_suburban, Sample 45

description: column in raw data file: BN25_K

value: MAL

tag: height

value: PB


title: Peripheral blood leukocyte_city, Sample 9

description: column in raw data file: BN33_B

source_name: Peripheral blood leukocyte, City

tag: age

value: city


title: Afp liver adult rep7

value: male


title: Peripheral blood leukocyte_suburban, Sample 48

description: column in raw data file: BN33_C

tag: bmi


title: Afp liver adult rep8

tag: mouse ids


title: Peripheral blood leukocyte_suburban, Sample 46

description: column in raw data file: BN25_L

tag: batch effect


title: PFBS_2


title: PFBS_5


title: PFBS_1


title: Peripheral blood leukocyte_suburban, Sample 43

description: column in raw data file: BN25_G

value: FEM

tag: life style


title: Afp liver adult rep6


title: QM 9414 on lactose_rep2

description:
SAMPLE 2
41639702_532

growth_protocol: Trichoderma reesei strains QM9414 (ATCC 26921) and the lae1 deleted strain were grown in 1 l Erlenmeyerflasks flasks on a rotary shaker (250 rpm) at 30 C in the medium described by Seiboth et al. (2004) [Mol Microbiol 51:1015-25] with lactose as a carbon source at a final concentration of 10 g l/1.

value: parent strain QM9414


title: delta-lae1 on lactose_1

description:
SAMPLE 3
41639802_532

value: delta-lae1 mutant


title: Peripheral blood leukocyte_suburban, Sample 44

description: column in raw data file: BN25_J


title: Peripheral blood leukocyte_suburban, Sample 40

description: column in raw data file: BN25_D


title: Afp liver adult rep4


title: Peripheral blood leukocyte_suburban, Sample 41

description: column in raw data file: BN25_E


title: delta-lae1 on lactose_2

description:
SAMPLE 4
41639602_532


title: Afp liver adult rep3


title: PFBS_4

value: liver


title: Afp liver adult rep5


title: QM 9414 on lactose_rep1

description:
SAMPLE 1
41639502_532


title: Afp liver adult rep2


title: PFBS_3


title: Peripheral blood leukocyte_suburban, Sample 39

description: column in raw data file: BN25_C


title: BMDM Kdo2 12h Expression (Cy3)

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
BMDM Expression in response to Kdo2 at 12 hours
Raw data file: US22502657_251486819800_S01_GE2-v5_95_Feb07_1_4.txt

hyb_protocol: 4x 44 k Agilent arrays were hybridized with 825 ng of each cDNA using the manufacturer's hybridization kit according to the instructions.

scan_protocol: Scanned on an Agilent Technologies Scanner using the extended dynamic range scan mode with a 5 µm pitch. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Data was further normalized between arrays using a multi-loess technique described in Corbeil et al (Journal of Molecular Endocrinology (2004) 33:1–9).
Dual-channel hybridization was analyzed as single-channel (ratios were not used). Each channel of biological replicates is therefore represented as a single Sample and the same raw data file is linked to two Sample records.

source_name: bone marrow-derived macrophages

label_protocol: Total RNA (250 ng) of two biological replicates was amplified and labeled using the Agilent Quick-Amp labeling kit according to the manufacturer's instructions.

growth_protocol: CD43-negative splenic B cells were isolated by magnetic depletion of CD43- and CD11b-expressing cells using MACS (Miltenyi, Bergisch Gladbach, Germany) according to the manufacturer's instructions. Peritoneal macrophages were harvested by peritoneal lavage with 10 ml ice-cold PBS 3 days after peritoneal injection of 3 ml thioglycollate broth. Peritoneal cells were washed once with PBS, and seeded in 10% fetal calf serum (FCS)/DMEM containing 100 U/ml penicillin/streptomycin in tissue culture-treated petri dishes overnight. Non-adherent cells were washed off with room temperature PBS. Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FCS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.

extract_protocol: Total RNA was extracted from 5 Mio cells on Rneasy columns (Qiagen) with on-column DNase digestion following the manufacturer's instructions. RNA quality was assessed on an Agilent 2100 BioAnalyzer.

tag: cell type

value: bone marrow-derived macrophages

tag: treatment

value: Kdo2 for 12 hours


title: Afp liver adult rep1


title: BMDM Kdo2 12h Expression (Cy5)


title: BMDM Ctrl 12h Expression (Cy5)

description:
BMDM Expression in response to mock treatment at 12 hours
Raw data file: US22502657_251486819800_S01_GE2-v5_95_Feb07_1_3.txt

value: dmso for 12 hours


title: wt cloned vs wt (ref)_spleen_rep8

value: 18-19 weeks

tag: genotype/variation

value: wt cloned

source_name: Reference pool wild type

value: wt


title: Peripheral blood leukocyte_city, Sample 8

description: column in raw data file: BN25_B


title: BMDM Ctrl 12h Expression (Cy3)


title: Peripheral blood leukocyte_suburban, Sample 42

description: column in raw data file: BN25_F

value: suburban


title: Peripheral blood leukocyte_suburban, Sample 37

description: column in raw data file: BN24_L


title: BMDM Kdo2 1h Expression (Cy5)

description:
BMDM Expression in response to Kdo2 at 1 hour
Raw data file: US22502657_251486819800_S01_GE2-v5_95_Feb07_1_2.txt

value: Kdo2 for 1 hour


title: Peripheral blood leukocyte_suburban, Sample 36

description: column in raw data file: BN24_K


title: wt cloned vs wt (ref)_spleen_rep7


title: Peripheral blood leukocyte_suburban, Sample 38

description: column in raw data file: BN25_A


title: wt cloned vs wt (ref)_spleen_rep6


title: BMDM Ctrl 1h Expression (Cy5)

description:
BMDM Expression in response to mock treatment at 1 hours
Raw data file: US22502657_251486819800_S01_GE2-v5_95_Feb07_1_1.txt

value: dmso for 1 hours


title: Macrophage Kdo2 12h Expression (Cy3)

description:
Macrophage Expression in response to Kdo2 at 12 hours
Raw data file: US22502657_251486819799_S01_GE2-v5_95_Feb07_1_4.txt


title: CD4 HIV+ 13_repl2

city: Charlestown

first: Matthew

last: Woods

state: MA

address: 149 13th Street

department: Computational Biology Core

institute: The Ragon Institute of MGH, MIT, and Harvard

description: HIV+ 13_repl2

hyb_protocol: Illumina standard iSCAN protocol

scan_protocol: Illumina standard iSCAN protocol

data_processing: Quantile Normalized, Background Corrected (BeadStudio).

source_name: CD4 HIV+

label_protocol: Illumina Whole Genome DASL assay per manufacturer protocol

extract_protocol: mRNA Extraction with RNAeasy kit from Qiagen

value: HLA-DR- CD4 cells, peripheral blood

tag: infection status

value: HAART Treated


title: CD4 HIV+ 15

description: HIV+ 14


title: wt cloned vs wt (ref)_spleen_rep3


title: wt cloned vs wt (ref)_spleen_rep5


title: Peripheral blood leukocyte_city, Sample 7

description: column in raw data file: BN24_I

value: MAL

value: PB

value: city


title: CD4 HIV+ 13_repl1

description: HIV+ 13_repl1


title: Peripheral blood leukocyte_suburban, Sample 35

description: column in raw data file: BN24_H


title: wt cloned vs wt (ref)_spleen_rep2

value: male


title: Macrophage Kdo2 12h Expression (Cy5)


title: BMDM Kdo2 1h Expression (Cy3)


title: BMDM Ctrl 1h Expression (Cy3)


title: CD4 HIV+ 12

description: HIV+ 12


title: Peripheral blood leukocyte_suburban, Sample 33

description: column in raw data file: BN24_F

value: FEM


title: wt cloned vs wt (ref)_spleen_rep1


title: CD4 HIV+ 11

description: HIV+ 11


title: Macrophage Ctrl 12h Expression (Cy5)

description:
Macrophage Expression in response to mock treatment at 12 hours
Raw data file: US22502657_251486819799_S01_GE2-v5_95_Feb07_1_3.txt


title: Macrophage Ctrl 12h Expression (Cy3)


title: Peripheral blood leukocyte_suburban, Sample 32

description: column in raw data file: BN24_E


title: CD4 HIV+ 10

description: HIV+ 10


title: wt cloned vs wt (ref)_liver_rep7


title: Peripheral blood leukocyte_city, Sample 6

description: column in raw data file: BN24_D


title: wt cloned vs wt (ref)_liver_rep6


title: PBMC control

description: GMC control

source_name: PBMC control

value: PBMC total RNA (ficoll extracted only)

value: Control


title: Peripheral blood leukocyte_suburban, Sample 31

description: column in raw data file: BN24_C


title: wt cloned vs wt (ref)_liver_rep8


title: wt cloned vs wt (ref)_liver_rep5


title: B cell Kdo2 12h Expression (Cy5)

description:
B cell Expression in response to Kdo2 at 12 hours
Raw data file: US22502657_251486819798_S01_GE2-v5_95_Feb07_1_4.txt

source_name: resting splenic B cells

value: resting splenic B cells

value: Kdo2 for 12 hours


title: wt cloned vs wt (ref)_liver_rep3

value: 18-19 weeks


title: CD4 HIV+ 06

description: HIV+ 06


title: wt cloned vs wt (ref)_liver_rep1

value: wt cloned


title: Macrophage Kdo2 1h Expression (Cy5)

description:
Macrophage Expression in response to Kdo2 at 1 hour
Raw data file: US22502657_251486819799_S01_GE2-v5_95_Feb07_1_2.txt


title: Peripheral blood leukocyte_city, Sample 5

description: column in raw data file: BN18_J


title: Peripheral blood leukocyte_suburban, Sample 29

description: column in raw data file: BN24_A


title: CD4 HIV+ 07

description: HIV+ 07


title: B cell Kdo2 12h Expression (Cy3)


title: wt cloned vs wt (ref)_liver_rep4

value: wt


title: Peripheral blood leukocyte_suburban, Sample 27

description: column in raw data file: BN18_K

value: suburban


title: Peripheral blood leukocyte_suburban, Sample 28

description: column in raw data file: BN18_L


title: B cell Kdo2 1h Expression (Cy5)

description:
B cell Expression in response to Kdo2 at 1 hour
Raw data file: US22502657_251486819798_S01_GE2-v5_95_Feb07_1_2.txt

value: Kdo2 for 1 hour


title: Macrophage Kdo2 1h Expression (Cy3)


title: B cell Ctrl 12h Expression (Cy5)

description:
B cell Expression in response to mock treatment at 12 hours
Raw data file: US22502657_251486819798_S01_GE2-v5_95_Feb07_1_3.txt

value: dmso for 12 hours


title: CD4 HIV+ 09

description: HIV+ 09

value: HLA-DR- CD4 cells, peripheral blood


title: Dll1 cloned vs Dll1 (ref)_spleen_rep8

value: Dll1 cloned

source_name: Reference pool Dll1 heterozygotes

value: Dll1 het


title: CD4 HIV+ 08

description: HIV+ 08

value: HAART Treated


title: CD4 HIV+ 05

description: HIV+ 05


title: Peripheral blood leukocyte_suburban, Sample 26

description: column in raw data file: BN18_H

value: PB


title: Peripheral blood leukocyte_suburban, Sample 30

description: column in raw data file: BN24_B


title: CD4 HIV+ 02

description: HIV+ 02


title: wt cloned vs wt (ref)_liver_rep2

value: male


title: Dll1 cloned vs Dll1 (ref)_spleen_rep7


title: B cell Ctrl 12h Expression (Cy3)


title: CD4 HIV+ 03

description: HIV+ 03


title: Gastric intestinal metaplasia P7686 V1

city: Padova

first: Matteo

last: Fassan

state: PD

address: via Gabelli 61

department: Department of Diagnostic Sciences & Special Therapies

country: Italy

institute: University of Padova

hyb_protocol: Hybridization of biotin-labeled complementary DNA was performed on the Ohio State University  miRNA microarray chip OSU_CCC version 4.0, which contains ~1100 miRNA probes, including 326 human and 249 mouse miRNA genes, spotted in duplicates. The hybridized chips were washed and processed to detect biotin-containing transcripts by streptavidin-Alexa647 conjugate and scanned on an Axon 4000B microarray scanner (Axon Instruments, Sunnyvale, CA).

scan_protocol: The microarrays were processed by using a method of direct detection of biotin-containing transcripts by streptavidin-Alexa647 conjugate. Processed slides were then scanned by using the PerkinElmer ScanArray XL5K Scanner, with the laser set to 635 nm, at power 80 and PMT 70 setting and a scan resolution of 10 nm. Microarray images were analyzed using GENEPIX PRO 6.0 (Axon Instruments).

data_processing: Average values of the replicate spots of each miRNA were background subtracted, normalized, and further analyzed. Normalization was performed using quantiles. miRNAs that are differentially expressed were identified using a random-variance t-test. The random-variance t-test is an improvement over the standard separate t-test as it permits sharing information among genes about within-class variation without assuming that all genes have the same variance. Genes were considered statistically significant if their p value was less than 0.01. A stringent significance threshold was used to limit the number of false positive findings.

source_name: H. pylori gastritis

label_protocol: Five μg of total RNA from each sample were reverse-transcribed using biotin end-labeled random-octamer oligonucleotide primer.

extract_protocol: Formalin-fixed paraffin-embedded biopsy samples were deparaffinized with xylene at 50°C for 3 minutes. Total RNA extraction was undertaken using the RecoverAll kit (Ambion Inc, Austin, Tex) according to manufacturer’s instructions.

tag: disease state

value: H. pylori gastritis

tag: histology

value: antral intestinal metaplasia

tag: tissue

value: antral intestinal metaplastic lesion


title: Gastric intestinal metaplasia P7684 T1

description: Hybridization of biotin-labeled complementary DNA was performed on the Ohio State University  miRNA microarray chip OSU_CCC version 4.0, which contains ~1100 miRNA probes, including 326 human and 249 mouse miRNA genes, spotted in duplicates.


title: Gastric intestinal metaplasia P7689 II1


title: CD4 HIV+ 04

description: HIV+ 04


title: Peripheral blood leukocyte_suburban, Sample 25

description: column in raw data file: BN18_G

value: MAL

tag: rna integrity score


title: Dll1 cloned vs Dll1 (ref)_spleen_rep6

tag: strain


title: CD4 HIV+ 01

description: HIV+ 01


title: Peripheral blood leukocyte_suburban, Sample 22

description: column in raw data file: BN18_D

tag: gender


title: Dll1 cloned vs Dll1 (ref)_spleen_rep5


title: Peripheral blood leukocyte_suburban, Sample 24

description: column in raw data file: BN18_F

value: FEM

tag: weight


title: Peripheral blood leukocyte_suburban, Sample 34

description: column in raw data file: BN24_G

tag: height


title: B cell Kdo2 1h Expression (Cy3)

value: resting splenic B cells


title: CD4 HIV- 08_repl1

description: HIV- 08_repl1

source_name: CD4 HIV-

value: HIV Negative


title: Peripheral blood leukocyte_city, Sample 4

description: column in raw data file: BN18_C

tag: age

value: city


title: Dll1 cloned vs Dll1 (ref)_spleen_rep4

value: 18-19 weeks


title: wt cloned vs wt (ref)_spleen_rep4

value: wt cloned

value: wt


title: CD4 HIV- 09

description: HIV- 09

value: HLA-DR- CD4 cells, peripheral blood


title: Peripheral blood leukocyte_suburban, Sample 23

description: column in raw data file: BN18_E

tag: bmi

value: suburban


title: CD4 HIV- 08_repl2

description: HIV- 08_repl2


title: Dll1 cloned vs Dll1 (ref)_spleen_rep3

value: Dll1 cloned

value: Dll1 het

tag: mouse ids


title: Peripheral blood leukocyte_suburban, Sample 21

description: column in raw data file: BN18_B

tag: batch effect

value: PB


title: Gastric intestinal metaplasia P7681 P1


title: Dll1 cloned vs Dll1 (ref)_spleen_rep2

value: male


title: Gastric intestinal metaplasia P7664 J1

value: H. pylori gastritis


title: Gastric intestinal metaplasia P7667 R1

value: antral intestinal metaplasia


title: Gastric intestinal metaplasia P7666 N1

value: antral intestinal metaplastic lesion


title: Gastric intestinal metaplasia P7659 D1


title: Gastric intestinal metaplasia P7662 H1


title: CD4 HIV- 07_repl2

description: HIV- 07_repl2


title: Gastric intestinal metaplasia P7658 B1


title: Dll1 cloned vs Dll1 (ref)_liver_rep8


title: CD4 HIV- 06

description: HIV- 06


title: Hp gastritis P7663 I1

value: non metaplastic antrum


title: CD4 HIV- 07_repl1

description: HIV- 07_repl1


title: Peripheral blood leukocyte_suburban, Sample 18

description: column in raw data file: BN13_K

value: MAL

tag: life style


title: Dll1 cloned vs Dll1 (ref)_liver_rep7


title: Dll1 cloned vs Dll1 (ref)_spleen_rep1


title: Peripheral blood leukocyte_suburban, Sample 20

description: column in raw data file: BN18_A

value: FEM


title: CD4 HIV- 04

description: HIV- 04

tag: cell type

value: HIV Negative


title: Dll1 cloned vs Dll1 (ref)_liver_rep5


title: CD4 HIV- 05

description: HIV- 05


title: Hp gastritis P7661 G1


title: Peripheral blood leukocyte_suburban, Sample 17

description: column in raw data file: BN13_J


title: Peripheral blood leukocyte_suburban, Sample 16

description: column in raw data file: BN13_I


title: Dll1 cloned vs Dll1 (ref)_liver_rep6


title: Peripheral blood leukocyte_suburban, Sample 15

description: column in raw data file: BN13_H


title: CD4 HIV- 03_repl1

description: HIV- 03_repl1


title: Hp gastritis P7678 C1


title: Hp gastritis P7677 A1


title: CD4 HIV- 02

description: HIV- 02


title: Peripheral blood leukocyte_suburban, Sample 14

description: column in raw data file: BN13_G


title: Hp gastritis P7671 BB1


title: Hp gastritis P7674 FF1


title: CD4 HIV- 03_repl2

description: HIV- 03_repl2


title: Hp gastritis P7685 U1


title: Dll1 cloned vs Dll1 (ref)_liver_rep4


title: Peripheral blood leukocyte_city, Sample 3

description: column in raw data file: BN13_C

value: city


title: CD4 EC 09

description: EC 09

source_name: CD4 EC

value: Elite Controller


title: CD4 EC 12

description: EC 12


title: Peripheral blood leukocyte_suburban, Sample 13

description: column in raw data file: BN13_D


title: Hp gastritis P7680 O1


title: Esophageal intestinal metaplasia P7650 DDD1

source_name: Barrett's esophagus

value: Barrett's esophagus

value: esophageal intestinal metaplasia

value: esophageal intestinal metaplastic lesion


title: Dll1 cloned vs Dll1 (ref)_liver_rep2

value: 18-19 weeks


title: Nox4_pancreas_rep7

tag: tissue type

value: pancreas

value: 17 weeks

tag: mutation

value: Nox4 knockout

source_name: Nox4 wild type pool

value: wild type


title: CD4 EC 10

description: EC 10

value: HLA-DR- CD4 cells, peripheral blood

tag: infection status


title: CD4 EC 11

description: EC 11


title: Nox4_pancreas_rep8

value: male

tag: genotype/variation


title: Dll1 cloned vs Dll1 (ref)_liver_rep3

value: Dll1 cloned

value: Dll1 het


title: Esophageal intestinal metaplasia P7670 AA1

tag: disease state

tag: histology


title: Hp gastritis P7688 HH1

value: H. pylori gastritis

value: non metaplastic antrum

tag: tissue


title: Hp gastritis P7682 Q1


title: CD4 EC 08

description: EC 08


title: CD4 HIV- 01

description: HIV- 01

value: HIV Negative


title: Peripheral blood leukocyte_city, Sample 2

description: column in raw data file: BN13_B

value: MAL

tag: rna integrity score

value: PB

value: city


title: Peripheral blood leukocyte_suburban, Sample 9

description: column in raw data file: BN07_I

tag: gender

value: PA

value: suburban


title: Dll1 cloned vs Dll1 (ref)_liver_rep1

value: 18-19 weeks

tag: strain


title: Peripheral blood leukocyte_city, Sample 1

description: column in raw data file: BN13_A

tag: weight

tag: height


title: Peripheral blood leukocyte_suburban, Sample 11

description: column in raw data file: BN07_K

value: FEM

tag: age

tag: bmi


title: Nox4_pancreas_rep5

value: pancreas

value: 17 weeks

tag: mouse ids


title: Nox4_pancreas_rep2

value: Nox4 knockout

value: wild type


title: Peripheral blood leukocyte_suburban, Sample 8

description: column in raw data file: BN07_H

tag: batch effect

tag: life style


title: Nox4_pancreas_rep6

tag: tissue type

value: male


title: Nox4_pancreas_rep4

tag: mutation


title: CD4 EC 07

description: EC 07

tag: cell type

value: HLA-DR- CD4 cells, peripheral blood

tag: infection status

value: Elite Controller


title: Esophageal intestinal metaplasia P7648 AAA1

tag: disease state

value: Barrett's esophagus

value: esophageal intestinal metaplasia

value: esophageal intestinal metaplastic lesion


title: Nox4_pancreas_rep3

tag: genotype/variation


title: Peripheral blood leukocyte_suburban, Sample 12

description: column in raw data file: BN07_L

value: MAL


title: CD4 EC 06

description: EC 06


title: Nox4_pancreas_rep1


title: CD4 EC 03

description: EC 03


title: Peripheral blood leukocyte_suburban, Sample 19

description: column in raw data file: BN13_L

value: PB


title: Esophageal intestinal metaplasia P7694 PP1

tag: histology

tag: tissue


title: Peripheral blood leukocyte_suburban, Sample 10

description: column in raw data file: BN07_J

tag: gender

tag: rna integrity score


title: Esophageal intestinal metaplasia P7690 JJ1


title: Esophageal intestinal metaplasia P7673 DD1


title: Esophageal intestinal metaplasia P7675 GG1


title: Esophageal intestinal metaplasia P7699 VV1


title: Peripheral blood leukocyte_suburban, Sample 5

description: column in raw data file: BN07_E

tag: weight


title: CD4 EC 01

description: EC 01


title: CD4 EC 04

description: EC 04


title: Nox4_muscle_rep7

value: muscle

tag: strain


title: Nox4_muscle_rep6

tag: age


title: Peripheral blood leukocyte_suburban, Sample 7

description: column in raw data file: BN07_G

tag: height

tag: bmi

value: PA


title: Nox4_muscle_rep8

tag: mouse ids


title: Nox4_muscle_rep5


title: CD4 EC 05

description: EC 05


title: Peripheral blood leukocyte_suburban, Sample 4

description: column in raw data file: BN07_D

tag: batch effect

tag: life style

value: suburban


title: 5103

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: human lymphoblast cell line was obtained from a patient with Golabi-Ito-Hall syndrome or from a healthy control person, matched for age, gender and race.

hyb_protocol: A mixture of 10pmol Cy5 incorporated dye and 14 pmol Cy3 incorporated dye was fragmented and resuspended in hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software (Agilent Technologies).

data_processing: We use the Agilent processed signal values (i.e., features gProcessedSignal and rProcessedSignal) from Agilent Feature Extraction software and compute log2-ratios.  We remove Agilent control probes. In case of multiple probes for the same Agilent ID, log2-ratios are averaged.

source_name: lymphoblast cell line_control_rep2

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy5 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

extract_protocol: Total RNA was isolated using the GenElute Total RNA miniprep kit from Sigma.

value: human lymphoblast cell line

tag: sample type

value: healthy control matched for age, gender and race

source_name: human lymphoblast cell line_GIH_rep4

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer's protocol (Agilent Technologies).

value: patient with Golabi-Ito-Hall syndrome


title: Peripheral blood leukocyte_suburban, Sample 6

description: column in raw data file: BN07_F

value: FEM


title: Esophageal intestinal metaplasia P7644 MM1


title: Nox4_muscle_rep4

tag: tissue type

value: 17 weeks

tag: mutation

value: Nox4 knockout


title: CD4 EC 02

description: EC 02

tag: cell type

tag: infection status


title: Peripheral blood leukocyte_suburban, Sample 1

description: column in raw data file: BN07_A


title: Esophageal gastric metaplasia P7646 ZZ1

tag: disease state

tag: histology

value: esophageal gastric metaplasia

value: esophageal gastric metaplastic lesion


title: Nox4_muscle_rep2

tag: gender

value: male

tag: genotype/variation

value: wild type


title: 5061

source_name: lymphoblast cell line_control_rep1

source_name: human lymphoblast cell line_GIH_rep3


title: Nox4_muscle_rep3


title: Esophageal gastric metaplasia P7665 M1

value: Barrett's esophagus

tag: tissue


title: 5102

source_name: lymphoblast cell line_GIH_rep2

source_name: human lymphoblast cell line_control_rep4


title: FP_sh86_120909

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

data_processing: Feature intensity was extracted and processed using MAS5 by Affymetrix GeneChip Command Console as CEL files. CHP files are generated by Affymetrix Expression Console.

source_name: HEL cells with shRNA against PRMT5

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: 10% fetal bovine serum with RPMI media, 37 degree 5% CO2 incubator

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with invitrogen superscriptase.

treatment_protocol: 0.5 micromolar of cep701 is added to the media for 16 hours. The lentivirus pLKO vector expression PRMT5 shRNA (TRCN0000107086) was used to make stable cell line knocking down PRMt5.

value: shRNA against PRMT5

tag: cell line

value: HEL cells


title: FP_LKO_scramble_120909

source_name: HEL cells with scramble shRNA

value: scramble shRNA


title: 5060

source_name: lymphoblast cell line_GIH_rep1

source_name: human lymphoblast cell line_control_rep3


title: Esophageal gastric metaplasia P7696 RR1


title: Nox4_kidney_rep8

value: kidney

tag: age

tag: strain


title: Nox4_muscle_rep1

value: muscle


title: Esophageal gastric metaplasia P7698 UU1


title: Nox4_kidney_rep5


title: D6-3

city: Columbia

first: Betul

middle: Fatma

last: Guloglu

state: MO

address: 1 Hospital Drive, M616 Medical Sciences Building

department: Microbiology and Immunology

institute: University of Missouri

description: Division 6 (experiment 3)

hyb_protocol: Antisense RNA was hybridized to Illumina beadchip array at 58C for 20hrs. After hybridization, the chips were washed and stained with streptavidin-Cy3.

scan_protocol: The image data was acquired by BeadArray reader (Illumina)

data_processing: The microarray data was processed by using BeadStudio v2.0 software, background substracted, and normalized using cubic spline algorithm. Genes with Detection p-val less than 0.05 were included. Genes differentially expressed between groups were identified using the Illumina custom error model implemented in BeadStudio. Division 4 (D4) was set as control group. Genes were considered significantly differentially expressed when p values were less than 0.05 (Diffscore 13) and the fold change was greater than 1.8 between D4 and D8 groups.

source_name: Division 6

label_protocol: Total RNA was used to make the biotin-labeled antisense RNA target using the Illumina TotalPrep RNA amplification kit  by following the manufacturer`s procedures.

growth_protocol: CFSE-labeled DO11.10 CD4 naïve T cells were transferred into Balb/c mice and the hosts were immunized with OVA peptide in CFA. 66-72 hrs later, the lymph node cells were harvested and Divisions 3, 4, 6 and 8 were sorted.

extract_protocol: total RNA was extracted using TRI reagent (Sigma Aldrich)

value: Balb/c

value: lymph node

value: DO11.10 CD4 T effectors divided 5 times


title: D8-3

description: Division 8 (experiment 3)

source_name: Division 8

value: DO11.10 CD4 T effectors divided 7 times


title: Esophageal gastric metaplasia P7693 OO1


title: Nox4_kidney_rep7


title: Nox4_kidney_rep6


title: D8-1

description: Division 8 (experiment 1)


title: D8-2

description: Division 8 (experiment 2)


title: D6-2

description: Division 6 (experiment 2)


title: FP_DMSO_16hrs_2

source_name: DMSO treated HEL cells

tag: treatment

value: DMSO

value: HEL cell


title: D6-1

description: Division 6 (experiment 1)


title: FP_LKO_scramble_111709


title: Esophageal gastric metaplasia P7700 CCC1


title: Esophageal gastric metaplasia P7692 LL1


title: Esophageal gastric metaplasia P7679 F1


title: FP_CEP701_16hrs_2

source_name: cep701 treated HEL cells


title: FP_sh86_111709


title: FP_DMSO_16hrs_1


title: Nox4_kidney_rep3

value: 17 weeks

value: Nox4 knockout

tag: mouse ids


title: Esophageal gastric metaplasia P7687 EE1

value: esophageal gastric metaplasia

value: esophageal gastric metaplastic lesion


title: D4-3

description: Division 4 (experiment 3)

source_name: Division 4

value: DO11.10 CD4 T effectors divided 3 times


title: Nox4_kidney_rep4

value: male

value: wild type


title: Esophageal intestinal metaplasia P7676 SS1

source_name: Barrett's esophagus

value: Barrett's esophagus

value: esophageal intestinal metaplasia

value: esophageal intestinal metaplastic lesion


title: Nox4_brain_rep7

value: brain

source_name: Nox4 wild type pool


title: Nox4_kidney_rep1

value: kidney


title: D4-1

description: Division 4 (experiment 1)

value: Balb/c

value: lymph node


title: Nox4_brain_rep8


title: D4-2

description: Division 4 (experiment 2)


title: C2M plus polystyrene beads, biological rep 2

city: Cork

first: John

middle: Andrew

last: Mac Sharry

state: Cork

address: College Road

department: APC, Biosciences Instiute

country: Ireland

institute: UCC

description: Gene expression data from C2M plus polystyrene beads

hyb_protocol: Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station

scan_protocol: Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000

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 data were further analysed using GeneSpring 7.3.1 software (Silicon Genetics) to determine significant changes, P <0.05, 1.5 fold difference.The data were falso analysed using Pathway Studio® Desktop version 7.0 (Ariadne Genomics, Rockville, MD) for differentially expressed genes and associated pathways.

source_name: C2-M plus polystyrene beads 2 hours

label_protocol: 1 ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences)

growth_protocol: C2BBe1 cells were cultured for 21 days on Transwell inserts and then co-cultured with Raji B cells for 72 hours to generate M cell-like cells (C2-M)

extract_protocol: mirVana extraction (Ambion) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: C2M cells were co-incubated with bacteria or beads for 2 hours

value: C2-M cell

tag: cell line source

value: polystyrene beads


title: C2M plus polystyrene beads, biological rep 1


title: C2M plus polystyrene beads, biological rep 3


title: D3-1

description: Division 3 (experiment 1)

source_name: Division 3

value: DO11.10 CD4 T effectors divided 2 times


title: Normal esophagus P7697 TT1

value: Normal esophagus


title: Normal esophagus P7695 QQ1


title: D3-2

description: Division 3 (experiment 2)


title: Normal esophagus P7649 BBB1


title: FP_CEP701_16hrs_1

value: HEL cells


title: C2M plus Bacteroides fragilis, biological rep 2

description: Gene expression data from C2M plus Bacteroides fragilis

source_name: C2-M plus Bacteroides fragilis 2 hours

value: Bacteroides fragilis


title: Nox4_brain_rep5

value: 17 weeks

value: Nox4 knockout


title: C2M plus Bacteroides fragilis, biological rep 1


title: Wild Type 9

city: Turku

first: Sonia

last: Bourguiba-Hachemi

address: Kiinamyllynkatu 10

department: Dept Physiology

country: Finland

institute: University of Turku

hyb_protocol: The labelled cRNA was purified and hybridized to the BeadChip at 58 deg.C, for 17 hours following the Illumina Whole-Genome Gene Expression Protocol for BeadStation. Hybridization was detected with Cyanine3-streptavidine (GE Healthcare, Little Chalfont, UK)

scan_protocol: The arrays were scanned with the Illumina BeadArray Reader. Normalization and statistical analyses of the microarray data were performed using the statistical software R package limma (http://www.R-project.org) or Sigma Stat 3.1 (SPSS Inc., Chicago, IL, USA).

data_processing: Data are normalized to remove variation between samples caused by non-biological reasons. This data set has been normalized using the quantile normalization method which is a standard method used for normalizing Illumina data.

source_name: Whole testis

label_protocol: Biotinylated cRNA were prepared with the Illumina RNA TotalPrep Amplification Kit (Ambion Inc., Austin, TX, USA).

growth_protocol: We used two established transgenic mouse lines: transgenic mice expressing Cre recombinase under the control of the AMH gene promoter selectively in Sertoli cells (Lecureuil C, Genesis 2002) and the floxed Rb mice were generously provided by Dr Anton Berns, of The Netherlands Cancer Institute (Vooijs M, Oncogene 1998). To generate the Sertoli cell-specific Rb conditional knockouts, transgenic Amh-Cre male mice were bred with female mice containing two floxed copies of Rb. These matings yielded SC-RbKO mice, along with other genotypes.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. The RNA concentrations were measured with Nanodrop ND-1000 (Thermo Fisher Scientific, Waltham, MA, USA) and RNA quality was controlled by Experion analysis (Bio-Rad Laboratories, Hercules, CA, USA). The microarray analysis were carried out at the Finnish DNA-Microarray Centre utilizing the MouseWG-6 v2 Expression BeadChips (Illumina, San Diego, CA, USA).

tag: age (days old)

tag: genotype


title: D3-3

description: Division 3 (experiment 3)


title: C2M plus Bacteroides fragilis, biological rep 3


title: Normal esophagus P7647 WW1


title: Nox4_brain_rep6

tag: tissue type

value: male


title: Normal esophagus P7683 S1


title: Nox4_brain_rep4

tag: mutation

value: wild type


title: SC-RbKO 2

value: SC-RbKO


title: Normal esophagus P7691 KK1

value: Barrett's esophagus


title: Nox4_brain_rep3


title: Nox4_brain_rep2


title: Normal esophagus P7672 CC1


title: Peripheral blood leukocyte_suburban, Sample 2

description: column in raw data file: BN07_B

source_name: Peripheral blood leukocyte, Suburban

value: FEM

tag: weight

tag: height

tag: bmi

tag: rna integrity score

tag: batch effect

value: PA

tag: life style

value: suburban


title: Normal esophagus P7660 E1

tag: disease state

tag: histology

tag: tissue


title: Normal esophagus P7668 W1


title: Peripheral blood leukocyte_suburban, Sample 3

description: column in raw data file: BN07_C

tag: gender

value: MAL

tag: age


title: Nox4_brain_rep1

value: brain

tag: strain

tag: genotype/variation

tag: mouse ids


title: C2M plus Escherichia coli, biological rep 3

description: Gene expression data from C2M plus Escherichia coli

source_name: C2-M plus Escherichia coli 2 hours

tag: cell type

value: C2-M cell

tag: cell line source

tag: treatment

value: Escherichia coli


title: EMP3_thymus_rep7

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse

source_name: EMP3 mutant (thymus)

tag: mouse id

tag: sex

value: thymus

source_name: EMP3 wild type pool


title: Wild Type 12

tag: age (days old)

tag: genotype


title: SC-Rb+/- 7

value: SC-Rb+/-


title: C2M plus Escherichia coli, biological rep 1


title: Wild Type 10


title: Normal esophagus P7645 NN1

value: Normal esophagus


title: C2M plus Lactobacillus salivarius, biological rep 1

description: Gene expression data from C2M plus Lactobacillus salviarius

source_name: C2-M plus Lactobacillus salivarius 2 hours

value: Lactobacillus salviarius


title: EMP3_thymus_rep8

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

value: 17 weeks


title: C2M plus Lactobacillus salivarius, biological rep 3


title: SC-RbKO 1


title: C2M plus Escherichia coli, biological rep 2


title: Wild Type 11


title: C2M plus Lactobacillus salivarius, biological rep 2


title: SC-RbKO 4


title: C2M control, biological rep 3

description: Gene expression data from C2M control cells

source_name: C2-M cell control

value: control


title: SC-Rb+/- 5


title: C2M control, biological rep 2


title: EMP3_thymus_rep5

value: male


title: EMP3_thymus_rep6


title: EMP3_thymus_rep2


title: SC-Rb+/- 6


title: SC-RbKO 3


title: EMP3_thymus_rep3


title: Wild Type 8

value: wild type


title: C2M control, biological rep 1


title: Mouse melanocytes 21d after NoUV treatment, rep3

city: Bethesda

first: Sean

last: Davis

state: MD

address: 37 Convent Drive, Room 6138

institute: National Cancer Institute

hyb_protocol: Per manufacturer recommendation.

scan_protocol: Per manufacturer recommendation.

data_processing: A variance stabilization transformation followed by quantile normalization and quality assessment were performed using the lumi bioconductor package.

source_name: Flow-sorted melanocytes, no UV, 21 days

label_protocol: Per manufacturer recommendation.

growth_protocol: A double homozygous Dct-rtTA/TRE-H2BGFP transgenic mouse line (Dct-GFP) was established in the albino FVB/N background, and males were crossed with wildtype FVB/N females to produce litters that were 100% Dct-GFP double heterozygous.

extract_protocol: Melanocytes were isolated from the dorsal skin of Dct-GFP mouse pups irradiated at P1 with either UVB or UVA. Doxycycline-induced GFP-labeled melanocytes were isolated via fluorescence-activated cell sorting (FACS) at 1 day, 6 days, and 21 days post irradiation. Following FACS collection of cells into PBS+1% BSA solution, the cells were centrifuged at 4C. Total RNA was isolated from the pelleted cells by Trizol (Invitrogen) organic extraction, followed by the RNeasy Micro Kit (Qiagen Sciences, MD, USA) procedure.

treatment_protocol: Precisely defined wideband wavelengths and physiologically relevant doses of UVB (output peak = 308 nm; total dose = 6 kJ/m2; equivalent to 15 times the Standard Erythemal Dose) and UVA (output peak = 375 nm; total dose = 150 kJ/m2) were used to irradiate Dct-GFP neonatal mice at postnatal day 1 (P1). To avoid potential complications of GFP expression, including toxicity associated with chronic expression and UV absorption, GFP was routinely induced by doxycycline administration only after UV irradiation, 24 hours prior to skin harvest.

tag: strain/background

value: FVB/N

value: double heterozygous Dct-rtTA/TRE-H2BGFP (Dct-GFP)

tag: developmental stage

value: postnatal

value: dorsal skin

value: melanocytes

tag: uv treatment

tag: days to harvest of cells

tag: group


title: carv_con

city: Atlanta

first: Michael

last: Zilliox

state: GA

address: 1510 Clifton Road

institute: Emory University School of Medicine

description: S. cerevisiae, strain BY4742, control

hyb_protocol: 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip human U133Plus 2.0 arrays for 16hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was then used to wash and stain the chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA.  The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was done through the GeneChip Operating System 1.4.1 (GCOS) software from Affymetrix, using the standard default settings.

data_processing: MAS 5.0 and PLIER

organism: Saccharomyces cerevisiae

source_name: yeast

label_protocol: RNA was processed using the RNA amplification protocol described by Affymetrix (Affymetrix Expression Manual). Briefly, 5 micrograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer (Proligo LLC, Boulder, Colorado) and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the product was purified by phenol-chloroform extraction, and biotinilated anti-sense cRNA was generated through in vitro transcription using the BioArray RNA High Yield Transcript Labelling kit (ENZO Life Sciences Inc., Farmingdale, New York).

extract_protocol: Hot acidic phenol extraction

value: untreated


title: SCAMD

description: S. cerevisiae, strain BY4742, treated with amiodarone for 1 hour

value: with amiodarone for 1 hour


title: carv_01

description: S. cerevisiae, BY4742 strain, treated with 0.01% carvacrol for 15 minutes

value: with 0.01% carvacrol for 15 minutes


title: carv_005

description: S. cerevisiae, strain BY4742, treated with 0.005% carvacrol for 15 minutes.

value: with 0.005% carvacrol for 15 minutes.


title: Mouse melanocytes 21d after NoUV treatment, rep1

tag: tissue


title: EMP3_spleen_rep8

source_name: EMP3 mutant (spleen)

tag: age

value: spleen


title: EMP3_thymus_rep4

value: thymus


title: EMP3_spleen_rep7


title: cnb1

description: S. cerevisiae, cnb1 knock out that is isogenic to strain BY4742, treated with amiodarone for 30 minutes.

value: cnb1 knock

tag: strain

value: with amiodarone for 30 minutes.


title: EMP3_spleen_rep6

value: 17 weeks


title: EMP3_thymus_rep1


title: Esophageal gastric metaplasia P7669 Z1

tag: disease state

value: Barrett's esophagus

tag: histology

value: esophageal gastric metaplasia

value: esophageal gastric metaplastic lesion


title: Mouse melanocytes 21d after UVB treatment, rep3

source_name: Flow-sorted melanocytes, UVB, 21 days

value: FVB/N

tag: cell type

value: UVB


title: EMP3_spleen_rep5

value: male


title: E15.5 mouse tg4

city: LYON

first: Jiri

last: ZAVADIL

state: Other

address: 150 COURS ALBERT THOMAS

country: France

institute: IARC WHO

description:
Total RNA extracted using RNeasy micro-elute columns (QIAGEN)
Total RNA

hyb_protocol: 2.2 micrograms of amplified/labeled cDNA was hybridized for 17 hr to the Affymetrix array. Genechips® were processed using protocol EukGE_WS2v4 450 for Genechip® fluidics station 450.

data_processing: Feature intensity was extracted by GeneChip Operating System as CEL files. The probe-level analysis of the CEL files was done by the RMA algorithm using GeneSpring 7.2 program. No further adjustments were made to the data in the table.

source_name: Total RNA from dnBrg1 mouse E15.5 lens

label_protocol: 50 ng total RNA was amplified using the NUGEN Ovation™ Biotin RNA Amplification and Labeling System. Amplified cDNA was fragmented and biotin labeled according to manufacturer's instructions.

growth_protocol: Embryonic day 15.5 Brg1 dominant-negative and wildtype embryos were used.

extract_protocol: Total RNA was extracted using RNeasy micro-elute columns (QIAGEN), according to manufacturer's instructions.

treatment_protocol: Embryonic day 15.5 Brg1 dominant-negative and wildtype lenses were dissected.

value: mixed background (Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J Exp Med. 2003 Dec 15;198(12):1937-49.)

value: αA-crystallin promoter driven dominant-negative Brg1

value: lens


title: Mouse melanocytes 21d after NoUV treatment, rep2

value: double heterozygous Dct-rtTA/TRE-H2BGFP (Dct-GFP)

value: postnatal

value: dorsal skin

value: melanocytes


title: BxPC-3 + PMA (1µM; 4h), biological rep 3

city: Dublin

first: Annamarie

last: Rogers

address: AMNCH

department: Surgery

institute: Trinity College Dublin

description: Human pancreatic cancer cells originally isolated from a primary tumour. Cells were treated with PMA (1µM) for 4 hours.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The probe arrays were scanned at 560nm using a confocal laser-scanning microscope - Affymetrix Scanner 3000.

data_processing: Data was 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: Human Pancreatic Cancer Cell Line (ATCC)

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

growth_protocol: All cell culture reagents were purchased from Sarstedt (Wexford, Ireland).  Human pancreatic cancer cell lines, AsPC-1 and BxPC-3, were purchased from the American Tissue Culture Collection (Manassas, VA, USA).  Cells were cultured to 80% confluence in RPMI-1640 (Sigma-Aldrich, Ireland)  supplemented with L-glutamine (2mM, All chemicals, unless otherwise stated, were purchased from Sigma-Aldrich, Ireland), HEPES (10mM; Invitrogen, NY, USA), sodium pyruvate (1mM), glucose (4.5g/L), sodium bicarbonate (1.5g/L) and foetal calf serum (10%; Invitrogen) in a humidified atmosphere at 37°C and 5% carbon dioxide.  At 80% confluency, cells were subcultured by trypsinization using 0.25% trypsin-EDTA. Cells were then counted and resuspended in phosphate buffered saline (PBS) (Sigma-Aldrich, Ireland) at a concentration of 5 x 105/mL. Experiments were performed using three different cell passages.

extract_protocol: Total RNA was extracted from cells and tissues with the Qiagen RNeasy Midi Kit (Qiagen, UK), including a DNase digestion step, according to the manufacturer’s instructions.

treatment_protocol: For gene expression studies, cells were serum starved overnight (2.5% foetal calf serum (FCS)) before treatment with a final concentration of PMA (1µM; reconsitituted in DMSO, 0.1%) for 4 hours. In parallel experiments, lysis buffer (350 μl; Qiagen, West Sussex, UK), containing β-mercaptoethanol (0.145 M) to avoid RNA degradation, was added to control and treated cells which were frozen at -80°C for isolation of total RNA

tag: cell passage

tag: cell line


title: BxPC-3 + PMA (1µM; 4h), biological rep 1


title: Mouse melanocytes 21d after UVB treatment, rep1


title: Nox4_kidney_rep2

tag: tissue type

value: kidney

tag: gender

tag: mutation

tag: genotype/variation

value: Nox4 knockout

source_name: Nox4 wild type pool

value: wild type

tag: mouse ids


title: E15.5 mouse tg3

tag: genotype


title: BxPC-3 + PMA (1µM; 4h), biological rep 2


title: E15.5 mouse tg2

description:
Total RNA extracted using RNeasy micro-elute columns (QIAGEN)
Polysome bound RNA


title: Mouse melanocytes 06d after NoUV treatment, rep3

source_name: Flow-sorted melanocytes, no UV, 6 days

tag: strain/background

tag: developmental stage

tag: uv treatment


title: EMP3_spleen_rep4

tag: mouse id

tag: sex

value: 17 weeks

tag: tissue

value: spleen


title: E15.5 mouse wt4

source_name: Total RNA from wild type mouse E15.5 lens

tag: strain

tag: age


title: E15.5 mouse tg1


title: Mouse melanocytes 21d after UVB treatment, rep2

tag: cell type

tag: days to harvest of cells

tag: group


title: E15.5 mouse wt3


title: Mouse melanocytes 01d after UVA treatment, rep3

source_name: Flow-sorted melanocytes, UVA, 1 day

value: UVA


title: EMP3_spleen_rep2


title: Mouse melanocytes 01d after UVB treatment, rep3

source_name: Flow-sorted melanocytes, UVB, 1 day


title: BxPC-3 control untreated cells, biological rep 3

description: Human pancreatic cancer cells originally isolated from a primary tumour. Untreated control cells

tag: cell passage

tag: cell line


title: BxPC-3 control untreated cells, biological rep 2


title: BxPC-3 control untreated cells, biological rep 1


title: EMP3_spleen_rep1


title: JR32 strain grown to exponential phase, replicate 5

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

description: L. pneumophila was grown to exponential phase in rich AYE broth. This is the E phase transcriptome obtained with standard protocol.

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461).

data_processing: The data was background subtracted and normalized by calculating the contribution of each spot to the total intensity and the ratio to gDNA was recorded.

label: AlexaFluor 546

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: RNA obtained from JR32 grown to exponential phase

label_protocol: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461).

extract_protocol: TRIzol reagent (Invitrogen).

tag: media

value: AYE broth, 37C

label: AlexaFluor 647

molecule: genomic DNA

source_name: Genomic DNA used as reference channel

label_protocol: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.

extract_protocol: Wizard Genomic Purification Kit (Promega).

tag: reference

value: genomic DNA


title: Mouse melanocytes 06d after UVB treatment, rep3

source_name: Flow-sorted melanocytes, UVB, 6 days

value: FVB/N

value: UVB


title: JR32 strain grown to exponential phase, replicate 6


title: AsPC-1 + PMA (1µM; 4h), biological rep 2

description: Human pancreatic cancer cells originally isolated from ascites. Cells were treated with PMA (1µM) for 4 hours.


title: Mouse melanocytes 01d after NoUV treatment, rep3

source_name: Flow-sorted melanocytes, no UV, 1 day


title: Mouse melanocytes 06d after UVA treatment, rep3

source_name: Flow-sorted melanocytes, UVA, 6 days


title: d4 deltaCnA replicate 1

city: Shanghai

first: Xiang

last: Li

state: Shanghai

address: 225 South Chongqing Road

country: China

institute: Institute of Health Sciences

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using cubic spline with IlluminaGUI in R

source_name: ideltaCnAES cells

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

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

tag: protocol

value: d4 deltaCnA


title: E15.5 mouse wt1

value: mixed background (Gebuhr TC, Kovalev GI, Bultman S, Godfrey V, Su L, Magnuson T. The role of Brg1, a catalytic subunit of mammalian chromatin-remodeling complexes, in T cell development. J Exp Med. 2003 Dec 15;198(12):1937-49.)

tag: genotype


title: JR32 strain grown to exponential phase, replicate 4


title: AsPC-1 + PMA (1µM; 4h), biological rep 3


title: AsPC-1 control untreated cells, biological rep 3

description: Human pancreatic cancer cells originally isolated from ascites. Untreated control cells.


title: Mouse melanocytes 01d after UVA treatment, rep1

tag: strain/background


title: JR32 strain grown to exponential phase, replicate 3


title: JR32 strain grown to exponential phase, replicate 2


title: d4 deltaCnA replicate 2

description: replicate 2


title: E15.5 mouse wt2

value: lens


title: Mouse melanocytes 01d after UVA treatment, rep2

value: double heterozygous Dct-rtTA/TRE-H2BGFP (Dct-GFP)

tag: developmental stage


title: d1 deltaCnA replicate 2

description: replicate 2

value: d1 deltaCnA


title: d1 deltaCnA replicate 1

description: replicate 1


title: Primary mouse keratinocytes, rep3

source_name: Primary mouse keratinocytes, no UV

value: postnatal

value: dorsal skin

value: keratinocytes

tag: uv treatment


title: JR32 strain grown to exponential phase, replicate 1


title: d0 deltaCnA replicate 2

description: replicate 2

value: d0 deltaCnA


title: AsPC-1 control untreated cells, biological rep 1


title: AsPC-1 + PMA (1µM; 4h), biological rep 1


title: d0 deltaCnA replicate 1

description: replicate 1


title: AsPC-1 control untreated cells, biological rep 2


title: Primary mouse keratinocytes, rep2


title: JR32 infection of THP-1 macrophage time 18h (SCOTS treated), replicate 6

description: L. pneumophila infection of human macrophages (THP-1) at time 18h.

source_name: 3XSCOTS cDNA obtained from JR32 infecting THP-1 macrophages at time 18

label_protocol: 2 µg of cDNA was labeled using amino-allyl dUTP (GE Healthcare) by random priming with Klenow (New England Biolabs) as previously described (Porwollik, S. 2001. Mutat Res 483:1-11.). Subsequently, the resulting cDNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 546.

extract_protocol: TRIzol reagent (Gibco BRL) was used according to the manufacturer instruction. RNA was treated with DNase I (Ambion). RNA sample was converted to cDNA in 5 independent reverse-transcription reactions as described previously (Graham, J. 1999. PNAS 96:11554-559). Bacterial transcript were purified from host transcript by using 3 rounds of the SCOTS procedure (Daigle, F. 2002. Methods Enzymol. 358:108-122).

tag: condition

value: L pneumophila inside human THP-1 macrophages


title: Primary mouse keratinocytes, rep1


title: Mouse melanocytes 06d after UVA treatment, rep1

value: melanocytes


title: d3 -LIF +CsA replicate 1

description: replicate 1

source_name: CGR8 ES cells

value: d3 -LIF +CsA


title: Mouse melanocytes 06d after UVA treatment, rep2

value: UVA


title: patient 1030-B,post

city: Durham

first: Christina

last: Augustine

state: NC

address: VAMC RmE4001 508 Fulton St.

institute: Duke University Medical Center

hyb_protocol: labeled cRNA waas hybridized to HU133plus2 Affymetrix genechip for 16hrs followed by washing and staining with biotinylated anti-streptavidin antibody according to standard Affymetrix protocols

scan_protocol: Stained array was scanned using the Affymetrix Microarray Suite (GeneChip Operating Software - GCOS) and the GeneChip Scanner 3000

data_processing: Expression values across 54675 probe sets were calculated as the difference between the perfect match (PM) and mismatch (MM) signals of each probe pair and normalized by MAS5.0 algorithm using the Affymetrix Expression Console software (v1.0).  A present/absent call is included.

source_name: melanoma

label_protocol: one-cycle cDNA synthesis of 1µg total RNA followed by in-vitro transcription and biotin labeling of antisense cRNA

extract_protocol: Tissue was homogenized and RNA isolated using Qiagen Rneasy kit.  A mini-beadbeater and disposable glass micro-beads were used to homogenize the tissue.  Each RNA isolation included treatment with DNase to minimize genomic DNA.

treatment_protocol: 4mm punch biopsies were obtained prior to ADH-1 and again prior to isolated-limb-infusion with melphalan following a protocol approved by the Duke University institutional review board.  Biopsies were snap frozen and stored at -130.

tag: disease

value: in-transit disease

tag: stage

tag: disease state

value: PR

tag: treatment

value: no previous ILI/ILP


title: JR32 infection of THP-1 macrophage time 18h (SCOTS treated), replicate 5

value: genomic DNA


title: patient 1026-B,post

value: LTF/U


title: d3 -LIF +CsA replicate 2

description: replicate 2

tag: strain


title: JR32 infection of THP-1 macrophage time 18h (SCOTS treated), replicate 3


title: JR32 infection of THP-1 macrophage time 18h (SCOTS treated), replicate 4


title: d1 -LIF +CsA replicate 1

description: replicate 1

value: d1 -LIF +CsA


title: d1 -LIF +CsA replicate 2

description: replicate 2


title: Mouse melanocytes 06d after NoUV treatment, rep1

value: FVB/N

tag: tissue

tag: cell type

tag: days to harvest of cells


title: Mouse melanocytes 01d after NoUV treatment, rep2

value: double heterozygous Dct-rtTA/TRE-H2BGFP (Dct-GFP)

tag: group


title: d0 -LIF +CsA replicate 2

description: replicate 2

tag: cell line

value: d0 -LIF +CsA


title: JR32 infection of THP-1 macrophage time 18h (SCOTS treated), replicate 2

tag: reference


title: patient 1030-A,pre


title: d0 -LIF +CsA replicate 1

description: replicate 1

tag: protocol


title: Mouse melanocytes 06d after NoUV treatment, rep2

tag: genotype

value: postnatal


title: Mouse melanocytes 01d after NoUV treatment, rep1

tag: strain/background

value: dorsal skin


title: JR32 infection of THP-1 macrophage time 18h (SCOTS treated), replicate 1


title: patient 1026-A,pre


title: JR32 infection of THP-1 macrophage time 6h (SCOTS treated), replicate 6

description: L. pneumophila infection of human macrophages (THP-1) at time 6h.

source_name: 3XSCOTS cDNA obtained from JR32 infecting THP-1 macrophages at time 6h


title: JR32 infection of THP-1 macrophage time 6h (SCOTS treated), replicate 5


title: patient 424-B,post

value: CR


title: Mouse melanocytes 06d after UVB treatment, rep1

tag: developmental stage

value: UVB


title: Mouse melanocytes 06d after UVB treatment, rep2

tag: uv treatment


title: JR32 infection of THP-1 macrophage time 6h (SCOTS treated), replicate 4

tag: condition

value: L pneumophila inside human THP-1 macrophages


title: patient 424-A,pre

tag: disease


title: d1 -LIF replicate 2

description: replicate 2

value: d1 -LIF


title: patient 423,post

tag: stage


title: JR32 infection of THP-1 macrophage time 6h (SCOTS treated), replicate 2


title: d1 -LIF replicate 1

description: replicate 1


title: d3 -LIF replicate 1

description: replicate 1

value: d3 -LIF


title: Mouse melanocytes 01d after UVB treatment, rep2

value: melanocytes


title: patient 421,post

value: in-transit disease

tag: disease state

value: previous ILI