title: P23_UVB

first: Vincent

last: Hearing

address: Bldg 37  Rm 2132

department: National Cancer Institute

institute: National Institutes of Health

description: Gene expression of human skin after 2 weeks UVB treatment

hyb_protocol: 1.65 ug of Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent's recommended hybridization chamber and oven. After hybridization, microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with preheated 0.06x SSPE buffer (37°) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System.

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. The signal intensities from the single-experiment raw data lists were normalized by dividing their median intensity values. The ratio lists of the array of each treatment sample versus the respective donor-matched control sample were generated using the RosettaResolver Software.

source_name: skin, UVB

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was checked using Agilent 2100 Bioanalyzer platform (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Dorsal skin of skin type II-III volunteers was irradiated with SSR or UVA or UVB for 2 weeks (5 times a week; total 10 times). Biopsies were taken 3 days after the last treatment with non-irradiated control skin.

value: skin

value: UVB


title: SF7093 p53 WT pten WT Map250kSty

status: Public on Apr 22 2010

type: genomic

city: South San Francisco

first: Anthony

middle: Steve

last: Guerrero

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech

description: SRCID:SRC107469,PRBID:PRB16766,SRCNAME:7093,RAWFILE:16766_7093_GBMTumors_SPR460_Map250kSty.CEL

hyb_protocol: According to manufacturer's protocol (Affymetrix)

data_processing: The genotyping copy number data were generated with Affymetrix's CNAT algorithm, version 4.  Nsp and Sty copy number data were also estimated using the dChip algorithm (2006 version, build Dec 22, 2005), normalized against normal hapmap samples (downloaded from affymetrix). Segmentation of copy number data was performed with GLAD, version: 1.16.0.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Affymetrix 500K Human Mapping 500K array manual

extract_protocol: Qiagen's  AllPrep DNA/RNA extraction kit (Catalog #80204) was used to extract DNA and RNA according to manufacturer's protocol

tag: source

value: UCSF

tag: sample id

tag: genome/variation

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:wt


title: SF7048 p53 MT pten WT Map250kSty

description: SRCID:SRC107463,PRBID:PRB16754,SRCNAME:7048,RAWFILE:16754_7048_GBMTumors_SPR460_Map250kSty.CEL

scan_protocol: According to manufacturer's protocol (Affymetrix)

value: p53 exon 4-8 mutation status:HETSUB.283R>C

value: pten exon 5-6 mutation status:WT


title: SF7201 p53 WT pten WT Map250kSty

description: SRCID:SRC107480,PRBID:PRB16788,SRCNAME:7201,RAWFILE:16788_7201_GBMTumors_SPR460_Map250kSty.CEL


title: SF7063 p53 WT pten WT Map250kSty

description: SRCID:SRC107466,PRBID:PRB16760,SRCNAME:7063,RAWFILE:16760_7063_GBMTumors_SPR460_Map250kSty.CEL


title: SF7113 p53 MT pten WT Map250kSty

description: SRCID:SRC107473,PRBID:PRB16774,SRCNAME:7113,RAWFILE:16774_7113_GBMTumors_SPR460_Map250kSty.CEL

value: p53 exon 4-8 mutation status:HETSUB.266G>R, HETSUB.267R>W


title: SF7082 p53 WT pten MT Map250kSty

description: SRCID:SRC107468,PRBID:PRB16764,SRCNAME:7082,RAWFILE:16764_7082_GBMTumors_SPR460_Map250kSty.CEL

value: pten exon 5-6 mutation status:HETSUB.67I>K


title: Crossbred 10 vs Crossbred 69-4

type: RNA

city: East Lansing

first: Catherine

middle: W.

last: Ernst

state: MI

address: 3330 Anthony Hall

department: Animal Science

institute: Michigan State University

description: The tissue samples compared on this array are part of an experiment to study muscle development at 40 and 70 days of gestation in a Brazilian local pig breed and crossbred pigs from the US using the swine protein-annotated oligonucleotide microarray.

hyb_protocol: Labeled aRNAs were purified and combined with 65 µl of Slide Hyb #1 solution (Ambion, Inc.) and denatured at 70C for 5 min. Hybridizations were performed in sealed hybridization cassettes (ArrayIt, TeleChem International, Inc., Sunnyvale, CA, USA) for 18 h at a humid 54C. Following hybridization, slides were washed in 2X SSC/0.5% SDS and 0.1X SSC/0.1% SDS solutions for 10 min each. The slides were rinsed in a 0.1X SSC solution and nuclease-free water and dried by centrifugation.

scan_protocol: Fluorescent images were detected by a GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA) and fluorescence intensity data were collected using GenePix software (Molecular Devices) after spot alignment. Median intensity values for each dye channel were stored as comma-separated values data files.

data_processing: Loess normalized log-ratio of Cy5 versus Cy3 intensities. No background correction.

molecule: total RNA

organism: Sus scrofa

source_name: Skeletal muscle Crossbred 10

label_protocol: One µg of total RNA was reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy3 (GE Healthcare, UK).

extract_protocol: Total RNA from 1.0 g of tissue was extracted using TRizol reagent (Invitrogen Corp., Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA, USA).

tag: breed type

value: Yorkshire x Landrace

tag: tissue type

value: Skeletal muscle – Longissimus dorsi

tag: age

value: 70 days of gestation

source_name: Skeletal muscle Crossbred 69-4

label_protocol: One µg of total RNA was reverse transcribed with a T7 oligo(dT) primer using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion Inc., Austin, TX, USA) according to the manufacturer’s instructions. Following first-strand and second-strand synthesis and purification, the cDNAs were in vitro transcribed to synthesize multiple copies of amino allyl-modified aRNAs. After purification, aRNAs were labeled with N-hydroxysuccinate (NHS) ester Cy5 (GE Healthcare, UK).

value: 40 days of gestation


title: Crossbred 56-1 vs Crossbred 12

source_name: Skeletal muscle Crossbred 56-1

source_name: Skeletal muscle Crossbred 12


title: P22_UVB

city: Bethesda

state: MD

tag: tissue

tag: treatment


title: P21_UVB


title: SF7228 p53 WT pten WT Map250kSty

description: SRCID:SRC107484,PRBID:PRB16796,SRCNAME:7228,RAWFILE:16796_7228_GBMTumors_SPR460_Map250kSty.CEL


title: SF7179 p53 WT pten WT Map250kSty

description: SRCID:SRC107475,PRBID:PRB16778,SRCNAME:7179,RAWFILE:16778_7179_GBMTumors_SPR460_Map250kSty.CEL


title: SF7081 p53 WT pten WT Map250kSty

description: SRCID:SRC107467,PRBID:PRB16762,SRCNAME:7081,RAWFILE:16762_7081_GBMTumors_SPR460_Map250kSty.CEL


title: SF7030 p53 WT pten WT Map250kSty

description: SRCID:SRC107461,PRBID:PRB16750,SRCNAME:7030,RAWFILE:16750_7030_GBMTumors_SPR460_Map250kSty.CEL


title: SF7054 p53 WT pten WT Map250kSty

description: SRCID:SRC107464,PRBID:PRB16756,SRCNAME:7054,RAWFILE:16756_7054_GBMTumors_SPR460_Map250kSty.CEL


title: Piau 241 vs Piau 308

source_name: Skeletal muscle Piau 241

extract_protocol: Total RNA from 30 mg of tissue was extracted using RNeasy Mini kit with on-column RNase-free DNase digestion (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA concentration and quality were determined with an RNA 6000 Pico LabChip® kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Palo Alto, CA, USA).

value: Piau

source_name: Skeletal muscle Piau 308


title: SF7095 p53 MT pten WT Map250kSty

description: SRCID:SRC107471,PRBID:PRB16770,SRCNAME:7095,RAWFILE:16770_7095_GBMTumors_SPR460_Map250kSty.CEL

value: p53 exon 4-8 mutation status:HOMSUB.282R>W


title: SF7034 p53 WT pten WT Map250kSty

description: SRCID:SRC107462,PRBID:PRB16752,SRCNAME:7034,RAWFILE:16752_7034_GBMTumors_SPR460_Map250kSty.CEL


title: SF6977 p53 MT pten WT Map250kSty

description: SRCID:SRC107459,PRBID:PRB16746,SRCNAME:6977,RAWFILE:16746_6977_GBMTumors_SPR460_Map250kSty.CEL

value: p53 exon 4-8 mutation status:HOMSUB.220Y>C


title: SF7180 p53 WT pten WT Map250kSty

description: SRCID:SRC107476,PRBID:PRB16780,SRCNAME:7180,RAWFILE:16780_7180_GBMTumors_SPR460_Map250kSty.CEL


title: SF7029 p53 MT pten WT Map250kSty

description: SRCID:SRC107460,PRBID:PRB16748,SRCNAME:7029,RAWFILE:16748_7029_GBMTumors_SPR460_Map250kSty.CEL

value: p53 exon 4-8 mutation status:HETSUB.216V>A


title: SF7059 p53 WT pten MT Map250kSty

description: SRCID:SRC107465,PRBID:PRB16758,SRCNAME:7059,RAWFILE:16758_7059_GBMTumors_SPR460_Map250kSty.CEL

value: pten exon 5-6 mutation status:HETSUB.32I>S


title: SF6969 p53 WT pten WT Map250kSty

description: SRCID:SRC107458,PRBID:PRB16744,SRCNAME:6969,RAWFILE:16744_6969_GBMTumors_SPR460_Map250kSty.CEL


title: P23_UVA

description: Gene expression of human skin after 2 weeks UVA treatment

source_name: skin, UVA

value: skin

value: UVA


title: P3_UVB

description: Gene expression of human skin after 2 weeks UVB treatment

value: UVB


title: Crossbred 11 vs Crossbred 3

source_name: Skeletal muscle Crossbred 11

source_name: Skeletal muscle Crossbred 3


title: P21_UVA


title: SF7225-2 p53 WT pten WT Map250kSty

description: SRCID:SRC107482,PRBID:PRB16792,SRCNAME:7225-2,RAWFILE:16792_7225_GBMTumors_SPR460_Map250kSty.CEL

value: UCSF

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:wt


title: Piau 148 vs Piau 492

source_name: Skeletal muscle Piau 148

source_name: Skeletal muscle Piau 492


title: NCI-H69

first: Jih-Hsiang

last: Lee

address: 9000 Rockville Pike, building 10 8N254

department: Medical oncology branch

institute: National Cancer Institute

hyb_protocol: Appropriate equal amoung of Cy5-labeled sample and Cy3-labeled reference DNAwere mixed to a 22ul final volumn. 61ul Hybridization Master Mix (1mg/ml Cot-1 DNA 5ul, Agilent 100X blocking agent 1ul, and Agilent 2X HiRPM Hybridization buffer 55ul) was added and incubated at 95'C for 3 min folloed by 37'C for 30min. 27ul of Agilent-CGHBlock was then added and mixed. The hybridization sample mixture was applied onto the microarray gasket well and was covered by a microarray slide. The slide was incubated in a 65'C rotator rack for 40 hours.  After hybridization, slide was washed sequential.

scan_protocol: Scanned on an Agilent DNA microarray scanner Images were quantified using Agilent Feature Extraction Software v10.5

data_processing: Agilent Feature Extraction Software v10.5 was used for background subtraction and data processing.  Data were normalized using Linear method.

source_name: Cell line

label_protocol: 500ng sample and reference genomic DNA were fragemented by incubation at 95'C up to 10 min and then were labeled with Cy5 and Cy3, respectively at 85'C for 30 min. Labeled DNA were purified using Agilent KREApure column. Degree of labeling was determined by measuring the absorbance at A260nm(DNA), A550nm(Cy3), and A650nmCy5).

extract_protocol: Total genomic DNA was isolated from cell lines, cytology specimens or deparaffinated FFPE specimens using reagents of the DNeasy Blood and Tissue Kit, QIAquick PCR Purification Kit (Qiagen, Gaithersburg, MD) as well as Dako Target Retrieval Solution (Dako, Carpinteria, CA) in protocols optimized for maximum yield from the various types of samples.

tag: gender

value: M

tag: sclc/carcinoid

value: SCLC

tag: sclc primary tumor/metastasis

tag: bronchial/gi carcinoid

tag: origin of sample

value: Pleural effusion

tag: growth pattern of cell line

value: SCLC-CLASSIC

tag: pathological review

source_name: Promega male human genomic DNA

tag: reference

value: Promega male human genomic DNA


title: P20_UVB


title: P2_UVB


title: NCI-H678


title: Crossbred 69-4 vs Piau 148

value: Yorkshire x Landrace

value: Skeletal muscle – Longissimus dorsi

value: 40 days of gestation.


title: NCI-H1173

value: F

value: Soft tissue


title: P20_UVA


title: NCI-H128


title: Piau 396 vs Piau 489

source_name: Skeletal muscle Piau 396

value: Piau

value: 70 days of gestation

source_name: Skeletal muscle Piau 489

value: 40 days of gestation


title: Piau 489 vs Crossbred 56-1


title: NCI-H82

value: SCLC-VARIANT


title: Piau 308 vs Crossbred 11


title: Crossbred 3 vs Piau 241


title: P22_UVA

value: skin

value: UVA


title: NCI-H620

value: Bone marrow


title: GLC4-CDDP

value: M


title: NCI-H146

value: SCLC

value: Bone marrow or PE


title: NCI-H526


title: NCI-N592

value: SCLC-CLASSIC


title: NCI-H187

value: Pleural effusion

value: Promega male human genomic DNA


title: GLC4


title: NCI-H792


title: P3_UVA


title: Crossbred 12 vs Piau 396

value: Yorkshire x Landrace

value: Skeletal muscle – Longissimus dorsi


title: P2_UVA


title: Piau 492 vs Crossbred 10


title: SCLC 11

source_name: Clinical sample

value: Primary tumor

value: Lung/nodulectomy

value: Small cell lung carcinoma


title: P23_SSR

description: Gene expression of human skin after 2 weeks SSR treatment

source_name: skin, SSR

value: SSR


title: P21_SSR


title: P22_SSR


title: SCLC 10

value: Lung/lobectomy


title: P20_SSR


title: Carcinoid 24

value: F

value: Carcinoid

value: Bronchial carcinoid

value: Right lower lobe lung

value: Typical carcinoid


title: SCLC 9

value: M

value: SCLC


title: SCLC 5


title: SCLC 6


title: SCLC 33

value: Metastasis

value: Mediastinum

value: Undifferentiated small cell carcinoma


title: Carcinoid 19

value: Promega male human genomic DNA


title: SCLC 7


title: SCLC 8


title: SCLC 29

value: Lung


title: SCLC 30

value: Liver


title: SCLC 31

value: Primary tumor

value: Right lung


title: SCLC 3

value: Lung/nodulectomy

value: Small cell lung carcinoma


title: Carcinoid 18

value: F

value: Lung/lobectomy


title: SCLC 4


title: P23_Control

description: Gene expression of human skin without treatment

source_name: skin, control

value: skin


title: Carcinoid 17

value: Carcinoid

value: Bronchial carcinoid


title: SCLC 28

value: M


title: Carcinoid 16

value: Typical carcinoid


title: SCLC 32

value: SCLC

value: Metastasis

value: Metastatic undifferentiated small cell carcinoma


title: P2_SSR

value: SSR


title: P21_Control


title: P22_Control


title: Carcinoid 14

value: Promega male human genomic DNA


title: Carcinoid 11


title: P3_Control


title: SCLC 27

value: Anterior mediastinum

value: Undifferentiated small cell carcinoma


title: P20_Control


title: Carcinoid 15


title: Carcinoid 13


title: SCLC 26

value: Primary tumor

value: Left lung mass


title: Carcinoid 12


title: P3_SSR


title: SCLC 23

value: Mediastinum


title: Carcinoid 10

value: F


title: SCLC 24


title: SCLC 25

value: Right middle lobe lung


title: P2_Control

value: skin


title: SCLC 20


title: SCLC 21

value: Anterior chest wall


title: SCLC 22

value: Scalp, breast, thigh


title: FPC88 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122569,PRBID:PRB21779,FILE:Agilent_251485025150_S01_GE2-v5_95_Feb07_1_3.txt

hyb_protocol: According to manufacturer's protocol (Agilent)

data_processing: Data were normalized using Agilent feature extraction software v9.5, with the Stratagene Universal Human Reference in the reference channel, according to manufacturer's protocol. Ratios are Cy5/Cy3, representing test/ref.

label_protocol: Agilent Low RNA Input Linear Amplification

value: UCSF

tag: cell type

value: 12454_Neurosphere Cultures

source_name: Universal Human Reference from Stratagene (#740000)

tag: type

value: reference


title: FPC44 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122563,PRBID:PRB21773,FILE:Agilent_251485025148_S01_GE2-v5_95_Feb07_1_2.txt

scan_protocol: According to manufacturer's protocol (Agilent)

tag: source

tag: sample id


title: FPC49 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122566,PRBID:PRB21776,FILE:Agilent_251485025152_S01_GE2-v5_95_Feb07_1_2.txt


title: SCLC 19

value: SCLC

value: Lung

value: M


title: FPC82 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122567,PRBID:PRB21777,FILE:Agilent_251485025148_S01_GE2-v5_95_Feb07_1_3.txt


title: FPC43 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122562,PRBID:PRB21772,FILE:Agilent_251485025152_S01_GE2-v5_95_Feb07_1_1.txt


title: FPC42 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122561,PRBID:PRB21771,FILE:Agilent_251485025150_S01_GE2-v5_95_Feb07_1_1.txt


title: SCLC 17

value: Metastasis

value: Right axillary lymp node

value: Promega male human genomic DNA


title: SCLC 18

value: Primary tumor

value: Right upper lobe lung

value: Undifferentiated small cell carcinoma


title: SCLC 16

value: Liver

value: Metastatic undifferentiated small cell carcinoma


title: 7179-NSP 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC108924,PRBID:PRB18965,FILE:Agilent_251485019099_S01_GE2-v5_95_Feb07_1_4.txt


title: FPC47 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122564,PRBID:PRB21774,FILE:Agilent_251485025149_S01_GE2-v5_95_Feb07_1_2.txt


title: FPC95 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122571,PRBID:PRB21781,FILE:Agilent_251485025148_S01_GE2-v5_95_Feb07_1_4.txt


title: SCLC 14

value: Cerebellum


title: FPC90 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122570,PRBID:PRB21780,FILE:Agilent_251485025152_S01_GE2-v5_95_Feb07_1_3.txt


title: SCLC 15


title: FPC85 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122568,PRBID:PRB21778,FILE:Agilent_251485025149_S01_GE2-v5_95_Feb07_1_3.txt


title: SCLC 13


title: 27335102

city: Tjele

first: Jakob

last: Hedegaard

address: PO-box 50

department: Department of Genetics and Biotechnology

country: Denmark

institute: Aarhus University, Faculty of Agricultural Sciences

hyb_protocol: Samples were co-hybridized with a MAUI hybridization system (BioMicro Systems).

scan_protocol: The arrays were scanned using a 5 µm scanner, and Nimblescan software (Roche Nimblegen, Madison, WI) was used to retrieve fluorescent intensity raw data from the scanned images of the oligonucleotide tiling arrays.

data_processing: First, spatial correction was applied to adjust position-dependent non-uniformity of signals across the array. Specifically, locally weighted polynomial regression (loess) was used to adjust signal intensities based on X,Y feature position. Normalization was then performed using the q-spline method, followed by segmentation using the segMNT CNV calling algorithm.

organism: Bos taurus

source_name: genomic DNA from bovine cattle

label_protocol: According to manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: Genomic DNA was purified from blood by salt precipitation. The precipitation was performed by adding 2.36volumes of cold 96% ethanol and 0.16volumes of 3M sodium acetate (pH 4.8). After 20 minutes of centrifugation at 4 degrees Celsius and 13.000 rpm, the precipitated DNA was washed with 70% ethanol, re-precipitated by 5 minutes of centrifugation at 4 degrees Celsius and 13.000 rpm. After precipitation, the isolated DNA was resuspended in 16TE-buffer. Following the isolation of the genomic DNA samples, the DNA quality was assessed by measuring the concentration and the purity on the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). DNA integrity and purity were also assessed by gel electrophoresis on a 1% agarose gel (SeaKemH GTGH Agarose, Cambrex Bio Science, and 16TBE buffer, Invitrogen) containing 0.15 mg/mL ethidium bromide.

tag: breed

value: Holstein

value: Blood

value: Male

tag: id

value: Simmental

value: blood

value: Female


title: 27578702


title: 27582302


title: 27558402


title: SCLC 2

value: F

tag: age

value: SCLC

value: Lymphnode paratracheal

value: Small cell anaplastic lung carcinoma


title: 27035102

tag: tissue


title: 25456002

value: Hereford


title: 27582602


title: 27035402

value: Red Danish


title: 24125302


title: 27329402


title: SCLC 12

value: Primary tumor

value: Lung

value: M

value: Promega male human genomic DNA


title: SCLC 1


title: 27579002


title: 27031702


title: 27031402


title: FPC48 12454_Neurosphere Cultures vs. reference GE2-v5

description: SRCID:SRC122565,PRBID:PRB21775,FILE:Agilent_251485025150_S01_GE2-v5_95_Feb07_1_2.txt

value: UCSF

value: 12454_Neurosphere Cultures

value: reference


title: 24125002

value: Holstein

value: Blood

value: Male


title: Carcinoid 28

value: Carcinoid

value: Bronchial carcinoid

value: Right middle lobe lung

value: Peripheral carcinoid


title: 24130002

value: Simmental

value: blood


title: 27034702

value: Red Danish


title: Carcinoid 27

value: F

value: Right lower lobe

value: Carcinoid tumor


title: 24124702

value: Female


title: 27034402


title: 7063NC18m13m90 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120200,PRBID:PRB20408,FILE:Agilent_251485019278_S01_GE2-v5_95_Feb07_1_4.txt

value: UCSF

value: 15394_In vivo passaged


title: 21197902


title: 25456302


title: 7063NC18m13m91 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120201,PRBID:PRB20409,FILE:Agilent_251485019279_S01_GE2-v5_95_Feb07_1_4.txt

value: reference


title: 7063c16m18m87 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC119845,PRBID:PRB20217,FILE:Agilent_251485019281_S01_GE2-v5_95_Feb07_1_2.txt


title: 7063c16m18m88 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC119846,PRBID:PRB20218,FILE:Agilent_251485019282_S01_GE2-v5_95_Feb07_1_2.txt


title: 19655402

value: Holstein


title: Carcinoid 26

value: Right mainstem bronchus

value: Endobronchial carcinoid focally extending through mucosa

value: M

value: Promega male human genomic DNA


title: 24130302

value: Blood

value: Male


title: 24124102

value: Simmental


title: 7113C20m32 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120194,PRBID:PRB20402,FILE:Agilent_251485019224_S01_GE2-v5_95_Feb07_1_3.txt


title: 19655102

value: blood


title: Carcinoid 23

value: Carcinoid

value: Bronchial carcinoid

value: Right lower lobe lung


title: 7113C13m24 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120193,PRBID:PRB20401,FILE:Agilent_251485019223_S01_GE2-v5_95_Feb07_1_3.txt


title: 7063c18m13 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117480,PRBID:PRB18967,FILE:Agilent_251485019205_S01_GE2-v5_95_Feb07_1_2.txt


title: Carcinoid 21

value: F


title: 19676602

value: Female

value: Hereford


title: 7063c16m18 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117479,PRBID:PRB18966,FILE:Agilent_251485019205_S01_GE2-v5_95_Feb07_1_1.txt

value: UCSF

value: 15394_In vivo passaged


title: Carcinoid 25

value: Left lower lobe lung

value: Carcinoid tumor


title: 19635102

value: Holstein


title: 19634802


title: 7113 neg c20 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110952,PRBID:PRB17619,FILE:Agilent_251485017476_S01_GE2-v5_95_Feb07_1_2.txt

value: 12474_CD133 Pos_Neg_Sorted_Populations

value: reference


title: 28203002

value: Blood


title: Carcinoid 9

value: M

value: GI carcinoid

value: Rectum

value: Submucosal carcinoid

value: Promega male human genomic DNA


title: 7113 neg c15 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110951,PRBID:PRB17618,FILE:Agilent_251485017476_S01_GE2-v5_95_Feb07_1_1.txt


title: Carcinoid 8

value: Carcinoid

value: Mid jejunum

value: Metastatic carcinoid tumor


title: 19635902

value: Male

value: blood


title: 19634502

value: Simmental


title: 7113 neg c13 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110950,PRBID:PRB17617,FILE:Agilent_251485017475_S01_GE2-v5_95_Feb07_1_4.txt

value: UCSF


title: Carcinoid 22

value: F

value: Bronchial carcinoid

value: Right lower lobe lung

value: Peripheral carcinoid


title: 28194802

value: Holstein

value: Blood


title: Carcinoid 7

value: GI carcinoid

value: Mesenteric lymph nodes, liver

value: Metastatic malignant carcinoid tumor

value: M


title: 27676602

value: Red Danish


title: 7063 neg c18 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110945,PRBID:PRB17612,FILE:Agilent_251485017474_S01_GE2-v5_95_Feb07_1_3.txt

value: 12474_CD133 Pos_Neg_Sorted_Populations

value: reference


title: Carcinoid 20

value: Carcinoid

value: Left lung

value: Carcinoid tumor

value: Promega male human genomic DNA


title: Carcinoid 6

value: Liver

value: Metastatic carcinoid


title: 27676902

value: Male

value: blood


title: 7063 neg c16 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110944,PRBID:PRB17611,FILE:Agilent_251485017474_S01_GE2-v5_95_Feb07_1_2.txt

value: UCSF


title: Carcinoid 5

value: Left inguinal lymph node

value: Metastatic small cell neuroendocrine carcinoma


title: 7063 neg c14 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110943,PRBID:PRB17610,FILE:Agilent_251485017474_S01_GE2-v5_95_Feb07_1_1.txt


title: Carcinoid 4

value: F

value: GI carcinoid

value: Small bowel

value: Metastatic carcinoid tumor


title: 7095NC20-PC2m141 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121793,PRBID:PRB21093,FILE:Agilent_251485025070_S01_GE2-v5_95_Feb07_1_4.txt

value: 15394_In vivo passaged


title: 27635302

value: Holstein

value: Blood


title: 27637402

value: Simmental


title: 27650902

value: Hereford


title: Carcinoid 3

value: M

value: Carcinoid

value: Carcinoid tumor

value: Promega male human genomic DNA


title: 7095NC20-PC11m139 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121792,PRBID:PRB21092,FILE:Agilent_251485025069_S01_GE2-v5_95_Feb07_1_4.txt

value: reference


title: 27675702

value: Male

value: blood


title: 27636802


title: 27674002

value: Red Danish


title: Carcinoid 2

value: F

value: Vermiform appendix

value: Focal carcinoid


title: 27667302


title: 27030102


title: 7095NC20-PC1m131 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121788,PRBID:PRB21088,FILE:Agilent_251485025070_S01_GE2-v5_95_Feb07_1_3.txt

value: UCSF


title: 27029102


title: 7095NC20-PC4m134 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121790,PRBID:PRB21090,FILE:Agilent_251485025047_S01_GE2-v5_95_Feb07_1_3.txt

value: 15394_In vivo passaged


title: Carcinoid 1

value: GI carcinoid

value: Small bowel, liver

value: Serosal carcinoid nodule, carcinoid


title: 28195102

value: Simmental

value: Blood

value: Holstein


title: 27645702


title: 28203302


title: 27667602


title: 27028802


title: 7095NC20-PC5m129 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121787,PRBID:PRB21087,FILE:Agilent_251485025069_S01_GE2-v5_95_Feb07_1_3.txt


title: 27027902


title: 7095NC20-PC8m126 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121786,PRBID:PRB21086,FILE:Agilent_251485025090_S01_GE2-v5_95_Feb07_1_3.txt


title: 27028202


title: SF7225-2 p53 WT pten WT Map250kNsp

description: SRCID:SRC107482,PRBID:PRB16791,SRCNAME:7225-2,RAWFILE:16791_7225_GBMTumors_SPR460_Map250kNsp.CEL

tag: genome/variation

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:wt


title: 7095NC20-PC9m123 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121784,PRBID:PRB21084,FILE:Agilent_251485025071_S01_GE2-v5_95_Feb07_1_2.txt

value: reference


title: 24143702

tag: gender

value: Male


title: 7095NC20-PC6m109 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121778,PRBID:PRB21078,FILE:Agilent_251485025070_S01_GE2-v5_95_Feb07_1_1.txt


title: 7095NC20-PC10m119 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121782,PRBID:PRB21082,FILE:Agilent_251485025069_S01_GE2-v5_95_Feb07_1_2.txt


title: 24426702

value: blood


title: SF7276 p53 WT pten MT Map250kNsp

description: SRCID:SRC107486,PRBID:PRB16799,SRCNAME:7276,RAWFILE:16799_7276_GBMTumors_SPR460_Map250kNsp.CEL

value: pten exon 5-6 mutation status:HETSUB.133V>I


title: 27025402


title: 27025102

value: Red Danish


title: 27651202


title: 7095NC20-PC7m105 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121776,PRBID:PRB21076,FILE:Agilent_251485025090_S01_GE2-v5_95_Feb07_1_1.txt


title: 24142702


title: 27667002


title: 24143402


title: 24143102


title: 7194PC7m57 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120202,PRBID:PRB20410,FILE:Agilent_251485019230_S01_GE2-v5_95_Feb07_1_3.txt


title: SF7228 p53 WT pten WT Map250kNsp

description: SRCID:SRC107484,PRBID:PRB16795,SRCNAME:7228,RAWFILE:16795_7228_GBMTumors_SPR460_Map250kNsp.CEL


title: 7063c3m21m66 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117485,PRBID:PRB18972,FILE:Agilent_251485019206_S01_GE2-v5_95_Feb07_1_3.txt


title: 24148402


title: SF7259 p53 WT pten WT Map250kNsp

description: SRCID:SRC107485,PRBID:PRB16797,SRCNAME:7259,RAWFILE:16797_7259_GBMTumors_SPR460_Map250kNsp.CEL


title: 7194C8m62 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120199,PRBID:PRB20407,FILE:Agilent_251485019229_S01_GE2-v5_95_Feb07_1_3.txt


title: 24141502


title: 7063c3m21m65 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117486,PRBID:PRB18973,FILE:Agilent_251485019206_S01_GE2-v5_95_Feb07_1_4.txt


title: 7194C8m61 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120198,PRBID:PRB20406,FILE:Agilent_251485019228_S01_GE2-v5_95_Feb07_1_3.txt


title: 7113c7m36 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117489,PRBID:PRB18976,FILE:Agilent_251485019207_S01_GE2-v5_95_Feb07_1_3.txt


title: SF7227 p53 WT pten WT Map250kNsp

description: SRCID:SRC107483,PRBID:PRB16793,SRCNAME:7227,RAWFILE:16793_7227_GBMTumors_SPR460_Map250kNsp.CEL


title: SF7223 p53 WT pten MT Map250kNsp

description: SRCID:SRC107481,PRBID:PRB16789,SRCNAME:7223,RAWFILE:16789_7223_GBMTumors_SPR460_Map250kNsp.CEL

value: pten exon 5-6 mutation status:HOMSUB.130R>G


title: 31041 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115719,PRBID:PRB18727,FILE:Agilent_251239150418_S01_GE2-SSPE_95_Feb07.txt

value: MD Anderson

value: p53 exon 4-8 mutation status:ND

value: pten exon 5-6 mutation status:ND


title: 19648702


title: SF7201 p53 WT pten WT Map250kNsp

description: SRCID:SRC107480,PRBID:PRB16787,SRCNAME:7201,RAWFILE:16787_7201_GBMTumors_SPR460_Map250kNsp.CEL

value: UCSF


title: 9957 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115718,PRBID:PRB18726,FILE:Agilent_251239150417_S01_GE2-SSPE_95_Feb07.txt


title: 7113c5m25 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117488,PRBID:PRB18975,FILE:Agilent_251485019207_S01_GE2-v5_95_Feb07_1_2.txt

value: 15394_In vivo passaged


title: SF7194 p53 WT pten WT Map250kNsp

description: SRCID:SRC107479,PRBID:PRB16785,SRCNAME:7194,RAWFILE:16785_7194_GBMTumors_SPR460_Map250kNsp.CEL


title: 7063c7m6 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117487,PRBID:PRB18974,FILE:Agilent_251485019207_S01_GE2-v5_95_Feb07_1_1.txt


title: 19640102

value: Hereford


title: 19639802


title: 3td-SMN vs 3WT

city: Montpellier

first: johann

last: Soret

address: 1919, route de Mende

department: Institut de Genetique Moleculaire

country: France

institute: CNRS

hyb_protocol: Approximately 6μg of DNA was hybridzed per array using the Affymetrix hybridization kit. Arrays were hybridized for 16 hours at 45° at 60rpm using an Affymetrix hybridization oven.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Data were processed with the TAS software with the following settings: Scale to target intensity 100; Signal scale Log2; p-value scale -10Log10; Bandwidth 40; Two sided test type; PM/MM intensities.Data were analyzed by two sample comparison, normalized using quantile normalization plus scaling. Both control and treatment groups were normalized together.

organism: Schizosaccharomyces pombe

source_name: RNA from td-SMN strain

label_protocol: Labelling was done according to the Affymetrix tiling array manufacturer instructions starting from 10μg of total RNA

growth_protocol: Both wild type and mutant strains were grown at 25°C in YES medium

extract_protocol: Total RNA were purified with Tri-Reagent (Sigma) and treated with RQ1 RNAse-free DNAse.

tag: strain

value: td-SMN

source_name: RNA from wild type strain

value: wild type


title: SF7186 p53 WT pten WT Map250kNsp

description: SRCID:SRC107477,PRBID:PRB16781,SRCNAME:7186,RAWFILE:16781_7184_GBMTumors_SPR460_Map250kNsp.CEL


title: 24141202

value: Simmental

value: Blood

value: Holstein


title: 19649002


title: 7063c4m9 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117484,PRBID:PRB18971,FILE:Agilent_251485019206_S01_GE2-v5_95_Feb07_1_2.txt

value: reference


title: 19639502

value: Male


title: SF7180 p53 WT pten WT Map250kNsp

description: SRCID:SRC107476,PRBID:PRB16779,SRCNAME:7180,RAWFILE:16779_7180_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:wt


title: 19638502

value: blood


title: 40152 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115717,PRBID:PRB18725,FILE:Agilent_251239150415_S01_GE2-SSPE_95_Feb07.txt


title: 24326 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115716,PRBID:PRB18724,FILE:Agilent_251239150414_S01_GE2-SSPE_95_Feb07.txt


title: 7063c3m21 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC117481,PRBID:PRB18968,FILE:Agilent_251485019205_S01_GE2-v5_95_Feb07_1_3.txt


title: SF7113 p53 MT pten WT Map250kNsp

description: SRCID:SRC107473,PRBID:PRB16773,SRCNAME:7113,RAWFILE:16773_7113_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:HETSUB.266G>R, HETSUB.267R>W


title: SF7179 p53 WT pten WT Map250kNsp

description: SRCID:SRC107475,PRBID:PRB16777,SRCNAME:7179,RAWFILE:16777_7179_GBMTumors_SPR460_Map250kNsp.CEL


title: SF7192 p53 MT pten WT Map250kNsp

description: SRCID:SRC107478,PRBID:PRB16783,SRCNAME:7192,RAWFILE:16783_7192_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:HETSUB.220Y>H

value: pten exon 5-6 mutation status:WT


title: 26460 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115715,PRBID:PRB18723,FILE:Agilent_251239150413_S01_GE2-SSPE_95_Feb07.txt

value: MD Anderson

value: p53 exon 4-8 mutation status:ND

value: pten exon 5-6 mutation status:ND


title: 27708902

value: Female


title: 7081C10siCtrl 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC120130,PRBID:PRB20230,FILE:Agilent_251485019281_S01_GE2-v5_95_Feb07_1_4.txt

value: UCSF

value: 12474_CD133 Pos_Neg_Sorted_Populations


title: 75A10 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115713,PRBID:PRB18721,FILE:Agilent_251239150411_S01_GE2-SSPE_95_Feb07.txt


title: 7194C7siCtrl 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC120135,PRBID:PRB20235,FILE:Agilent_251485019282_S01_GE2-v5_95_Feb07_1_4.txt


title: 27681502


title: 31A6 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115712,PRBID:PRB18720,FILE:Agilent_251239150410_S01_GE2-SSPE_95_Feb07.txt


title: 7113 pos c9 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110949,PRBID:PRB17616,FILE:Agilent_251485017475_S01_GE2-v5_95_Feb07_1_3.txt


title: 71I p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115714,PRBID:PRB18722,FILE:Agilent_251239150412_S01_GE2-SSPE_95_Feb07.txt


title: SF7101 p53 WT pten MT Map250kNsp

description: SRCID:SRC107472,PRBID:PRB16771,SRCNAME:7101,RAWFILE:16771_7101_GBMTumors_SPR460_Map250kNsp.CEL

value: pten exon 5-6 mutation status:HOMSUB.173R>C


title: 27681202

value: Blood


title: SF7093 p53 WT pten WT Map250kNsp

description: SRCID:SRC107469,PRBID:PRB16765,SRCNAME:7093,RAWFILE:16765_7093_GBMTumors_SPR460_Map250kNsp.CEL


title: 7113 pos c7 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110948,PRBID:PRB17615,FILE:Agilent_251485017475_S01_GE2-v5_95_Feb07_1_2.txt


title: SF7095 p53 MT pten WT Map250kNsp

description: SRCID:SRC107471,PRBID:PRB16769,SRCNAME:7095,RAWFILE:16769_7095_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:HOMSUB.282R>W


title: 27680502

value: Holstein


title: 27676002

value: Male


title: 7202-NSP p53 HETSUB. MT pten WT vs. reference CGH-v4

description: SRCID:SRC111511,PRBID:PRB17934,SRCNAME:7202-NSP,RAWFILE:Agilent_251469333145_S01_CGH-v4_95_Feb07.txt

data_processing: Data were processed using Agilent feature extraction software v9.5, with Promega male gDNA in the reference channel, according to manufacturer's protocol. The genotyping copy number data were generated with Affymetrix's CNAT algorithm, version 4. Segmentation of copy number data was performed with GLAD, version: 1.16.0.

label_protocol: Agilent Genomic DNA Labeling Kit Plus

value: p53 exon 4-8 mutation status:HETSUB. 273R>L

source_name: Promega male gDNA (catalog number G147A)

value: reference


title: 6969-NSP p53 WT pten WT vs. reference CGH-v4

description: SRCID:SRC108918,PRBID:PRB17934,SRCNAME:6969-NSP,RAWFILE:Agilent_251469332909_S01_CGH-v4_95_Feb07.txt

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:wt


title: 7063 pos c7 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110942,PRBID:PRB17609,FILE:Agilent_251485017473_S01_GE2-v5_95_Feb07_1_4.txt


title: 7101-NSP p53 WT pten MT vs. reference CGH-v4

description: SRCID:SRC115700,PRBID:PRB17934,SRCNAME:7101-NSP,RAWFILE:Agilent_251469333238_S01_CGH-v4_95_Feb07.txt


title: 27680902

value: blood


title: 27588602

value: Simmental


title: 40A6 p53 ND pten ND vs. reference GE2_44k

description: SRCID:SRC115709,PRBID:PRB18716,FILE:Agilent_251239150409_S01_GE2-SSPE_95_Feb07.txt


title: SF7063 p53 WT pten WT Map250kNsp

description: SRCID:SRC107466,PRBID:PRB16759,SRCNAME:7063,RAWFILE:16759_7063_GBMTumors_SPR460_Map250kNsp.CEL


title: SF7082 p53 WT pten MT Map250kNsp

description: SRCID:SRC107468,PRBID:PRB16763,SRCNAME:7082,RAWFILE:16763_7082_GBMTumors_SPR460_Map250kNsp.CEL

value: pten exon 5-6 mutation status:HETSUB.67I>K


title: SF7179-2 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC108926,PRBID:PRB17120,FILE:Agilent_251239150384_S01_GE2_44k_1005.txt


title: SF7225-2 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107482,PRBID:PRB17122,FILE:Agilent_251239150343_S01_GE2_44k_1005.txt


title: 7113 pos c5 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110947,PRBID:PRB17614,FILE:Agilent_251485017475_S01_GE2-v5_95_Feb07_1_1.txt


title: SF7081 p53 WT pten WT Map250kNsp

description: SRCID:SRC107467,PRBID:PRB16761,SRCNAME:7081,RAWFILE:16761_7081_GBMTumors_SPR460_Map250kNsp.CEL


title: SF7284 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC108928,PRBID:PRB17123,FILE:Agilent_251239150408_S01_GE2-SSPE_95_Feb07.txt


title: 27677502


title: 7063 pos c3 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110940,PRBID:PRB17607,FILE:Agilent_251485017473_S01_GE2-v5_95_Feb07_1_2.txt


title: SF7034 p53 WT pten WT Map250kNsp

description: SRCID:SRC107462,PRBID:PRB16751,SRCNAME:7034,RAWFILE:16751_7034_GBMTumors_SPR460_Map250kNsp.CEL


title: 7095NC20-NC17m142 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121794,PRBID:PRB21094,FILE:Agilent_251485025071_S01_GE2-v5_95_Feb07_1_4.txt

value: 15394_In vivo passaged


title: SF7054 p53 WT pten WT Map250kNsp

description: SRCID:SRC107464,PRBID:PRB16755,SRCNAME:7054,RAWFILE:16755_7054_GBMTumors_SPR460_Map250kNsp.CEL


title: 7095NC20-NC23m137 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121791,PRBID:PRB21091,FILE:Agilent_251485025090_S01_GE2-v5_95_Feb07_1_4.txt


title: SF7259 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107485,PRBID:PRB16820,FILE:Agilent_251239150109_S01_GE2_44k_1005.txt


title: SF7227 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107483,PRBID:PRB16818,FILE:Agilent_251239150107_S01_GE2_44k_1005.txt


title: 7095NC20-NC21m132 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121789,PRBID:PRB21089,FILE:Agilent_251485025071_S01_GE2-v5_95_Feb07_1_3.txt


title: PBMC_AuNP_24hr_3

city: Chicago

first: Eun-Young

last: Kim

state: IL

address: 303 E Superior Street

department: Feinberg School of Medicine

institute: Northwestern University

description: Gene expression data from PBMCs treated with AuNP EGFP oligonucleotide complex for 24 hours

hyb_protocol: Following fragmentation, 35 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Agilent GeneArray Scanner.

data_processing: Normalization for biological and technical replicates and probe-level analysis were performed using FlexArray with the GC-Robust Multichip Average (RMA) option. Probe sets whose absolute expression value did not exceed 5.0 for all arrays were excluded.

source_name: PBMCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PBMCs derived from healthy donors were isolated on Ficoll-Paque gradient, and PBMC and 293T cells were grown in 5% CO2 at 37°C in RPMI1640 medium and DMEM (Invitrogen) with 10% fetal bovine serum supplemented with 100 U/ml penicillin, 100 μg/ml streptomycin, and 200 μM l-glutamine, respectivley.

extract_protocol: Total RNA were extracted from cells by using Qiagen RNeasy kit

treatment_protocol: Cells were seeded at 50% confluent in 24-well plates and treated with 10nM AuNP for 6-, 24, and 48hr and washed twice with PBS

value: PBMCs

tag: treatment group


title: CAF22

city: Baltimore

first: Kim

last: Walter

address: 1550 Orleans St.

institute: Johns Hopkins University

hyb_protocol: Samples were hybridized with the GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the JHMI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Relative gene expression values were obtained after using the RMA method to normalize the raw intensity measurements of all probe sets.  RMA expression value derived from Expression Console software; core-exon analysis using default settings.

source_name: Pancreatic ductal adenocarcinoma

label_protocol: Single stranded cDNA was generated from the amplified cRNA using the WT cDNA Synthesis kit (Affymetrix) and then fragmented and labeled using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were maintained in culture at 37degrees C in DMEM containing 10% FBS and 2% penicillin-streptomycin.

extract_protocol: RNA was isolated from fibroblast cultures using the Ambion mirVana RNA extraction kit, according to the manufacturer's instructions.

value: pancreas

value: fibroblasts

tag: disease status

value: ductal adenocarcinoma


title: SF7223 p53 WT pten MT vs. reference GE2_44k

description: SRCID:SRC107481,PRBID:PRB18719,FILE:Agilent_251239150407_S01_GE2-SSPE_95_Feb07.txt

value: UCSF

value: pten exon 5-6 mutation status:HOMSUB.130R>G


title: CAF21

description: RMA expression value derived from Expression Console software; core-exon analysis


title: PBMC_Control_3

description: Gene expression data from control PBMCs

value: control


title: 7186 nsp psg35 p53 WT pten WT vs. reference CGH-v4

description: SRCID:SRC120185,PRBID:PRB17934,SRCNAME:7186 nsp psg35,RAWFILE:Agilent_251469333265_S01_CGH-v4_95_Feb07.txt

value: 7186 nsp psg35


title: 27596902

value: Holstein

value: Blood

value: Male

value: Female


title: 7276-NSP p53 WT pten MT vs. reference CGH-v4

description: SRCID:SRC115702,PRBID:PRB17934,SRCNAME:7276-NSP,RAWFILE:Agilent_251469333385_S01_CGH-v4_95_Feb07.txt

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:HETSUB.133V>I

value: reference


title: CAF19


title: 7259 nsp psg30 p53 WT pten WT vs. reference CGH-v4

description: SRCID:SRC120203,PRBID:PRB17934,SRCNAME:7259 nsp psg30,RAWFILE:Agilent_251469333266_S01_CGH-v4_95_Feb07.txt

value: 7259 nsp psg30

value: pten exon 5-6 mutation status:wt


title: CAF18


title: 7095NC20-NC15m125 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121785,PRBID:PRB21085,FILE:Agilent_251485025047_S01_GE2-v5_95_Feb07_1_2.txt

value: 15394_In vivo passaged


title: 7095NC29-NC22m116 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121781,PRBID:PRB21081,FILE:Agilent_251485025090_S01_GE2-v5_95_Feb07_1_2.txt


title: SF7201 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107480,PRBID:PRB16817,FILE:Agilent_251239150106_S01_GE2_44k_1005.txt


title: SF7186 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107477,PRBID:PRB17129,FILE:Agilent_251239150350_S01_GE2_44k_1005.txt


title: 7095NC20-NC14m121 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121783,PRBID:PRB21083,FILE:Agilent_251485025070_S01_GE2-v5_95_Feb07_1_2.txt


title: 7095NC20-NC20m114 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121780,PRBID:PRB21080,FILE:Agilent_251485025047_S01_GE2-v5_95_Feb07_1_1.txt


title: SF7029 p53 MT pten WT Map250kNsp

description: SRCID:SRC107460,PRBID:PRB16747,SRCNAME:7029,RAWFILE:16747_7029_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:HETSUB.216V>A

value: pten exon 5-6 mutation status:WT


title: naïve-WIBR3.3 hESC

city: Cambridge

first: Albert

middle: W

last: Cheng

state: MA

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data of cell linenaïve-WIBR3.3 hESC

hyb_protocol: Samples were prepared for hybridization using 12.5 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human U133 2.0) were hybridized in a GeneChip Hybridization Oven at 45°C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 and images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console.

data_processing: The data were analyzed with Affy and limma package (MAS5)

source_name: naïve-WIBR3.3 hESC

label_protocol: 100 ng total RNA was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (Affymetrix 3’ IVT Express Kit). Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Naïve and conventional human ESCs and iPSCs were propagated as described in Hanna et al. PNAS 2010

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

treatment_protocol: RNA was feshly extracted from MEF depleted different human embryonic stem cells grown at optimal confluency.

value: Human embryonic stem cells (hESC)

tag: cell subtype

value: naïve-WIBR3.3 hESC


title: SF7030 p53 WT pten WT Map250kNsp

description: SRCID:SRC107461,PRBID:PRB16749,SRCNAME:7030,RAWFILE:16749_7030_GBMTumors_SPR460_Map250kNsp.CEL

value: UCSF


title: 7192-NSP p53 MT pten WT vs. reference CGH-v4

description: SRCID:SRC111508,PRBID:PRB17934,SRCNAME:7192-NSP,RAWFILE:Agilent_251469333269_S01_CGH-v4_95_Feb07.txt

value: p53 exon 4-8 mutation status:HETSUB.220Y>H


title: 19639102

value: blood


title: naïve-WIBR3.1 hESC

description: Gene expression data of cell linenaïve-WIBR3.1 hESC

source_name: naïve-WIBR3.1 hESC

value: naïve-WIBR3.1 hESC


title: SF7059 p53 WT pten MT Map250kNsp

description: SRCID:SRC107465,PRBID:PRB16757,SRCNAME:7059,RAWFILE:16757_7059_GBMTumors_SPR460_Map250kNsp.CEL

value: pten exon 5-6 mutation status:HETSUB.32I>S


title: SF7194 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107479,PRBID:PRB16816,FILE:Agilent_251239150105_S01_GE2_44k_1005.txt


title: CAF13

description: RMA expression value derived from Expression Console software; core-exon analysis

value: pancreas

value: fibroblasts

value: ductal adenocarcinoma


title: CAF15


title: SF6969 p53 WT pten WT Map250kNsp

description: SRCID:SRC107458,PRBID:PRB16743,SRCNAME:6969,RAWFILE:16743_6969_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:wt


title: 7095NC20-NC24m112 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121779,PRBID:PRB21079,FILE:Agilent_251485025047_S01_GE2-v5_95_Feb07_1_4.txt

value: reference


title: 7227-NSP p53 WT pten WT vs. reference CGH-v4

description: SRCID:SRC115703,PRBID:PRB17934,SRCNAME:7227-NSP,RAWFILE:Agilent_251469333384_S01_CGH-v4_95_Feb07.txt


title: CAF12


title: SF7048 p53 MT pten WT Map250kNsp

description: SRCID:SRC107463,PRBID:PRB16753,SRCNAME:7048,RAWFILE:16753_7048_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:HETSUB.283R>C


title: SF7113 p53 MT pten WT vs. reference GE2_44k

description: SRCID:SRC107473,PRBID:PRB16813,FILE:Agilent_251239150102_S01_GE2_44k_1005.txt

value: p53 exon 4-8 mutation status:HETSUB.266G>R, HETSUB.267R>W

value: pten exon 5-6 mutation status:wt


title: naïve-C1.10 hiPSC

description: Gene expression data of cell linenaïve-C1.10 hiPSC

source_name: naïve-C1.10 hiPSC

value: naïve-C1.10 hiPSC


title: SF7180 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107476,PRBID:PRB17128,FILE:Agilent_251239150349_S01_GE2_44k_1005.txt


title: CAF16


title: CAF11


title: 7095NC20-NC18m107 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC121777,PRBID:PRB21077,FILE:Agilent_251485025069_S01_GE2-v5_95_Feb07_1_1.txt

value: 15394_In vivo passaged


title: PBMC_AuNP_48hr_3

description: Gene expression data from PBMCs treated with AuNP EGFP oligonucleotide complex for 48 hours

value: PBMCs


title: SF7276 p53 WT pten MT vs. reference GE2_44k

description: SRCID:SRC107486,PRBID:PRB16821,FILE:Agilent_251239150110_S01_GE2_44k_1005.txt

value: pten exon 5-6 mutation status:HETSUB.133V>I


title: 7194C16m59 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120196,PRBID:PRB20404,FILE:Agilent_251485019226_S01_GE2-v5_95_Feb07_1_3.txt

value: UCSF


title: 7225 nsp psg33 p53 WT pten WT vs. reference CGH-v4

description: SRCID:SRC120184,PRBID:PRB17934,SRCNAME:7225 nsp psg33,RAWFILE:Agilent_251469333264_S01_CGH-v4_95_Feb07.txt

value: 7225 nsp psg33


title: NF1-3

source_name: Chronic pancreatitis tissue

value: chronic pancreatitis


title: SF7095 p53 MT pten WT vs. reference GE2_44k

description: SRCID:SRC107471,PRBID:PRB16811,FILE:Agilent_251239150100_S01_GE2_44k_1005.txt

value: p53 exon 4-8 mutation status:HOMSUB.282R>W


title: SF7101 p53 WT pten MT vs. reference GE2_44k

description: SRCID:SRC107472,PRBID:PRB16812,FILE:Agilent_251239150112_S01_GE2_44k_1005.txt

value: pten exon 5-6 mutation status:HOMSUB.173R>C


title: 7194C16m60 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120197,PRBID:PRB20405,FILE:Agilent_251485019227_S01_GE2-v5_95_Feb07_1_3.txt


title: 7095c20c21m86 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120154,PRBID:PRB20254,FILE:Agilent_251485019230_S01_GE2-v5_95_Feb07_1_2.txt


title: SC-2

description: RMA expression value derived from Expression Console software; core-exon analysis

source_name: Pancreatic IPMN tumor

value: pancreas

value: IPMN tumor


title: SF7093 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107469,PRBID:PRB16809,FILE:Agilent_251239150098_S01_GE2_44k_1005.txt


title: 7063 pos c4 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC110941,PRBID:PRB17608,FILE:Agilent_251485017473_S01_GE2-v5_95_Feb07_1_3.txt

value: 12474_CD133 Pos_Neg_Sorted_Populations


title: SF6977 p53 MT pten WT Map250kNsp

description: SRCID:SRC107459,PRBID:PRB16745,SRCNAME:6977,RAWFILE:16745_6977_GBMTumors_SPR460_Map250kNsp.CEL

value: p53 exon 4-8 mutation status:HOMSUB.220Y>C


title: SF7082 p53 WT pten MT vs. reference GE2_44k

description: SRCID:SRC107468,PRBID:PRB16808,FILE:Agilent_251239150097_S01_GE2_44k_1005.txt

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:HETSUB.67I>K

value: reference


title: 7095c20c19m79 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120152,PRBID:PRB20252,FILE:Agilent_251485019229_S01_GE2-v5_95_Feb07_1_2.txt


title: 7194c19m54 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120150,PRBID:PRB20250,FILE:Agilent_251485019227_S01_GE2-v5_95_Feb07_1_2.txt


description: Gene expression data of cell lineC1 hiPSC (exposed to PD/CH/FK/Lif for 48 hours)

value: Human embryonic stem cells (hESC)


title: naïve-WIBR3.2 hESC

description: Gene expression data of cell linenaïve-WIBR3.2 hESC

source_name: naïve-WIBR3.2 hESC

value: naïve-WIBR3.2 hESC


title: SF7081 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107467,PRBID:PRB16807,FILE:Agilent_251239150096_S01_GE2_44k_1005.txt

value: pten exon 5-6 mutation status:wt


title: naïve-WIBR3.5 hESC

description: Gene expression data of cell linenaïve-WIBR3.5 hESC

source_name: naïve-WIBR3.5 hESC

value: naïve-WIBR3.5 hESC


title: 7095c20c20m82 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120149,PRBID:PRB20249,FILE:Agilent_251485019226_S01_GE2-v5_95_Feb07_1_2.txt

value: 15394_In vivo passaged


title: SF7054 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107464,PRBID:PRB16804,FILE:Agilent_251239150093_S01_GE2_44k_1005.txt

value: UCSF


title: 7095C20C20siCtrl 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC120131,PRBID:PRB20231,FILE:Agilent_251485019224_S01_GE2-v5_95_Feb07_1_2.txt


title: SF7063 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107466,PRBID:PRB16806,FILE:Agilent_251239150095_S01_GE2_44k_1005.txt


title: C1 hiPSC

description: Gene expression data of cell lineC1 hiPSC

source_name: C1 hiPSC

value: C1 hiPSC


title: SF7059 p53 WT pten MT vs. reference GE2_44k

description: SRCID:SRC107465,PRBID:PRB16805,FILE:Agilent_251239150094_S01_GE2_44k_1005.txt

value: pten exon 5-6 mutation status:HETSUB.32I>S


title: SF7030 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107461,PRBID:PRB16802,FILE:Agilent_251239150091_S01_GE2_44k_1005.txt


title: 7201C14siCtrl 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC120136,PRBID:PRB20236,FILE:Agilent_251485019225_S01_GE2-v5_95_Feb07_1_2.txt


title: SF7034 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107462,PRBID:PRB16803,FILE:Agilent_251239150092_S01_GE2_44k_1005.txt


title: 7095c20m77 15394_In vivo passaged vs. reference GE2-v5

description: SRCID:SRC120151,PRBID:PRB20251,FILE:Agilent_251485019228_S01_GE2-v5_95_Feb07_1_2.txt


title: 7194 NC16 unsorted 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC120122,PRBID:PRB20222,FILE:Agilent_251485019225_S01_GE2-v5_95_Feb07_1_1.txt

value: 7194 NC16 unsorted


title: SF6977 p53 MT pten WT vs. reference GE2_44k

description: SRCID:SRC107459,PRBID:PRB16801,FILE:Agilent_251239150090_S01_GE2_44k_1005.txt


title: HPNE

description: RMA expression value derived from Expression Console software; core-exon analysis

source_name: Normal pancreas immortalized fibroblasts (ATCC available)

value: fibroblasts

value: normal


title: Gracilis - ischemia 4h reperfusion 7d

city: Kaohsiung Hsien

first: Ching-Hua

last: Hsieh

state: Kaohsiung

address: 123, Ta-Pei road, Naio-Sung Hsiang

department: Plastic and Reconstructive Surgery

country: Taiwan

institute: Kaohsiung Chang Gung Memorial Hospital

description: Biological replicate 1 of 3rd condition. Gracilis muscle ischemia 4h and reperfusion for 7d

hyb_protocol: Scanned on an Agilent G2565AA scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.9.5.3).

data_processing: Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.

organism: Rattus norvegicus

source_name: Gracilis muscle

label_protocol: The RNA from the experimental muscle was labeled with Cy5 and the RNA from the sham-operated control muscle RNA was labeled with Cy3.

growth_protocol: The harvested muscles were frozen in isopentane chilled in liquid nitrogen and stored at -80°C.

extract_protocol: 0.5 μg of total RNA was amplified using a Fluorescent Linear Amplification Kit (Agilent Technologies) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, CA, USA) during the in vitro transcription process.

treatment_protocol: Total RNA was extracted using the mirVana miRNA Isolation kit (Ambion, Austin, TX, USA) following manufacturer's instructions

value: Sprague-Dawley

value: male

value: Gracilis muscle

tag: treatment

value: ischemia 4h reperfusion 7d

value: sham-operated control


title: 7194 NC20 unsorted 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC120121,PRBID:PRB20221,FILE:Agilent_251485019224_S01_GE2-v5_95_Feb07_1_1.txt

value: 7194 NC20 unsorted

value: 12474_CD133 Pos_Neg_Sorted_Populations

source_name: Universal Human Reference from Stratagene (#740000)

value: reference


title: Gracilis - ischemia 4h reperfusion 14d

description: Biological replicate 1 of 4th condition. Gracilis muscle ischemia 4h and reperfusion for 14d

value: ischemia 4h reperfusion 14d


title: Gracilis - ischemia 4h reperfusion 3d

description: Biological replicate 1 of 2ndt condition. Gracilis muscle ischemia 4h and reperfusion for 3d

value: ischemia 4h reperfusion 3d


title: 7194 NC19 unsorted 12474_CD133+/- vs. reference GE2-v5

description: SRCID:SRC120120,PRBID:PRB20220,FILE:Agilent_251485019223_S01_GE2-v5_95_Feb07_1_1.txt

value: 7194 NC19 unsorted


title: Gracilis - ischemia 4h reperfusion 1d

description: Biological replicate 1 of 1st condition. Gracilis muscle ischemia 4h and reperfusion for 1d

value: ischemia 4h reperfusion 1d


title: SF6969 p53 WT pten WT vs. reference GE2_44k

description: SRCID:SRC107458,PRBID:PRB17119,FILE:Agilent_251239150383_S01_GE2_44k_1005.txt

value: UCSF

value: p53 exon 4-8 mutation status:wt

value: pten exon 5-6 mutation status:wt


title: naïve-C1.2 hiPSC

description: Gene expression data of cell linenaïve-C1.2 hiPSC

source_name: naïve-C1.2 hiPSC

value: Human embryonic stem cells (hESC)

value: naïve-C1.2 hiPSC


title: Lymph node metastasis MT-15

status: Public on Apr 21 2010

city: Stockholm

first: Stefano

last: Caramuta

address: CMM L8:01, Karolinska University Hospital

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

description: miRNA expression profile

hyb_protocol: Labeled RNA was hybridized onto Agilent miRNA array (G4470A) for 18-20 hours at 55°C

scan_protocol: Slides were scanned in an Agilent microarray scanner (G2565BA, Agilent Technologies) using default settings for miRNA microarray v1.0. Images obtained after scanning were processed with Feature Extraction Software 9.5.3.1 (Agilent, Santa Clara, CA)

data_processing: Processing of the intensity values was done using Cluster 3.0 software whereby data were normalized, log transformed and median centered. Only normalized miRNAs with less than 20% missing values across the samples were included in the further analysis.

source_name: Lymph node metastasis from patient with malignant cutaneous melanoma

label_protocol: 120 ng of total RNA were were dephosphorylated and fluorescence-labeled with Cyanine 3-pCp by using T4 RNA Ligase. Labeled RNA was purified using Micro Bio Spin 6 Columns (Bio-Rad, 732-6221)

growth_protocol: Normal human melanocyte cultures were bough from PromoCell (Heidelberg, Germany). Melanoma cell lines were obtained from surgical melanoma samples and cultured in RPMI medium supplemented with 10% FCS, HEPES buffer, glutamine and antibiotics (Biowhittaker).

extract_protocol: Total RNA was extracted using mirVana miRNA Isolation Kit (Applied Biosystem/Ambion, Austin, TX) according to the protocol recommended by the manifacturer.

value: Fresh frozen lymph nodes


title: Lymph node metastasis MT-16

description: miRNA expression profile


title: Lymph node metastasis MT-14

description: miRNA expression profile


title: Lymph node metastasis MT-13

description: miRNA expression profile


title: Lymph node metastasis MT-11

description: miRNA expression profile


title: Lymph node metastasis MT-12

description: miRNA expression profile


title: Lymph node metastasis MT-10

description: miRNA expression profile


title: Lymph node metastasis MT-9

description: miRNA expression profile


title: AYX011

city: TOURS

first: Jérome

last: Rollin

address: av de la republique

department: Hematology-Hemostasis

institute: CHU-Tours

description: Not relevant.

hyb_protocol: According to Direct hybridization protocol (Cy5 vs Cy3)

scan_protocol: Arrays were scanned with Agilent G2505B Scanner. Feature extraction was performed with Genepix Pro 6.0 software (Axon Instruments).

data_processing: The data in the VALUE column correspond to lowess normalized log ratio of F635_MEDIAN vs F532_MEDIAN.

organism: Mus musculus

label_protocol: Labeling were performed using 2.5 ug of aRNA per reaction and were carried out according to the manufacturer's rpotocol (Ambion) using the MessageAmp kit with 1/2 quantity.

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen) according to the manufacturer's protocol and the integrity of the RNAs was verified using the Agilent Bioanalyzer.
Message RNA amplification with T7 RNA Polymerase was carried out according to the manufacturer's protocol (Ambion) using the MessageAmp kit with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies).

value: Murine Embryonic Fibroblast

source_name: WT


title: AYY015

description: Not relevant.


title: AYT044

description: Not relevant.


title: AYY018

description: Not relevant.


title: AYT048

description: Not relevant.


title: AYX027

description: Not relevant.


title: AYX010

description: Not relevant.


title: AYY002

description: Not relevant.


title: AYX006

description: Not relevant.


title: AYT050

description: Not relevant.


title: AYT024

description: Not relevant.


title: AYT046

description: Not relevant.


title: AYY004

description: Not relevant.


title: AYX033

description: Not relevant.


title: AYT036

description: Not relevant.


title: Lymph node metastasis MT-7

description: miRNA expression profile


title: AYT035

description: Not relevant.


title: Lymph node metastasis MT-5

description: miRNA expression profile


title: Lymph node metastasis MT-6

description: miRNA expression profile


title: Lymph node metastasis MT-4

description: miRNA expression profile


title: Lymph node metastasis MT-8

description: miRNA expression profile


title: Lymph node metastasis MT-3

description: miRNA expression profile


title: AYT005

description: Not relevant.


title: Lymph node metastasis MT-1

description: miRNA expression profile


title: AYT004

description: Not relevant.


title: AYT051

description: Not relevant.

tag: tissue type

value: Thymus

source_name: ICF5 m3/m24

extract_protocol: Message RNA amplification with T7 RNA Polymerase was carried out according to the manufacturer's protocol (Ambion) using the MessageAmp kit with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies).


title: Lymph node metastasis MT-2

description: miRNA expression profile


title: Melanoma cell line MCc-9

description: miRNA expression profile

source_name: Culture derived from cutaneous metastasis of patient with cutaneous malignant melanoma

tag: cell line

value: melanoma

tag: sample

value: cutaneous


title: Melanoma cell line MCc-8

description: miRNA expression profile


title: Melanoma cell line MCc-7

description: miRNA expression profile


title: AYT042

description: Not relevant.

source_name: ICF2 m3/m24


title: AYT007

description: Not relevant.

tag: cell type


title: Melanoma cell line MCc-3

description: miRNA expression profile


title: AYT034

description: Not relevant.


title: Melanoma cell line MCc-4

description: miRNA expression profile


title: Melanoma cell line MCc-5

description: miRNA expression profile


title: AYT041

description: Not relevant.

source_name: ICF4 m3/m24


title: Melanoma cell line MCc-6

description: miRNA expression profile


title: Melanoma cell line MCc-2

description: miRNA expression profile


title: AYT033

description: Not relevant.


title: Melanoma cell line MCc-1

description: miRNA expression profile


title: Melanoma cell line MCn-8

description: miRNA expression profile

source_name: Culture derived from lymph node metastasis of patient with cutaneous malignant melanoma

value: lymph node


title: AYT031

description: Not relevant.


title: pri-WIBR3.1 hESC

description: Gene expression data of cell linepri-WIBR3.1 hESC

source_name: pri-WIBR3.1 hESC

value: pri-WIBR3.1 hESC


title: Melanoma cell line MCn-7

description: miRNA expression profile


title: Melanoma cell line MCn-6

description: miRNA expression profile


title: Melanoma cell line MCn-5

description: miRNA expression profile


title: Melanoma cell line MCn-3

description: miRNA expression profile


title: AYT018

description: Not relevant.


title: AYT021

description: Not relevant.


title: AYT016

description: Not relevant.


title: AYT022

description: Not relevant.

source_name: ICF3 m3/m24


title: Melanoma cell line MCn-2

description: miRNA expression profile


title: AYT029

description: Not relevant.


title: AYT030

description: Not relevant.


title: AYT026

description: Not relevant.


title: AYT032

description: Not relevant.


title: AYT012

description: Not relevant.


title: AYT010

description: Not relevant.


title: ethanol (vehicle) treated monosome-associated RNA, biological rep2

city: PROVIDENCE

first: Alexander

last: Brodsky

state: RI

address: 593 Eddy St.

department: MCB

institute: Rhode Island Hospital/Brown University

description: Gene expression data from monosome-associated RNA collected from ethanol treated MCF7 cells

hyb_protocol: Following fragmentation,  of about 2.3 ug cRNA were hybridized for 17 hr at 45C on each GeneST 1.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using fluidics script FS450_007

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner equipped with an autoloader.

data_processing: The data were analyzed with plier-gcbg from Affymetrix Power Tools using  HuGene-1_0-st-v1.r3.bgp, HuGene-1_0-st-v1.r3.pgf, and HuGene-1_0-st-v1.r3.clf f iles from Affymetrix.

source_name: 300 nanograms MCF7 monosome-associated RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix).

growth_protocol: Cells maintained in DMEM with 10% FBS, split 1:4 every 3 days.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Polysome-associated RNA was collected from fractionation of a sucrose gradient and then purified by precipitating in guanadine-HCL and ethanol.  Both sets were cleaned up using RNeasy with on-the-column DNase I treatment.

treatment_protocol: Cells were split on day 0, then switched to phenol red free DMEM with 5% charcol-dextran-treated serum on day 1.  The media was changed daily.  On day 4, the cells were treated with 10nM estradiol (E2) or vehicle control (etoh) for one hour.

tag: agent

value: ethanol

tag: fraction

value: monosome-associated RNA


title: AYT017

description: Not relevant.

source_name: ICF1 m3/m24


title: estrogen treated monosome-associated RNA, biological rep3

description: Gene expression data from monosome-associated RNA collected from estrogen treated MCF7 cells

value: estrogen


title: Melanoma cell line MCp-3

description: miRNA expression profile

source_name: Culture derived from primary melanoma tumor

value: primary melanoma tumor


title: Melanoma cell line MCn-1

description: miRNA expression profile


title: ethanol (vehicle) treated monosome-associated RNA, biological rep3


title: ethanol (vehicle) treated monosome-associated RNA, biological rep1


title: AYT009

description: Not relevant.


title: Melanoma cell line MCp-2

description: miRNA expression profile


title: Normal human melanocyte 1

description: miRNA expression profile

source_name: primary culture 1

value: melanocyte


title: Melanoma cell line MCn-4

description: miRNA expression profile


title: Normal human melanocyte 3

description: miRNA expression profile

source_name: primary culture 3


title: Normal human melanocyte 2

description: miRNA expression profile

source_name: primary culture 2


title: Melanoma cell line MCp-4

description: miRNA expression profile


title: Melanoma cell line MCp-1

description: miRNA expression profile


title: estrogen treated monosome-associated RNA, biological rep1


title: estrogen treated monosome-associated RNA, biological rep2


title: ethanol (vehicle) treated polysome-associated RNA, biological rep1

description: Gene expression data from polysome-associated RNA collected from ethanol treated MCF7 cells

source_name: 300 nanaograms MCF7 polysome-associated RNA

value: polysome-associated RNA


title: ethanol (vehicle) treated polysome-associated RNA, biological rep2


title: ethanol (vehicle) treated total RNA, biological rep3

description: Gene expression data from total RNA collected from ethanol treated MCF7 cells

source_name: 300 nanaograms MCF7 total RNA

value: total RNA


title: ethanol (vehicle) treated total RNA, biological rep1


title: estrogen treated polysome-associated RNA, biological rep3

description: Gene expression data from polysome-associated RNA collected from estrogen treated MCF7 cells


title: ovary_Low prolificacy level_animal5

city: Madrid

first: Amanda

last: Fernández Rodríguez

state: Madrid

address: Ctra Coruña km 7.5

department: Mejora Genética Animal

country: Spain

institute: INIA

description: OVARY L-5

hyb_protocol: standard Affymetrix hybridization protocol

scan_protocol: standard Affymetrix scanning protocol using GCOS

data_processing: Expression data were generated with GeneChip Operating Software (GCOS, Affymetrix) and GCRMA normalization was carried out with BRB-Array Tools (v.3.6.0), by filtering out those probes with more than 50% of missing values.

source_name: ovary sample at 30 days after fertilization, low

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

growth_protocol: Sows were slaughtered after 30 days of pregnancy

extract_protocol: RiboPure RNA isolation kit

treatment_protocol: Ovary samples were mantained at -80ºC

tag: breed

value: Iberian x Meishan F2 cross

value: ovary

tag: prolificacy

value: lower EBV (LOW prolificacy)


title: ethanol (vehicle) treated polysome-associated RNA, biological rep3


title: ovary_Low prolificacy level_animal1

description: OVARY L-1


title: ovary_High prolificacy level_animal3

description: OVARY H-3

source_name: ovary sample at 30 days after fertilization, high

value: higher EBV (HIGH prolificacy)


title: DUR3_24hrs_rep2

city: Vancouver

first: Matthew

last: Dahabieh

address: 2205 East Mall

department: Wine Research Centre

country: Canada

institute: University of British Columbia

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Array Scanner

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

organism: Saccharomyces cerevisiae

source_name: DUR3 replicate 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Strains innoculated into 200 mL filter sterilized (0.22 um) Calona Chardonnay must to final OD600=0.1 and incubated at 20 deg celsius for 24 hrs

extract_protocol: Total RNA was harvested by hot acidic phenol method as per Short protocols in Molecular Biology

treatment_protocol: Cells were harvested by centrifugation and snap frozen in liquid nitrogen until processing


title: ovary_High prolificacy level_animal6

description: OVARY H-6


title: ovary_Low prolificacy level_animal6

description: OVARY L-6


title: ovary_Low prolificacy level_animal4

description: OVARY L-4


title: ovary_Low prolificacy level_animal2

description: OVARY L-2


title: ovary_High prolificacy level_animal1

description: OVARY H-1


title: ovary_High prolificacy level_animal2

description: OVARY H-2


title: ovary_Low prolificacy level_animal3

description: OVARY L-3


title: AYT008

description: Description Not relevant.

tag: age

source_name: WT

extract_protocol:
Agilent Bioanalyzer.
Message RNA amplification with T7 RNA Polymerase was carried out according to the manufacturer's protocol (Ambion) using the MessageAmp kit with 1/2 quantity. aRNA integrity and yield were assessed by electrophoretic fractionation on a Bioanalyzer 2100 and a RNA6000 Nano chip (Agilent Technologies).


title: estrogen treated polysome-associated RNA, biological rep1


title: estrogen treated polysome-associated RNA, biological rep2


title: ethanol (vehicle) treated total RNA, biological rep2


title: estrogen treated total RNA, biological rep2

description: Gene expression data from total RNA collected from estrogen treated MCF7 cells


title: DUR3_24hrs_rep1

source_name: DUR3 replicate 1


title: Kinetic 3, Time point 24H day 1, technical replicates 1-3

status: Public on Apr 20 2010

city: Rennes

first: annabelle

last: monnier

address: 2 avenue du Professeur Léon Bernard

institute: UMR 6061 Génétique et Développement

description: Biological replicate 3 (kinetic 3 of 3)

hyb_protocol: Hybridization was performed using Agilent In Situ Hybridization Kit Plus. 1 microg of each test and reference cRNAs were mixed and subjected to fragmentation (30 min at 60°C). Samples were diluted in Nexterion Hyb buffer (Schott Nexterion) and hybridized using Gasket Slides in an Agilent Hybridization rotation oven (60°C, 17 h at 4 rpm in the dark). Slides were disassembled, washed according to the Schott protocol

scan_protocol: Scanned with the dynamic autofocus Agilent G2565BA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 9.1).

data_processing:
Normalization was performed using the print-tip loess method and scaled with the Gquantile method
The value of each biological time point is calculate as an average of the technical triplicate.

organism: Ostreococcus tauri

source_name: Ostreococcus tauri strain isolated from the Thau lagoon; 12:12  light/dark cycles (kinetic point)

label_protocol: Total RNAs (350 ng) were ampliﬁed and labeled using a two-color labeling protocol Low Input Linear RNA ampliﬁcation kit (Agilent) according to the manufacturer recommendations . Test and reference samples were respectively labeled with Cyanine-5 and Cyanine-3 CTP (10 mM, Perkin-Elmer/NENLife Science)

growth_protocol: Growth in Keller medium at 25°C under light/dark cycles

extract_protocol: Total RNA extracted with RNeasy Plant Mini Kit (Qiagen) following manufacturer's instructions

treatment_protocol: LIGHT OFF

tag: time

value: 24H, day 1

tag: protocol

value: LIGHT OFF

source_name: Ostreococcus tauri strain isolated from the Thau lagoon (reference)

tag: reference

value: pooled samples (3 kinetics)


title: Wildtype_24hrs_rep1

source_name: Wildtype replicate 1

tag: strain

value: WT


title: ovary_High prolificacy level_animal5

description: OVARY H-5

tag: tissue


title: estrogen treated total RNA, biological rep1


title: Kinetic 3, Time point 21H day 1, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

value: 21H, day 1


title: ovary_High prolificacy level_animal4

description: OVARY H-4


title: Wildtype_24hrs_rep2

source_name: Wildtype replicate 2


title: Kinetic 3, Time point 3H day 1, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

value: 3H, day 1


title: DUR1,2_24hrs_rep2

source_name: DUR1,2 replicate 2


title: Kinetic 3, Time point 18H day 1, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

treatment_protocol: LIGHT ON

value: 18H, day 1

value: LIGHT ON


title: Kinetic 3, Time point 6H day 1, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

value: 6H, day 1


title: Kinetic 3, Time point 9H day 2, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

value: 9H, day 2


title: DUR1,2_24hrs_rep1

source_name: DUR1,2 replicate 1


title: estrogen treated total RNA, biological rep3

value: estrogen


title: Kinetic 3, Time point 15H day 1, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

value: 15H, day 1


title: Kinetic 3, Time point 12H day 1, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

value: 12H, day 1


title: Kinetic 2, Time point 12H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 2, Time point 21H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 2, Time point 3H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 2, Time point 24H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 2, Time point 18H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 2, Time point 15H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 3, Time point 9H day 1, technical replicates 1-3

description: Biological replicate 3 (kinetic 3 of 3)

value: 9H, day 1


title: Kinetic 2, Time point 9H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 1, Time point 9H day 2, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)


title: Kinetic 2, Time point 9H day 2, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 2, Time point 6H day 1, technical replicates 1-3

description: Biological replicate 2 (kinetic 2 of 3)


title: Kinetic 1, Time point 3H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)


title: Kinetic 1, Time point 15H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)


title: RA-4 passage 1 vs. passage 7 b oncogene array

city: Bad Nauheim

first: Elena

last: Neumann

address: Benekestr. 2-8

department: Internal Medicine and Rheumatolgy

country: Germany

description: Array comparison evaluation using BD AtlasImageTM 2.7 Software providing data of differentially regulated genes (equally expressed genes are not provided by the software)

hyb_protocol: The PCR products were purified from unincorporated nucleotides and small cDNA fragments by column chromatography. The filters were prehybridized in prewarmed hybridization solution with 100 µg/ml fragmented denatured salmon sperm DNA. The labeled cDNA probe was denatured and 1 µg/µl sheared human genomic DNA was added with an equal volume of neutralizing solution (1M NaH2PO4, pH 7.0). The mixture was added to the filters and hybridized over night.

scan_protocol: The filters were exposed to a Phosphor-Imager-Screen for 3-5 days depending on the intensity of radiation. Data analysis was performed using the Ambis software.

data_processing:
Evaluation was performed using the AtlasImageTM 2.7 software, developed specifically for analysis of the AtlasTM cDNA Expression Arrays. Background and signal intensity was normalized. The default signal threshold was kept constant for all analyses. After background correction, the median signal intensity for all spots on an array were used to calculate the correction coefficient (global normalization). Comparison of the arrays was performed using the “Compare two arrays” setting and resulting .txt-files were saved as .xls-files. Genes spotted on both arrays were evaluated on the GLP139 array only.
*********Only differentially expressed genes are reported in the Sample data tables. Complete data tables were requested and reported to be unavailable by the submitter.*********

source_name: Rheumatoid arthritis synovial fibroblasts from Patient #4 (RA-4)

label_protocol: RAP-PCR of total cellular RNA was performed using 250 ng RNA. First strand synthesis was carried out using MuLV reverse transcriptase (Promega) and 2 µM first strand arbitary primer. Second strand synthesis was performed using AmpliTaq Stoffel Fragment 2.8 µl [32P]dATP (3,000 Ci/mmol, 10 mCi/ml), and 4 µM arbitrary second primer. The reaction was cycled through 30 low stringency cycles 94°C, 35°C, 72°C). Primer combination: OPN23 (5'- CAG GGG CAC C-3') and OPN21 (5'-ACC AGG GGC A-3').

growth_protocol: Synovial tissues were obtained from synovial biopsies of RA patients undergoing joint surgery. Following enzymatic digestion, fibroblasts were seeded in culture flasks (= passage 0) and grown in DMEM containing 10% heat inactivated fetal calf serum and cultured at 37°C in 10% CO2. At 85-95% confluency, cells were passaged 1:2 and a part of the cells was harvested and total RNA was extracted and stored at -70°C.

extract_protocol: Total cellular RNA was extracted using the RNeasy spin column purification kit. To remove contaminating genomic DNA, total RNA was treated with DNase I (0.2 U/µl for 40 minutes at 37°C. RNA concentrations were measured, adjusted to 200 ng/µl and stored at -70°C.

treatment_protocol: Culture conditions were kept constant during the experiments.

tag: passage

value: passage 1

value: passage 7


title: Kinetic 1, Time point 18H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)


title: RA-4 passage 1 vs. passage 7 a oncogene array

value: Rheumatoid arthritis synovial fibroblasts from Patient #4 (RA-4)


title: Kinetic 1, Time point 12H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)


title: RA-4 passage 1 vs. passage 6 b oncogene array

value: passage 6


title: RA-4 passage 1 vs. passage 8 a oncogene array

value: passage 8


title: RA-4 passage 1 vs. passage 8 b oncogene array


title: RA-4 passage 1 vs. passage 5 b oncogene array

value: passage 5


title: Kinetic 1, Time point 6H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)

value: LIGHT OFF

value: pooled samples (3 kinetics)


title: RA-3 passage 1 vs. passage 7 b oncogene array

source_name: Rheumatoid arthritis synovial fibroblasts from Patient #3 (RA-3)


title: RA-4 passage 1 vs. passage 6 a oncogene array


title: RA-4 passage 1 vs. passage 3 a oncogene array

value: passage 3


title: RA-3 passage 1 vs. passage 8 b oncogene array

value: Rheumatoid arthritis synovial fibroblasts from Patient #3 (RA-3)


title: RA-4 passage 1 vs. passage 2 a oncogene array

value: passage 2


title: RA-3 passage 1 vs. passage 8 a oncogene array


title: RA-4 passage 1 vs. passage 4 a oncogene array

value: passage 4


title: RA-4 passage 1 vs. passage 4 b oncogene array


title: RA-4 passage 1 vs. passage 5 a oncogene array


title: RA-3 passage 1 vs. passage 7 a oncogene array


title: RA-4 passage 1 vs. passage 2 b oncogene array


title: RA-4 passage 1 vs. passage 3 b oncogene array


title: RA-3 passage 1 vs. passage 6 a oncogene array


title: Kinetic 1, Time point 21H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)

value: 21H, day 1


title: RA-3 passage 1 vs. passage 6 b oncogene array


title: Kinetic 1, Time point 9H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)

value: LIGHT ON


title: Kinetic 1, Time point 24H day 1, technical replicates 1-3

description: Biological replicate 1 (kinetic 1 of 3)

value: 24H, day 1


title: RA-3 passage 1 vs. passage 5 a oncogene array


title: RA-3 passage 1 vs. passage 5 b oncogene array


title: RA-3 passage 1 vs. passage 4 b oncogene array


title: RA-3 passage 1 vs. passage 4 a oncogene array


title: RA-3 passage 1 vs. passage 3 a oncogene array


title: RA-3 passage 1 vs. passage 2 a oncogene array


title: RA-2 passage 1 vs. passage 8 b oncogene array

source_name: Rheumatoid arthritis synovial fibroblasts from Patient #2 (RA-2)


title: RA-3 passage 1 vs. passage 2 b oncogene array


title: RA-2 passage 1 vs. passage 7 b oncogene array

value: Rheumatoid arthritis synovial fibroblasts from Patient #2 (RA-2)


title: RA-2 passage 1 vs. passage 6 b oncogene array


title: RA-2 passage 1 vs. passage 5 a oncogene array


title: RA-2 passage 1 vs. passage 6 a oncogene array


title: RA-2 passage 1 vs. passage 4 b oncogene array


title: RA-2 passage 1 vs. passage 5 b oncogene array


title: RA-2 passage 1 vs. passage 3 a oncogene array


title: RA-2 passage 1 vs. passage 7 a oncogene array


title: RA-2 passage 1 vs. passage 8 a oncogene array


title: RA-2 passage 1 vs. passage 4 a oncogene array


title: RA-2 passage 1 vs. passage 2 b oncogene array


title: RA-1 passage 1 vs. passage 7 b oncogene array

source_name: Rheumatoid arthritis synovial fibroblasts from Patient #1 (RA-1)


title: RA-1 passage 1 vs. passage 5 b oncogene array

value: Rheumatoid arthritis synovial fibroblasts from Patient #1 (RA-1)


title: RA-1 passage 1 vs. passage 8 a oncogene array

value: passage 1


title: RA-2 passage 1 vs. passage 3 b oncogene array


title: RA-1 passage 1 vs. passage 5 a oncogene array


title: RA-1 passage 1 vs. passage 6 a oncogene array


title: RA-1 passage 1 vs. passage 6 b oncogene array


title: RA-3 passage 1 vs. passage 3 b oncogene array


title: RA-1 passage 1 vs. passage 7 a oncogene array

value: passage 7


title: RA-1 passage 1 vs. passage 4 b oncogene array


title: RA-1 passage 1 vs. passage 8 b oncogene array


title: RA-1 passage 1 vs. passage 3 a oncogene array


title: RA-1 passage 1 vs. passage 3 b oncogene array


title: RA-1 passage 1 vs. passage 4 a oncogene array


title: RA-1 passage 1 vs. passage 2 b oncogene array


title: RA-1 passage 1 vs. passage 2 a oncogene array


title: RA-2 passage 1 vs. passage 2 a oncogene array


title: Ls174T si b-catenin (dye swap)

city: London

first: Vivian

last: Li

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description: Dye swap of 1. Ls174T cells transfected with si-b-catenin

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Ls174T colorectal cancer cells

label_protocol: 2µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

growth_protocol: Ls174T or HEK293T cells were seeded on 6-well plates and transfected with control/human b-catenin/MLLT10/DOT1L/BRG1/P300 15nM siRNA for 72 hours

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions

treatment_protocol: Control or Wnt3A conditioned medium was added to the HEK293T cells and incubate for 9 hours before RNA extraction

tag: transfection

value: si-control

value: si-b-catenin


title: si MLLT10 + 9hr Wnt

description: 293T cells transfected with si-MLLT10, induced with Wnt3A medium for 9 hours.

source_name: HEK293T human embryonic kidney cells

tag: induction

value: +Wnt3A, 9 hours

source_name: Human reference RNA

value: Human reference RNA


title: NA19172/NA15510

city: Santa Clara

first: Nick

last: Sampas

address: 5301 Stevens Creek Blvd

department: Life Science and Nanotechnology Department

institute: Agilent Technologies

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling for Blood, Cells, Tissues or FFPE Protocol

scan_protocol: Scanned on an Agilent G2505A Scanner

data_processing: Agilent Feature Extraction v9.1, default CGH parameters. This data represents probes not in the reference assembly (novel probe sequences).  All filtering of novel probes begins with those 54,931 sequences represented in the Sample data tables.

extract_protocol: Performed by the Coriell Cell Repository

value: Coriell Lymphoblastoid

tag: coriell sample

tag: population

value: YRI Female

value: Unknown Female Fosmid library:G248


title: NA19240/NA15510

label_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis ULS Labeling for Blood, Cells, Tissues or FFPE Protocol

tag: cell line

value: YRI Female Fosmid library:ABC10


title: Ls174T si P300

description: Ls174T cells transfected with si-P300


title: NA19132/NA15510


title: si control + 9hr Wnt

description: 293T cells transfected with si-control, induced with Wnt3A medium for 9 hours.


title: si BRG1 + 9hr Wnt

description: 293T cells transfected with si-BRG1, induced with Wnt3A medium for 9 hours.


title: Ls174T si control

description: Ls174T cells transfected with si-control


title: Ls174T si b-catenin

description: Ls174T cells transfected with si-b-catenin


title: si control + 9hr CM

description: 293T cells transfected with si-control, induced with control medium for 9 hours.

value: +CM, 9 hours


title: NA19129/NA15510

value: YRI Female Fosmid library:ABC13


title: NA15510/NA15510


title: si P300 + 9hr Wnt

description: 293T cells transfected with si-P300, induced with Wnt3A medium for 9 hours.


title: Ls174T si BRG1

description: Ls174T cells transfected with si-BRG1


title: NA18980/NA15510

value: JPT Female


title: Ls174T si MLLT10

description: Ls174T cells transfected with si-MLLT10


title: NA19116/NA15510


title: NA18947/NA15510

value: JPT Female Fosmid library:ABC16


title: NA18573/NA15510

value: CHB Female Fosmid library:ABC19


title: NA18861/NA15510


title: NA18507/NA15510

value: YRI Male Fosmid library:ABC8


title: NA18555/NA15510

value: CHB Female Fosmid library:ABC11


title: NA18523/NA15510

value: YRI Female Fosmid library:ABC23


title: NA18956/NA15510

value: JPT Female Fosmid library:ABC9


title: NA18564/NA15510

value: CHB Female Fosmid library:ABC17


title: NA18517/NA15510

value: YRI Female Fosmid library:ABC7


title: NA18942/NA15510

value: JPT Female Fosmid library:ABC27


title: NA18502/NA15510

value: YRI Female Fosmid library:ABC24


title: NA19102/NA15510

value: Coriell Lymphoblastoid

value: YRI Female Fosmid library:ABC20


title: RA-4 passage 1 vs. passage 5 a cancer array

value: Rheumatoid arthritis synovial fibroblasts from Patient #4 (RA-4)

value: passage 1

value: passage 5


title: RA-4 passage 1 vs. passage 5 b cancer array


title: RA-4 passage 1 vs. passage 4 b cancer array

value: passage 4


title: RA-4 passage 1 vs. passage 6 a cancer array

value: passage 6


title: RA-4 passage 1 vs. passage 7 a cancer array

value: passage 7


title: RA-4 passage 1 vs. passage 4 a cancer array


title: RA-3 passage 1 vs. passage 8 a cancer array

value: Rheumatoid arthritis synovial fibroblasts from Patient #3 (RA-3)

value: passage 8


title: RA-4 passage 1 vs. passage 3 b cancer array

value: passage 3


title: RA-4 passage 1 vs. passage 2 a cancer array

value: passage 2


title: RA-4 passage 1 vs. passage 2 b cancer array


title: RA-4 passage 1 vs. passage 3 a cancer array


title: RA-3 passage 1 vs. passage 8 b cancer array


title: RA-3 passage 1 vs. passage 7 b cancer array


title: RA-3 passage 1 vs. passage 6 b cancer array


title: RA-3 passage 1 vs. passage 6 a cancer array


title: RA-3 passage 1 vs. passage 7 a cancer array


title: RA-4 passage 1 vs. passage 8 b cancer array


title: RA-4 passage 1 vs. passage 8 a cancer array


title: NA12878/NA15510

value: CEU Female Fosmid library:ABC12

value: Unknown Female Fosmid library:G248


title: NA12156/NA15510

value: CEU Female Fosmid library:ABC14


title: RA-4 passage 1 vs. passage 6 b cancer array


title: RA-4 passage 1 vs. passage 7 b cancer array


title: RA-3 passage 1 vs. passage 5 a cancer array


title: RA-3 passage 1 vs. passage 5 b cancer array


title: RA-3 passage 1 vs. passage 4 b cancer array


title: RA-3 passage 1 vs. passage 4 a cancer array


title: RA-3 passage 1 vs. passage 3 b cancer array


title: NA10847/NA15510

value: CEU Female Fosmid library:ABC18


title: RA-3 passage 1 vs. passage 2 b cancer array


title: RA-3 passage 1 vs. passage 3 a cancer array


title: NA10851/NA15510

value: CEU Male Fosmid library:Redon Ref


title: RA-2 passage 1 vs. passage 7 a cancer array

value: Rheumatoid arthritis synovial fibroblasts from Patient #2 (RA-2)


title: RA-2 passage 1 vs. passage 7 b cancer array


title: RA-2 passage 1 vs. passage 8 b cancer array


title: RA-2 passage 1 vs. passage 8 a cancer array


title: RA-2 passage 1 vs. passage 6 b cancer array


title: RA-3 passage 1 vs. passage 2 a cancer array


title: RA-2 passage 1 vs. passage 4 b cancer array


title: RA-2 passage 1 vs. passage 5 a cancer array


title: RA-2 passage 1 vs. passage 5 b cancer array


title: RA-2 passage 1 vs. passage 3 b cancer array


title: RA-2 passage 1 vs. passage 3 a cancer array


title: RA-2 passage 1 vs. passage 6 a cancer array


title: RA-2 passage 1 vs. passage 2 a cancer array


title: RA-2 passage 1 vs. passage 2 b cancer array


title: RA-1 passage 1 vs. passage 8 b cancer array

value: Rheumatoid arthritis synovial fibroblasts from Patient #1 (RA-1)


title: RA-1 passage 1 vs. passage 8 a cancer array


title: RA-1 passage 1 vs. passage 7 a cancer array


title: RA-1 passage 1 vs. passage 7 b cancer array


title: RA-1 passage 1 vs. passage 6 b cancer array


title: NA11832/NA15510

value: Coriell Lymphoblastoid

value: CEU Female


title: NA18552/NA15510

value: CHB Female Fosmid library:JVI1


title: NA12004/NA15510


title: RA-2 passage 1 vs. passage 4 a cancer array

value: passage 1

value: passage 4


title: NA11993/NA15510


title: NA11840/NA15510

value: CEU Female Fosmid library:ABC22


title: RA-1 passage 1 vs. passage 2 a cancer array


title: RA-1 passage 1 vs. passage 4 a cancer array


title: RA-1 passage 1 vs. passage 5 a cancer array

growth_protocol: Synovial tissues were obtained fr!Sample_growth_protocol_ch2 = Synovial tissues were obtained from synovial biopsies of RA patients undergoing joint surgery. Following enzymatic digestion, fibroblasts were seeded in culture flasks (= passage 0) and grown in DMEM containing 10% heat inactivated fetal calf serum and cultured at 37°C in 10% CO2. At 85-95% confluency, cells were passaged 1:2 and a part of the cells was harvested and total RNA was extracted and stored at -70°C.

value: passage 5


title: RA-1 passage 1 vs. passage 5 b cancer array


title: RA-1 passage 1 vs. passage 4 b cancer array


title: RA-1 passage 1 vs. passage 2 b cancer array


title: RA-1 passage 1 vs. passage 6 a cancer array

value: passage 6


title: RA-1 passage 1 vs. passage 3 a cancer array

value: passage 3