title: MDD, S89.BA44.1.S

city: Vancouver

first: Paul

last: Pavlidis

state: British Columbia

address: 177 Michael Smith Laboratories 2185 East Mall

department: Centre for High-Throughput Biology / Psychiatry

institute: University of British Columbia

hyb_protocol: Samples were dried using a vacuum concentrator at 50°C on the medium-high heat setting for one hour. All samples were resuspended in 17 uL of nuclease-free water, 1 uL of Hyb spike-in solution, 4.5 uL of 10X GE Blocking agent and 22.5 uL of 2X Hi-RPM Hybridization Buffer , incubated at 100°C for 5 minutes followed by a 5 minute ice water bath, as suggested by the manufacturer's instructions. Samples were hybridized on Agilent-021827 slides at 55°C and rotated at 20rpm for 20 hours. After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (warmed to 37°C, Agilent) and GE Wash Buffer 2 (warmed to 37°C, Agilent) ), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color scan setting on the Unrestricted Human miRNA microarray V3 (Agilent Design ID: 021827; Product Number: G4470C). Format 8x15K, Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR low 5%.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. We used the AgiMicroRna package in Bioconductor to summarize the data followed by quantile normalization.

source_name: Brain tissue (BA44), MDD

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the microRNA complete labeling and hybridization kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification. This method involves the ligation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule with greater than 90% efficiency. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA (including miRNA fraction) was isolated from frozen brain using the miRNeasy Mini Kit protocol (Qiagen, Canada) with no modifications. RNA and miRNA yield and quality were determined using the Nanodrop 1000 (Thermo Scientific, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, USA), respectively.

treatment_protocol: Post-mortem prefrontal cortex (BA44) brain tissue was obtained in collaboration with the Quebec Coroner's Office and the Suicide section of the Douglas-Bell Canada Brain Bank (Douglas Mental Health University Institute, Montreal, Quebec, Canada). A total of 25 brain samples were included in the present study. All individuals were of French-Canadian origin, a homogeneous population with a well-documented founder effect, and were matched for refrigeration delay, age and pH. Refrigeration delay refers to the difference between the estimated time of death (determined by the pathologist through external body examination details) and the time at which the body was refrigerated. Psychological autopsies were performed post-mortem on both cases and controls by a panel of psychiatrists and diagnoses were assigned based on DSM-IV criteria. The control group had no history of suicidal behavior or major mood or psychotic disorders.

value: ventrolateral prefrontal cortex (PFC)

tag: diagnosis

value: major depressive disorder

tag: gender

value: male

tag: population

value: French-Canadian

tag: age

tag: ph

tag: rin


title: MS341 normal appearing white matter

status: Public on May 30 2014

type: RNA

city: Lyon

first: Serge

last: Nataf

address: 8 Rue Guillaume Paradin

department: Inserm U1028 - CNRS UMR5292

country: France

institute: Neuroscience Research Center of Lyon

hyb_protocol: Following an Affymetrix protocol, 10 ug of labeled cRNA were fragmented and hybridized on GeneChip Human Genome U133 plus 2.0 array (Affymetrix) during 16 hours at 45°C. Arrays were washed and stained with streptavidin-phycoerythrin (GeneChip Hybridization Wash and Stain kit) in the Affymetrix Fluidics Station 450.

scan_protocol: The arrays were read with the GeneChip scanner 3000 7G (Affymetrix).

data_processing: The CEL Files were generated using the Affymetrix GeneChip Command Console (AGCC) software 3.0. Data were normalized using Affymtrix Expression Console software using MAS5 statistical algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: normal appearing white matter from MS spinal cord 341

label_protocol: Total RNA was triple amplified using an ExpressArt mRNA amplification Pico kit (Amptec GmbH) and biotin-labelled by a round of in vitro transcription using a BioArray HighYield RNA transcript Labeling kit (Enzo Life Sciences) following he manufacturer's protocol.

growth_protocol: Snap frozen spinal cord samples were used.

extract_protocol: RNA extraction were performed using the Rneasy Micro kit (Qiagen).

treatment_protocol: Spinal cord sections were dehydrated and microdissected using the PixCell LCM System (Arcturus)

tag: tissue

tag: organ

value: spinal cord

tag: disease course

value: secondary progressive multiple sclerosis

tag: Sex

value: F

tag: age at death

tag: disease duration


title: MS207 periplaque region

source_name: periplaque region from MS spinal cord 207

value: periplaque region from MS spinal cord


title: MS157 periplaque region

source_name: periplaque region from MS spinal cord 157


title: MS207 normal appearing white matter

source_name: normal appearing white matter from MS spinal cord 207


title: MS157 normal appearing white matter

source_name: normal appearing white matter from MS spinal cord 157


title: P23

city: Rio de Janeiro

first: Renata

last: Binato

state: Rio de Janeiro

address: Praça Cruz Vermelha 23/ 6 andar ala C

country: Brazil

institute: INCA

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

hyb_protocol: The biotinylated cRNA was subsequently hybridized to a GeneChip Human Exon 1.0 ST Array (Affymetrix, CA, USA).

scan_protocol: The GeneChip arrays were washed and stained according to the manufacturer’s protocols and scanned using a GeneChip® Scanner 3000 (Affymetrix)

data_processing: Affymetrix Expression Console Software version 1.0 was used to create summarized expression values (CHP-files). The Robust Multichip Analysis (RMA) algorithm was applied. The data were analyzed with Partek® software (http://www.partek.com). Hierarchical clustering of chip array data was based on the PAM 50 classifier genes

source_name: woman with breast cancer

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

growth_protocol: The breast cancer tissues were obtained from patients diagnosed with unilateral primary ductal infiltrative carcinoma of the breast at Instituto do Câncer de Londrina (Londrina, Paraná, Brazil) and Instituto Nacional de Câncer (Rio de Janeiro, Brazil).

extract_protocol: Total RNA from all breast cancer tissues used in this study was obtained using the RNeasy Mini Kit (Qiagen, CA, USA) according to the manufacturer's instructions.

value: breast cancer


title: P20


title: MS166 normal appearing white matter

source_name: normal appearing white matter from MS spinal cord 166


title: P19


title: MS413 periplaque region

source_name: periplaque region from MS spinal cord 413

value: M


title: P22


title: MS402 periplaque region

source_name: periplaque region from MS spinal cord 402


title: MDD, S87.BA44.1.S

country: Canada


title: P18


title: MDD, S38.BA44.1.S


title: MDD, S84.BA44.1.S


title: MDD, S85.BA44.1.S


title: MDD, S28.BA44.1.S


title: P21


title: P17


title: P15


title: P14


title: P13


title: MDD, S81.BA44.1.S


title: P12


title: MDD, S31.BA44.4.S


title: P16


title: MDD, S26.BA44.1.S


title: P11


title: MDD, S67.BA44.1.S


title: P10


title: MDD, S65.BA44.1.S


title: MDD, S68.BA44.1.S


title: MDD, S63.BA44.4.S


title: case poor response 11002

type: genomic

city: Shanghai

first: Weili

last: Yan

address: 399 Wanyuan Road

country: China

institute: Department of Clinical Epidemiology, Children's Hospital of Fudan University

hyb_protocol: Illumina HumanMethylation450 BeadChip Protocol

scan_protocol: Arrays were imaged using Illumina iScan on a two-color channel

data_processing:
background corrected and normalized average beta; the normalization was done by GenomeStudio using control normalization
AVG.BETA: methylaiton level signal intensities; Detection.Pval: detection p-value

label: Cy5 and Cy3

molecule: genomic DNA

source_name: PBMC

extract_protocol: Genomic DNA was purified using the Dneasy Blood and Tissue kit followed by bisufite conversion using the ES DNA methylation kit following manufacturer's protocols.

value: Male

tag: vaccine response

value: poor

value: blood

tag: sample type

value: case


title: P8


title: P6


title: P7


title: P9


title: Control, S16.BA44.1.C

source_name: Brain tissue (BA44), control

value: psychiatrically healthy


title: P5


title: Control, S13.BA44.4.C


title: P4


title: P3


title: P2


title: MDD, S77.BA44.4.S


title: case poor response 22099

label_protocol: Illumina HumanMethylation450 BeadChip Protocol

value: Female


title: Control, S58.BA44.4.C


title: case poor response 11119


title: case poor response 76


title: case poor response 20011


title: case poor response 12124


title: case poor response 89


title: case poor response 49


title: U2OS_Control_RNAi_biological_replicate_3

city: Martinsried/Munich

first: Tim

last: Ammon

address: Am Klopferspitz 18

department: Dept. of Molecular Cell Biology

country: Germany

institute: Max-Planck-Institute of Biochemistry

description: After RNAi transfection and isolation of total RNA subsequent steps were conducted by the at ATLAS Biolabs GmbH (Berlin, Germany)

hyb_protocol: Hybridization solution was prepared using the Affymetrix HWS Kit (Affymetrix P/N 900720) according to Affymetrix GeneChip Expression Wash, Stain and Scan User Manual.Hybridization to the GeneChip Human Exon 1.0 ST Arrays (Affymetrix) was performed for 18+/-2 hours at 45°C and 60 rpm in a rotating hybridization oven (Hybridization Oven 640, Affymetrix). Washing and staining was performed using the Affymetrix HWS Kit (Affymetrix P/N 900720) with a fluidics station (GeneChip Fluidics Station 450, Affymetrix), which is controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4.Fluidics protocol: FS450_0001 (Exon 1.0 ST Array).

scan_protocol: Scanning was performed with the GeneChip Scanner 3000 7G (Affymetrix), which is controlled by Affymetrix´ software GeneChip Operating System (GCOS) v1.4.

data_processing: Primary data analysis was performed with Affymetrix´ software GeneChip Operating System (GCOS) v1.4. CEL files were processed using Affymetrix Powertools (apt-probeset-summarize 1.12.0.) and the core sets were analyzed according to the ARH-Method (A. Rasche and R. Herwig. Arh: predicting splice variants fromgenome-wide data with modified entropy. Bioinformatics, 26(1):84, 2010.)

label_protocol: cDNA synthesis followed by IVT and second round cDNA synthesis was done with Ambion’s WT Expression Kit (Cat. No. #4411973) according to the manufacturers’ instructions, starting with 200 ng of total RNA. Affymetrix WT Terminal Labeling Kit (# 900671) was used to fragment 5,5 µg cDNA followed by Biotin-labeling according to the manufacturers’ instructions.

growth_protocol: The human osteosarcoma cell line U2OS was maintained at 37°C, 6% CO2 in DMEM (Invitrogen) supplemented with 10% fetal calf serum (FCS; Biochrom).

extract_protocol: After cell harvest total RNA was isolated from transfected U2OS using the RNeasy Kit (Qiagen) with including RNase-free DNase (Qiagen) on column digestion. RNA quality was tested using the Agilent 2100 Bioanalyzer, Assay Eukaryote (or Plant) total RNA Nano; Nanodrop for exact quantification and purity assessment

treatment_protocol: U2OS cells were transfected with Hub1-targeting siRNA or control GL2 oligos by electroporation using the Amaxa Nucleofector II system (Lonza) according to suppliers protocol (final concentration 300 nM siRNA ).

tag: cell line

tag: transfection

value: Control RNAi


title: U2OS_Hub1_RNAi_biological_replicate_3

value: Hub1 RNAi


title: U2OS_Control_RNAi_biological_replicate_2


title: Control, S59.BA44.4.C

value: ventrolateral prefrontal cortex (PFC)


title: Control, S12.BA44.1.C

value: male


title: P1


title: case poor response 133


title: U2OS_Control_RNAi_biological_replicate_1


title: Control, S56.BA44.4.C

value: French-Canadian


title: Control, S6.BA44.1.C


title: case poor response 3


title: case poor response 29


title: U2OS_Hub1_RNAi_biological_replicate_1


title: Control, S54.BA44.4.C


title: Control, S3.BA44.1.C


title: Control, S4.BA44.1.C


title: U2OS_Hub1_RNAi_biological_replicate_2


title: Control, S1.BA44.1.C


title: case poor response 20201


title: control good response 22184

value: good

value: control


title: control good response 4


title: case poor response 40272


title: UCC2003 grown on ribose v. UCC2003 grown on sialic acid

status: Public on May 29 2014

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown in mMRS supplemented with 0.05% cysteine and 0.5% ribose

label_protocol: Labelling was performed as described in van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77.

growth_protocol: Bifidobacterium breve UCC2003  was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), , supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing either 0.5% ribose or 0.5% sialic acid .The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5

extract_protocol: Method for cell disruption, RNA isolation, RNA quality control and complementary DNA synthesis was performed as described in:  van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77.

tag: strain

tag: medium supplement

value: 0.05% cysteine and 0.5% ribose

source_name: Bifidobacterium breve UCC200 grown in mMRS supplemented with 0.05% cysteine and 0.5% sialic acid

value: 0.05% cysteine and 0.5% sialic acid


title: UCC2003 grown on sialic acid v. UCC2003 grown on ribose

description: gene expression array

source_name: Bifidobacterium breve UCC2003 grown in mMRS supplemented with 0.05% cysteine and 0.5% sialic acid


title: control good response 69

tag: gender


title: Genomic DNA from whole blood TWPID1221.Beta

city: London

first: Pei-Chien

last: Tsai

address: 3rd Floor South Wing Block D, St Thomas’ Campus, Lambeth Palace Road

department: Twin Research and Genetic Epidemiology

country: United Kingdom

institute: King's College London

description: Family 59 Monozygotic twin

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: BeadStudio software for 27k data.

source_name: Whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from whole blood samples

tag: disease state

value: Normal

tag: 27k chip

tag: order on 27k chip

value: L

tag: twin

value: Family 59 Monozygotic twin


title: Genomic DNA from whole blood TWPID6819.Beta

description: Family 94 Monozygotic twin

tag: tissue

tag: age

value: H

value: Family 94 Monozygotic twin


title: Genomic DNA from whole blood TWPID8477.Beta

description: Family 95 Singleton

value: blood

value: J

value: Family 95 Singleton


title: Genomic DNA from whole blood TWPID6233.Beta

description: Family 5 Monozygotic twin

value: Female

value: C

value: Family 5 Monozygotic twin


title: control good response 92


title: Genomic DNA from whole blood TWPID1147.Beta

description: Family 96 Singleton

value: K

value: Family 96 Singleton


title: Genomic DNA from whole blood TWPID1218.Beta

description: Family 63 Monozygotic twin

value: E

value: Family 63 Monozygotic twin


title: control good response 21033

value: Male

value: good

value: control


title: Genomic DNA from whole blood TWPID5225.Beta

description: Family 44 Dizygotic twin

value: Normal

value: I

value: Family 44 Dizygotic twin


title: Genomic DNA from whole blood TWPID6811.Beta

description: Family 92 Dizygotic twin

value: G

value: Family 92 Dizygotic twin


title: Genomic DNA from whole blood TWPID4223.Beta

description: Family 53 Dizygotic twin

value: blood

value: H

value: Family 53 Dizygotic twin


title: Genomic DNA from whole blood TWPID6799.Beta

description: Family 94 Monozygotic twin

value: Female

value: F

value: Family 94 Monozygotic twin


title: Genomic DNA from whole blood TWPID10001.Beta

description: Family 93 Singleton

value: L

value: Family 93 Singleton


title: Genomic DNA from whole blood TWPID5451.Beta

description: Family 90 Dizygotic twin

value: K

value: Family 90 Dizygotic twin


title: Genomic DNA from whole blood TWPID5342.Beta

description: Family 91 Dizygotic twin

value: Family 91 Dizygotic twin


title: Genomic DNA from whole blood TWPID4793.Beta

description: Family 32 Dizygotic twin

value: C

value: Family 32 Dizygotic twin


title: Genomic DNA from whole blood TWPID5038.Beta

description: Family 62 Dizygotic twin

value: Normal

value: J

value: Family 62 Dizygotic twin


title: Genomic DNA from whole blood TWPID5257.Beta

description: Family 91 Dizygotic twin

value: D


title: Genomic DNA from whole blood TWPID6901.Beta

description: Family 92 Dizygotic twin

value: blood

value: E

value: Family 92 Dizygotic twin


title: Genomic DNA from whole blood TWPID9838.Beta

description: Family 83 Dizygotic twin

value: Female

value: A

value: Family 83 Dizygotic twin


title: Genomic DNA from whole blood TWPID11699.Beta

description: Family 88 Dizygotic twin

value: L

value: Family 88 Dizygotic twin


title: control good response 28

value: good

value: control


title: control good response 6


title: Genomic DNA from whole blood TWPID11698.Beta

description: Family 88 Dizygotic twin


title: control good response 45

value: Male


title: control good response 12


title: control good response 10


title: Genomic DNA from whole blood TWPID4751.Beta

description: Family 89 Singleton

value: K

value: Family 89 Singleton


title: Genomic DNA from whole blood TWPID11096.Beta

description: Family 85 Singleton

value: Normal

value: C

value: Family 85 Singleton


title: Genomic DNA from whole blood TWPID5364.Beta

description: Family 80 Dizygotic twin

value: F

value: Family 80 Dizygotic twin


title: Genomic DNA from whole blood TWPID4220.Beta

description: Family 45 Dizygotic twin

value: blood

value: E

value: Family 45 Dizygotic twin


title: Genomic DNA from whole blood TWPID2318.Beta

description: Family 86 Singleton

value: Female

value: Family 86 Singleton


title: Genomic DNA from whole blood TWPID11091.Beta

description: Family 81 Monozygotic twin

value: I

value: Family 81 Monozygotic twin


title: Genomic DNA from whole blood TWPID2884.Beta

description: Family 78 Dizygotic twin

value: A

value: Family 78 Dizygotic twin


title: Genomic DNA from whole blood TWPID3950.Beta

description: Family 82 Dizygotic twin

value: J

value: Family 82 Dizygotic twin


title: Genomic DNA from whole blood TWPID4864.Beta

description: Family 82 Dizygotic twin

value: L


title: Genomic DNA from whole blood TWPID1994.Beta

description: Family 84 Dizygotic twin

value: Normal

value: B

value: Family 84 Dizygotic twin


title: Genomic DNA from whole blood TWPID1995.Beta

description: Family 84 Dizygotic twin

value: D


title: Genomic DNA from whole blood TWPID11092.Beta

description: Family 81 Monozygotic twin

value: K


title: Genomic DNA from whole blood TWPID6970.Beta

description: Family 87 Dizygotic twin

value: blood

value: Family 87 Dizygotic twin


title: Genomic DNA from whole blood TWPID8446.Beta

description: Family 77 Monozygotic twin

value: E

value: Family 77 Monozygotic twin


title: Genomic DNA from whole blood TWPID9848.Beta

description: Family 83 Dizygotic twin

value: Female

value: Family 83 Dizygotic twin


title: Genomic DNA from whole blood TWPID8445.Beta

description: Family 77 Monozygotic twin

value: C


title: Genomic DNA from whole blood TWPID6979.Beta

description: Family 79 Dizygotic twin

value: Family 79 Dizygotic twin


title: Genomic DNA from whole blood TWPID6980.Beta

description: Family 79 Dizygotic twin


title: Genomic DNA from whole blood TWPID8751.Beta

description: Family 12 Monozygotic twin

value: A

value: Family 12 Monozygotic twin


title: Genomic DNA from whole blood TWPID1878.Beta

description: Family 50 Monozygotic twin

value: Family 50 Monozygotic twin


title: Genomic DNA from whole blood TWPID3489.Beta

description: Family 78 Dizygotic twin

value: Family 78 Dizygotic twin


title: Genomic DNA from whole blood TWPID4767.Beta

description: Family 80 Dizygotic twin

value: Normal

value: H

value: Family 80 Dizygotic twin


title: Genomic DNA from whole blood TWPID10085.Beta

description: Family 48 Dizygotic twin

value: Family 48 Dizygotic twin


title: Genomic DNA from whole blood TWPID5955.Beta

description: Family 90 Dizygotic twin

value: B

value: Family 90 Dizygotic twin


title: Genomic DNA from whole blood TWPID10872.Beta

description: Family 76 Singleton

value: blood

value: J

value: Family 76 Singleton


title: Genomic DNA from whole blood TWPID10909.Beta

description: Family 87 Dizygotic twin

value: Female

value: G

value: Family 87 Dizygotic twin


title: Genomic DNA from whole blood TWPID12433.Beta

description: Family 74 Dizygotic twin

value: I

value: Family 74 Dizygotic twin


title: Genomic DNA from whole blood TWPID12432.Beta

description: Family 74 Dizygotic twin


title: Genomic DNA from whole blood TWPID10928.Beta

description: Family 73 Singleton

value: F

value: Family 73 Singleton


title: Genomic DNA from whole blood TWPID1691.Beta

description: Family 60 Dizygotic twin

value: D

value: Family 60 Dizygotic twin


title: Genomic DNA from whole blood TWPID10861.Beta

description: Family 75 Singleton

value: Normal

value: H

value: Family 75 Singleton


title: Genomic DNA from whole blood TWPID9830.Beta

description: Family 72 Dizygotic twin

value: C

value: Family 72 Dizygotic twin


title: Genomic DNA from whole blood TWPID6832.Beta

description: Family 64 Dizygotic twin

value: blood

value: Family 64 Dizygotic twin


title: Genomic DNA from whole blood TWPID6632.Beta

description: Family 71 Monozygotic twin

value: L

value: Family 71 Monozygotic twin


title: Genomic DNA from whole blood TWPID9834.Beta

description: Family 72 Dizygotic twin

value: Female

value: E


title: Genomic DNA from whole blood TWPID12523.Beta

description: Family 70 Monozygotic twin

value: Family 70 Monozygotic twin


title: control good response 17

value: Male

value: good

value: control


title: Genomic DNA from whole blood TWPID1884.Beta

description: Family 69 Dizygotic twin

value: D

value: Family 69 Dizygotic twin


title: Genomic DNA from whole blood TWPID6790.Beta

description: Family 36 Dizygotic twin

value: Normal

value: K

value: Family 36 Dizygotic twin


title: Genomic DNA from whole blood TWPID8457.Beta

description: Family 67 Monozygotic twin

value: J

value: Family 67 Monozygotic twin


title: Genomic DNA from whole blood TWPID12590.Beta

description: Family 70 Monozygotic twin

value: blood

value: G


title: Genomic DNA from whole blood TWPID9398.Beta

description: Family 38 Dizygotic twin

value: Family 38 Dizygotic twin


title: Genomic DNA from whole blood TWPID7761.Beta

description: Family 68 Monozygotic twin

value: I

value: Family 68 Monozygotic twin


title: Genomic DNA from whole blood TWPID8456.Beta

description: Family 67 Monozygotic twin

value: Female

value: F


title: Genomic DNA from whole blood TWPID5561.Beta

description: Family 16 Dizygotic twin

value: Family 16 Dizygotic twin


title: control good response 5

value: Male

value: good


title: Genomic DNA from whole blood TWPID8232.Beta

description: Family 24 Monozygotic twin

value: C

value: Family 24 Monozygotic twin


title: Genomic DNA from whole blood TWPID8415.Beta

description: Family 33 Monozygotic twin

value: Normal

value: Family 33 Monozygotic twin


title: Genomic DNA from whole blood TWPID11102.Beta

description: Family 41 Monozygotic twin

value: L

value: Family 41 Monozygotic twin


title: Genomic DNA from whole blood TWPID3222.Beta

description: Family 69 Dizygotic twin

value: B

value: Family 69 Dizygotic twin


title: Genomic DNA from whole blood TWPID2552.Beta

description: Family 39 Monozygotic twin

value: blood

value: K

value: Family 39 Monozygotic twin


title: Genomic DNA from whole blood TWPID6663.Beta

description: Family 71 Monozygotic twin

value: A

value: Family 71 Monozygotic twin


title: Genomic DNA from whole blood TWPID8628.Beta

description: Family 66 Monozygotic twin

value: Female

value: D

value: Family 66 Monozygotic twin


title: Genomic DNA from whole blood TWPID8632.Beta

description: Family 66 Monozygotic twin

value: H


title: Genomic DNA from whole blood TWPID7499.Beta

description: Family 68 Monozygotic twin

value: G

value: Family 68 Monozygotic twin


title: Genomic DNA from whole blood TWPID2289.Beta

description: Family 40 Dizygotic twin

value: Normal

value: Family 40 Dizygotic twin


title: Genomic DNA from whole blood TWPID9287.Beta

description: Family 65 Monozygotic twin

value: E

value: Family 65 Monozygotic twin


title: Genomic DNA from whole blood TWPID1844.Beta

description: Family 11 Monozygotic twin

value: Family 11 Monozygotic twin


title: Genomic DNA from whole blood TWPID9276.Beta

description: Family 65 Monozygotic twin

value: C


title: Genomic DNA from whole blood TWPID5602.Beta

description: Family 9 Monozygotic twin

value: blood

value: B

value: Family 9 Monozygotic twin


title: Genomic DNA from whole blood TWPID9286.Beta

description: Family 19 Dizygotic twin

value: I

value: Family 19 Dizygotic twin


title: Genomic DNA from whole blood TWPID1692.Beta

description: Family 60 Dizygotic twin

value: Female

value: L

value: Family 60 Dizygotic twin


title: Genomic DNA from whole blood TWPID1646.Beta

description: Family 37 Monozygotic twin

value: A

value: Family 37 Monozygotic twin


title: Genomic DNA from whole blood TWPID1217.Beta

description: Family 63 Monozygotic twin

value: G

value: Family 63 Monozygotic twin


title: Genomic DNA from whole blood TWPID2003.Beta

description: Family 21 Monozygotic twin

value: Normal

value: K

value: Family 21 Monozygotic twin


title: Genomic DNA from whole blood TWPID6072.Beta

description: Family 22 Dizygotic twin

value: Family 22 Dizygotic twin


title: Genomic DNA from whole blood TWPID1222.Beta

description: Family 59 Monozygotic twin

value: Family 59 Monozygotic twin


title: Genomic DNA from whole blood TWPID3283.Beta

description: Family 25 Monozygotic twin

value: blood

value: F

value: Family 25 Monozygotic twin


title: Genomic DNA from whole blood TWPID5127.Beta

description: Family 64 Dizygotic twin

value: H

value: Family 64 Dizygotic twin


title: Genomic DNA from whole blood TWPID11425.Beta

description: Family 47 Monozygotic twin

value: Female

value: I

value: Family 47 Monozygotic twin


title: Genomic DNA from whole blood TWPID7209.Beta

description: Family 20 Dizygotic twin

value: J

value: Family 20 Dizygotic twin


title: Genomic DNA from whole blood TWPID11786.Beta

description: Family 57 Singleton

value: B

value: Family 57 Singleton


title: Genomic DNA from whole blood TWPID1860.Beta

description: Family 26 Dizygotic twin

value: Normal

value: Family 26 Dizygotic twin


title: Genomic DNA from whole blood TWPID5115.Beta

description: Family 51 Dizygotic twin

value: C

value: Family 51 Dizygotic twin


title: Genomic DNA from whole blood TWPID2285.Beta

description: Family 49 Monozygotic twin

value: K

value: Family 49 Monozygotic twin


title: Genomic DNA from whole blood TWPID7009.Beta

description: Family 55 Dizygotic twin

value: blood

value: Family 55 Dizygotic twin


title: Genomic DNA from whole blood TWPID6154.Beta

description: Family 62 Dizygotic twin

value: E

value: Family 62 Dizygotic twin


title: Genomic DNA from whole blood TWPID4110.Beta

description: Family 61 Singleton

value: Female

value: Family 61 Singleton


title: Genomic DNA from whole blood TWPID2427.Beta

description: Family 52 Monozygotic twin

value: D

value: Family 52 Monozygotic twin


title: Genomic DNA from whole blood TWPID7189.Beta

description: Family 55 Dizygotic twin

value: H


title: Genomic DNA from whole blood TWPID2140.Beta

description: Family 30 Monozygotic twin

value: Family 30 Monozygotic twin


title: Genomic DNA from whole blood TWPID2117.Beta

description: Family 58 Singleton

value: Family 58 Singleton


title: Genomic DNA from whole blood TWPID5255.Beta

description: Family 31 Dizygotic twin

value: Normal

value: L

value: Family 31 Dizygotic twin


title: Genomic DNA from whole blood TWPID5239.Beta

description: Family 56 Singleton

value: A

value: Family 56 Singleton


title: Genomic DNA from whole blood TWPID9016.Beta

description: Family 54 Singleton

value: G

value: Family 54 Singleton


title: Genomic DNA from whole blood TWPID3368.Beta

description: Family 13 Monozygotic twin

value: blood

value: B

value: Family 13 Monozygotic twin


title: Genomic DNA from whole blood TWPID11743.Beta

description: Family 29 Dizygotic twin

value: Female

value: J

value: Family 29 Dizygotic twin


title: Genomic DNA from whole blood TWPID10024.Beta

description: Family 8 Dizygotic twin

value: Family 8 Dizygotic twin


title: Genomic DNA from whole blood TWPID7553.Beta

description: Family 28 Monozygotic twin

value: I

value: Family 28 Monozygotic twin


title: Genomic DNA from whole blood TWPID3440.Beta

description: Family 46 Dizygotic twin

value: F

value: Family 46 Dizygotic twin


title: Genomic DNA from whole blood TWPID2814.Beta

description: Family 53 Dizygotic twin

value: Normal

value: E

value: Family 53 Dizygotic twin


title: Genomic DNA from whole blood TWPID5179.Beta

description: Family 52 Monozygotic twin

value: D

value: Family 52 Monozygotic twin


title: Genomic DNA from whole blood TWPID3528.Beta

description: Family 23 Dizygotic twin

value: A

value: Family 23 Dizygotic twin


title: Genomic DNA from whole blood TWPID4413.Beta

description: Family 7 Monozygotic twin

value: blood

value: G

value: Family 7 Monozygotic twin


title: Genomic DNA from whole blood TWPID4846.Beta

description: Family 45 Dizygotic twin

value: Female

value: Family 45 Dizygotic twin


title: Genomic DNA from whole blood TWPID3546.Beta

description: Family 49 Monozygotic twin

value: K

value: Family 49 Monozygotic twin


title: Genomic DNA from whole blood TWPID2288.Beta

description: Family 40 Dizygotic twin

value: J

value: Family 40 Dizygotic twin


title: Genomic DNA from whole blood TWPID1518.Beta

description: Family 43 Monozygotic twin

value: B

value: Family 43 Monozygotic twin


title: Genomic DNA from whole blood TWPID10260.Beta

description: Family 34 Monozygotic twin

value: Normal

value: Family 34 Monozygotic twin


title: Genomic DNA from whole blood TWPID6004.Beta

description: Family 51 Dizygotic twin

value: C

value: Family 51 Dizygotic twin


title: Genomic DNA from whole blood TWPID11196.Beta

description: Family 6 Dizygotic twin

value: H

value: Family 6 Dizygotic twin


title: Genomic DNA from whole blood TWPID1519.Beta

description: Family 43 Monozygotic twin

value: blood


title: Genomic DNA from whole blood TWPID2075.Beta

description: Family 44 Dizygotic twin

value: Family 44 Dizygotic twin


title: Genomic DNA from whole blood TWPID10086.Beta

description: Family 48 Dizygotic twin

value: Family 48 Dizygotic twin


title: Genomic DNA from whole blood TWPID6296.Beta

description: Family 1 Dizygotic twin

value: Female

value: A

value: Family 1 Dizygotic twin


title: Genomic DNA from whole blood TWPID1645.Beta

description: Family 37 Monozygotic twin

value: G

value: Family 37 Monozygotic twin


title: Genomic DNA from whole blood TWPID11103.Beta

description: Family 41 Monozygotic twin

value: K

value: Family 41 Monozygotic twin


title: Genomic DNA from whole blood TWPID9396.Beta

description: Family 38 Dizygotic twin

value: Family 38 Dizygotic twin


title: Genomic DNA from whole blood TWPID3863.Beta

description: Family 42 Singleton

value: Normal

value: L

value: Family 42 Singleton


title: Genomic DNA from whole blood TWPID4224.Beta

description: Family 36 Dizygotic twin

value: F

value: Family 36 Dizygotic twin


title: Genomic DNA from whole blood TWPID11426.Beta

description: Family 47 Monozygotic twin

value: I

value: Family 47 Monozygotic twin


title: Genomic DNA from whole blood TWPID4095.Beta

description: Family 39 Monozygotic twin

value: blood

value: Family 39 Monozygotic twin


title: non-tumor tissues replicate 7

city: guangzhou

first: Chuanhui

last: Cao

state: guangdong

address: 1838 guangzhoudadaobeiroad

department: Department of Radiation Oncology

institute: Nanfang Hospital, Southern Medical University, Guangzhou, China

description: gene expression of non-tumor tissue ajacent HCC tumor from Xiaolong Xiao

hyb_protocol: 1 μg of each labeled cRNA was  fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505B).

scan_protocol: Scanned on Agilent Microarray Scanner (Agilent p/n G2565BA).

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies).

source_name: non-tumor tissues from patients whose name was Xiaolong Xiao

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from 1 μg total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Fresh HCC tissues and adjacent non-tumor tissues were collected and stores at from 7 patients who underwent initial hepatectomy and were diagnosed with HCC between January 2011 and July 2012 at the Nanfang Hospital of the Southern Medical University (Guangzhou, China).

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

value: male

value: 39 years

tag: tumor stage

value: Barcelona Clinic Liver Cancer:A

tag: source

value: non-tumor tissue ajacent HCC tumor


title: Genomic DNA from whole blood TWPID8436.Beta

description: Family 35 Singleton

value: Female

value: E

value: Family 35 Singleton


title: tumor tissues replicate 7

description: gene expression of HCC tumor from Xiaolong Xiao

source_name: tumor tissues from patients whose name was Xiaolong Xiao

value: HCC tumor from Xiaolong Xiao

value: HCC tumor


title: Genomic DNA from whole blood TWPID10826.Beta

description: Family 34 Monozygotic twin

value: Normal

value: D

value: Family 34 Monozygotic twin


title: tumor tissues replicate 6

description: gene expression of HCC tumor from Ruodi Chen

source_name: tumor tissues from patients whose name was Ruodi Chen

value: 49 years

value: Barcelona Clinic Liver Cancer:C

value: HCC tumor from Ruodi Chen


title: tumor tissues replicate 5

description: gene expression of HCC tumor from Zhichang Liu

source_name: tumor tissues from patients whose name was Zhichang Liu

value: 36 years

value: HCC tumor from Zhichang Liu


title: non-tumor tissues replicate 6

description: gene expression of non-tumor tissue ajacent HCC tumor from Ruodi Chen

source_name: non-tumor tissues from patients whose name was Ruodi Chen

value: male


title: Genomic DNA from whole blood TWPID4667.Beta

description: Family 3 Dizygotic twin

value: blood

value: C

value: Family 3 Dizygotic twin


title: non-tumor tissues replicate 4

description: gene expression of non-tumor tissue ajacent HCC tumor from Chunxian Liao

source_name: non-tumor tissues from patients whose name was Chunxian Liao

value: 39 years

value: Barcelona Clinic Liver Cancer:D

value: non-tumor tissue ajacent HCC tumor


title: Genomic DNA from whole blood TWPID7453.Beta

description: Family 28 Monozygotic twin

value: Female

value: I

value: Family 28 Monozygotic twin


title: non-tumor tissues replicate 5

description: gene expression of non-tumor tissue ajacent HCC tumor from Zhichang Liu

source_name: non-tumor tissues from patients whose name was Zhichang Liu


title: Genomic DNA from whole blood TWPID2114.Beta

description: Family 26 Dizygotic twin

value: Normal

value: F

value: Family 26 Dizygotic twin


title: Genomic DNA from whole blood TWPID8499.Beta

description: Family 27 Singleton

value: G

value: Family 27 Singleton


title: Genomic DNA from whole blood TWPID7442.Beta

description: Family 15 Dizygotic twin

value: E

value: Family 15 Dizygotic twin


title: Genomic DNA from whole blood TWPID8414.Beta

description: Family 33 Monozygotic twin

value: B

value: Family 33 Monozygotic twin


title: Genomic DNA from whole blood TWPID5254.Beta

description: Family 31 Dizygotic twin

value: blood

value: L

value: Family 31 Dizygotic twin


title: tumor tissues replicate 3

description: gene expression of HCC tumor from Xiaojun Wang

source_name: tumor tissues from patients whose name was Xiaojun Wang

value: male

value: 33 years

value: Barcelona Clinic Liver Cancer:A

value: HCC tumor from Xiaojun Wang

value: HCC tumor


title: Genomic DNA from whole blood TWPID11742.Beta

description: Family 29 Dizygotic twin

value: Female

value: Normal

value: J

value: Family 29 Dizygotic twin


title: tumor tissues replicate 4

description: gene expression of HCC tumor from Chunxian Liao

source_name: tumor tissues from patients whose name was Chunxian Liao

value: 39 years

value: Barcelona Clinic Liver Cancer:D

value: HCC tumor from Chunxian Liao


title: Genomic DNA from whole blood TWPID1877.Beta

description: Family 50 Monozygotic twin

value: Family 50 Monozygotic twin


title: Genomic DNA from whole blood TWPID4670.Beta

description: Family 32 Dizygotic twin

value: A

value: Family 32 Dizygotic twin


title: Genomic DNA from whole blood TWPID4757.Beta

description: Family 30 Monozygotic twin

value: blood

value: K

value: Family 30 Monozygotic twin


title: non-tumor tissues replicate 2

description: gene expression of non-tumor tissue ajacent HCC tumor from Yinquan Zhao

source_name: non-tumor tissues from patients whose name was Yinquan Zhao

value: male

value: 40 years

value: non-tumor tissue ajacent HCC tumor


title: tumor tissues replicate 2

description: gene expression of HCC tumor from Yinquan Zhao

source_name: tumor tissues from patients whose name was Yinquan Zhao

value: Barcelona Clinic Liver Cancer:A

value: HCC tumor from Yinquan Zhao

value: HCC tumor


title: non-tumor tissues replicate 3

description: gene expression of non-tumor tissue ajacent HCC tumor from Xiaojun Wang

source_name: non-tumor tissues from patients whose name was Xiaojun Wang

value: 33 years


title: non-tumor tissues replicate 1

description: gene expression of non-tumor tissue ajacent HCC tumor from Yongping Xun

source_name: non-tumor tissues from patients whose name was Yongping Xun

value: 36 years


title: unknown (7911739007_I)

city: New Haven

first: Victoria

middle: Elizabeth

last: Clark

state: CT

address: 300 Cedar Street TAC S330

department: Departments of Neurosurgery and Genetics

country: USA

institute: Yale University School of Medicine

description: unknown

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using normal-exponential convolution model-based background correction and quantile normalization. Merging of the data, background removal and normalization processes were performed using the limma R package.  All of the batches were normalized at once after excluding probes with low quality.

source_name: meningioma

label_protocol: Standard Illumina

extract_protocol: RNA was extracted from human meningioma samples using the Allprep DNA/RNA/protein Mini Kit (Qiagen Science, MD).

tag: isprimary

value: PRIMARY

tag: grade

tag: radiation

value: No

tag: center

tag: rin

tag: batch

tag: ID


title: unknown (7911747005_C)

description: unknown


title: tumor tissues replicate 1

description: gene expression of HCC tumor from Yongping Xun

source_name: tumor tissues from patients whose name was Yongping Xun

value: HCC tumor from Yongping Xun


title: Genomic DNA from whole blood TWPID8152.Beta

description: Family 24 Monozygotic twin

value: Female

value: Normal

value: B

value: Family 24 Monozygotic twin


title: Genomic DNA from whole blood TWPID2546.Beta

description: Family 25 Monozygotic twin

value: blood

value: D

value: Family 25 Monozygotic twin


title: unknown (7911739007_A)

description: unknown


title: Genomic DNA from whole blood TWPID4866.Beta

description: Family 18 Dizygotic twin

value: H

value: Family 18 Dizygotic twin


title: unknown (7911739004_K)

description: unknown


title: Genomic DNA from whole blood TWPID6073.Beta

description: Family 22 Dizygotic twin

value: L

value: Family 22 Dizygotic twin


title: unknown (7911739035_A)

description: unknown


title: Genomic DNA from whole blood TWPID1542.Beta

description: Family 14 Dizygotic twin

value: C

value: Family 14 Dizygotic twin


title: Genomic DNA from whole blood TWPID4259.Beta

description: Family 23 Dizygotic twin

value: A

value: Family 23 Dizygotic twin


title: unknown (7754315064_L)

description: unknown

value: PRIMARY

value: No


title: Genomic DNA from whole blood TWPID2004.Beta

description: Family 21 Monozygotic twin

value: Female

value: K

value: Family 21 Monozygotic twin


title: unknown (7911739023_E)

description: unknown


title: Genomic DNA from whole blood TWPID4865.Beta

description: Family 18 Dizygotic twin

value: Normal


title: Genomic DNA from whole blood TWPID2514.Beta

description: Family 17 Singleton

value: blood

value: G

value: Family 17 Singleton


title: unknown (7754315088_C)

description: unknown


title: unknown (7754315088_E)

description: unknown

value: unknown

value: Yes


title: unknown (7754315064_J)

description: unknown


title: unknown (7911739023_D)

description: unknown


title: Genomic DNA from whole blood TWPID9300.Beta

description: Family 19 Dizygotic twin

value: I

value: Family 19 Dizygotic twin


title: unknown (7754315064_E)

description: unknown


title: Genomic DNA from whole blood TWPID7246.Beta

description: Family 15 Dizygotic twin

value: E

value: Family 15 Dizygotic twin


title: Genomic DNA from whole blood TWPID7223.Beta

description: Family 20 Dizygotic twin

value: J

value: Family 20 Dizygotic twin


title: TRAF7 (7911747005_A)

value: PRIMARY


title: Genomic DNA from whole blood TWPID3369.Beta

description: Family 13 Monozygotic twin

value: B

value: Family 13 Monozygotic twin


title: unknown (7754315086_I)

description: unknown

value: No


title: TRAF7 (7911739001_J)


title: Genomic DNA from whole blood TWPID15891.Beta

description: Family 4 Monozygotic twin

value: Female

value: D

value: Family 4 Monozygotic twin


title: Genomic DNA from whole blood TWPID8737.Beta

description: Family 12 Monozygotic twin

value: blood

value: Normal

value: L

value: Family 12 Monozygotic twin


title: unknown (7911739005_G)

description: unknown


title: unknown (7911739005_E)

description: unknown


title: Genomic DNA from whole blood TWPID1541.Beta

description: Family 14 Dizygotic twin

value: C

value: Family 14 Dizygotic twin


title: Genomic DNA from whole blood TWPID12170.Beta

description: Family 10 Singleton

value: Family 10 Singleton


title: TRAF7 (7911739023_A)


title: TRAF7 (7911739001_D)


title: Genomic DNA from whole blood TWPID3992.Beta

description: Family 9 Monozygotic twin

value: I

value: Family 9 Monozygotic twin


title: TRAF7 (7911739003_J)


title: Genomic DNA from whole blood TWPID4434.Beta

description: Family 7 Monozygotic twin

value: G

value: Family 7 Monozygotic twin


title: Genomic DNA from whole blood TWPID6066.Beta

description: Family 5 Monozygotic twin

value: E

value: Family 5 Monozygotic twin


title: SMO (7911747005_G)

description: SMO

value: PRIMARY

value: No


title: SMO (7911739035_G)

description: SMO


title: Genomic DNA from whole blood TWPID11197.Beta

description: Family 6 Dizygotic twin

value: Female

value: F

value: Family 6 Dizygotic twin


title: Genomic DNA from whole blood TWPID10027.Beta

description: Family 8 Dizygotic twin

value: blood

value: Normal

value: H

value: Family 8 Dizygotic twin


title: Genomic DNA from whole blood TWPID1591.Beta

description: Family 11 Monozygotic twin

value: K

value: Family 11 Monozygotic twin


title: Genomic DNA from whole blood TWPID3682.Beta

description: Family 46 Dizygotic twin

value: Family 46 Dizygotic twin


title: Genomic DNA from whole blood TWPID4668.Beta

description: Family 3 Dizygotic twin

value: C

value: Family 3 Dizygotic twin


title: SMO (7911739001_G)

description: SMO


title: Genomic DNA from whole blood TWPID15890.Beta

description: Family 4 Monozygotic twin

value: D

value: Family 4 Monozygotic twin


title: Genomic DNA from whole blood TWPID6692.Beta

description: Family 1 Dizygotic twin

value: A

value: Family 1 Dizygotic twin


title: SMO (7754315014_E)

description: SMO

value: Recurrent

value: No


title: SMO (7754315014_A)

description: SMO

value: PRIMARY


title: SMO (7911739023_I)

description: SMO


title: SMO (7754315064_H)

description: SMO


title: Genomic DNA from whole blood TWPID8368.Beta

description: Family 2 Singleton

value: Female

value: B

value: Family 2 Singleton


title: SMO (7754315014_C)

description: SMO


title: SMO (7911739001_E)

description: SMO


title: SMO (7911739003_H)

description: SMO


title: TRAF7 (7754315014_L)


title: KLF4+TRAF7 (7911739035_K)


title: SMO (7911739003_F)

description: SMO


title: KYSE170 treated E2

city: Beijing

first: Yang

last: Xu

address: No.17 Panjiayuan Nanli, Chaoyang district

institute: Cancer Hospital

description: Gene expression data from KYSE170 treated with ethyl-3,4-dihydroxybenzoate for 12 hrs.

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

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

data_processing: The data were normalized using Robust Multi-array Average (RMA).

source_name: KYSE170 treated with EDHB for 12 hrs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA (3' IVT Express Kit User Manual, 2008, Affymetrix).

growth_protocol: KYSE170 cells were clutured in RPMI 1640 media with 10% fetal bovin serum (FBS) and antibiotics

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

treatment_protocol: KYSE170 cells were treated with 50μg/ml ethyl-3,4-dihydroxybenzoate  for 12 hrs or left untreated

tag: cell line

tag: treatment


title: KLF4+TRAF7 (7911739035_I)


title: KYSE170 untreated 2

description: Gene expression data from KYSE170 untreated.

source_name: KYSE170 untreated

value: Untreated


title: KYSE170 treated E1

value: 50μg/ml ethyl-3,4-dihydroxybenzoate  for 12 hrs


title: KYSE170 untreated 1


title: KLF4+TRAF7 (7911739035_C)


title: KLF4+TRAF7 (7911739023_L)


title: Panc2-MMP3 2

city: Jacksonville

first: Derek

middle: Charles

last: Radisky

state: Florida

address: 4500 San Pablo Road

department: Cancer Biology

institute: Mayo Clinic

description: Gene expression data from cell culture

hyb_protocol: cRNA was hybridized onto chips for 18 h at 45 degrees C.  GeneChips were washed in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4_450 wash protocol.

scan_protocol: Chips were scanned in an Affymetrix 3000 (7G) Confocal Scanner.

data_processing: The data were analyzed with Genespring GX 7.3.1 using Affymetrix default analysis settings and standard Genespring normalizations (per chip normalize to 50th percentile, per gene normalize to median)

source_name: Panc2 cells treated with 100U/ml MMP3

label_protocol: This project used the Affymetrix Mouse 430 2.0 GeneChip 200 ng of total RNA was used as input

growth_protocol: Cells were grown in DMEM+10% FCS

extract_protocol: Phenol/Chloroform

treatment_protocol: Treatment with 100U/ml rMMP3

value: pancreas

value: 100U/ml MMP3


title: Panc2-control 2

description: Gene expression data from cell culture

source_name: Untreated Panc2 cells

value: untreated


title: Panc2-control 1

description: Gene expression data from cell culture


title: KLF4+TRAF7 (7911739023_J)


title: KLF4+TRAF7 (7911739001_B)


title: Panc2-MMP3 1

description: Gene expression data from cell culture


title: KLF4+TRAF7 (7754315086_H)


title: KLF4+TRAF7 (7911747016_J)


title: CBA-Kid_Diet_B_d3

city: Leicester

first: Yuri

middle: E

last: Dubrova

address: University Road

department: Genetics

institute: University of Leicester

description: 2 techinical replicates

hyb_protocol: Hybridization was performed using the NimbleGen Hybridization System 4 following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed using GenePix Axon 4200 AL scanner, following their standard operating protocol.

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

organism: Mus musculus

source_name: Group B Diet male 3

label_protocol: Labeling was performe using the NimbleGen One-Color DNA Labeling Kit.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

treatment_protocol: Diet low in methionine and lacking choline and folic acid (Diet #518892, Dyets Inc, Bethelhem, USA)

tag: strain

value: CBA/Ca

value: Methyl-deficient diet for 8 weeks + 2 weeks on normal diet

value: Kidney


title: CBA-Kid_Diet_B_d4

description: 2 techinical replicates

source_name: Group B Diet male 4


title: CBA-Kid_Diet_B_d2

description: 2 techinical replicates

source_name: Group B Diet male 2


title: CBA-Kid_Diet_B_d5

description: 2 techinical replicates

source_name: Group B Diet male 5


title: CBA-Kid_Con_B_s6

description: 2 techinical replicates

source_name: Group B Control male 6

value: Control


title: CBA-Kid_Diet_B_d6

description: 2 techinical replicates

source_name: Group B Diet male 6


title: CBA-Kid_Con_B_s4

description: 2 techinical replicates

source_name: Group B Control male 4


title: KLF4+TRAF7 (7754315014_D)


title: KLF4+TRAF7 (7754315064_D)


title: KLF4+TRAF7 (7911739003_B)


title: KLF4+TRAF7 (7911747016_H)


title: CBA-Kid_Con_B_s1

description: 2 techinical replicates

source_name: Group B Control male 1


title: KLF4+TRAF7 (7754315086_K)


title: CBA-Kid_Diet_B_d1

description: 2 techinical replicates

source_name: Group B Diet male 1


title: KLF4+TRAF7 (7911739003_K)


title: CBA-Kid_Con_B_s5

description: 2 techinical replicates

source_name: Group B Control male 5


title: chr22loss+TRAF7+NF2 (7911739007_E)


title: CBA-Kid_Con_B_s3

description: 2 techinical replicates

source_name: Group B Control male 3


title: KLF4+TRAF7 (7911739003_G)

source_name: meningioma


title: CBA-Kid_Con_B_s2

description: 2 techinical replicates

source_name: Group B Control male 2


title: Genomic DNA from whole blood TWPID5410.Beta

description: Family 16 Dizygotic twin

source_name: Whole blood

value: blood

tag: gender

tag: disease state

value: Normal

tag: 27k chip

value: F

value: Family 16 Dizygotic twin


title: KLF4+TRAF7 (7911739003_D)

value: PRIMARY

value: No


title: chr22loss+TRAF7+NF2 (7754315064_I)


title: KLF4+TRAF7 (7911739003_I)


title: CBA-Kid_Diet_A_d3

description: 2 techinical replicates

source_name: Group A Diet male 3

value: Methyl-deficient diet for 8 weeks

tag: tissue


title: CBA-Kid_Diet_A_d6

description: 2 techinical replicates

source_name: Group A Diet male 6


title: CBA-Kid_Diet_A_d5

description: 2 techinical replicates

source_name: Group A Diet male 5


title: chr22loss+TRAF7+NF2 (7754315088_G)

value: Recurrent

value: Yes


title: CBA-Kid_Con_A_s6

description: 2 techinical replicates

source_name: Group A Control male 6


title: chr22loss+NF2 (7911739004_I)


title: CBA-Kid_Con_A_s3

description: 2 techinical replicates

source_name: Group A Control male 3


title: chr22loss+NF2 (7911739001_C)


title: chr22loss+NF2 (7911739007_K)


title: chr22loss+NF2 (7911739001_A)


title: chr22loss+NF2 (7911739023_F)


title: CBA-Kid_Diet_A_d2

description: 2 techinical replicates

source_name: Group A Diet male 2


title: chr22loss+NF2 (7911739023_H)


title: chr22loss+NF2 (7911739001_F)


title: CBA-Kid_Con_A_s5

description: 2 techinical replicates

source_name: Group A Control male 5


title: CBA_Liv_Diet_B_d3

description: 2 techinical replicates

source_name: Group B Diet male 3

value: Liver


title: CBA-Kid_Con_A_s2

description: 2 techinical replicates

source_name: Group A Control male 2


title: CBA-Kid_Diet_A_d1

description: 2 techinical replicates

source_name: Group A Diet male 1


title: CBA_Liv_Diet_B_d5

description: 2 techinical replicates

source_name: Group B Diet male 5


title: CBA_Liv_Diet_B_d4

description: 2 techinical replicates

source_name: Group B Diet male 4


title: chr22loss+NF2 (7754315014_I)


title: chr22loss+NF2 (7754315086_F)

value: unknown

value: Unknown


title: CBA-Kid_Con_A_s4

description: 2 techinical replicates

source_name: Group A Control male 4


title: chr22loss+NF2 (7754315088_A)


title: chr22loss+NF2 (7911739001_I)


title: CBA-Kid_Con_A_s1

description: 2 techinical replicates

source_name: Group A Control male 1


title: chr22loss+NF2 (7754315014_H)

source_name: meningioma


title: chr22loss+NF2 (7754315086_J)


title: chr22loss+NF2 (7911739023_C)


title: CBA_Liv_Diet_B_d2

description: 2 techinical replicates

source_name: Group B Diet male 2


title: chr22loss+NF2 (7754315088_B)


title: chr22loss+NF2 (7754315014_K)


title: chr22loss+NF2 (7754315088_K)


title: chr22loss+NF2 (7754315014_G)


title: chr22loss+NF2 (7754315086_E)


title: chr22loss+NF2 (7754315014_J)


title: CBA_Liv_Con_B_s4

description: 2 techinical replicates

source_name: Group B Control male 4


title: chr22loss+NF2 (7911739005_B)


title: chr22loss+NF2 (7911739003_L)


title: CBA_Liv_Con_B_s2

description: 2 techinical replicates

source_name: Group B Control male 2


title: CBA_Liv_Con_B_s3

description: 2 techinical replicates

source_name: Group B Control male 3


title: chr22loss+NF2 (7911739005_J)


title: CBA_Liv_Diet_A_d5

description: 2 techinical replicates

source_name: Group A Diet male 5


title: CBA_Liv_Con_A_s4

description: 2 techinical replicates


title: CBA_Liv_Diet_A_d6

description: 2 techinical replicates

source_name: Group A Diet male 6


title: CBA_Liv_Diet_A_d1

description: 2 techinical replicates


title: CBA_Liv_Con_B_s5

description: 2 techinical replicates

source_name: Group B Control male 5


title: chr22loss+NF2 (7911739005_A)


title: CBA_Liv_Con_A_s3

description: 2 techinical replicates

source_name: Group A Control male 3


title: CBA_Liv_Diet_B_d1

description: 2 techinical replicates

source_name: Group B Diet male 1


title: CBA_Liv_Diet_A_d2

description: 2 techinical replicates

source_name: Group A Diet male 2


title: CBA_Liv_Con_A_s5

description: 2 techinical replicates

source_name: Group A Control male 5


title: chr22loss (7911739004_E)


title: CBA_Liv_Diet_A_d4

description: 2 techinical replicates

source_name: Group A Diet male 4


title: CBA_Liv_Con_B_s1

description: 2 techinical replicates

source_name: Group B Control male 1


title: CBA_Liv_Con_A_s6

description: 2 techinical replicates

source_name: Group A Control male 6


title: CBA_Liv_Con_A_s2

description: 2 techinical replicates

source_name: Group A Control male 2


title: chr22loss (7911739004_G)


title: chr22loss (7911739007_G)


title: chr22loss (7754315064_A)


title: Kid_Def_F1_d51

description: 2 techinical replicates

source_name: Offspring of treated male 5

value: BALB/c

value: Offspring of treated male


title: chr22loss (7911747005_I)

source_name: meningioma


title: Kid_Def_F1_d41

description: 2 techinical replicates

source_name: Offspring of treated male 4


title: CBA_Liv_Con_A_s1

description: 2 techinical replicates

source_name: Group A Control male 1

value: CBA/Ca


title: Kid_Def_F1_d31

description: 2 techinical replicates

source_name: Offspring of treated male 3

value: Kidney


title: Kid_Con_F1_s61

description: 2 techinical replicates

source_name: Offspring of control male 6

value: Offspring of control partents


title: chr22loss (7911739023_K)


title: Kid_Def_F1_d21

description: 2 techinical replicates

source_name: Offspring of treated male 2


title: Kid_Def_F1_d11

description: 2 techinical replicates

source_name: Offspring of treated male 1


title: Kid_Con_F1_s31

description: 2 techinical replicates

source_name: Offspring of control male 3


title: chr22loss (7911739005_C)


title: chr22loss (7754315086_C)


title: Kid_Con_F1_s51

description: 2 techinical replicates

source_name: Offspring of control male 5


title: Kid_Con_F1_s41

description: 2 techinical replicates

source_name: Offspring of control male 4


title: chr22loss (7754315014_F)


title: Kid_Con_F1_s21

description: 2 techinical replicates

source_name: Offspring of control male 2


title: chr22loss (7911739005_K)


title: chr22loss (7911739005_I)


title: chr22loss (7754315064_K)


title: chr*loss (7911747005_K)

description: chr*loss


title: chr22loss (7754315086_L)


title: Kid_Con_F1_s11

description: 2 techinical replicates

source_name: Offspring of control male 1


title: Liv_Def_F1_d31

description: 2 techinical replicates


title: Liv_Def_F1_d51

description: 2 techinical replicates


title: chr*loss (7754315064_C)

description: chr*loss


title: chr*loss (7754315088_L)

description: chr*loss


title: Liv_Def_F1_d11

description: 2 techinical replicates


title: chr*loss (7754315086_A)

description: chr*loss


title: AKT1+TRAF7+SMO (7911739040_A)


title: AKT1+TRAF7+SMO (7754315064_B)


title: Liv_Def_F1_d21

description: 2 techinical replicates


title: AKT1+TRAF7 (7911739035_E)


title: chr22loss+NF2 (7754315086_G)


title: Liv_Con_F1_s41

description: 2 techinical replicates


title: chr22loss (7911739023_B)


title: Liv_Def_F1_d41

description: 2 techinical replicates


title: Liv_Con_F1_s51

description: 2 techinical replicates


title: AKT1+TRAF7 (7911739007_C)


title: Liv_Con_F1_s21

description: 2 techinical replicates


title: Liv_Con_F1_s31

description: 2 techinical replicates


title: AKT1+TRAF7 (7754315064_G)


title: CBA_Spleen_Diet_A_d5

description: 2 techinical replicates

source_name: Group A Diet male 5


title: AKT1+TRAF7 (7911739023_G)


title: AKT1+TRAF7 (7911747016_F)


title: AKT1+TRAF7 (7911747005_E)


title: AKT1+TRAF7 (7911747016_L)


title: AKT1+TRAF7 (7911747016_D)


title: AKT1+TRAF7 (7754315088_I)


title: Liv_Con_F1_s11

description: 2 techinical replicates


title: AKT1+TRAF7 (7911739003_E)


title: CBA_Spleen_Diet_A_d3

description: 2 techinical replicates

source_name: Group A Diet male 3

value: Spleen


title: AKT1+TRAF7 (7911739003_C)


title: CBA_Spleen_Diet_A_d4

description: 2 techinical replicates

source_name: Group A Diet male 4


title: CBA_Spleen_Con_A_s4

description: 2 techinical replicates

source_name: Group A Control male 4

value: Control


title: CBA_Spleen_Con_A_s5

description: 2 techinical replicates

source_name: Group A Control male 5


title: chr22loss+NF2 (7911739005_L)

source_name: meningioma


title: AKT1+TRAF7 (7754315086_D)


title: CBA_Spleen_Con_A_s3

description: 2 techinical replicates

source_name: Group A Control male 3


title: CBA_Spleen_Con_A_s8

description: 2 techinical replicates

source_name: Group A Control male 8


title: AKT1+TRAF7 (7754315086_B)


title: CBA_Spleen_Con_A_s2

description: 2 techinical replicates

source_name: Group A Control male 2


title: CBA_Spleen_Diet_A_d1

description: 2 techinical replicates

source_name: Group A Diet male 1


title: AKT1 (7911747016_B)


title: CBA_Liv_Diet_A_d3

description: 2 techinical replicates


title: CBA_Spleen_Con_A_s1

description: 2 techinical replicates

source_name: Group A Control male 1


title: BALB_Spleen_Diet_A_d5

description: 2 techinical replicates


title: TS vs. TGCs (7 days differentiation) rep2

city: Stanford

first: Roberta

middle: L

last: Hannibal

state: CA

address: 300 Pasteur Drive

institute: Stanford University

hyb_protocol: The standard steps of the Agilent arrayCGH hybridization protocol were performed by the Biomedical Genomics Core at the Research Institute at Nationwide Children’s Hospital (Columbus, OH) using the SurePrint G3 Mouse CGH Microarray Kit, 4x180k (Agilent).

scan_protocol: The standard steps of the Agilent arrayCGH scan protocol were performed by the Biomedical Genomics Core at the Research Institute at Nationwide Children’s Hospital (Columbus, OH) using the SurePrint G3 Mouse CGH Microarray Kit, 4x180k (Agilent).

data_processing: The standard steps of the Agilent arrayCGH data processing were performed by the Biomedical Genomics Core at the Research Institute at Nationwide Childrens Hospital (Columbus, OH). Log ratios from the data were then transformed into normalized log 2 ratios.

source_name: Trophoblast stem cells - cultured

label_protocol: For each condition, approximately 4 μg DNA was sent to the Biomedical Genomics Core at the Research Institute at Nationwide Children’s Hospital (Columbus, OH) for processing with the SurePrint G3 Mouse CGH Microarray Kit, 4x180k (Agilent).  When possible (ie: all arrays performed on DNA from in vivo tissue), to ensure that the arrays detect copy number variation, duplicates consist of 1) female test versus male control and 2) male test versus female control.

extract_protocol: Genomic DNA was extracted from fresh tissue and cultured cells using the DNeasy Blood & Tissue Kit (Qiagen).  Before column purification, we digested in vivo and in vitro samples with proteinase-K (600 mAU/ml solution or 40 mAU/mg protein) overnight and for 10 minutes, respectively, at 56C, followed by 4 minute incubation with RNase A (100 mg/mL) (Qiagen DNeasy Blood & Tissue Kit).  For arrays performed on DNA from TGCs and embryonic controls, genomic DNA from two individuals in the same litter were pooled for each condition.  For megakaryocyte arrays, cells derived from 5-6 livers from a single litter were pooled for each condition.  For controls for the megakaryocyte array, three embryos (subset of the litter from which livers were collected from) were pooled for each condition.  For arrays performed on DNA from cultured cells, two replicates from different passages were used (5 million cells each).

treatment_protocol: Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004).  Trophoblast stem cells were differentiated into trophoblast giant cells by replacing the FGF, Activin and Heparin in the media with retinoic acid (Yan et al., 2001; Erlebacher et al., 2004).  Mature TGCs are seen after 4-6 days of differentiation (Carney et al., 1993).  Cells were trypsinized for 4 minutes before the extract protocol.

tag: Stage

source_name: Trophoblast giant cells - cultured

value: differentiated 7 days


title: BALB_Spleen_Diet_A_d8

description: 2 techinical replicates

source_name: Group A Diet male 8


title: BALB_Spleen_Diet_A_d2

description: 2 techinical replicates

source_name: Group A Diet male 2


title: TS vs. TGCs (7 days differentiation) rep1


title: BALB_Spleen_Diet_A_d1

description: 2 techinical replicates


title: BALB_Spleen_Diet_A_d7

description: 2 techinical replicates

source_name: Group A Diet male 7


title: BALB_Spleen_Con_A_s10

description: 2 techinical replicates

source_name: Group A Control male 10


title: BALB_Spleen_Con_A_s6

description: 2 techinical replicates

source_name: Group A Control male 6


title: BALB_Spleen_Con_A_s7

description: 2 techinical replicates

source_name: Group A Control male 7


title: TS vs. TGCs (5 days differentiation) rep2

value: differentiated 5 days


title: BALB_Spleen_Con_A_s9

description: 2 techinical replicates

source_name: Group A Control male 9


title: TS vs. ES rep2

treatment_protocol:
Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004).  Trophoblast stem cells were differentiated into trophoblast giant cells by replacing the FGF, Activin and Heparin in the media with retinoic acid (Yan et al., 2001; Erlebacher et al., 2004).  Mature TGCs are seen after 4-6 days of differentiation (Carney et al., 1993).  Cells were trypsinized for 4 minutes before the extract protocol.
The embryonic stem cell line CGR8 is a germ-line competent cell line established from the inner cell mass of a 129 e3.5 male pre-implantation embryo (Nichols et al., 1990).  Cells were cultured feeder-free on 0.1% gelatin coated plates.  The ES cell medium was prepared by supplementing knockout DMEM (Invitrogen) with 15% FBS, 1mM glutamax, 0.1mM nonessential amino acids, 1mM sodium pyruvate, 0.1mM 2-mercaptoethanol, penicillin/streptomycin, and 1000 units of leukemia inhibitory factor (LIF; Millipore).  Cell culture was maintained at 37°C with 5% CO2.

source_name: Embryonic stem cells - cultured


title: BALB_Spleen_Diet_A_d6

description: 2 techinical replicates

source_name: Group A Diet male 6


title: BALB_Spleen_Con_A_s5

description: 2 techinical replicates

source_name: Group A Control male 5


title: TS vs. ES rep1


title: TS vs. TGCs (5 days differentiation) rep1


title: BALB_Spleen_Con_A_s2

description: 2 techinical replicates


title: TS vs. TGCs (3 days differentiation) rep1

value: differentiated 3 days


title: BALB_Spleen_Con_A_s1

description: 2 techinical replicates


title: e16.5 vs. embryos (FvM)

source_name: Trophoblast giant cells - e16.5

treatment_protocol: Pregnant C57BL/6 mice were obtained from Charles River.  Copulation was determined by the presence of a vaginal plug the morning after mating, and embryonic day 0.5 (e0.5) was defined as noon of that day.  TGCs and embryos were dissected in 1X PBS (1:10 10X PBS, pH=7.4; Gibco) and stored on ice until further processing.  TGCs were dissected away from the placental disk, decidua, and, if possible, Reichert’s membrane.  For gathering 2N genomic DNA, at e9.5-10.5, the embryo body, after removal of obvious organs and head (removed at otic vesicle), was collected; and at later stages, limbs, or a mixture of limbs and the tail, were collected.   All experimental procedures were carried out in accordance with the APLAC protocol and the institutional guidelines set by the Veterinary Service Center at Stanford University.

value: female

source_name: Embryo - e16.5

value: male


title: placenta disk vs. embryos (MvF)

source_name: Placenta disk cells

source_name: Embryo - e13.5


title: TS vs. TGCs (3 days differentiation) rep2


title: placenta disk vs. embryos (FvM)


title: e16.5 vs. embryos (MvF)


title: e13.5 vs. embryos (MvF)

source_name: Trophoblast giant cells - e13.5


title: AKT1+TRAF7 (7911739003_A)

source_name: meningioma

value: PRIMARY

value: No


title: Th2+IFNa_Donor3_Day5+4hours

city: PAris

first: Maxime

last: Touzot

address: 26 rue d'ULM

institute: Institut Curie

description:
Th2 CD4 T cells + IFNa
IS08_ARN0068

hyb_protocol: Labelled DNA was hybridized on the Affymetrix human Gene ST1.1, processed on an Affymetrix GeneTitan device

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

data_processing: The data were normalized using the RMA algorithm and bioinformatics analysis was performed using GeneSpring GX 7.3 (Agilent, Palo Alto, CA). Probes with an expression lower than 20 Units were filtered out. Differential gene expression was defined according to the two following criteria: Fold Change > 2; p-value < 0.05 (T-test).

source_name: Th2 CD4 T cells + IFNa

label_protocol: Not provided

growth_protocol: Naive CD4+ T cells were cultured in 48-well plates (Falcon) at a density of 8 x 104 cells per well in X-VIVO 15 serum free medium (Lonza) in the presence of Dynabeads CD3/CD28 T cell expander (Invitrogen) and polarized into Th0, Th1, Th2, Th17 with the following cytokines: none for Th0; IL-12 (10 ng/ml; R&D Systems) for Th1; IL-4 (25 ng/ml; R&D Systems) for Th2; IL-1β (10 ng/ml; Peprotech), IL-6 (20 ng/ml; Peprotech), IL-23 (100 ng/ml; R&D Systems) and TGF-β (1 ng/ml; Peprotech) for Th17. IFN-α (Miltenyi) was added at 10 ng/m

extract_protocol: RNA was extracted using Rneasy Microquit (Qiagen).  For each condition, 500pg of RNA were used to synthesize targets using the WT-Ovation™ Pico RNA amplification system (Nugen, Bemmel,The Netherlands).

tag: cell type

value: T cells


title: Th17_Donor3_Day5+4hours

description:
Th17 CD4 T cells
IS08_ARN0070

source_name: Th17 CD4 T cells


title: e11.5 vs. embryos (MvF)

source_name: Trophoblast giant cells - e11.5

source_name: Embryo - e11.5


title: Th17+IFNa_Donor3_Day5+4hours

description:
Th17 CD4 T cells + IFNa
IS08_ARN0071

source_name: Th17 CD4 T cells + IFNa


title: CBA_Spleen_Diet_A_d6

description: 2 techinical replicates

value: Methyl-deficient diet for 8 weeks


title: Th1_Donor3_Day5+4hours

description:
Th1 CD4 T cells
IS08_ARN0064

source_name: Th1 CD4 T cells


title: Th0+IFNa_Donor3_Day5+4hours

description:
Th0 CD4 T cells + IFNa
IS08_ARN0062

source_name: Th0 CD4 T cells + IFNa


title: Th1+IFNa_Donor3_Day5+4hours

description:
Th1 CD4 T cells + IFNa
IS08_ARN0065

source_name: Th1 CD4 T cells + IFNa


title: Th2_Donor3_Day5+4hours

description:
Th2 CD4 T cells
IS08_ARN0067

source_name: Th2 CD4 T cells


title: e11.5 vs. embryos (FvM)


title: CBA_Spleen_Diet_A_d8

description: 2 techinical replicates

source_name: Group A Diet male 8


title: Th0_Donor3_Day5+4hours

description:
Th0 CD4 T cells
IS08_ARN0061

source_name: Th0 CD4 T cells


title: AKT1+TRAF7 (7754315064_F)


title: e13.5 vs. embryos (FvM)


title: e9.5 vs. embryos (FvM)

source_name: Trophoblast giant cells - e9.5

source_name: Embryo - e9.5


title: Megakaryocytes vs. embryos (MvF)

source_name: Megakaryocytes

treatment_protocol:
Pregnant C57BL/6 mice were obtained from Charles River.  Copulation was determined by the presence of a vaginal plug the morning after mating, and embryonic day 0.5 (e0.5) was defined as noon of that day.  TGCs and embryos were dissected in 1X PBS (1:10 10X PBS, pH=7.4; Gibco) and stored on ice until further processing.  TGCs were dissected away from the placental disk, decidua, and, if possible, Reichert’s membrane.  For gathering 2N genomic DNA, at e9.5-10.5, the embryo body, after removal of obvious organs and head (removed at otic vesicle), was collected; and at later stages, limbs, or a mixture of limbs and the tail, were collected.   All experimental procedures were carried out in accordance with the APLAC protocol and the institutional guidelines set by the Veterinary Service Center at Stanford University.
Megakaryocytes were derived and cultured as described in (Shivdasani and Schulze, 2005).  Briefly, fetal livers were dissected from e13.5 C57BL/6 embryos in Hanks’ Balanced Salt Solution and placed in DMEM with 10% FBS supplemented with 100 ug/mL penicillin-streptomycin (Invitrogen).  Livers were pooled based on sex of the embryo (males pooled and females pooled).  To make a single cell solution, Livers were aspirated through a progression of 18G, 21G and 23G needles.  To promote differentiation into megakaryocytes, cells were cultured for five days in media containing thrombopoietin (TPO; R&D Systems) at 37C with 5% CO2.  Successful differentiation was identified by 1) the presence of large cells (megakaryocytes) and by 2) FACS to confirm up to 32N ploidy.  Megakaryocytes were further isolated by placing cultured cells over a two-step density gradient (1.5% BSA over 3% BSA in a 15mL tube).  Megakaryocytes sank to the bottom of the tube while smaller, undifferentiated, cells stayed in the upper portion.


title: Th17_Donor2_Day5+4hours

description:
Th17 CD4 T cells
IS08_ARN0046


title: e9.5 vs. embryos (MvF)


title: Megakaryocytes vs. embryos (FvM)

source_name: Embryo - e13.5


title: Th2_Donor2_Day5+4hours

description:
Th2 CD4 T cells
IS08_ARN0043


title: Th17+IFNa_Donor2_Day5+4hours

description:
Th17 CD4 T cells + IFNa
IS08_ARN0047


title: miR1792-DOX

city: stanford

first: Dean

last: Felsher

address: 269 Campus Drive

department: Medicine

description: MYC OFF

data_processing: The data were normalised using rank invarient normalisation with using GenomeStudio.

source_name: MYC lymphoma with MSCV-miR-17-92, MYC OFF

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

growth_protocol: CL4188 cultured in RPMI 1640 with 10%FBS and 2-mercaptoethanol

extract_protocol: Qiagen RNeasy kit

treatment_protocol: doxycycline 20ng/ml for 48 hours

tag: agent

value: DOX (20ng/ml)

value: FVB/N


title: Control-DOX

description: MYC OFF

source_name: MYC lymphoma with MSCV control, MYC OFF


title: miR1792-No DOX

description: MYC ON

source_name: MYC lymphoma with MSCV-miR-17-92


title: Th1_Donor2_Day5+4hours

description:
Th1 CD4 T cells
IS08_ARN0040


title: Th0+IFNa_Donor2_Day5+4hours

description:
Th0 CD4 T cells + IFNa
IS08_ARN0038


title: WT_Tconv.IL6.TGFβ.Rapa_18h#1

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

institute: GSK

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 18 hours and treated with 10 nM rapamycin

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16-18 hours in GeneChip Hybridization oven 640 at 45 °C with rotation (60 rpm).  The hybridized samples were washed and stained using Affymetrix fluidics station 450. The first stain with streptavidin-R-phycoerythrin (SAPE) was followed by signal amplification using a biotinilated goat anti-streptavidin antibody and another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix).

scan_protocol: Standard Affymetrix protocol on an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental .MPS file)

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, rapamycin-treated, 18 hour timepoint

label_protocol: biotin

growth_protocol: Murine CD4+ CD25- T cells were cultured in 96-well plates at a density of 10^5 cells per mL in standard IMDM medium supplemented with 10% FBS, 2 mM L-glutamine, 50 mM 2-mercapthoethanol, 1 mM Pyruvate, 10 mM HEPES, and 10 U/10 mg Penicillin/Streptomycin. Cells were activated by adding 0.3 mg/ mL hamster-anti-mouse CD3 and 0.5 mg/mL hamsanti-CD28 antibodies to cells in wells pre-coated with 0.3 mg/ mL goat-anti-hamster IgG. Th17-polarization was induced using 3 ng/mL recombinant human TGF-b1 and 30 ng/ mL recombinant mouse IL-6. Cells were transferred from antibody-coated wells to fresh, uncoated 96- or 48-well plate wells after 48 hours, and fresh TGF-b1 and IL-6 were added

extract_protocol: Total RNA was extracted using the Qiagen RNeasy with on-column DNase treatment method.

treatment_protocol: 10 nM Halofuginone or 10 nM rapamycin or equal concentration (0.01% v/v DMSO) was prepared in medium and was added to the cells in culture immediately before anti-CD3/ anti-CD28 activation. For 72 hour timepoints, compoudns were re-added alongside TGF-b1 and IL-6 when cells were split at 48 hours

value: CD4+ CD25- T cells


title: Th0_Donor2_Day5+4hours

description:
Th0 CD4 T cells
IS08_ARN0037


title: WT_Tconv.IL6.TGFβ.Rapa_18h#2


title: Th1+IFNa_Donor2_Day5+4hours

description:
Th1 CD4 T cells + IFNa
IS08_ARN0041


title: Control-No DOX

description: MYC ON

source_name: MYC lymphoma with MSCV control


title: WT_Tconv.IL6.TGFβ.Rapa_72h#1

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 72 hours and treated with 10 nM rapamycin

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, rapamycin-treated, 72 hour timepoint


title: Th2+IFNa_Donor2_Day5+4hours

description:
Th2 CD4 T cells + IFNa
IS08_ARN0044

source_name: Th2 CD4 T cells + IFNa


title: Th2_Donor1_Day5+4hours

description:
Th2 CD4 T cells
IS08_ARN0019


title: WT_Tconv.IL6.TGFβ.Rapa_3h#1

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 4 hours and treated with 10 nM rapamycin

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, rapamycin-treated, 4 hour timepoint


title: Th2+IFNa_Donor1_Day5+4hours

description:
Th2 CD4 T cells + IFNa
IS08_ARN0020


title: WT_Tconv.IL6.TGFβ.HF_72h#1

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 72 hours and treated with 10 nM halofuginone

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, halofuginone-treated, 72 hour timepoint


title: WT_Tconv.IL6.TGFβ.HF_18h#2

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 18 hours and treated with 10 nM halofuginone

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, halofuginone-treated, 18 hour timepoint


title: Th17_Donor1_Day5+4hours

description:
Th17 CD4 T cells
IS08_ARN0022

source_name: Th17 CD4 T cells


title: Th17+IFNa_Donor1_Day5+4hours

description:
Th17 CD4 T cells + IFNa
IS08_ARN0023

source_name: Th17 CD4 T cells + IFNa


title: Th1+IFNa_Donor1_Day5+4hours

description:
Th1 CD4 T cells + IFNa
IS08_ARN0017

source_name: Th1 CD4 T cells + IFNa


title: WT_Tconv.IL6.TGFβ.HF_72h#2


title: WT_Tconv.IL6.TGFβ.HF_18h#1


title: WT_Tconv.IL6.TGFβ.HF_3h#1

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 4 hours and treated with 10 nM halofuginone

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, halofuginone-treated, 4 hour timepoint


title: WT_Tconv.IL6.TGFβ.Rapa_4h#1


title: Th1_Donor1_Day5+4hours

description:
Th1 CD4 T cells
IS08_ARN0016

source_name: Th1 CD4 T cells


title: WT_Tconv.IL6.TGFβ.HF_4h#1


title: Th0_Donor1_Day5+4hours

description:
Th0 CD4 T cells
IS08_ARN0013

source_name: Th0 CD4 T cells


title: WT_Tconv.IL6.TGFβ.DMSO_72h#2

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 72 hours and treated with vehicle

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, vehicle-treated, 72 hour timepoint


title: Th17_Donor3_Day5

description:
Th17 CD4 T cells
IS08_ARN0058


title: WT_Tconv.IL6.TGFβ.DMSO_18h#2

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 18 hours and treated with vehicle

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, vehicle-treated, 18 hour timepoint


title: Th2_Donor3_Day5

description:
Th2 CD4 T cells
IS08_ARN0055

source_name: Th2 CD4 T cells


title: Th2+IFNa_Donor3_Day5

description:
Th2 CD4 T cells + IFNa
IS08_ARN0056


title: Th0+IFNa_Donor1_Day5+4hours

description:
Th0 CD4 T cells + IFNa
IS08_ARN0014

source_name: Th0 CD4 T cells + IFNa


title: GCN2KO_Tconv.IL6.TGFβ.Rapa_72h#1

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 72 hours and treated with 10 nM rapamycin

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, rapamycin-treated, 72 hour timepoint


title: Th1+IFNa_Donor3_Day5

description:
Th1 CD4 T cells + IFNa
IS08_ARN0053


title: WT_Tconv.IL6.TGFβ.DMSO_4h#1

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 4 hours and treated with vehicle

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, vehicle-treated, 4 hour timepoint


title: GCN2KO_Tconv.IL6.TGFβ.Rapa_18h#1

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 18 hours and treated with 10 nM rapamycin

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, rapamycin-treated, 18 hour timepoint


title: Th1_Donor3_Day5

description:
Th1 CD4 T cells
IS08_ARN0052


title: Th17+IFNa_Donor3_Day5

description:
Th17 CD4 T cells + IFNa
IS08_ARN0059


title: WT_Tconv.IL6.TGFβ.DMSO_3h#1


title: Th0+IFNa_Donor3_Day5

description:
Th0 CD4 T cells + IFNa
IS08_ARN0050


title: GCN2KO_Tconv.IL6.TGFβ.Rapa_4h#2

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 4 hours and treated with 10 nM rapamycin

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, rapamycin-treated, 4 hour timepoint


title: WT_Tconv.IL6.TGFβ.DMSO_18h#1


title: GCN2KO_Tconv.IL6.TGFβ.Rapa_4h#1


title: GCN2KO_Tconv.IL6.TGFβ.Rapa_18h#2


title: Th0_Donor3_Day5

description:
Th0 CD4 T cells
IS08_ARN0049


title: Th2_Donor2_Day5

description:
Th2 CD4 T cells
IS08_ARN0031


title: WT_Tconv.IL6.TGFβ.DMSO_72h#1


title: GCN2KO_Tconv.IL6.TGFβ.Rapa_72h#2


title: GCN2KO_Tconv.IL6.TGFβ.HF_72h#1

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 72 hours and treated with 10 nM halofuginone

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, halofuginone-treated, 72 hour timepoint


title: Th17_Donor2_Day5

description:
Th17 CD4 T cells
IS08_ARN0034


title: Th17+IFNa_Donor2_Day5

description:
Th17 CD4 T cells + IFNa
IS08_ARN0035


title: GCN2KO_Tconv.IL6.TGFβ.HF_72h#2


title: Th2+IFNa_Donor2_Day5

description:
Th2 CD4 T cells + IFNa
IS08_ARN0032

source_name: Th2 CD4 T cells + IFNa


title: Th0+IFNa_Donor2_Day5

description:
Th0 CD4 T cells + IFNa
IS08_ARN0026


title: Th1+IFNa_Donor2_Day5

description:
Th1 CD4 T cells + IFNa
IS08_ARN0029


title: Th0_Donor2_Day5

description:
Th0 CD4 T cells
IS08_ARN0025


title: GCN2KO_Tconv.IL6.TGFβ.HF_4h#2

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 4 hours and treated with 10 nM halofuginone

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, halofuginone-treated, 4 hour timepoint


title: atypical NF1 deletion patient_8

city: Ulm

first: Julia

last: Vogt

address: Albert-Einstein Allee 11

department: Institute of Human Genetics

institute: Ulm University

hyb_protocol: Sample hybridization and washing of the microarrays was carried out by means of the Oligo aCGH-on-chip Hybridization and Wash Buffer Kits (Agilent Technologies).

scan_protocol: Fluorescent intensities were detected with Scan Control A.8.4.1 Software on the Agilent DNA MicroarrayScanner and extracted from the images using Feature Extraction 10.7.3.1 Software (Agilent Technologies) and the design file 033151_D_F_20110323.xml.

data_processing: The software tools Feature Extraction 10.7.3.1 and Genomic Workbench Lite 6.0.130.24 (CGH module) were used for quality control by means of quality metrics, for annotation, statistical data analysis and visualization. The microarray data were normalized according to the following procedure: The expected average μ was subtracted from all log2 ratios vi. These modified log2 ratios vi are divided by the estimated variance σ. This transforms the log2 ratio scores into a normal distribution with a mean of 0 under the null model assumption. μ and σ were calculated from one or more microarrays according to the formula: vi  → (vi - µ) / σ. The identification of aberrant regions was performed with the analysis software Genomic Workbench Lite using the aberration algorithm ADM-2 in combination with a centralization algorithm. The analysis of the microarrays was performed by IMGM Laboratories (Martinsried, Germany).

source_name: genomic DNA isolated from blood samples

label_protocol: Restriction enzymatic digestion of 0.5 µg genomic DNA from the patient as well as from a sex-matched control was performed with a mixture of AluI and RsaI at 37°C for two hours. Sample labelling of the restriction-digested genomic DNA samples with Cy5-dUTP or Cy3-dUTP, respectively, was performed using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies).

extract_protocol: Total genomic DNA was extracted from blood samples after cell lysis, proteinase treatment and purification of the DNA by ethanol precipitation.

value: blood

source_name: human genomic DNA, female (#1521, Promega)


title: atypical NF1 deletion patient_9


title: Th17+IFNa_Donor1_Day5

description:
Th17 CD4 T cells + IFNa
IS08_ARN0011

source_name: Th17 CD4 T cells + IFNa


title: GCN2KO_Tconv.IL6.TGFβ.HF_4h#1


title: GCN2KO_Tconv.IL6.TGFβ.DMSO_72h#1

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 72 hours and treated with vehicle

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, vehicle-treated, 72 hour timepoint


title: GCN2KO_Tconv.IL6.TGFβ.HF_18h#1

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 18 hours and treated with 10 nM halofuginone

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, halofuginone-treated, 18 hour timepoint


title: GCN2KO_Tconv.IL6.TGFβ.DMSO_18h#2

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 18 hours and treated with vehicle

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, vehicle-treated, 18 hour timepoint


title: GCN2KO_Tconv.IL6.TGFβ.DMSO_72h#2


title: Th1_Donor2_Day5

description:
Th1 CD4 T cells
IS08_ARN0028

source_name: Th1 CD4 T cells


title: atypical NF1 deletion patient_12

source_name: human genomic DNA, male (#1471, Promega)


title: atypical NF1 deletion patient_7


title: GCN2KO_Tconv.IL6.TGFβ.HF_18h#2


title: atypical NF1 deletion patient_10


title: atypical NF1 deletion patient_11


title: atypical NF1 deletion patient_6


title: Th2_Donor1_Day5

description:
Th2 CD4 T cells
IS08_ARN0007

source_name: Th2 CD4 T cells


title: siSLU7_48H_rep3

city: Pamplona

first: Victor

last: Segura

state: Navarra

address: Avda. Pío XII, 55

department: Unit of Proteomics, Genomics and Bioinformatics

country: Spain

institute: FIMA

description:
siSlu73
Affymetrix GeneChip Human Exon 1.0 ST (HuEx-1_0-st-v2_core.cdf from aroma.affymetrix)

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuExon-1_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing:
The data were normalized with Bioconductor software using RMA algorithm.
probe group file: HuEx-1_0-st-v2.r2.pgf

source_name: PLC/PRF/5 cell line

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: PLC/PRF/5 cells were cultured in DMEM supplemented with 10%FCS.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: The siRNAs targeting human SLU7 gene (siSLU7) and the control siRNA (siGL) were from Sigma Chemical and have been previously described. Transfections were performed using Lipofectamine RNAiMAX transfection reagent (Invitrogen) following manufacturer’s instructions.

value: hepatocellular carcinoma cell line PLC/PRF/5

tag: genotype/variation

value: SLU7 knockdown


title: Th17_Donor1_Day5

description:
Th17 CD4 T cells
IS08_ARN0010

source_name: Th17 CD4 T cells


title: GCN2KO_Tconv.IL6.TGFβ.DMSO_18h#1


title: Th2+IFNa_Donor1_Day5

description:
Th2 CD4 T cells + IFNa
IS08_ARN0008


title: siSLU7_48H_rep2

description:
siSlu72
Affymetrix GeneChip Human Exon 1.0 ST (HuEx-1_0-st-v2_core.cdf from aroma.affymetrix)


title: Th1+IFNa_Donor1_Day5

description:
Th1 CD4 T cells + IFNa
IS08_ARN0005

source_name: Th1 CD4 T cells + IFNa


title: atypical NF1 deletion patient_5


title: Th1_D1_Day5

description:
Th1 CD4 T cells
IS08_ARN0004


title: siSLU7_48H_rep1

description:
siSlu71
Affymetrix GeneChip Human Exon 1.0 ST (HuEx-1_0-st-v2_core.cdf from aroma.affymetrix)


title: Th0+IFNa_Donor1_Day5

description:
Th0 CD4 T cells + IFNa
IS08_ARN0002

source_name: Th0 CD4 T cells + IFNa


title: WT_Tconv.IL6.TGFβ.Rapa_72h#2

description: Magnetically-isolated wild-type CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 72 hours and treated with 10 nM rapamycin

source_name: Wild-type CD4+CD25- T cells, Th17-polarized, rapamycin-treated, 72 hour timepoint


title: GCN2KO_Tconv.IL6.TGFβ.DMSO_4h#2

description: Magnetically-isolated Gcn2-/- CD4+ CD25- T cells cultured in presence of Th17-inducing cytokines for 4 hours and treated with vehicle

source_name: Gcn2-/- CD4+CD25- T cells, Th17-polarized, vehicle-treated, 4 hour timepoint


title: GCN2KO_Tconv.IL6.TGFβ.DMSO_4h#1


title: atypical NF1 deletion patient_2


title: CONTROL_48H_rep2

description:
siGL2
Affymetrix GeneChip Human Exon 1.0 ST (HuEx-1_0-st-v2_core.cdf from aroma.affymetrix)

value: control


title: Th0_Donor1_day5

description:
Th0 CD4 T cells
IS08_ARN0001

source_name: Th0 CD4 T cells

extract_protocol: RNA was extracted using Rneasy Microquit (Qiagen).  For each condition, 500pg of RNA were used to synthesize targets using the WT-Ovation™ Pico RNA amplification system (Nugen, Bemmel,The Netherlands)..For each condition, 500pg of RNA were used to synthesize targets using the WT-Ovation™ Pico RNA amplification system (Nugen, Bemmel,The Netherlands).


title: atypical NF1 deletion patient_1


title: atypical NF1 deletion patient_3


title: CONTROL_48H_rep1

description:
siGL1
Affymetrix GeneChip Human Exon 1.0 ST (HuEx-1_0-st-v2_core.cdf from aroma.affymetrix)


title: atypical NF1 deletion patient_4


title: Replication timing of TS cells, replicate 2 (TSC 3)

hyb_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing one oligonucleotide probe every 3.5 kb across the entire mouse genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: NimbleScan software was used to obtain .pair raw data per manufacturer's instructions. Raw early/late data (i.e. from .pair files) from three independent biological replicates in which early and late replicating DNA were labeled were loess-normalized to remove signal intensity-dependent bias, scaled to a reference data set to have the same median absolute deviation and averaged (limma package, R/Bioconductor).The mean early/late ratios were used to generate a smoothed profile (i.e. processed data) using local polynomial smoothing (loess, 300-kb span) for each chromosome using basic functions in the statistical language R. Processed data sets can be graphically displayed (and are also downloadable) on our web site (http://www.replicationdomain.org). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

source_name: Early-replicating DNA of TSCs

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

growth_protocol: Mouse TSCs were obtained from Dr. Janet Rossant, Hospital for Sick Children, (Toronto, Canada) and maintained in DMEM/F12 with 15 mM Hepes, 20% FBS, 2 mM glutamine, 100 ug/ml streptomycin, 1 mM sodium pyruvate, 100 uM BME, supplemented with Activin, FGF4, and Heparin following (Erlebacher et al, Developmental Biology 2004).  Trophoblast stem cells were differentiated into trophoblast giant cells by replacing the FGF, Activin and Heparin in the media with retinoic acid (Yan et al., 2001; Erlebacher et al., 2004).  Mature TGCs are seen after 4-6 days of differentiation (Carney et al., 1993).  Cells were trypsinized for 4 minutes before the extract protocol.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as described in Hiratani et al [PLoS Biology (2008) 6: e245]. Briefly, replication intermediates are prepared from cells that are first pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245].

value: Early-replicating DNA of TSCs

source_name: Late-replicating DNA of TSCs

value: Late-replicating DNA of TSCs


title: CONTROL_48H_rep3

description:
siGL3
Affymetrix GeneChip Human Exon 1.0 ST (HuEx-1_0-st-v2_core.cdf from aroma.affymetrix)


title: Myanmar10

status: Public on May 28 2014

city: Baltiomore

first: Christopher

last: Jacob

state: MD

address: 685 W. Baltimore St.

department: Center for Vaccine Development

institute: University of Maryland School of Medicine

hyb_protocol: described in Jacob et al, 2014

scan_protocol: Arrays were scanned on a NimbleGen MS 200 scanner using autogain setting per manufacturer's protocol (www.NimbleGen.com)

data_processing: data were processed by both a previously published method (PMCID: PMC3218861), and by a custom algorithm (Jacob et al, 2014, Submitted)

organism: Plasmodium falciparum

source_name: clincal isolate

label_protocol: described in Jacob et al, 2014

extract_protocol: all samples were extracted using a Qiagen blood extraction mini prep (qiagen.com)

tag: country

value: Myanmar


title: Replication timing of TS cells, replicate 3 (TSC 4)


title: Myanmar8


title: Myanmar7


title: Replication timing of TS cells, replicate 1 (TSC 2b)


title: Myanmar3


title: Myanmar5


title: Myanmar9


title: Bangladesh140

value: Bangladesh


title: Myanmar6


title: Bangladesh139


title: Bangladesh142


title: Bangladesh146


title: Myanmar4


title: Bangladesh147


title: Myanmar2


title: Bangladesh138


title: Myanmar12


title: Myanmar11


title: Bangladesh145


title: Myanmar1


title: Bangladesh144


title: Bangladesh143


title: Bangladesh135


title: Bangladesh137


title: Bangladesh134


title: Bangladesh141


title: Bangladesh129


title: Bangladesh128


title: Bangladesh127