title: Serum sample 137

description: no additional information


title: Serum sample 135

status: Public on Jan 03 2012

type: protein

city: Perugia

first: tania

last: dottorini

address: via del Giochetto

department: Dept. Exp.Medicine and Bichem. Sci.

country: Italy

institute: University of Perugia

description: no additional information

hyb_protocol: Printed slides were blocked with PBS containing 2% BSA for 1 h at room temperature. Slides were then incubated with serum samples (100 µl) for 60 minutes at 37°C. To reveal bound IgE, the slides were incubated with a secondary mouse monoclonal antibody directed against human IgE (0.14 µg/ml - 100µl) for 45 minutes at 37°C, followed by an incubation with anti-mouse IgG HRP conjugated antibody (1.6 µg/mL - 100µl) for 45 minutes at 37°C and finally incubated with tyramide-Alexa 555 (TSA™ Kit #42 *with HRP—streptavidin and Alexa Fluor® 555 tyramide* *50-150 slides*) (Invitrogen) diluted 1:200 (100µl), for 15 minutes at 37°C. Slides were dried at 37°C before measuring the fluorescence signal.

scan_protocol: The processed slides were scanned using a fluorescence-detecting scanner ScanArray™ Gx and the images were generated with the ScanArray™ software provided by Perkin Elmer Life Sciences Inc. All the slides were scanned under identical settings: 90 % laser power and 60 % photomultiplier gain.

data_processing: Quantification of bound IgE: The fluorescence signal was acquired using ProScanArray Express™ version 3.0 software. PMC reading values of individual spots were corrected against the internal negative control to identify signals above background. Duplicate measurements of individual allergens were utilized. The signal collected from the allergens was interpolated with an external calibration curve to obtain the IU/ml value (see supplementary file GSE20020_IU_ml values.txt on the GSE20020 record), and translated into a Class Score by plotting the data in a standard reactivity scale (see Sample data tables). Class Score values: CLASS 0 (less than 0.35 IU/ml); CLASS 1 (0.35-0.7 IU/ml); CLASS 2 (0.71-3.5 IU/ml); CLASS 3 (3.51-17.5 IU/ml); CLASS 4 (17.51-50 IU/ml); CLASS 5 (50.01-100 IU/ml).

label: Alexa 555

molecule: protein

organism: Homo sapiens

source_name: Human sera

label_protocol: TSA™ Kit #42 *with HRP—streptavidin and Alexa Fluor® 555 tyramide* *50-150 slides* (Invitrogen)

extract_protocol: At the recruitment sessions, each subject was interviewed, disease status was ascertained by physical examination, permission was asked to access personal health records, and blood samples were collected

tag: fluid

value: Human serum

tag: gender

value: F

tag: clinical status

value: non-asthmatic

tag: eczema

value: negative

tag: conjunctivitis

tag: rhinitis


title: Serum sample 132

description: no additional information


title: Serum sample 134

description: no additional information

value: M

value: asthmatic


title: Serum sample 133

description: no additional information

value: positive


title: Serum sample 129

description: no additional information


title: Serum sample 130

description: no additional information


title: Serum sample 131

description: no additional information


title: Serum sample 123

description: no additional information


title: Serum sample 125

description: no additional information


title: Serum sample 126

description: no additional information


title: Serum sample 127

description: no additional information


title: Serum sample 124

description: no additional information


title: Serum sample 122

description: no additional information


title: Serum sample 120

description: no additional information


title: Serum sample 121

description: no additional information


title: Serum sample 128

description: no additional information


title: Serum sample 116

description: no additional information


title: Serum sample 118

description: no additional information


title: Serum sample 117

description: no additional information

value: undefined diagnosis


title: Serum sample 115

description: no additional information


title: Serum sample 109

description: no additional information


title: Serum sample 114

description: no additional information


title: Serum sample 108

description: no additional information


title: Serum sample 111

description: no additional information


title: Serum sample 112

description: no additional information


title: Serum sample 113

description: no additional information


title: Serum sample 107

description: no additional information


title: Serum sample 106

description: no additional information


title: Serum sample 110

description: no additional information


title: Serum sample 119

description: no additional information


title: Serum sample 102

description: no additional information


title: Serum sample 103

description: no additional information


title: Serum sample 101

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title: Serum sample 105

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title: Serum sample 104

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title: Serum sample 98

description: no additional information


title: Serum sample 100

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title: Serum sample 95

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title: Serum sample 94

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title: Serum sample 87

description: no additional information


title: Serum sample 88

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title: Serum sample 86

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title: Serum sample 89

description: no additional information


title: Serum sample 90

description: no additional information


title: Serum sample 91

description: no additional information


title: Serum sample 92

description: no additional information


title: Serum sample 93

description: no additional information


title: Serum sample 77

description: no additional information


title: Serum sample 79

description: no additional information


title: Serum sample 78

description: no additional information


title: Serum sample 73

description: no additional information


title: Serum sample 74

description: no additional information


title: Serum sample 75

description: no additional information


title: Serum sample 76

description: no additional information


title: Serum sample 97

description: no additional information


title: Serum sample 99

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title: Serum sample 81

description: no additional information


title: Serum sample 83

description: no additional information


title: Serum sample 80

description: no additional information


title: Serum sample 82

description: no additional information


title: Serum sample 96

description: no additional information


title: Serum sample 85

description: no additional information


title: Serum sample 84

description: no additional information


title: Serum sample 71

description: no additional information


title: Serum sample 72

description: no additional information


title: Serum sample 66

description: no additional information


title: Serum sample 67

description: no additional information


title: Serum sample 65

description: no additional information


title: Serum sample 64

description: no additional information


title: Serum sample 68

description: no additional information


title: Serum sample 70

description: no additional information


title: Serum sample 63

description: no additional information


title: Serum sample 62

description: no additional information


title: Serum sample 61

description: no additional information


title: Serum sample 60

description: no additional information


title: Serum sample 69

description: no additional information


title: Serum sample 58

description: no additional information


title: Serum sample 57

description: no additional information


title: Serum sample 56

description: no additional information


title: Serum sample 55

description: no additional information


title: Serum sample 53

description: no additional information


title: Serum sample 52

description: no additional information


title: Serum sample 51

description: no additional information


title: Serum sample 48

description: no additional information


title: Serum sample 50

description: no additional information


title: Serum sample 54

description: no additional information


title: Serum sample 59

description: no additional information


title: Serum sample 49

description: no additional information


title: Serum sample 44

description: no additional information


title: Serum sample 46

description: no additional information


title: Serum sample 45

description: no additional information


title: Serum sample 47

description: no additional information


title: Serum sample 41

description: no additional information


title: Serum sample 43

description: no additional information


title: Serum sample 42

description: no additional information


title: Serum sample 35

description: no additional information


title: Serum sample 37

description: no additional information


title: Serum sample 40

description: no additional information


title: Serum sample 38

description: no additional information


title: Serum sample 31

description: no additional information


title: Serum sample 32

description: no additional information


title: Serum sample 30

description: no additional information


title: Serum sample 29

description: no additional information


title: Serum sample 39

description: no additional information


title: Serum sample 24

description: no additional information


title: Serum sample 36

description: no additional information


title: Serum sample 25

description: no additional information


title: Serum sample 26

description: no additional information


title: Serum sample 28

description: no additional information


title: Serum sample 27

description: no additional information


title: Cortical neurons-Lact-24h-Rep 1

type: RNA

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description: Replicate 1

hyb_protocol: 15μg of fragmented cRNA produced above was hybridized to the GeneChip Murine genome U74A and U74Av2 arrays for 16h at 45°C. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The hybridized arrays were washed, stained, and scanned using the Hewlett-Packard GeneArray Scanner G2500A according to the manufacturer’s instructions.

data_processing: The data from each array were collected and initially analyzed using Affymetrix Microarray Suite 5.0 software. For comparison of multiple arrays, the signal intensity of each array was scaled to 500. The regulated genes were filtered on fold change 1.5 fold against controls in at least one of three time-points. One-way ANOVA (p<0.05) approach was used to find differentially expressed genes using GeneSpring™ GX 7.3 software (Agilent Technologies, CA, USA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Murine primary cortical neurons

label_protocol: According to technical manual form Affymetrix, 7μg of extracted total RNA was used for cDNA synthesis. Double-stranded cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) with a T7-dT24 primer. After cleanup, Biotin-labeled cRNA was synthesized by in vitro transcription (Enzo Diagnostic, Inc., NY, USA) and fragmented subsequently.

growth_protocol: Neocortical neurons (gestational days 15 or 16) obtained from foetal cortices of Swiss albino mice were used to prepare the primary cultures employing previous described procedures with modifications [Cheung NS, Beart PM, Pascoe CJ, John CA, Bernard O. Human Bcl-2 protects against AMPA receptor-mediated apoptosis. J Neurochem. 2000; 74: 1613-1620.].

extract_protocol: RNA from samples was extracted using RNeasy Mini Kit (Qiagen Cat. No. 74104) according to the manufacturer’s instructions. 1.5μl of the RNA sample was aliquoted for spectrophotometric quantification using Nanodrop ND-1000 Version 3.2.1 and 1μl for RNA quality analysis using E-gene HDAGT12 genetic analyzer.

treatment_protocol: Lactacystin was prepared as 1mM stock solution in DMSO stored at -20°C. Desired concentrations were achieved by dilution with serum-free NB. On day 5 in vitro, the cultured neurons were treated with 1uM lactacystin in NB medium.

tag: strain

value: Swiss Albino mice

tag: age

value: Gestation day 15-16

tag: tissue

value: Primary cortical neurons

tag: age of culture

value: Day 5

tag: time point

tag: agent

value: lactacystin


title: Serum sample 34

description: no additional information


title: Serum sample 33

description: no additional information


title: Serum sample 23

description: no additional information


title: Serum sample 13

description: no additional information


title: Cortical neurons-Lact-48h-Rep 1

description: Replicate 1


title: Serum sample 11

description: no additional information


title: Serum sample 10

description: no additional information


title: Serum sample 12

description: no additional information


title: Serum sample 22

description: no additional information


title: Serum sample 21

description: no additional information


title: Serum sample 16

description: no additional information


title: Serum sample 17

description: no additional information


title: Serum sample 15

description: no additional information


title: Serum sample 18

description: no additional information


title: Serum sample 20

description: no additional information


title: Cortical neurons-Ctrl-24h-Rep 1

description: Replicate 1

value: control


title: Serum sample 8

description: no additional information


title: Serum sample 6

description: no additional information


title: Cortical neurons-Lact-48h-Rep 2

description: Replicate 2


title: Serum sample 9

description: no additional information


title: Cortical neurons-Lact-48h-Rep 3

description: Replicate 3


title: Serum sample 14

description: no additional information


title: Serum sample 19

description: no additional information


title: Cortical neurons-Ctrl-48h-Rep 1

description: Replicate 1


title: Cortical neurons-Ctrl-24h-Rep 2

description: Replicate 2


title: Cortical neurons-Ctrl-48h-Rep 2

description: Replicate 2


title: Cortical neurons-Lact-24h-Rep 3

description: Replicate 3


title: Cortical neurons-Lact-24h-Rep 2

description: Replicate 2


title: Serum sample 7

description: no additional information


title: Serum sample 4

description: no additional information


title: Serum sample 5

description: no additional information


title: Serum sample 2

description: no additional information


title: Serum sample 3

description: no additional information


title: Serum sample 1

description: no additional information


title: C2C12-MBNL1i-0h

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

country: Japan

institute: Nagoya University Graduate School of Medicine

description: C2C12 treated with MBNL1-siRNA; time point; 0 h

hyb_protocol: Samples were hybridized with GeneChip mouse Gene 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip 3000 7G

data_processing: The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software.

source_name: C2C12 -MBNL1-siRNA- time point-0 h

label_protocol: 100ng of total RNA were used to generate labeled cDNA. Biotinylated DNA probes were prepared using Affymetrix WT Expression kit for Affymetrix Whole Transcript Sense Expression arrays and Affymetrix geneChip WT Terminal Labeling kit according to the manufacture's protocol.

growth_protocol: C2C12 mouse myoblast cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum at 37C in 5% CO2.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: To stop transcription, 5 ug/ml actinomycin-D was added to the culture medium of  C2C12 cells treated with siRNA, and total RNA was harvested at 0, 2.5 or 5 hrs.

tag: cell type

value: myoblast

tag: cell line


title: C2C12-conti-5h

description: C2C12 treated with control siRNA; time point; 5 h

source_name: C2C12-control-siRNA- time point-5h


title: C2C12-CUGi-5h

description: C2C12 treated with CUGBP1-siRNA; time point; 5 h

source_name: C2C12-CUGBP1-siRNA-time point-5 h


title: C2C12-MBNL1i-2.5h

description: C2C12 treated with MBNL1-siRNA; time point; 2.5 h

source_name: C2C12 -MBNL1-siRNA- time point-2.5h


title: C2C12-MBNL1i-5h

description: C2C12 treated with MBNL1-siRNA; time point; 5 h

source_name: C2C12 -MBNL1-siRNA- time point-5 h


title: TCP_Rep2

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

description: Biological replicate 2 of 2.

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 825 ng / 1.65 ug cy-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, and then Agilent 2X hybridization buffer was added to the cocktail prior to application to the array. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor oven set to maximum speed.

scan_protocol: Arrays were scanned using an Agilent scanner G2565BA and the data was extracted using Agilent’s Feature Extraction software v10.1.1.1.

data_processing: Data was extracted using Agilent’s Feature Extraction software v10.1.1.1 set to the default two-color gene expression protocol.

source_name: Embyonic stem cells

label_protocol: Cy-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 1 µg total RNA. Briefly, first and second strand cDNA are generated using MMLV-RT enzyme and an oligo-dT based primer. In vitro transcription is performed using T7 RNA polymerase and either cyanine 3-CTP or cyanine 5-CTP, creating a direct incorporation of dye into the cRNA.

growth_protocol: ZHBTc4 Oct4 shutdown inducible cells were grown on irradiated MEFs and split onto gelatin coated dishes for 2 passages in mES media. Oct4 shutdown was induced by addition of 2ug doxycycline for 48hours

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

value: ZHBTc4 cells

tag: treatment

value: 48hr +dox +tcp


title: C2C12-conti-2.5h

description: C2C12 treated with control siRNA; time point; 2.5 h

source_name: C2C12-control-siRNA- time point-2.5 h


title: C2C12-conti-0h

description: C2C12 treated with control siRNA; time point; 0 h

source_name: C2C12-control-siRNA- time point-0 h


title: high fat diet, DLP lobe, rep 3

status: Public on Jan 02 2012

city: Bethesda

first: Yoshitaka

last: Sekine

state: Maryland

address: 10 Center Dr

institute: NHLBI

description: mouse prostate

hyb_protocol: Fragmented RNA was assessed for relative length on Agilent 2100 bioanalyzer and hybridized to Affymetrix Mouse 430 2.0 chips for 16 hours.

scan_protocol: Affymetrix GeneChip scanner

data_processing: Intensities were pre-processed with MAS5.0, and further processed with variance stablization transformation

source_name: mouse prostate tissue

label_protocol: Biotin labeled with Affymetrix's IVT labeling kits (Affymetrix, Santa Clara, CA).

growth_protocol: After 12-weeks, the ventral (VP), dorsolateral (DLP) and anterior (AP) prostate lobes from control group and the group fed with high fat diet were removed and placed in RNase-free PBS and snapped-frozen in liquid nitrogen and stored at -70 °C.

extract_protocol: Total RNA was extracted from VP and DLP lobes of mice.

treatment_protocol: Control group: 5 C57BL/6J mice, 8-weeks of age fed with control diet ad libitum for 12 weeks. Experimental group: 5 C57BL/6J mice, 8-weeks of age  fed with ad libitum high fat diet for 12 weeks.

tag: prostate tissue

value: DLP lobe

tag: group

value: high fat diet


title: Control_Rep1

description: Biological replicate 1 of 2.

value: 48hr +dox


title: C2C12-CUGi-0h

description: C2C12 treated with CUGBP1-siRNA; time point; 0 h

source_name: C2C12-CUGBP1-siRNA-time point-0 h


title: Control_Rep2

description: Biological replicate 2 of 2.


title: C2C12-CUGi-2.5h

description: C2C12 treated with CUGBP1-siRNA; time point; 2.5 h

source_name: C2C12-CUGBP1-siRNA-time point-2.5 h


title: high fat diet, DLP lobe, rep 1

description: mouse prostate


title: control, DLP lobe, rep 5

description: mouse prostate


title: TCP_Rep1

description: Biological replicate 1 of 2.


title: high fat diet, DLP lobe, rep 2

description: mouse prostate


title: control, DLP lobe, rep 3

description: mouse prostate


title: high fat diet, DLP lobe, rep 4

description: mouse prostate


title: control, DLP lobe, rep 4

description: mouse prostate


title: Non-transgenic (NTG) mouse treated with vehicle (veh) replicate 3

city: San Diego

first: Peter

middle: J

last: Belmont

state: CA

address: 10724 Science Center Drive

institute: Pfizer

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase Version 13, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between SNK6 and “SNT16” samples using the probe repeats as individual samples. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: NTG mouse veh treated heart RNA replicate 3

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy3/Cy5 dye staining.

growth_protocol: 12 adult male mice (C57BL6 background) were used for this study

extract_protocol: Mouse heart ventricles were extracted and total RNA was isolated

treatment_protocol: Mice were treated once per day with vehicle or tamoxifen (20mg/kg in 95% ethanol and sunflower oil) for 5 days

value: male

tag: genotype/variation

value: NTG

tag: treatment type

value: vehicle

source_name: NTG mouse tam treated heart RNA replicate 3

value: tamoxifen


title: Transgenic (TG) mouse treated with vehicle (veh) replicate 2

source_name: TG mouse veh treated heart RNA replicate 2

tag: gender

value: TG

source_name: TG mouse tam treated heart RNA replicate 2


title: Transgenic (TG) mouse treated with vehicle (veh) replicate 3

source_name: TG mouse veh treated heart RNA replicate 3

source_name: TG mouse tam treated heart RNA replicate 3


title: Non-transgenic (NTG) mouse treated with vehicle (veh) replicate 1

source_name: NTG mouse veh treated heart RNA replicate 1

source_name: NTG mouse tam treated heart RNA replicate 1


title: control, VP lobe, rep 5

description: mouse prostate

value: VP lobe


title: high fat diet, VP lobe, rep 2

description: mouse prostate


title: high fat diet, VP lobe, rep 3

description: mouse prostate


title: high fat diet, VP lobe, rep 1

description: mouse prostate


title: control, VP lobe, rep 1

description: mouse prostate


title: control, DLP lobe, rep 2

description: mouse prostate


title: control, VP lobe, rep 3

description: mouse prostate


title: control, VP lobe, rep 4

description: mouse prostate


title: control, DLP lobe, rep 1

description: mouse prostate


title: HEK293 F18_doxycycline untreated

status: Public on Jan 01 2012

city: Charlestown

first: Woo

middle: Jae

last: Kim

state: Ma

department: Cancer Center

institute: Massachusetts General Hospital

hyb_protocol: Affymetrix standard protocol for 3'-IVT expression microarrays

scan_protocol: Affymetrix scanner G7

data_processing:
Affymetrix GCOS
Target scaling = 150

label: ENZO 3'-labeling kit

source_name: HEK293 F18 WTX inducible

label_protocol: ENZO 3'-labeling kit manufacturer's instruction

extract_protocol: Qiagen RNeasy Kit

treatment_protocol: untreatment

value: HEK293 cells WTX inducible clone F18


title: Non-transgenic (NTG) mouse treated with vehicle (veh) replicate 2

source_name: NTG mouse veh treated heart RNA replicate 2

source_name: NTG mouse tam treated heart RNA replicate 2


title: control, VP lobe, rep 2

description: mouse prostate


title: HEK293 F18_doxycycline treated

treatment_protocol: 1 μg/ml doxycycline for 12 hr treatment

value: doxycycline


title: Minimally invasive adenocarcinoma (MIA) Replicate 1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: normalized log2 ratio ( BAC typeC No.1/BAC typeB No.1)

hyb_protocol: Hybridized for 16h at 37C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: BAC typeB No.1

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: The patient with 1cm minimally invaisve adenocarcinoma (MIA) of the lung was selected.

extract_protocol: Total RNA was extracted from each cell pool using NucleoSpin RNA XS (Macherey-Nagel GmbH & Co., KG, Germany).

treatment_protocol: The frozen sections were prepared from surgically resected MIA tumor and applied to laser microdissection for collecting cancer cells of both lepidic growth (LG) and micro-invasion (MI) components.

tag: tissue origin

value: lung

value: Control lepidic growth (LG) cancer cell pool

source_name: BAC typeC No.1

value: Micro-invasion (MI) cancer cell pool


title: Transgenic (TG) mouse treated with vehicle (veh) replicate 1

source_name: TG mouse veh treated heart RNA replicate 1

source_name: TG mouse tam treated heart RNA replicate 1


title: HEK293 F5_doxycycline untreated

source_name: HEK293 F5 WTX inducible

treatment_protocol: untreated

value: HEK293 cells WTX inducible clone F5

value: control


title: PNET cell line 5

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

country: Netherlands

institute: Erasmus MC

description: Gene expression data of PNET cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU 133 Plus2.0 arrays. GeneChips were washed and stained according to Affymetrix protocol

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (TGT value 500) as normalization method.

source_name: PNET cell line 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cultured in DMEM or RPMI at 37 C and 5% CO2 in non-hypoxic conditions

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

treatment_protocol: no treatment

value: female

value: EWS-FLI translocation


title: PNET cell line 4

description: Gene expression data of PNET cell line

source_name: PNET cell line 4


title: high fat diet, VP lobe, rep 4

description: mouse prostate

source_name: mouse prostate tissue

value: high fat diet


title: HEK293 F5_doxycycline treated


title: C2C12-Cugbp1 siRNA-2

description:
C2C12 treated with Cugbp1 siRNA; replicate 2
CUGi5

hyb_protocol: Samples were hybridized with GeneChip mouse exon 1.0 ST Arrays (Affymetrix) and scanned accoding to the manufacture's protocol.

data_processing:
The data were background corrected and normalized using the robust multiarray average (RMA) procedure implemented in the Affymetrix Expression Console software.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dtl.mm9.full.ps

source_name: C2C12, Cugbp1 siRNA

treatment_protocol: C2C12 cells were treated with  control-, Cugbp1- or Mbnl1-siRNA. After 48 hrs, total RNA was harvested.

value: myoblast

tag: sirna

value: Cugbp1 siRNA


title: DU-145-rep2

city: Barcelona

first: Mercedes

last: Marín-Aguilera

address: Villarroel 170

country: Spain

institute: Fundació Clínic per a la Recerca Biomèdica

hyb_protocol: GeneChip Hybridization wash and stain kit

scan_protocol: GeneChip 3000 Scanner 3000 7G system; software: GeneChip  Command Console (AGCC 1.1)

data_processing: Raw expression measures were summarized after background correction and normalization steps using the rma methodology in the affy package from the Bioconductor project.

source_name: DU-145 cell line original

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix IVT Labeling kit from  2ug total RNA.

growth_protocol: DU-145 and DU-145R cell lines were cultured in RPMI 1640 medium (Invitrogen), and PC-3 and PC-3R in F-12K nutrient mixture medium (Invitrogen), both supplemented with 10% fetal bovine serum.

treatment_protocol: The human prostate carcinoma cell lines DU-145 and PC-3 (obtained from American Tissue Culture Collection) were converted to docetaxel-resistant cells by exposing them to an initial dose of 5 nM docetaxel and culturing surviving cells during 1 yr and 6 mo, respectively, with increasing doses in an intermittent regimen. Docetaxel (Sigma) was dissolved in DMSO (10mM).

tag: disease state

value: metastatic prostate cancer


title: PNET cell line 3

description: Gene expression data of PNET cell line

source_name: PNET cell line 3


title: PC3-docetaxel resistant-rep1

source_name: PC3 cell line resistant to docetaxel

value: converted to docetaxel-resistant cells


title: high fat diet, VP lobe, rep 5

description: mouse prostate

tag: strain


title: DU-145-docetaxel resistant-rep1

source_name: DU-145 cell line resistant to docetaxel


title: PNET cell line 1

description: Gene expression data of PNET cell line

source_name: PNET cell line 1


title: DU-145-docetaxel resistant-rep2


title: C2C12-Mbnl1 siRNA-3

description:
C2C12 treated with MBNL1 siRNA; replicate 3
MBNi9

source_name: C2C12, Mbnl1 siRNA

value: Mbnl1 siRNA


title: DU-145-docetaxel resistant-rep3


title: prostatecancer_xenograft_MDAPCa146-10_rep3

city: Houston

first: Jiexin

last: Zhang

state: TX

address: 1515 Holcombe Blvd

department: Bioinformatics & Computational Biology

institute: UT MD Anderson Cancer Center

hyb_protocol: Hydrization was done with fragmented cRNA with herring sperm DNA, acetylated BSA in a buffer at 45 oC for overnight with rotation using GeneChip Fuidics station

scan_protocol: GeneArray Scanne using Microarray Suit software

data_processing: We used RMA (Robust Multichip Analysis) for the normalization and quantification of the data.

source_name: xenografted prostate cancer grown subcutaneously in the flanks of CB17 SCID intact mice

label_protocol: ENZO BioArray High Yield RNA Transcript Labeling Kit

growth_protocol: tumors were grown subcutaneously in the flanks of CB17 SCID intact mice

extract_protocol: The RNeasy mini kit (Qiagen, Inc. Valencia, CA) was used for total RNA extraction

value: prostate cancer

tag: tumor stage

value: castration-resistant prostate cancer (CRPC)

tag: histologic type

value: small cell carcinoma


title: C2C12-control siRNA-2

description:
C2C12 treated with control siRNA; replicate 2
cont2

source_name: C2C12, control siRNA


title: PNET cell line 2

description: Gene expression data of PNET cell line

source_name: PNET cell line 2


title: prostatecancer_xenograft_MDAPCa155-2_rep1

tag: tissue


title: DU-145-rep3


title: prostatecancer_xenograft_MDAPCa144-13_rep4


title: prostatecancer_xenograft_MDAPCa155-12_rep1


title: DU-145-rep1


title: prostatecancer_xenograft_MDAPCa144-13_rep2


title: C2C12-Mbnl1 siRNA-1

description:
C2C12 treated with MBNL1 siRNA; replicate 1
MBNi7


title: prostatecancer_xenograft_MDAPCa146-10_rep1


title: C2C12-Cugbp1 siRNA-3

description:
C2C12 treated with Cugbp1 siRNA; replicate 3
CUGi6


title: C2C12-control siRNA-3

description:
C2C12 treated with control siRNA; replicate 3
cont3


title: C2C12-control siRNA-1

description:
C2C12 treated with control siRNA; replicate 1
cont1


title: C2C12-Cugbp1 siRNA-1

description:
C2C12 treated with Cugbp1 siRNA; replicate 1
CUGi4


title: C2C12-Mbnl1 siRNA-2

description:
C2C12 treated with MBNL1 siRNA; replicate 2
MBNi8


title: dlp_1669 CDM vs. WT CDM hyb3

city: Ede

first: Michiel

last: Wels

address: Kernhemseweg 2

institute: NIZO food research

hyb_protocol: Hybridization buffer (Agilent In Situ Hybridization Kit Plus) was added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers at 65 degrees Celcius for 17 h. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.7.5)

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244). Interslide scaling was performed using Postprep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).

organism: Lactiplantibacillus plantarum WCFS1

source_name: lp_1669 deletion mutant grown in 2*CDM

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 3 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Cultures were grown in MRS or 2-times concentrated CDM (2*CDM) at

extract_protocol: Cultures were lysed by beat-beating and total RNA was isolated by subsequent fenol extraction

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

value: grown in 2*CDM

tag: genotype

value: lp_1669 deletion

source_name: wt grown in 2*CDM

value: WT


title: prostatecancer_xenograft_MDAPCa144-4_rep3

value: large cell neuroendocrine carcinoma


title: dlp_1669 MRS vs. dlp_1669 CDM hyb2

source_name: lp_1669 deletion mutant grown in MRS

value: grown in MRS


title: WT CDM vs. WT MRS hyb1

source_name: wt grown in MRS


title: prostatecancer_xenograft_MDAPCa144-4_rep4


title: prostatecancer_xenograft_MDAPCa144-13_rep1


title: prostatecancer_xenograft_MDAPCa117-9_rep3

value: adenocarcinoma


title: prostatecancer_xenograft_MDAPCa144-13_rep3


title: prostatecancer_xenograft_MDAPCa117-9_rep1


title: prostatecancer_xenograft_MDAPCa130_rep2


title: prostatecancer_xenograft_MDAPCa117-9_rep2


title: prostatecancer_xenograft_MDAPCa130_rep1


title: SKBR3_G15

city: Heraklion

first: George

last: Notas

address: PO BOX 2208

department: Medicine

country: Greece

institute: University of Crete

description: G15 treated cells 3h

hyb_protocol: RNA was hybridized according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual), on HGU133A plus 2 chips.

scan_protocol: Signals were detected by an Affymetrix microarray chip reader.

data_processing: Normalization and analysis was performed with the raw data using Genespring GX V11.0 (Agilent, Foster City, CA).

source_name: treated for 3 hours with 10-5M G15

label_protocol: RNA was labeled according to the Affymetrix protocol (Affymetrix Gene-Chip Expression Analysis Technical Manual).

growth_protocol: The human breast cancer cell line SKBR3 was obtained from DSMZ (Braunschweig, Germany) and cultured in McCoy′s 5A supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer’s instructions.

treatment_protocol: SKBR3 cells were incubated with or without Estradiol, E2-BSA, ICI, G15 or combinations of E2-BSA with ICI or G15 for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS.

value: breast cancer derived cells


title: prostatecancer_xenograft_MDAPCa79_rep2


title: prostatecancer_xenograft_MDAPCa79_rep3


title: WT MRS vs. dlp_1669 MRS hyb4


title: prostatecancer_xenograft_MDAPCa79_rep1


title: SKBR3_BSA

description: BSA treated cells 3h

source_name: treated for 3 hours with 10-6M BSA


title: SKBR3_E2-BSA+G15

description: E2-BSA plus G15 treated cells 3h

source_name: treated for 3 hours with 10-6M E2-BSA plus 10-5M G15


title: prostatecancer_xenograft_MDAPCa144-4_rep1


title: SKBR3_E2-BSA+ICI

description: E2-BSA plus ICI treated cells 3h

source_name: treated for 3 hours with 10-6M E2-BSA plus 10-5M ICI


title: SKBR3_E2-BSA

description: E2-BSA treated cells 3h

source_name: treated for 3 hours with 10-6M E2-BSA


title: prostatecancer_xenograft_MDAPCa144-4_rep5


title: SKBR3_Ethanol

description: ethanol treated cells (vehicle for estradiol) 3h

source_name: treated for 3 hours with 0.1% Ethanol


title: MDA-MB-231_G15

description: G15 treated cells 3h

data_processing: Normalization and analysis was performed with the raw data using Genespring GX V11.0 (Agilent, Foster City, CA)

growth_protocol: The human breast cancer cell line MDA-MB-231 was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

treatment_protocol: MDA-MB-231 cells were incubated with or without Estradiol, E2-BSA, ICI, G15 or combinations of E2-BSA with ICI or G15 for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS.


title: MDA-MB-231_BSA

description: BSA treated cells 3h


title: MDA-MB-231_E2-BSA+ICI

description: E2-BSA plus ICI treated cells 3h


title: SKBR3_control

description: control sample (3 hours post change of medium)

source_name: untreated control (3 hours post change of medium)


title: SKBR3_Estradiol

description: estradiol treated cells 3h

source_name: treated for 3 hours with 10-6M estradiol


title: 5.4 over 24hr

hyb_protocol: Agilent hybridization protocol for Two-color microarray-based Gene expression analysis. Version 5.5

scan_protocol: Scanned on an ScanArray Express 4000 scanner (Perkin Elmer, Wellesley, MA). Images were quantified using ImaGene Version 7.5 software (BioDiscovery Inc., Marina Del Rey, CA, USA).

data_processing: scanned slides were Lowess normalised using Prep (van Hijum, Applied Bioinformatics 2003 2(4):241-244).

growth_protocol: pH controlled Batch cultivation CDM-broth

extract_protocol: Quenching Buffer 66.7 mM HEPES (pH 6.5) 60%Methanol Extraction Mixture (Prepared in a screw-cap tube) -500 µl phenol/Chloroform -30 µl10% SDS -30 µl 3 M NaAc (pH 5.2) -500 mg glass-beads (75-150 µm) -400 µl TE buffer  1.For each sample prepare a tube with Extraction Mixture  2.Harvest cells and quench them immediately in Quenching Buffer. Add 4 volumes of Quenching Buffer ( 40°C) to 1 volume of cell culture  3.Mix and store the sample at -40°C  4.Centrifuge cells at -20°C at 9000 rpm for 10 minutes (Centrifuge RC5B)  5.Discard the supernatant; keep the cell pellet cooled and work quickly to prevent condensation of water. Transfer the pellet with a pre-cooled spatula to a screw-crap tube with Extraction Mixture  6.Mix the cell pellet thoroughly with Extraction Mixture by shaking by hand  7.Freeze the tube immediately in liquid nitrogen  8.Break cells in the Savant FastPrep FP120. Three times 40 seconds at speed 4.0 (cool cells between steps if necessary)  9.Centrifuge for 5 minutes at 4°C in an Eppendorf centrifuge at 10.000 rpm  10.Transfer 500 µl of the supernatant to a new tube. Add 400 µl chloroform (chloroform should be cooled at 4°C)  11.Centrifuge for 2 minutes in an Eppendorf centrifuge at full speed (4°C)  12.Continue with the High Pure RNA Isolation Kit from Roche (order # 1 828 665)  13.Incubate for 60 minutes with DnaseI, elute with 50 µl elution buffer   14.Store the RNA in at least 2 aliquots, one of 20 µl (for concentration and quality analysis and labelling) and one back-up of 30 µl at -80°C.

treatment_protocol: sampled at different OD600

tag: growth phase

source_name: 24hr sample

value: 24hr sample


title: MDA-MB-231_ICI

description: ICI treated cells 3h

source_name: treated for 3 hours with 10-5M ICI

tag: cell type


title: 24hr over 24hr


title: MDA-MB-231_E2-BSA (2)

description: E2-BSA treated cells 3h

tag: cell line


title: 5.2 over 5.1


title: MDA-MB-231_Ethanol


title: prostatecancer_xenograft_MDAPCa144-4_rep2

source_name: xenografted prostate cancer grown subcutaneously in the flanks of CB17 SCID intact mice


title: 5.3 over 5.2


title: MCF-7_E2-BSA

description: E2-BSA treated cells 3h

growth_protocol: The human breast cancer cell line MCF-7 was obtained from DSMZ (Braunschweig, Germany) and cultured in DMEM/F12 (1:1) supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

treatment_protocol: MCF-7 cells were incubated with or without Estradiol, E2-BSA or combinations of E2-BSA with ICI or G15 for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS.


title: 5.1 over 5.0


title: MCF-7_control (2)


title: 5.0 over 3.0


title: MCF-7_E2-BSA+G15

description: E2-BSA plus G15 treated cells 3h


title: MDA-MB-231_E2-BSA+G15

description: E2-BSA plus G15 treated cells 3h


title: MCF-7_E2-BSA+ICI

description: E2-BSA plus ICI treated cells 3h


title: MDA-MB-231_control (2)


title: MCF-7_E2-BSA (2)

description: E2-BSA treated cells 3h


title: 5.0 over 5.2


title: MDA-MB-231_E2-BSA

description: E2-BSA treated cells 3h


title: 5.4 over 5.3


title: 3.0 over 1.5


title: 5.2 over 5.4


title: MCF-7_BSA

description: BSA treated cells 3h


title: 1.5 over 5.0


title: MCF-7_Estradiol

description: estradiol treated cells 3h


title: T47D_E2-BSA+G15

description: E2-BSA plus G15 treated cells 3h

growth_protocol: The human breast cancer cell line T47D was obtained from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal bovine serum, at 37 °C, 5% CO2.

extract_protocol: Total RNA was isolated using Nucleospin II columns (Macheray-Nagel, Dttren, Germany), according to the manufacturer's instructions.

treatment_protocol: T47D cells were incubated with or without Estradiol, E2-BSA, ICI, G15 or combinations of E2-BSA with ICI or G15 for 3 hours after preincubation for 4 hours with medium containing 10% charcoal stripped FBS


title: prostatecancer_xenograft_MDAPCa146-10_rep2


title: MCF-7_control


title: T47D_BSA

description: BSA treated cells 3h


title: T47D_E2-BSA+ICI

description: E2-BSA plus ICI treated cells 3h


title: T47D_E2-BSA (2)

description: E2-BSA treated cells 3h


title: T47D_ICI

description: ICI treated cells 3h


title: Srsf1 ChIP in Psip1-/- using anti Srsf1 antibody (Invitrogen 32-4500) rep1

type: genomic

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

description: Chip-chip MEFs Srsf1 (in Psip1-/-)

hyb_protocol: Samples were hybridized according to standard protocol (http://www.nimblegen.com/products/lit/NG_ChIP-chip_Guide_v6p2.pdf)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: The media signal intensity of the 8 replicate probes,on each array was taken. Loess normalization was used within arrays to correct for the dye bias, and scale normalization was used, within replicates group, to control inter array variability. The log enrichment for each group was calculated by subtracting the mean of log2 input intensities from the mean of log2 enriched intensities.

molecule: genomic DNA

source_name: Input DNA from  Psip1-/- MEFs

label_protocol: 0.6 to 1.5 µg ChIP DNA or Input DNA was directly labeled by Klenow random priming with Cy3/Cy5 nonamers as per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Immortalized MEFs were used

extract_protocol: MEFs were harvested by trypsinizing and immediately fixed with 1% formaldehyde (25C, 10 min) in PBS, and stopped with 0.125M Glycine. Chromatin immunoprecipitation (ChiP) was performed as described previously (Johnson et al 2007). The nuclei were sonicated using a Diagenode Bioruptor (Liege, full power 30s on, 30s off, in an icebath for 50 min) to produce fragments of < 300bp. An arbitrary concentration of 200 µg chromatin was incubated with 4µg rabit IgG (Santa Cruz, sc-2025) or 4 µg Psip1 antibodies (A300-847) and washed and eluted as described in (Johnson et al 2007). Reverse cross-linked DNA was purified as described above.

value: immortalized MEFs (Psip1 -/-)

value: Psip1 -/-

source_name: Srsf1 ChIP DNA from Psip1-/-MEFS


title: Srsf1 ChIP in Psip1-/- using anti Srsf1 antibody (Invitrogen 32-4500) rep2

description: Chip-chip MEFs Srsf1 (in Psip1-/-)

value: immortalized MEFs (Psip1-/-)


title: T47D_E2-BSA

description: E2-BSA treated cells 3h


title: Srsf1 ChIP in WT mefs using anti Srsf1 antibody (Invitrogen 32-4500) rep2

description: Chip-chip MEFs Srsf1

source_name: Srsf1 ChIP DNA from MEFS

value: immortalized MEFs

value: wild type

source_name: Input DNA from MEFs


title: Patient 3_Om

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

hyb_protocol: The labeled and fragmented cRNA (10mg) was used for the hybridization to the Affymetrix (Santa Clara, CA) gene chips U133 plus 2 for 16 hr at 45C. An automated process of washing and staining in the Affymetrix Fluidics Station 400 was performed.

scan_protocol: Affymetrix arrays were scanned using the Affymetrix 3000G scanner. Absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v1 software.

data_processing: CEL files were transferred to MadMax website (https://madmax.bioinformatics.nl), and data analysis was performed using the statistical programming language R and the R libraries offered by the Bioconductor project. The data were first explored for quality control purposes and were normalized the GCRMA method within Bioconductor.

source_name: Patient 3_Om

label_protocol: 2 μg of high quality total RNA, verified using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies), was used with the Affymetrix Eukaryotic One-Cylce Target Labeling and Control reagents (#900493) following the manufacturers instructions to generate Biotin-labeled antisense cRNA.

extract_protocol: Total RNA was extracted from the adipose tissue tissue using an RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA following the manufacturer's instructions.

value: Female

value: omental adipose tissue


title: Patient 2_Sub C

source_name: Patient 2_Sub C

value: sub cutaneous adipose tissue


title: Srsf1 ChIP in WT mefs using anti Srsf1 antibody (Invitrogen 32-4500) rep1

description: Chip-chip MEFs Srsf1


title: Patient 1_Sub C

source_name: Patient 1_Sub C


title: Nipponbare genomic DNA,  biological rep3

city: Wuhan

first: Weiwei

last: Tie

state: Hubei Province

address: Shizishan Street, Hongshan District

department: College of Life Science and Technology

country: China

institute: Huazhong Agricultural University

hyb_protocol: Microarray hybridization were conducted by the CapitalBio Corporation (Beijing, China) according to the Affymetrix standard protocols (Affymetrix GeneChip Expression Analysis Technical Manual).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: Probe-pairs from the gDNA .cel files were selected using a .cel file parser script (Xspecies .cel file parser Version 2, http://affymetrix.arabidopsis.info/xspecies), which produced two sets of probe-mask files (custom .cdf files) under a series of intensity thresholds (ranging from 0–150), one for Nipponbare and the other for Zhenshan97. The mask file contains only probe-pairs whose corresponding perfect-match probe has a signal intensity greater than the user-defined gDNA hybridisation intensity threshold. These two sets of custom .cdf files were used to analyze the corresponding 30 RNA .cel files in R using the RMA normalisation algorithm. According to the method described in the paper, we select a gDNA hybridization intensity threshold of 50 for Nipponbare and an intensity threshold of 45 for Zhenshan 97 in the subsequent analysis of transcriptional data.

organism: Oryza sativa Japonica Group

source_name: Nipponbare genomic DNA

label_protocol: The genomic DNA was labeled using the Bioprime DNA Labeling System (Invitrogen).

growth_protocol: The germinated seeds were cultured hydroponically.

extract_protocol: The genomic DNA (gDNA) of Nip and ZS were extracted from 2-week old seedlings using the Plant Genomic DNA Kit (TIANGEN, Beijing, China).

treatment_protocol: Untreated.

tag: cultivar

value: Nipponbare


title: Zhenshan 97 genomic DNA, biological rep1

organism: Oryza sativa Indica Group

source_name: Zhenshan 97 genomic DNA

value: Zhenshan 97


title: Zhenshan 97 genomic DNA, biological rep2


title: T47D_control (2)


title: Patient 1_Om

source_name: Patient 1_Om


title: Patient 3_Sub C

source_name: Patient 3_Sub C


title: EcCo3 U133 Plus 2.0

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Gene expression data from HT-29 cells

hyb_protocol: Following fragmentation, 10 microg of cRNA was hybridized for 16 hr at 45C on Affymetrix HGU133 Plus 2.0 chip. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip 3000 Scanner

data_processing: The data were preprocessed by the function mas5 from the Bioconductor affy package

source_name: cell culture: Control HT29

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 3 microg total RNA

extract_protocol: Qiagen RNeasy Mini extraction of total RNA was performed according to the manufacturer instructions

value: colorectal adenocarcinoma


title: T47D_Ethanol

source_name: treated for 3 hours with 0.1% Ethanol


title: Nipponbare genomic DNA,  biological rep1


title: EcCo2 U133 Plus 2.0

description: Gene expression data from HT-29 cells


title: Zhenshan 97, callus 24hr, biological rep1

data_processing: The RNA probe intensity files (.cel files) for expression profiles were read into R. Background correction, quantile normalization and summarization were performed using the RMA method in Bioconductor affy package. During .cel file loading and pre-normalisation, the Nipponbare and Zhenshan97 RNA .cel files were interpreted using corresponding custom .cdf files generated from the genomic DNA .cel file with a gDNA hybridization intensity threshold of 50 for Nipponbare and an intensity threshold of 45 for Zhenshan97.

source_name: Zhenshan 97 callus, 24 h after Agrobacterium tumefaciens infection

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Sterilized dehusked seeds were cultured on callus induction medium at 27±1°C in the dark. After 4-5 wk, the proliferating white hard embryogenic calli were subcultured onto the subculture medium and cultured under dark at 27±1°C for another 2-3 wk. The vigorously growing embryogenic calli of approximately 2-3 mm size were transferred onto the precultivation medium 4 d before infection with Agrobacterium.

extract_protocol: Total RNA extraction was performed using Trizol, according to the manufacturer's instructions.

treatment_protocol: Precultivated embryogenic calli of approximately 2-3 mm size were infected by the Agrobacterium Strain EHA105(pCAMBIA 1301) suspension with an optical density (OD) of 0.35 to 0.4 at 600 nm for 30 mins. Then the calli were blotted dry using sterile filter paper for removal of excess bacteria. Afterwards, the agroinfected calli were transferred onto the co-cultivation medium under dark at 20±1°C for 3 days.

tag: time point

tag: infection

value: Agrobacterium tumefaciens


title: Zhenshan 97, callus 24hr, biological rep3


title: Zhenshan 97 genomic DNA, biological rep3


title: Psip1 ChIP using A300-847 antibody (recognizes p52 isoform of Psip1)

description: Chip-chip MEFs Psip1 (A300-847)

tag: genotype/variation

source_name: Psip1 ChIP DNA from MEFs


title: Nipponbare genomic DNA,  biological rep2


title: Patient 2_Om

source_name: Patient 2_Om


title: Zhenshan 97, callus 24hr, biological rep2


title: Zhenshan 97, callus 12hr, biological rep3

source_name: Zhenshan 97 callus, 12 h after Agrobacterium tumefaciens infection


title: H3K36me3 ChIP using anti H3K36me3 (Abcam Ab 9050-100)

description: Chip-chip MEFs H3K36me3

source_name: H3K36me3 ChIP DNA from MEFS


title: T47D_G15

description: G15 treated cells 3h

source_name: treated for 3 hours with 10-5M G15


title: Zhenshan 97, callus 1hr, biological rep2

source_name: Zhenshan 97 callus, 1 h after Agrobacterium tumefaciens infection

value: 1 h


title: H460cri-CCDP 1hour

city: Pamplona

first: Eva

last: Bandres

address: Avda Pio XII, 55

department: Cancer Research Program

institute: Center for Applied Medical Research (CIMA), University of Navarra

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133A 2.0 chip according to the protocols provided by the manufacturer.

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

data_processing: RMA

source_name: H460cri-CCDP 1hour

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).

growth_protocol: The human non small lung cancer cell line H460 used in this study was from ATCC (American Type Culture Collection). The cell line was maintained in Roswell Park Memorial Institute (RPMI) (Gibco, Invitrogen) supplemented with 10% bovine serum and transfected by Lipofectamine Plus Reagent from Life Technologies as directed by the manufacturer.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany). The RNA quality was confirmed by the ratio of 28S and 18S rRNA after agarose gel electrophoresis.

treatment_protocol: The DUSP1 pSuperRetro-derived vectors were constructed as described (Chattoppadhyay et al., 2006). Clones expressing siRNA for DUSP1 were selected for their ability to grow in the presence of puromycin and kept for selection. Stable transfection was confirmed by qRT-PCR and Western Blot.Cisplatin (CCDP) was purchased by Farma Ferrer (Barcelona, Spain). Cells were treated with 10 µg/mL CDDP for 1, 3 and 6 hours.

value: non small cell lung cancer cell line H460

value: DUSP1 knockdown (siRNA-mediated)

tag: agent

value: CCDP

tag: time

value: 1 hour


title: Aza 2 U133 Plus 2.0

description: Gene expression data from HT-29 cells

source_name: cell culture: Aza treatment


title: Zhenshan 97, callus 1hr, biological rep3


title: Zhenshan 97, callus 1hr, biological rep1


title: Nipponbare, callus 24hr, biological rep3

source_name: Nipponbare callus, 24 h after Agrobacterium tumefaciens infection


title: Zhenshan 97, callus 0, biological rep2

source_name: Zhenshan 97 callus, right before Agrobacterium tumefaciens infection


title: H460cri-CCDP 6hour

source_name: H460cri-CCDP 6hour

value: 6 hour


title: EcCo1 U133 Plus 2.0

description: Gene expression data from HT-29 cells


title: Aza 3 U133 Plus 2.0

description: Gene expression data from HT-29 cells


title: Nipponbare, callus 12hr, biological rep3

source_name: Nipponbare callus, 12 h after Agrobacterium tumefaciens infection


title: H460cri-control

value: untreated (control)


title: H460v-CCDP 6hour

source_name: H460v-CCDP 6hour


title: Zhenshan 97, callus 0, biological rep1


title: Nipponbare, callus 24hr, biological rep2


title: Huh7 NTC

city: Hong Kong

first: Kin Wah

last: Lee

address: 21 Sassoon Road

institute: The University of Hong Kong

hyb_protocol: Service by Genome Research Centre of the University of Hong Kong

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method; and Ingenuity Pathway Analysis

source_name: Huh7 non-target control

growth_protocol: Huh7 cells grown in DMEM medium supplemented with 10% FBS and 1% penicillin and streptomycin

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

treatment_protocol: Huh7 cells lentivirally transduced with shRNA CD24 (knockdown) or non-target control

value: Liver


title: Nipponbare, callus 24hr, biological rep1


title: Zhenshan 97, callus 6hr, biological rep2

source_name: Zhenshan 97 callus, 6 h after Agrobacterium tumefaciens infection

value: 6 h


title: Zhenshan 97, callus 0, biological rep3


title: Zhenshan 97, callus 12hr, biological rep2


title: Zhenshan 97, callus 6hr, biological rep3


title: Aza 1 U133 Plus 2.0

description: Gene expression data from HT-29 cells


title: H460cri-CCDP 3 hour

source_name: H460cri-CCDP 3 hour

value: 3 hour


title: Zhenshan 97, callus 6hr, biological rep1


title: H460v-CCDP 1hour

source_name: H460v-CCDP 1hour

value: wild type


title: H460v-CCDP 3 hour

source_name: H460v-CCDP 3 hour


title: H460v-control


title: Zhenshan 97, callus 12hr, biological rep1


title: Nipponbare, callus 12hr, biological rep2


title: Nipponbare, callus 12hr, biological rep1


title: Nipponbare, callus 6hr, biological rep1

source_name: Nipponbare callus, 6 h after Agrobacterium tumefaciens infection


title: Anc midlog R4

city: Grenoble

first: Mickael

last: Le Gac

address: Institut Jean Roget

country: France

institute: CNRS

hyb_protocol: The of biotinylated cDNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix E. coli Genome 2.0 Microarray for 16 hours at 45ºC. 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: Quality check and data analysis were carried out using Affymetrix GeneChip Command Console (AGCC) and Expression Console

organism: Escherichia coli B str. REL606

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA

growth_protocol: Bacteria were acclimated during 24h, 37°C, 120rpm in DM25, then diluted 100 times  in 200mL DM25 and grown until mid exponential phase (6 hours for the ancestor, 4,5 hours for the evolved clones)

extract_protocol: RNA was extracted using Qiagen RNeasy mini kit as per the manufacturer's protocol

treatment_protocol: Bacteria were pelleted at 4°C

value: E. coli B REL606

tag: population

value: ancestor

tag: lineage


title: PBS Treated Cells 3

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Affimetrix standard hyb protocol

scan_protocol: Affimetrix standard scan protocol

data_processing: RMA by software Parteck

source_name: PBS Treated Cells 3

label_protocol: Affimetrix standard label protocol

growth_protocol: Cells were grown in 12 well dishes in DMEM, 10% FBS, 1% Antibiotic. 150,000 cells were seeded.

extract_protocol: RNA was extracted using the Quiagen RNeasy RNA isolation kit (Valencia, CA)

treatment_protocol: Ribavirin was added directly to the media and cells were expoed to drug for 24 hours at a concentration of 100 ug/mL

value: liver

value: PBS


title: Nipponbare, callus 1hr, biological rep2

source_name: Nipponbare callus, 1 h after Agrobacterium tumefaciens infection

value: Nipponbare


title: Nipponbare, callus 1hr, biological rep3

value: Agrobacterium tumefaciens


title: Ribavirin Treated Cells 1

source_name: Ribavirin Treated Cells 1

value: Ribavirin


title: Anc midlog R5


title: 6.5KS midlog R3

source_name: Four S clones isolated at 6500 generations from population ara-2, pooled

value: E. coli B REL606 derivative

value: S

tag: generation


title: 6.5KS midlog R2

tag: strain


title: 6.5KS midlog R4


title: Nipponbare, callus 6hr, biological rep2


title: Ribavirin Treated Cells 2

source_name: Ribavirin Treated Cells 2


title: Anc midlog R2


title: Anc midlog R3


title: PBS Treated Cells 2

source_name: PBS Treated Cells 2


title: Ribavirin Treated Cells 3

source_name: Ribavirin Treated Cells 3


title: Nipponbare, callus 0, biological rep3

source_name: Nipponbare callus, right before Agrobacterium tumefaciens infection


title: Nipponbare, callus 1hr, biological rep1

value: 1 h


title: PBS Treated Cells 1

source_name: PBS Treated Cells 1


title: Anc midlog R1


title: 6.5KS midlog R6


title: 6.5KS midlog R1


title: Nipponbare, callus 0, biological rep1


title: 6.5KS midlog R5


title: Nipponbare, callus 6hr, biological rep3


title: 6.5KL midlog R6

source_name: Four L clones isolated at 6500 generations from population ara-2, pooled

value: L


title: 6.5KL midlog R5


title: 6.5KL midlog R4


title: 40KS midlog R1

source_name: Four S clones isolated at 40000 generations from population ara-2, pooled


title: 40KS midlog R3


title: 6.5KL midlog R3


title: 6.5KL midlog R2


title: 40KS midlog R6


title: 40KS midlog R5


title: 40KS midlog R2


title: 17KS midlog R6

source_name: Four S clones isolated at 17000 generations from population ara-2, pooled


title: 40KS midlog R4


title: 17KS midlog R4


title: 17KL midlog R1

source_name: Four L clones isolated at 17000 generations from population ara-2, pooled


title: 40KL midlog R2

source_name: Four L clones isolated at 40000 generations from population ara-2, pooled


title: Huh7 shRNA CD24

scan_protocol: Service by Genome Research Centre of the University of Hong Kong

source_name: Huh7 shRNA CD24 (knockdown)


title: 40KL midlog R3


title: 17KL midlog R2


title: 17KL midlog R5


title: 6.5KL midlog R1


title: 17KL midlog R3


title: 17KS midlog R5


title: 40KL midlog R1


title: 17KL midlog R4


title: 17KS midlog R1


title: 40KL midlog R5


title: 40KL midlog R4


title: 17KS midlog R2


title: 17KS midlog R3


title: Leaf H3K27me3

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

description: H3K27me3 profile in leaves

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
CEL files were analyzed by CisGenome.
ma.bar files were genenrated by CisGenome.

label: Biotin

organism: Arabidopsis thaliana

source_name: Leaf

label_protocol: standard Affymetrix protocol

extract_protocol: The ChIP assay was performed by using the the anti H3 trimethyl-Lys 27 antibody (Upstate, USA, Cat. 07-449).

treatment_protocol: For callus induction, leaf explants were harvested from 20-day-old plants grown in sterile culture on Murashige and Skoog basal salt mixture (MS) plates. Explants were cultured on the callus induction medium (CIM, Gamborg’s B5 medium with 0.5 g/L MES, 2% glucose, 0.2 mmol/L kinetin, and 2.2 mmol/L 2,4-dichlorophenoxyacetic acid and 0.8% agar), and incubated for 20 days in the dark.

value: leaf

tag: chip antibody

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #

source_name: Leaf negative expt1

value: input

value: Leaf


title: Nipponbare, callus 0, biological rep2


title: Callus H3K27me3

description: H3K27me3 profile in the callus

source_name: Callus

tag: tissue

value: callus

source_name: Callus negative expt1

value: Callus


title: Mesenchymal stem cells from human bone marrow_P6

city: Nagoya

first: Akihito

last: Yamamoto

state: Aichi-ken

address: 65 Tsurumai-Cho, Showa-Ku

department: Department of Oral and Maxillofacial Surgery

institute: Nagoya University Graduate School of Medicine

description: We followed manufacturer's protocol.

hyb_protocol: We followed manufacturer's protocol. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf Briefly, Hybridization is performed overnight in a temperature-controlled shaking incubator. Optimized hybridization buffer components are also included in CodeLink Expression Assay Reagent Kit for use at this step. Post-hybridization processing includes a stringent wash to remove unbound and non-specifically hybridized target molecules, a staining step with a Cy5-Streptavidin conjugate, and several non-stringent washing steps to remove unbound conjugate

scan_protocol: We followed manufacturer's protocol, and used GenePix 4000B. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf Following a final rinse, the bioarrays are dried by centrifugation and scanned. Analysis of the bioarrays with the CodeLink Expression Analysis software is described in the Help accessible in the software.

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

label_protocol:
We followed manufacturer's protocol.
http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf
Biotin-labelled cRNA target is prepared by a linear amplification method. The poly(A)+ RNA subpopulation (within the total RNA population) is primed for reverse transcription by a DNA oligonucleotide containing the T7 RNA polymerase promoter 5' to a d(T)24 sequence (Fig 1). After second-strand cDNA synthesis, the cDNA serves as the template for an in vitro transcription (IVT) reaction to produce the target cRNA. The IVT is performed in the presence of biotinylated nucleotides to label the target cRNA. This method produces approximately 1000-fold to 5000-fold linear amplification of the input poly(A)+ RNA.

growth_protocol: DMEM supplemented with 10% fetal calf serum, then incubated at 37°C in 5% CO2.

extract_protocol: We followed TRIzol Method. This is a modification of the procedure originally described by Chomczynski P and Sacchi N. 1987.Signal-Step Method of RNA Isolation by Acid Guanidinium Thiocyanate - Phenol -Chloroform Extraction.

value: mesenchymal stem cells from human bone marrow

tag: gender

value: female

tag: age


title: Dental stem cells from human milk teeth_P6

description: We followed manufacturer's protocol.

source_name: Dental stem cells from human milk teeth

tag: cell type

value: dental stem cells from human milk teeth


title: Kidney_FHH.Pkhd1_30dayold_technical rep2

city: Milwaukee

first: Caitlin

middle: C

last: OMeara

state: WI

address: 8701 Watertown Plank Rd

department: Physiology

institute: Medical College of Wisconsin

hyb_protocol: following fragmentation, 10ug of cRNA were hybridized for 16hr at 45oC on Affymetrix Rat Genome 230 2.0 arrays.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics station 450, and scanned using a 7G GeneChip Scanner 3000.  Image data were quantified with Affymetrix Expression Console Software.

data_processing: The quantified raw signal intensites were normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios.  Analysis of variation (ANOVA) was conducted using Partek Genomics Suite 6.2 (Partek Incorporated).  Differentially expressed probe sets were defined as those possessing ANOVA p<0.05, and a log2 ratio >0.5 between the compared groups.  Biological network analysis was performed with the Ingenuity Pathway Analysis (IPA; http://www.ingenuity.com/).

organism: Rattus norvegicus

source_name: Kidney_30 day old FHH.Pkhd1

label_protocol: biotinylated cRNA were prepared from 100ng starting material, using Affymetrix protocol and Affymetrix 3' IVT Express Kit (GeneChip Expression Analysis Technical Manual, 2005-2009, Affymetrix)

growth_protocol: SD, FHH, PCK, FHH.Pkhd1 animals sacrificed at 30 days of age, and kidneys removed and stored in RNAleter (Ambion).

extract_protocol: RNA was extracted using the Trizol (Invitrogen, Carlsbad, CA) method according to manufacturer’s instructions.

treatment_protocol: All rats were fed 5LOD diet (Purina, Jefferson, WI) for the duration of the experiments.

tag: organ

value: Kidney

value: 30 days


title: Kidney_SD_30dayold_technical rep2

source_name: Kidney_30 day old SD

value: SD


title: pancreatic cancer patient 134

city: Homburg

first: Andreas

last: Keller

address: Building 60

country: Germany

institute: Saarland University

hyb_protocol: According to manufacturer's instructions (febit biomed).

scan_protocol: Images were detected inside the geniom rt analyzer version 3. Wizard software on standard Microsoft Windows Workstation PC.

data_processing: Summarizing of technical replica by median and quantile normalization. Following BG correction, negative values were corrected to 1. All analyses were carried out using R.

source_name: Pancreas RNA from pancreatic cancer patient

label_protocol: MPEA, microfluidic primer extension assay, biotin labeling.

growth_protocol: Stored at -20 degrees Celsius.

extract_protocol: Standard extraction of miRNAs from tissue samples using the miRNeasy kit (Qiagen, Hilden).

value: pancreas

tag: disease state

value: pancreatic cancer


title: pancreatic cancer patient 135


title: pancreatic cancer patient 136


title: Kidney_FHH_30dayold_technical rep3

source_name: Kidney_30 day old FHH

value: FHH


title: WT/WT_SC_rep2

city: Giessen

first: Eveline

last: Baumgart-Vogt

state: Hesse

address: Aulweg 123

department: Institute for Anatomy and Cell Biology II

institute: Justus Liebig University Giessen

description: Sertoli cells isolated from 14 day-old mice, cultured for 7 days

hyb_protocol: The samples were hybridized for 18 h in a Minitron shaker incubator (Infors AG, Bottmingen, Germany) at 37C°/300 rpm and using microarrays for the mouse whole genome analysis, according to the manufacturer’s protocol (300033-6PK, CodeLink™ Mouse Whole Genome Bioarray, Applied Microarrays, Tempe AZ, USA)

scan_protocol: GenePix 4000 B scanner and GenePix Pro 4.0 Software (Axon Instruments, Arlington, USA)

data_processing: Images were analyzed using CodeLink Expression Analysis Software. Data were normalized by quantile normalization.

source_name: Sertoli cells from testis

label_protocol: 1 µg RNA of every sample was labelled using the MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (AM1791, Ambion) according to the manufacturer’s protocol.

growth_protocol: At 34ºC in a humidified atmosphere of 5% CO2 and 95% air for seven days

extract_protocol: Using the RNeasy Mini Kit from Qiagen, according to the manufacturer’s protocol (Qiagen, Hilden, Germany)

treatment_protocol: To remove germ cells and increase the purity of the Sertoli cell preparation, after 2 days of culture the Sertoli cell monolayer was subjected to hypotonic shock by incubation with 20 mM Tris-HCl (pH 7.5) for 2 min at room temperature.

tag: sex

value: male

tag: genotyping

value: WT/WT

value: 14 day-old


title: Kidney_SD_30dayold_technical rep3


title: AMH-Cre/WT_SC_rep1

value: AMH-Cre/WT


title: Kidney_FHH_30dayold_technical rep2


title: Kidney_PCK_30dayold_technical rep3

source_name: Kidney_30 day old PCK

value: PCK


title: Kidney_SD_30dayold_technical rep1


title: Kidney_FHH.Pkhd1_30dayold_technical rep3


title: Kidney_FHH_30dayold_technical rep1


title: AMH-Cre/WT_SC_rep2


title: WT/WT_SC_rep1


title: Kidney_FHH.Pkhd1_30dayold_technical rep1


title: Kidney_PCK_30dayold_technical rep1


title: Kidney_PCK_30dayold_technical rep2


title: pancreatic cancer patient 132


title: pancreatic cancer patient 131


title: pancreatic cancer patient 129


title: pancreatic cancer patient 130


title: pancreatic cancer patient 128


title: normal rat (Zhengchang), biol rep1

city: Beijing

first: Li

last: Xiaoguang

address: No.37 of Xueyuan Road, Haidian District

department: School of Biological Science and Medical Engineering

institute: Beihang University

description: Gene expression data from corresponding segments in normal rat

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Expression Console Software using RMA algorithm.

source_name: 5 mm long segments from normal rats, T7-8

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

growth_protocol: The experimental rats were kept at a temperature of 24-26ºC, and humidity of 35-45% with twelve h light-dark cycles. Food and water were provided ad libitum. Supplemental oral feedings were given as necessary.

extract_protocol: The samples for microarray analysis were homogenized in 1 ml Trizol (Invitrogen, Carlsbad, CA), and RNA extracted using RNEasy miniprep columns (Qiagen, Valencia, CA) according to the manufacturer’s instructions. An average of 40-60 ug RNA was obtained from 80-120 mg of tissue pooled from four animals for microarray analysis which was performed using an Affymetrix GeneChipÒ Rat Genome 230 2.0 chip for each time point. All assays were performed at least in triplicate biological independent pooled samples.

treatment_protocol: Wistar rats weighing 250-300 g each were anaesthetized , followed by transection at the T7-8 level removing a spinal cord segment 5.0 mm in length. The blade was repeatedly scraped along the ventral surface of the spinal canal, and any residual fibers at the lesion site were removed by aspiration. The animals were divided into 3 groups. One group (NT-3-chitosan tube) received a chitosan tube of 5 mm in length, with a 2.2 mm outer diameter and 2.0   mm in inner diameter, seeded with the NT-3-chitosan carriers, implanted into the lesioned area. A second group (tube alone) had implanted only an empty chitosan tube. A third group (lesion control) received no treatment after the operation.

value: spinal cord

tag: treatment

value: no lesion

value: Wistar rat

value: adult rat, i.e. 2 months after birth


title: anti-TNF non-responder (biological rep 23)

city: Nijmegen

first: Erik

last: Toonen

address: Geert Grooteplein-zuid 10

institute: Radboud University Nijmegen Medical Centre

description: Patient was treated with anti-TNF medication

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: RMA + GC correction by Partek software

label_protocol: GeneChip WT Terminal Labeling Kit

extract_protocol: Rneasy column purification

value: white blood cells

value: anti-TNF drugs infliximab and adalimumab

tag: response

value: anti-TNF non-responder

value: rheumatoid arthritis


title: anti-TNF non-responder (biological rep 21)


title: anti-TNF non-responder (biological rep 20)


title: universal rat reference RNA, technical rep5

description: Gene expression data for monitoring and controlling batch variation

source_name: rat reference RNA purchased from the Stratagen Co.(Agilent Co., Cat# 740200)

tag: sample type

value: Stratagene universal reference of 14 rat cell lines

value: female

value: pools of RNA from individual cell lines representing different rat tissues


title: normal rat (Zhengchang), biol rep2


title: anti-TNF non-responder (biological rep 19)


title: normal rat (Zhengchang), biol rep3


title: anti-TNF non-responder (biological rep 22)


title: universal rat reference RNA, technical rep4


title: Vector H3 ChIP vs. Input DNA Rep2

city: Los Angeles

first: Xiao-Fen

state: California

address: 615 Charles E. Young Dr

department: Biological Chemistry

institute: University of California Los Angeles

description: Tiling Array, biological replicate 2 of 2

hyb_protocol: Performed according to Agilent Yeast Tiling Array (G4491A) manufacturer's instructions.

scan_protocol: According to Agilent manufacturer's instructions.

data_processing: Following scanning, features were extracted using Agilent Feature Extraction and normalized using Agilent ChIP Analytics with default settings.

organism: Saccharomyces cerevisiae

source_name: H3-Myc ChIP

label_protocol: 500 ng of amplified DNA were primed with 20 µl of 2.5x random primer (BioPrime kit; Invitrogen) at 95°C for 5 min, then dNTP mix (each 1.2mM, dCTP 0.6 mM), Cy3-dCTP or Cy5-dCTP and Klenow (40U) were added and incubated at 37°C for 3 hours.

growth_protocol: Cells were grown in 50mL Ura- Trp- SD medium t to OD600 0.8-1.0.

extract_protocol: The ChIP were performed as previously described (Hecht et al. Nature 1996 [PMID 8779721]). Briefly, formaldehyde cross-linked, sonicated whole-cell extract was incubated overnight with antibodies directed against myc-H3 (9E10, Abcam), together with Protein A-agarose beads. The beads were washed and the crosslinked DNA was eluted. After reverse crosslinking, eluate samples were purified with Qiagen column.

treatment_protocol: Crosslink with 1% formaldehyde for 15 min at room temperature,quenche by 125 mM glycine at  room temperature for 5min. Pellet cells 3500 rpm, 3 min., and wash 2 x 20 ml PBS.

tag: genetic background

tag: genotype

value: anti-myc H3

value: Abcam

source_name: Input DNA

value: input DNA


title: universal rat reference RNA, technical rep3


title: pancreatic cancer patient 127

value: pancreas

value: pancreatic cancer


title: WT H3 ChIP vs. Input DNA Rep1

description: Tiling Array, biological replicate 1 of 2

value: wild type


title: H150A H3 ChIP vs. Input DNA Rep1

value: rpd3 H150A


title: Vector H3 ChIP vs. Input DNA Rep1


title: pancreatic cancer patient 126


title: WT H3 ChIP vs. Input DNA Rep2


title: H150A H3 ChIP vs. Input DNA Rep2


title: anti-TNF non-responder (biological rep 24)


title: anti-TNF non-responder (biological rep 17)


title: anti-TNF non-responder (biological rep 16)


title: pancreatic cancer patient 125


title: anti-TNF non-responder (biological rep 15)


title: anti-TNF non-responder (biological rep 18)


title: anti-TNF non-responder (biological rep 14)


title: anti-TNF non-responder (biological rep 10)


title: universal rat reference RNA, technical rep1


title: anti-TNF non-responder (biological rep 11)


title: anti-TNF non-responder (biological rep 13)


title: pancreatic cancer patient 124


title: pancreatic cancer patient 123


title: anti-TNF non-responder (biological rep 12)


title: SigA4stat_35021002

city: Jouy en Josas

first: Nathalie

last: Pigeonneau

address: domaine de Vilvert

department: Micalis

institute: INRA

description: Stationary phase, replicate 4.

hyb_protocol: Standard NimbleGen protocol.

scan_protocol: Standard NimbleGen protocol.

data_processing:
Identification of peaks corresponding to SigA binding sites on the Bacillus subtilis chromosome was done as described previously (Reppas et al., 2006, Mol Cell 24: 747-757 [PMID 17157257]).
Signal intensities were converted as log2 ratio (ChIP-DNA/Control-DNA) and corrected for dye bias using Loess regression on the MA plot.
The signal was smoothed by two rounds of sliding window averaging. The sliding window contained 29 probes (the middle probe and 14 probes on each side) corresponding to approximately 320 bp.

organism: Bacillus subtilis

source_name: ChIP_DNA from BSB1 strain expressing SigA-SPA protein, stationary phase

label_protocol: Standard NimbleGen protocol. ChIP DNA is labelled with Cy5 and control DNA is labelled with Cy3.

growth_protocol: BSB1 cells expressing the SigA-SPA protein were grown in 2 liters of LB medium (Erythromycin 0.6 mg/L, IPTG 0.5mM) supplemented with 0.3% glucose with vigorous shaking at 37°C. At stationary growth phase (OD600nm ≈ 1.5), 400mL was treated with formaldehyde.

extract_protocol: Cells were treated with formaldehyde 0.6 % final concentration, and cross-linking was carried out for 20 minutes at room temperature before quenching with 125 mM glycine (final concentration). Cells were harvested, washed twice with buffer A (10 mM Tris-HCl pH 7.5, 150 mM NaCl) and treated with lysozyme (1 mg/mL) in buffer B (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 0.2 mM EDTA, 0.1% (v/v) TritonX-100) supplemented with 0.1 mg/mL of RNase A. DNA was then sheared by sonication in order to obtain 0.2 to 1 Kbp fragments. Cell debris were removed by centrifugation at 20’000g for 30 minutes. 400 μL of Anti-FLAG M2 agarose beads (Sigma) washed with buffer B were added to the supernatant and incubation was continued for 2 h with rotation at 4 °C. Beads were then harvested, washed 3 times with large volumes of buffer B and resuspended in 500 μL of buffer C (100 mM Tris-HCl pH 8, 100 g/L SDS, 10 mM EDTA). Cross-links were dissociated by incubation at 65 °C for 18 hours. DNA fragments co-purified with SigA-SPA were extracted using the QIAquick PCR Purification kit (Qiagen). Contaminating RNA was treated with RNase A and a second purification of the DNA fragments was done. These fragments (ChIP-DNA) and DNA isolated from the whole cell extract fraction before the immunopurification (control DNA) were sent to NimbleGen.

tag: strain

tag: growth phase

value: stationary

value: mouse anti-FLAG M2

tag: antibody vendor

value: Sigma

tag: antibody catalog number

tag: antibody lot number

source_name: Control_DNA from BSB1 strain expressing SigA-SPA protein, stationary phase


title: Lesion control (D), caudal to the lesion (C), 90 days post-op, biol rep3

description: Gene expression data from adult rat of  lesion control

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 90 days after operation

tag: tissue

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and no control treatment

tag: time

value: 90 days after operation

value: Wistar rat

tag: gender

value: adult rat, i.e. 2 months after birth


title: pancreatic cancer patient 122


title: Lesion control (D), caudal to the lesion (C), 90 days post-op, biol rep2

value: female

tag: age


title: pancreatic cancer patient 121

tag: disease state


title: pancreatic cancer patient 133


title: anti-TNF non-responder (biological rep 9)

tag: cell type

value: white blood cells

value: anti-TNF drugs infliximab and adalimumab

value: anti-TNF non-responder

value: rheumatoid arthritis


title: Lesion control (D), caudal to the lesion (C), 60 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 60 days after operation

value: 60 days after operation


title: pancreatic cancer patient 119

value: pancreas

value: pancreatic cancer


title: anti-TNF non-responder (biological rep 7)


title: anti-TNF non-responder (biological rep 8)


title: anti-TNF non-responder (biological rep 4)


title: Lesion control (D), caudal to the lesion (C), 60 days post-op, biol rep2


title: universal rat reference RNA, technical rep2

value: Stratagene universal reference of 14 rat cell lines

value: pools of RNA from individual cell lines representing different rat tissues


title: anti-TNF non-responder (biological rep 5)


title: pancreatic cancer patient 120


title: SigA3stat_33779602

description: Stationary phase, replicate 3.

value: stationary

tag: chip antibody

value: mouse anti-FLAG M2


title: pancreatic cancer patient 117


title: anti-TNF non-responder (biological rep 3)

tag: treatment


title: Lesion control (D), caudal to the lesion (C), 90 days post-op, biol rep1

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord


title: pancreatic cancer patient 118


title: Lesion control (D), caudal to the lesion (C), 30 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 30 days after operation

value: spinal cord injury and no control treatment

value: 30 days after operation


title: pancreatic cancer patient 115


title: SigA4expo_33793802

description: Exponential phase, replicate 4.

source_name: ChIP_DNA from BSB1 strain expressing SigA-SPA protein, exponential phase

growth_protocol: BSB1 cells expressing the SigA-SPA protein were grown in 2 liters of LB medium (Erythromycin 0.6 mg/L, IPTG 0.5mM) supplemented with 0.3% glucose with vigorous shaking at 37°C. At mid-log growth phase (OD600nm ≈ 0.4), 1 liter was treated with formaldehyde.

value: exponential

value: Sigma

source_name: Control_DNA from BSB1 strain expressing SigA-SPA protein, exponential phase


title: anti-TNF responder (biological rep 17)

source_name: anti-TNF responder (biological rep 17)

tag: response

value: anti-TNF responder


title: anti-TNF responder (biological rep 18)

source_name: anti-TNF responder (biological rep 18)

value: white blood cells


title: anti-TNF non-responder (biological rep 1)

value: anti-TNF drugs infliximab and adalimumab


title: SigA4trans_33805002

description: Transition phase, replicate 4.

source_name: ChIP_DNA from BSB1 strain expressing SigA-SPA protein, transitive phase

growth_protocol: BSB1 cells expressing the SigA-SPA protein were grown in 2 liters of LB medium (Erythromycin 0.6 mg/L, IPTG 0.5mM) supplemented with 0.3% glucose with vigorous shaking at 37°C. At the transition growth phase (OD600nm ≈ 1.2), 400 mL was treated with formaldehyde.

value: transition

source_name: Control_DNA from BSB1 strain expressing SigA-SPA protein, transitive phase


title: pancreatic cancer patient 116

source_name: Pancreas RNA from pancreatic cancer patient


title: pancreatic cancer patient 114


title: anti-TNF responder (biological rep 11)

source_name: anti-TNF responder (biological rep 11)

value: rheumatoid arthritis


title: pancreatic cancer patient 113


title: SigA3expo_33780302

description: Exponential phase, replicate 3.


title: anti-TNF responder (biological rep 13)

source_name: anti-TNF responder (biological rep 13)


title: anti-TNF non-responder (biological rep 2)

value: anti-TNF non-responder


title: anti-TNF responder (biological rep 16)

source_name: anti-TNF responder (biological rep 16)


title: anti-TNF responder (biological rep 15)

source_name: anti-TNF responder (biological rep 15)


title: anti-TNF responder (biological rep 12)

source_name: anti-TNF responder (biological rep 12)


title: anti-TNF responder (biological rep 14)

source_name: anti-TNF responder (biological rep 14)


title: anti-TNF responder (biological rep 10)

source_name: anti-TNF responder (biological rep 10)


title: Lesion control (D), caudal to the lesion (C), 60 days post-op, biol rep1

value: 60 days after operation

value: Wistar rat

value: female

value: adult rat, i.e. 2 months after birth


title: Lesion control (D), caudal to the lesion (C), 30 days post-op, biol rep1


title: Lesion control (D), caudal to the lesion (C), 30 days post-op, biol rep2


title: anti-TNF responder (biological rep 9)

source_name: anti-TNF responder (biological rep 9)


title: anti-TNF responder (biological rep 7)

source_name: anti-TNF responder (biological rep 7)


title: Lesion control (D), caudal to the lesion (C), 20 days post-op, biol rep1

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 20 days after operation

value: 20 days after operation


title: pancreatic cancer patient 112

value: pancreas

value: pancreatic cancer


title: Lesion control (D), caudal to the lesion (C), 10 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 10 days after operation

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and no control treatment

value: 10 days after operation


title: anti-TNF responder (biological rep 8)

source_name: anti-TNF responder (biological rep 8)


title: anti-TNF responder (biological rep 6)

source_name: anti-TNF responder (biological rep 6)


title: Lesion control (D), caudal to the lesion (C), 20 days post-op, biol rep3


title: pancreatic cancer patient 111


title: SigA3trans_33809802

description: Transition phase, replicate 3.

value: mouse anti-FLAG M2

value: Sigma


title: anti-TNF responder (biological rep 5)

source_name: anti-TNF responder (biological rep 5)

value: white blood cells

value: anti-TNF responder


title: pancreatic cancer patient 110


title: Lesion control (D), caudal to the lesion (C), 20 days post-op, biol rep2


title: anti-TNF responder (biological rep 4)

source_name: anti-TNF responder (biological rep 4)

value: anti-TNF drugs infliximab and adalimumab


title: IL-17A-stimulated normal fibroblasts

city: Kumamoto

first: Taiji

last: Naashima

address: 1-1-1 Honjo

department: Department of Dermatology and Plastic Surgery

institute: Faculty of Life Sciences, Kumamoto University

description:
Test
SAMPLE 2

data_processing: The raw threshold cycle (Ct) was normalized using the value of housekeeping gene ; deltaCt = (Ct_Target − Ct_HKG)]. For the normalization, it uses the average of five housekeeping genes ; B2M, HPRT1, RPL13A, GPADH,ACTB. Fold Change worksheet reports 1/2^the normalized Ct of each mRNA – the normalized Ct of housekeeping genes [ available as a Series Supplementary file]

label: SYBR Green

source_name: IL-17A-stimulated normal fibroblasts

label_protocol: For PCR array (SABioscience), first-strand cDNA was synthesized using RT2 First Strand Kit (SABiosciences). cDNA was mixed with RT2 SYBR Green/ROX qPCR Master Mix and the mixture was added into a 96-well Extracellular Matrix and Adhesion Molecules PCR Array (SA Biosciences) that included primer pairs for 84 human RNAs.

extract_protocol: Total RNA was extracted from culture cells with ISOGEN (Nippon Gene, Tokyo, Japan).

value: dermal fibroblasts obtained by skin biopsy from healthy donors

tag: activation agent


title: Not stimulated normal fibroblasts

description:
control
SAMPLE 1

source_name: Not stimulated normal fibroblasts

value: no activation


title: pancreatic cancer patient 109

source_name: Pancreas RNA from pancreatic cancer patient


title: pancreatic cancer patient 108


title: IL-17F-stimulated normal fibroblasts

description:
Test
SAMPLE 3

source_name: IL-17F-stimulated normal fibroblasts


title: anti-TNF responder (biological rep 3)

source_name: anti-TNF responder (biological rep 3)

value: rheumatoid arthritis


title: anti-TNF responder (biological rep 2)

source_name: anti-TNF responder (biological rep 2)


title: Lesion control (D), caudal to the lesion (C), 10 days post-op, biol rep2

value: Wistar rat


title: pancreatic cancer patient 107


title: Lesion control (D), caudal to the lesion (C), 3 days post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 3 days after operation

value: 3 days after operation

value: female


title: Lesion control (D), caudal to the lesion (C), 10 days post-op, biol rep1

value: adult rat, i.e. 2 months after birth


title: pancreatic cancer patient 106

value: pancreas


title: Lesion control (D), caudal to the lesion (C), 3 days post-op, biol rep1


title: pancreatic cancer patient 105

value: pancreatic cancer


title: anti-TNF responder (biological rep 1)

source_name: anti-TNF responder (biological rep 1)


title: pancreatic cancer patient 103


title: pancreatic cancer patient 104


title: anti-TNF non-responder (biological rep 6)

value: anti-TNF non-responder


title: Lesion control (D), caudal to the lesion (C), 3 days post-op, biol rep2

value: 5mm long segments caudal to the T7-T8 lesioned area of the spinal cord

value: spinal cord injury and no control treatment


title: Patient 5_Sub C_4 months

first: Claus

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

hyb_protocol: The labeled and fragmented cRNA (10mg) was used for the hybridization to the Affymetrix (Santa Clara, CA) gene chips HS 1a520180 for 16 hr at 45C. An automated process of washing and staining in the Affymetrix Fluidics Station 400 was performed.

data_processing: CEL files were transferred to MadMax website (https://madmax.bioinformatics.nl), and data analysis was performed using the statistical programming language R and the R libraries offered by the Bioconductor project. The data were first explored for quality control purposes and were normalized the GCRMA method within Bioconductor.

source_name: Patient 5_Sub C_4 months

label_protocol: 2 μg of high quality total RNA, verified using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies), was used with the Affymetrix Eukaryotic One-Cylce Target Labeling and Control reagents (#900493) following the manufacturers instructions to generate Biotin-labeled antisense cRNA.

extract_protocol: Total RNA was extracted from the adipose tissue tissue using an RNeasy Lipid tissue mini kit followed by incubation with RNase free DNase (Qiagen, Crawley, West Sussex) for DNA-free RNA following the manufacturer's instructions.

value: Female

value: sub cutaneous adipose tissue

tag: time post vbg

value: 4 months


title: Patient 5_Om_Day 0

source_name: Patient 5_Om_Day 0

value: omental adipose tissue

value: Day 0


title: Lesion control (D), caudal to the lesion (C), 1 day post-op, biol rep3

source_name: 5 mm long segments caudal to the lesioned area were sampled under RNAase-free conditions 1 day after operation

value: 1 day after operation


title: Patient 5_Sub C_Day 0

source_name: Patient 5_Sub C_Day 0


title: Lesion control (D), caudal to the lesion (C), 1 day post-op, biol rep2


title: Lesion control (D), caudal to the lesion (C), 1 day post-op, biol rep1


title: Patient 4_Om_Day 0

source_name: Patient 4_Om_Day 0


title: Patient 5_Sub C_12 months

source_name: Patient 5_Sub C_12 months

value: 12 months


title: pancreatic cancer patient 101


title: pancreatic cancer patient 102


title: Lesion control (D), in the lesion (M), 90 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 90 days after operation

value: 5mm long segments in the T7-T8 lesioned area of the spinal cord

value: 90 days after operation


title: Patient 4_Sub C_Day 0

source_name: Patient 4_Sub C_Day 0


title: pancreatic cancer patient 99


title: Lesion control (D), in the lesion (M), 60 days post-op, biol rep3

source_name: 5 mm long segments in the lesioned area were sampled under RNAase-free conditions 60 days after operation

value: 60 days after operation

value: Wistar rat


title: Patient 4_Sub C_4 months

source_name: Patient 4_Sub C_4 months


title: Lesion control (D), in the lesion (M), 90 days post-op, biol rep2

value: female

value: adult rat, i.e. 2 months after birth


title: Lesion control (D), in the lesion (M), 60 days post-op, biol rep2


title: pancreatic cancer patient 100

value: pancreas

value: pancreatic cancer


title: Patient 3_Om_Day 0

source_name: Patient 3_Om_Day 0


title: Patient 4_Sub C_12 months

source_name: Patient 4_Sub C_12 months


title: pancreatic cancer patient 98

source_name: Pancreas RNA from pancreatic cancer patient