title: THP1 human monocyte cell line treated with GA/RS for 24HRs AFFY_CEL_6803f7cbce2.CEL


title: P2_M8

status: Public on May 22 2015

type: RNA

city: Dallas

first: Jason

middle: A

last: Skinner

state: TX

address: 3434 Live Oak

country: USA

institute: Baylor Institute for Immunology Research

description:
6116733017_F
Baseline
Total RNA (globin reduced)

hyb_protocol: Standard Illumina HT-12 V4 hybridization protocol.

scan_protocol: Standard Illumina iScan protocol.

data_processing: We first applied a normal-exponential convolution model (Xie et al., Bioinformatics, 2009; Shi et al., Nucleic Acids Research, 2010) to correct for the background noise.  An offset of 16 (the default value) was then added to the data (to improve precision and avoid a compression of the fold changes) before they were log2 transformed (to stabilize the variance). Finally, a quantile-quantile normalization was performed. The ComBat method (Johnson et al., Biostatistics, 2007) was used on those normalized data to correct for batch effects (namely a small hybridization chamber effect that was identified through Principal Variance Component Analysis - Li et al., chap. 12, Batch Effects and Noise in Microarray Experiments: Sources and Solutions, Wiley, 2009). At last, only probes which pval detection (provided by Genome Studio) was below 0.01 in at least one sample were kept for analysis.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood, P2, week -8

label_protocol: Biotinylated cRNA were prepared using Illumina Totalprep-96 Amplification Kits with 250ng input.

extract_protocol: RNA was extracted from Applied Biosystems Tempus Blood RNA Tubes using the Ambion MagMax-96 total RNA Isolation kits. Globin message reduction was conducted using Ambion GlobinClear Human 96 Kits.

tag: patient

tag: week

tag: dataset

value: treatment

tag: tissue

value: whole blood


title: THP1 human monocyte cell line treated with Probioglat for 12HRs AFFY_CEL_6804343a60d.CEL

city: Natanya

first: Tal

middle: Haim

last: Hasson

address: Hatrufa 12

department: Analytical R&D

country: Israel

institute: Teva Pharmaceuticals

hyb_protocol: This cDNA was purified and used as a template for in vitro transcription using T7 RNA polymerase and biotinylated ribonucleotides. The resulting cRNA was purified using magnetic beads and quantified using spectrophotometry. Purified cRNA was fragmented using a 5X Fragmentation buffer, then hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 arrays.

scan_protocol: standard Affymetrix procedures

data_processing: Data was normalized using RMA from Bioconductor's AFFY package. The normalize matrix was then batch corrected using COMBAT. The processing batch characteristic was utilized as the batch and the timepoint and treatment_by_lot characteristics were utilized as covariates during the batch-correction step

source_name: THP-1 human monocyte cell line

label_protocol: All specimens were amplified and labeled using the Enzo BioArray Single-Round RNA amplification and Biotin labeling system.

growth_protocol: THP-1 cells are routinely cultivated according to the ATCC recommendations. The cells are split up and fed with fresh culture medium 24 – 48 hours before each test. The usual cell split ratio is 1.5-2 (depending on the metabolic and reproducing activity of the cells)

extract_protocol: Total RNA was isolated from the Qiagen miRNEasy Kit according to the manufacturer’s instructions.

treatment_protocol: In-vitro assay is performed in a 6-well, flat-bottomed cell culture sterile test plates. Each treatment at each time point was replicated 6 times to ensure robustness of the result. 1mL from the prepared 100 microgram/mL treated glatiramoid (or 200 microgram/mL mannitol control) activation solution were transferred into the THP-1 6-well plate. The 6-well plate was then plated in a humidified 37°C, 5% CO2 incubator. Incubation was conducted for 6, 12 or 24 hours. The final treatment concentration is 50 ug/mL for drug and 100ug/mL for placebo

tag: processing batch

tag: timepoint

tag: treatment

value: Probioglat

tag: cell line


title: THP1 human monocyte cell line treated with GA/RS for 6HRs AFFY_CEL_6802d944f9d.CEL

value: GA/RS


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 12HRs AFFY_CEL_680de7ca40.CEL

value: Other glatiramoid


title: P8_16

description:
6116733015_B
APH2
Total RNA (globin reduced)

source_name: whole blood, P8, week 16


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 12HRs AFFY_CEL_68061a92558.CEL


title: P10_16

description:
6116733015_F
APH2
Total RNA (globin reduced)

source_name: whole blood, P10, week 16


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_6804c69695e.CEL

value: Copaxone


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 6HRs AFFY_CEL_680284a79ab.CEL


title: P8_4

description:
6116733017_C
DC2
Total RNA (globin reduced)

source_name: whole blood, P8, week 4


title: P1_22, pre-ATI

description:
6116733017_E
W22 (Treatment Baseline)
Total RNA (globin reduced)

source_name: whole blood, P1, week 22

value: follow-up and treatment


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_68067a0ce93.CEL


title: P18_0

description:
6116733017_K
DC1
Total RNA (globin reduced)

source_name: whole blood, P18, week 0


title: P19_8

description:
6116733013_F
DC3
Total RNA (globin reduced)

source_name: whole blood, P19, week 8


title: P17_M8

description:
6116733014_J
Baseline
Total RNA (globin reduced)

source_name: whole blood, P17, week -8


title: P14_16

description:
6116733015_L
APH2
Total RNA (globin reduced)

source_name: whole blood, P14, week 16


title: P14_12

description:
6116733014_C
DC4
Total RNA (globin reduced)

source_name: whole blood, P14, week 12


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 6HRs AFFY_CEL_68066000d07.CEL


title: P13_12

description:
6116733013_G
DC4
Total RNA (globin reduced)

source_name: whole blood, P13, week 12


title: P14_4

description:
6116733015_H
DC2
Total RNA (globin reduced)

source_name: whole blood, P14, week 4


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 24HRs AFFY_CEL_68012ae5dd9.CEL


title: THP1 human monocyte cell line treated with GA/RS for 6HRs AFFY_CEL_6804562bf08.CEL


title: P11_22, pre-ATI

description:
6116733011_K
W22 (Treatment Baseline)
Total RNA (globin reduced)

source_name: whole blood, P11, week 22


title: P11_0

description:
6116733014_A
DC1
Total RNA (globin reduced)

source_name: whole blood, P11, week 0


title: P9_0

description:
6116733013_H
DC1
Total RNA (globin reduced)

source_name: whole blood, P9, week 0


title: P19_0

description:
6116733013_A
DC1
Total RNA (globin reduced)

source_name: whole blood, P19, week 0


title: P7_4

description:
6116733013_E
DC2
Total RNA (globin reduced)

source_name: whole blood, P7, week 4


title: P9_12

description:
6116733011_L
DC4
Total RNA (globin reduced)

source_name: whole blood, P9, week 12


title: P15_4

description:
6116733014_D
DC2
Total RNA (globin reduced)

source_name: whole blood, P15, week 4


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 12HRs AFFY_CEL_680786c9f8.CEL

source_name: THP-1 human monocyte cell line


title: P11_12

description:
6116733014_G
DC4
Total RNA (globin reduced)

source_name: whole blood, P11, week 12


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 12HRs AFFY_CEL_680754e1ac7.CEL


title: P16_4

description:
6116733011_J
DC2
Total RNA (globin reduced)

source_name: whole blood, P16, week 4


title: P5_0

description:
6116733011_D
DC1
Total RNA (globin reduced)

source_name: whole blood, P5, week 0


title: P16_M4

description:
6116733008_K
APH1
Total RNA (globin reduced)

source_name: whole blood, P16, week -4


title: P14_M8

description:
6116733008_E
Baseline
Total RNA (globin reduced)

source_name: whole blood, P14, week -8


title: THP1 human monocyte cell line treated with Probioglat for 24HRs AFFY_CEL_68055c38d0.CEL


title: P14_M4

description:
6116733008_I
APH1
Total RNA (globin reduced)

source_name: whole blood, P14, week -4


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 12HRs AFFY_CEL_6803ded28fe.CEL


title: P3_8

description:
6116733011_H
DC3
Total RNA (globin reduced)

source_name: whole blood, P3, week 8


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_680446b25ff.CEL


title: P4_M8

description:
6116733006_H
Baseline
Total RNA (globin reduced)

source_name: whole blood, P4, week -8


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 24HRs AFFY_CEL_68018f03edf.CEL


title: P13_0

description:
6116733006_C
DC1
Total RNA (globin reduced)

source_name: whole blood, P13, week 0


title: P8_M4

description:
6116733008_G
APH1
Total RNA (globin reduced)

source_name: whole blood, P8, week -4


title: P17_4

description:
6116733008_L
DC2
Total RNA (globin reduced)

source_name: whole blood, P17, week 4


title: P5_22, pre-ATI

description:
6116733006_E
W22 (Treatment Baseline)
Total RNA (globin reduced)

source_name: whole blood, P5, week 22


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_680538d7fd7.CEL


title: P8_8

description:
6116733005_H
DC3
Total RNA (globin reduced)

source_name: whole blood, P8, week 8


title: P7_12

description:
6116733006_A
DC4
Total RNA (globin reduced)

source_name: whole blood, P7, week 12


title: P1_8

description:
6116733005_K
DC3
Total RNA (globin reduced)

source_name: whole blood, P1, week 8


title: THP1 human monocyte cell line treated with Mannitol for 24HRs AFFY_CEL_6807cf47fe2.CEL

value: Mannitol


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_68024085a04.CEL


title: P16_8

description:
6116733006_F
DC3
Total RNA (globin reduced)

source_name: whole blood, P16, week 8


title: P7_M4

description:
6116733005_E
APH1
Total RNA (globin reduced)

source_name: whole blood, P7, week -4


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_68069da9ad8.CEL

source_name: THP-1 human monocyte cell line


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_6809b928ce.CEL


title: P5_12

description:
6116733006_D
DC4
Total RNA (globin reduced)

source_name: whole blood, P5, week 12


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 24HRs AFFY_CEL_6804c06613c.CEL


title: NACMIRNA-36-CNTRL

city: Richmond

first: Vladimir

last: Vladimirov

state: VA

address: 800 E Leigh ST

department: Psychiatry

institute: Virginia Commonwealth University

hyb_protocol: Each labeled sample was hybridized onto a GeneChip® miRNA 3.0 Array.

scan_protocol: Each array was scanned on the Affymetrix GeneChip® Scanner 3000 7G (Affymetrix) and raw probe intensities stored in .CEL files by the GeneChip® Operating Software (GCOS v1.4).

data_processing: Array quality was assessed by monitoring the 3′/5′ ratios of GAPDH and by the percentage of “Present” genes (%P) and array exhibiting GAPDH 3′/5′ < 3.0 and %P > 40% were considered of good quality. Expression values were calculated following the pre-processing procedure: 1) GCRMA background correction, 2) log2 transformation, 3) quantile normalization and 4) median-polish probeset summarization using Partek Genomics Suite (PGS) v6.23 (PGS; Partek Inc., St. Louis, MO). The batch effect removal option in PGS was used to control for batch effect. mRNA and miRNA microarray quality was further assessed using a principal components analysis (PCA) which was conducted on the expression values for both array types in which samples were plotted along the first three principle components (PCs) to identify potential microarray outliers.

source_name: Nucleus Accumbens

label_protocol: Total RNA (500ng) from each specimen was labeled using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix). Each RNA sample was spiked with 5 different oligonucleotides as positive endogenous controls to assess the efficiency of the labeling reaction. The RNA samples were subjected to a brief Poly(A) tailing reaction followed by ligation of a biotinylated signal molecule.

growth_protocol: none used

extract_protocol: Total RNA containing the small RNA fraction was isolated from 100mg fresh frozen tissue from the nucleus accumbens (NAc) using the mirVana-PARIS kit (Life Technologies, Carlsbad, CA) following manufacturer's protocols. RNA concentration was measured using the Quant-iT Broad Range RNA Assay kit (Life Technologies) and the RNA Integrity Number (RIN) was measured on the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).

treatment_protocol: none used

tag: diagnosis

value: Control

tag: tissue type

value: post mortem brain


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_680395e864d.CEL


title: P6_12

description:
6116733005_A
DC4
Total RNA (globin reduced)

source_name: whole blood, P6, week 12


title: P11_8

description:
6116733004_C
DC3
Total RNA (globin reduced)

source_name: whole blood, P11, week 8


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 6HRs AFFY_CEL_68073207cbc.CEL


title: NACMIRNA-34-CNTRL


title: P6_22, pre-ATI

description:
6116733004_B
W22 (Treatment Baseline)
Total RNA (globin reduced)

source_name: whole blood, P6, week 22


title: P13_M4

description:
6116733005_G
APH1
Total RNA (globin reduced)

source_name: whole blood, P13, week -4


title: NACMIRNA-35-AD

value: alcohol dependence (AD)


title: P9_4

description:
6116733004_D
DC2
Total RNA (globin reduced)

source_name: whole blood, P9, week 4


title: NACMIRNA-33-AD


title: NACMRNA-33-AD

hyb_protocol: Ten µg of fragmented cRNA were hybridized on the Affymetrix GeneChip® Human Genome U133A 2.0 (HG-U133A 2.0).

label_protocol: Starting from 300ng of total RNA, cDNA synthesis and cRNA labelling were performed using the GeneChip® 3' IVT Express Kit (Affymetrix).


title: NACMRNA-35-AD


title: NACMRNA-36-CNTRL


title: NACMRNA-32-CNTRL


title: NACMRNA-31-AD


title: NACMRNA-34-CNTRL


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_680392ab2da.CEL


title: NACMIRNA-31-AD


title: NACMIRNA-32-CNTRL


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_68074bf8cda.CEL


title: NACMRNA-30-CNTRL


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_6807dbe1025.CEL


title: NACMRNA-28-CNTRL


title: NACMIRNA-30-CNTRL


title: NACMRNA-26-CNTRL


title: THP1 human monocyte cell line treated with Mannitol for 6HRs AFFY_CEL_68014cd0b87.CEL


title: NACMRNA-27-AD


title: THP1 human monocyte cell line treated with Probioglat for 6HRs AFFY_CEL_6805e51b6f3.CEL


title: NACMRNA-25-AD


title: NACMRNA-29-AD


title: NACMIRNA-28-CNTRL


title: NACMRNA-24-CNTRL


title: NACMIRNA-29-AD


title: NACMRNA-23-AD


title: NACMIRNA-27-AD


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_680429cc0e.CEL


title: NACMIRNA-25-AD


title: THP1 human monocyte cell line treated with Probioglat for 6HRs AFFY_CEL_68023d5dee8.CEL


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_6801c453e43.CEL


title: NACMRNA-21-AD


title: NACMRNA-20-CNTRL


title: NACMRNA-22-CNTRL


title: NACMIRNA-24-CNTRL


title: NACMRNA-15-AD


title: NACMRNA-16-CNTRL


title: NACMRNA-17-AD


title: NACMRNA-13-AD


title: NACMIRNA-26-CNTRL


title: THP1 human monocyte cell line treated with Mannitol for 24HRs AFFY_CEL_68048850b38.CEL


title: NACMRNA-11-AD


title: NACMRNA-9-AD


title: NACMRNA-10-CNTRL


title: NACMRNA-8-CNTRL


title: NACMRNA-12-CNTRL


title: NACMIRNA-20-CNTRL


title: NACMIRNA-21-AD


title: NACMRNA-14-CNTRL


title: NACMRNA-18-CNTRL


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_68026d80920.CEL


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 24HRs AFFY_CEL_68070cb4e8d.CEL


title: THP1 human monocyte cell line treated with Mannitol for 24HRs AFFY_CEL_6802a1252d8.CEL


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 12HRs AFFY_CEL_6807ab62a0e.CEL


title: NACMIRNA-22-CNTRL


title: NACMIRNA-23-AD


title: NACMRNA-19-AD


title: NACMRNA-7-AD


title: NACMIRNA-19-AD


title: NACMRNA-5-AD


title: NACMRNA-6-CNTRL


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_6806b99b2c3.CEL


title: NACMIRNA-18-CNTRL


title: NACMRNA-4-CNTRL


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 6HRs AFFY_CEL_68042883cff.CEL


title: NACMIRNA-16-CNTRL


title: NACMIRNA-17-AD


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_6801a4f3136.CEL


title: THP1 human monocyte cell line treated with Other_glatiramoid_2 for 12HRs AFFY_CEL_68066428bd.CEL


title: NACMRNA-2-CNTRL


title: NACMIRNA-15-AD


title: NACMIRNA-12-CNTRL


title: NACMRNA-1-AD


title: NACMIRNA-13-AD


title: NACMIRNA-14-CNTRL


title: THP1 human monocyte cell line treated with Probioglat for 24HRs AFFY_CEL_68046263c61.CEL


title: THP1 human monocyte cell line treated with Mannitol for 6HRs AFFY_CEL_68018243241.CEL


title: Relative gene expressions in Flk1+PDGFRα+CAR+ cells to Flk1+PDGFRα-CAR- cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: normalized log2 ratio (Flk1+PDGFRα+CAR+ / Flk1+PDGFRα-CAR-)

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

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

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

organism: Mus musculus

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

growth_protocol: ES cells were plated onto a round-bottom Lipidure-coated 96-well plate in differentiation medium (DMEM supplemented with 15% FCS, non-essential amino acids, 2 mM L-glutamine , 100 uM 2-mercaptoethanol and penisillin/streptomycin) to form embryoiod bodies, and were cultured for 7 days.

extract_protocol: Total RNA was extracted from each cell using ISOGEN (Nippon Gene) or RNAiso plus (TAKARA).

treatment_protocol: Single cell suspensions were prepared from 7-days-cultured embryioid bodies with 0.25% trypsin-EDTA, and were stained with anti-Flk1, anti-PDGFRa and anti-CAR antibodies. F+Pα-C-, F+Pα-C+ and F+Pα+C+ cells were sorted using FACSAria.

tag: cell type

value: ES cells

tag: strain

tag: sample type

value: 7 days-cultured EBs

tag: population


title: THP1 human monocyte cell line treated with GA/RS for 12HRs AFFY_CEL_6804ddbdac5.CEL


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 6HRs AFFY_CEL_68049170d0d.CEL


title: NACMIRNA-11-AD


title: Relative gene expressions in Flk1+PDGFRα-CAR+ cells to Flk1+PDGFRα+CAR+ cells

description: normalized log2 ratio (Flk1+PDGFRα-CAR+ / Flk1+PDGFRα+CAR+)


title: siGL3_vs_siAGO1

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: Equal amounts of differentially labeled specimens from siAGO1_PC3 cell line and siGL3_PC3 cell line were put together, fragmented and hybridized to oligonucleotide glass arrays representing 19,596 Entrez Gene RNAs (Whole Human Genome Microarray, 4x44K, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the Agilent wash procedure. For each sample, a dye-swap replicate was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B.

data_processing: Images were analyzed using Feature Extraction software (Agilent Technologies) version 9.5. Raw data elaboration was carried out with Bioconductor (Gentleman et al., 2004), using R statistical language. Background correction was performed with the normexp method with an offset of 50, loess was used for the within array normalization and Aquantile for between-array normalization. The limma package was used to identify differentially expressed genes. The empirical Bayes method was used to compute a moderated t-statistics.

label_protocol: mRNA was amplified and labeled by means of Quick Amp Labeling Kit (Agilent Technologies) which simultaneously amplifies target material and incorporates cyanine 3/5-labeled CTP. Briefly: mRNA was reverse transcribed in cDNA and then in vitro transcribed in cRNA including cyanine 3/5-labeled CTP. cRNA underwent a purification step using RNeasy Mini Kit (Qiagen). mRNA quantity and labeling efficiency were checked by means of NanoDrop 1000 Spectrophotometer (Thermo Scientific).

growth_protocol: PC3 cells were maintained under standard conditions in RPMI medium with 10% FBS. Cells were plated in 6-well plates at a density of 40’000 cells/well 24 hours prior transfection.

extract_protocol: Total RNA was extracted from cell lines using SV Total RNA Isolation System (Promega) 72 hours following the transfection with a scramble siRNA (siGL3) and a siRNA targeting Ago1(siAgo1); totRNA quality and quantity were checked by means of RNA 6000 nano chip assays (Agilent Technologies) and NanoDrop 1000 Spectrophotometer (Thermo Scientific), respectively.

treatment_protocol: Cell were transfected with siRNAs (20 nM) using Interferin (Polyplus) in serum-free OPTIMEM medium. Cells were harvested after 72 hours to extract RNA. These conditions ensured effective knockdown of the target as indicated by previous studies.

value: PC3 metastatic prostate cancer cell line

value: PC3 cells 72 hours following the transfection with a scramble siRNA (siGL3)

tag: genotype/variation

value: control

value: PC3 cells 72 hours following the transfection with a siRNA targeting Ago1(siAgo1)

value: Ago1 knockdown


title: NACMRNA-3-AD


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_6805e4c353f.CEL


title: NACMIRNA-9-AD


title: NACMIRNA-6-CNTRL


title: NACMIRNA-8-CNTRL


title: siAGO1_vs_siGL3

value: PC3 cells 72 hours following the transfection with a siRNA targeting Ago1 (siAgo1)


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_6806b768f65.CEL


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_6807f9cf7de.CEL


title: NACMIRNA-7-AD


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 24HRs AFFY_CEL_680574c9f7e.CEL


title: Relative gene expressions in Flk1+PDGFRα-CAR+ cells to Flk1+PDGFRα-CAR- cells

description: normalized log2 ratio (Flk1+PDGFRα-CAR+ / Flk1+PDGFRα-CAR-)


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_68056b579a4.CEL


title: NACMIRNA-5-AD


title: NACMIRNA-4-CNTRL


title: NACMIRNA-10-CNTRL


title: NACMIRNA-2-CNTRL


title: NACMIRNA-3-AD


title: NACMIRNA-1-AD


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 24HRs AFFY_CEL_68031e6a2f.CEL


title: THP1 human monocyte cell line treated with GA/RS for 6HRs AFFY_CEL_680109d6849.CEL


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_6806bf0d768.CEL


title: THP1 human monocyte cell line treated with GA/RS for 24HRs AFFY_CEL_6801237c219.CEL


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_6805f30bd42.CEL


title: THP1 human monocyte cell line treated with Probioglat for 6HRs AFFY_CEL_680281271c9.CEL

value: Probioglat


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 6HRs AFFY_CEL_680376cc840.CEL


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_6803f5654e8.CEL


title: THP1 human monocyte cell line treated with Other_glatiramoid_1 for 24HRs AFFY_CEL_6801dc4d8d2.CEL


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_68066dbe5df.CEL


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_680124b55b7.CEL


title: THP1 human monocyte cell line treated with Copaxone for 12HRs AFFY_CEL_6805e86d929.CEL


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_68044a02ada.CEL


title: THP1 human monocyte cell line treated with Mannitol for 12HRs AFFY_CEL_6802c08e185.CEL


title: ESC-derived neural precursors, replicate B

status: Public on May 21 2015

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

hyb_protocol: Biotinylated cRNA was hybridized onto GeneChip® HG-U133 Plus 2.0 Arrays according to the protocol supplied by the manufacturer (Affymetrix)

scan_protocol: standard Affymetrix protocol

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: ESC-derived neural precursors

label_protocol: cRNA was biotinilated by IVT labeling kit standard protocol (Affymetrix)

growth_protocol: ESCs were maintained on irradiated mouse embryonic fibroblasts (MEFs) at 5% CO2 in Knockout-DMEM (Invitrogen), containing 20% FCS, 1% non-essential amino acids, 1 mM glutamine, 0.1mM ß-mercaptoethanol and 10 ng/mL FGF2 (Invitrogen). NESCs were grown in DMEM/F12 with 20 μg/mL insulin (Sigma–Aldrich), 1.6 g/L glucose, 10 ng/mL FGF2 (R&D Systems), 10 ng/mL EGF (R&D Systems), and 1 μl/ml B27 supplement (Invitrogen)

extract_protocol: total RNA was extracted by RNeasy Mini Kit (QIAGEN) standard protocol and DNAse treated by RNase-Free DNase Set (QIAGEN)

value: ESC-derived neural precursors


title: Human embryonic stem cells (H9), replicate C

source_name: Human embryonic stem cells (H9)

value: Human embryonic stem cells (H9)


title: Human embryonic stem cells (H9), replicate B


title: Human embryonic stem cells (H9), replicate A


title: PD12_pre, rep2

city: London

first: Lilach

last: Soreq

address: Queen Square

department: Molecular  Neuroscience

country: United Kingdom

institute: UCL

description:
J97=J69_pd12S1.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.

hyb_protocol: HJAY profiling of blood leukocytes conducted using exon array pre- prepared hybridization samples using the GeneChip Whole Transcript Sense Target Labeling assay kit (Affymetrix), as per manufacturer's instructions.

scan_protocol: The microarrays were scanned on an Affymetrix GeneChip Scanner 3000 7G scanner, according to the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay protocol.

data_processing:
Affymetrix Power Tools (APT version-1.10.1 ) using the RMA algorithm.

Probe group file: HJAY_r2.pgf

source_name: Blood leukocytes, PD patient, pre-DBS

label_protocol: HJAY profiling of blood leukocytes conducted using exon array pre- prepared labeled samples using the GeneChip Whole Transcript Sense Target Labeling assay kit (Affymetrix), as per manufacturer's instructions.

extract_protocol: RNA extraction conducted from LeukoLock filters (Ambion, Applied Biosystems, Inc., Foster City, CA) following de-freezing. The extraction followed the manufacturers' alternative protocol instructions. Briefly, cells were flushed (TRI-ReagentTM, Ambion) into 1-bromo-3-chloropropane-containing 15ml tubes and centrifuged. 0.5 and 1.25 volume water and ethanol were added to the aqueous phase. Samples were filtered through spin cartridges, and stored in pre-heated 150 µl EDTA. RNA was quantified and examined on Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and frozen in -80⁰C.

value: blood leukocytes

tag: gender

value: male

tag: disease status

value: Parkinson’s disease (PD)

tag: treatment stage

value: pre-DBS

tag: individual identifier


title: Control patient 46

city: Warsaw

first: Monika

last: Gora

address: Pawinskiego 5A

department: Genetics

country: Poland

institute: Institute of Biochemistry and Biophysics

hyb_protocol: Following fragmentation, 5.5 ug ssDNA were hybridized for 16 hr at 45˚C on GeneChip® Human Gene 1.0 ST Array according to standard Affymetrix protocol. Chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GCS 3000 GeneArray Scanner.

data_processing: The data were analyzed with the Partek Genomics Suite software (Partek Inc, St. Louis, MO, USA) using RMA (robust multiarray average) background correction, quantile normalization, median polish method for probesets summarization, and log values of probes signals using base 2.

source_name: peripheral blood mononuclear cells

label_protocol: Biotin-labeled ssDNA were prepared from 100 ng total RNA by using the Ambion® WT Expression Kit followed by Affymetrix® GeneChip® WT Terminal Labeling Kit according to the manufacturer's instruction.

extract_protocol: Total RNA from peripheral blood mononuclear cells (PBMCs) samples was isolated using MagNA Pure Compact System (Roche Diagnostics GmbH, Germany) according to the manufacturer's recommendations. The amount of RNA was quantified by UV absorption (Nanodrop, LabTech International, UK) and its quality was determined using an Agilent 2100 Bioanalizer© and RNA 6000 Nano Kit (Agilent, Santa Clara, CA, USA). For all RNA samples the RNA integrity number value was above eight.

value: PBMC

tag: samples collection

tag: hf progression

value: stable CAD


title: THP1 human monocyte cell line treated with Copaxone for 6HRs AFFY_CEL_6805a3d24a3.CEL

tag: processing batch

value: Copaxone


title: CCR6 ILC3 4

city: New York

first: Gregory

middle: F

last: Sonnenberg

state: NY

address: 413 East 69th Street, Belfer Research Building 512

institute: Weill Cornell Medical College

description: Array was performed at the University of Pennsylvania Microarray core

data_processing: RMA

source_name: mesenteric lymph node

extract_protocol: Lymph nodes were mechanically disrupted in a cell strainer, cells were sort purified into Trizol.

tag: tissue

value: mesenteric lymph node

value: CCR6+ innate lymphoid cells

tag: cell markers


title: ESC-derived neural precursors, replicate A


title: Control patient 45


title: PD12_pre

description:
J97=J69_pd12S1_restain.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.


title: PD8_pre

description:
J95=H89_pd8S1.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.


title: HC2

source_name: Blood leukocytes, healthy control volunteer

value: healthy


title: PD8_post

description:
J96=J44_pd8S2.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.

source_name: Blood leukocytes, PD patient, post-DBS on electrical stimulation

value: post-DBS


title: CCR6 ILC3 3

hyb_protocol: Array was performed at the University of Pennsylvania Microarray core


title: Control patient 42


title: Control patient 43


title: THP1 human monocyte cell line treated with Copaxone for 24HRs AFFY_CEL_680579e9c70.CEL

tag: timepoint

tag: treatment

tag: cell line


title: HC1

tag: cell type


title: Control patient 41


title: Control patient 40


title: Control patient 38


title: Control patient 39


title: PD1_post

description:
J06=H55_pd1S2.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.


title: PD7_pre

description:
J05=H90_pd7S1.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.


title: PD7_post

description:
J04=H91_pd7S2.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.


title: Control patient 37


title: ESC-derived neural precursors, replicate C


title: HC3


title: Control patient 44


title: Control patient 35


title: Control patient 30


title: Control patient 31


title: PD1_pre

description:
J03=G97_pd1S1.CEL
DBS: deep brain stimulation neurosurgery conducted to target the subthalamic nucleous (STN) brain region.


title: Control patient 32


title: Control patient 28


title: Control patient 36


title: Control patient 26


title: Control patient 24


title: Control patient 25


title: Control patient 27


title: Control patient 23


title: Control patient 34


title: Control patient 29


title: Control patient 21


title: Control patient 20


title: Control patient 22


title: Control patient 18


title: Control patient 19


title: Control patient 17


title: Control patient 16


title: Control patient 12


title: Control patient 13


title: Control patient 11


title: Control patient 8


title: Control patient 14


title: Control patient 10


title: Control patient 7


title: Control patient 15


title: Control patient 9


title: Brain tumor 6752625107_R05C01

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

description:
Methylation data from ependymal tumor sample.
Location: 1: infratentorial; 2: spinal; 3: supratentorial.

hyb_protocol: Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Data analysis was performed using the open source statistical programming language R (R Core Team, 2014; http://www.R-project.org/). Raw data files generated by the iScan array scanner were read and preprocessed using the capabilities of the Bioconductor (Version 2.9) package minfi (Version 1.12; Aryee et al., 2014 (PMID 24478339)). With the minfi package using function 'preprocessIllumina', the same preprocessing steps, i.e., background subtraction and normalization using control probes, as in Illumina's GenomeStudio software were performed.

label: biotin/DNP

molecule: genomic DNA

source_name: brain tumor, PF-EPN-B

label_protocol: Illumina protocol.

extract_protocol: Extraction of high molecular weight DNA from frozen tumor samples was carried out by use of a salting-out method or by ultracentrifugation over cesium chloride. DNA was isolated from formalin-fixed and paraffin-embedded (FFPE)  tissue using the blackPREP FFPE DNA Kit (Analytik Jena, Jena, Germany) according to the manufacturer's instructions.

value: ependymal tumor

tag: tumor type

value: relapse

tag: molecular subtype

value: PF-EPN-B

tag: material

value: frozen

tag: location

tag: who grade


title: Brain tumor 9403904109_R06C02

source_name: brain tumor, PF-EPN-A

value: PF-EPN-A


title: Brain tumor 9403904109_R04C02

value: primary


title: Brain tumor 6026818094_R06C02

source_name: brain tumor, ST-EPN-RELA

value: ST-EPN-RELA


title: Control patient 5


title: Control patient 6


title: Brain tumor 9403904109_R03C01

value: relapse 2


title: Brain tumor 9403904109_R05C01


title: Control patient 4


title: Brain tumor 9403904071_R04C02


title: Control patient 1


title: Control patient 3


title: Brain tumor 9403904111_R04C01


title: Patient 111Z,sampling 3

value: 1 month after MI


title: Patient 110Z,sampling 3


title: Patient 110Z,sampling 4

value: 6 months after MI


title: Patient 111Z,sampling 1

value: PBMC

value: on the 1st day of MI (admission)


title: Brain tumor 9403904071_R02C01

source_name: brain tumor, PF-SE

value: PF-SE


title: Patient 110Z,sampling 1


title: Patient 109Z,sampling 4

value: HF


title: Patient 110Z,sampling 2

value: after 4-6 days of MI (discharge)


title: Patient 109Z,sampling 2


title: Patient 109Z,sampling 3


title: Patient 108Z,sampling 4


title: Control patient 33

value: stable CAD


title: Brain tumor 9403904111_R02C01


title: Patient 111Z,sampling 2


title: Patient 109Z,sampling 1


title: Control patient 2


title: Patient 108Z,sampling 2


title: Patient 108Z,sampling 1


title: Patient 108Z,sampling 3


title: Patient 107Z,sampling 3


title: Brain tumor 9403904071_R04C01


title: Brain tumor 9403904125_R03C01


title: Patient 107Z,sampling 4


title: Brain tumor 9403904125_R03C02


title: Brain tumor 9403904125_R01C02


title: Brain tumor 9403904111_R05C02


title: Brain tumor 9403904109_R03C02


title: Brain tumor 9403904125_R05C02


title: Patient 107Z,sampling 2


title: Brain tumor 9403904071_R02C02


title: Brain tumor 9403904111_R03C02


title: Patient 107Z,sampling 1


title: Brain tumor 9403904125_R05C01


title: Brain tumor 9403904111_R01C01


title: Patient 106Z,sampling 4


title: Patient 106Z,sampling 2


title: Patient 106Z,sampling 3


title: Brain tumor 6752625106_R06C02


title: Brain tumor 6752625107_R02C01


title: Brain tumor 6969568124_R04C01

source_name: brain tumor, SP-MPE

value: SP-MPE


title: Brain tumor 6969568124_R03C01

value: ependymal tumor

value: relapse 1


title: Patient 105Z,sampling 2


title: Patient 106Z,sampling 1


title: Brain tumor 8622007099_R06C02

value: relapse


title: Brain tumor 9403904125_R04C02

value: frozen


title: Patient 105Z,sampling 4


title: Patient 104Z,sampling 3


title: Patient 104Z,sampling 2


title: Brain tumor 6752625107_R02C02


title: Patient 104Z,sampling 4


title: Brain tumor 6752625107_R06C01


title: Patient 105Z,sampling 1


title: Patient 103Z,sampling 1


title: Brain tumor 6752625106_R03C01

value: PF-EPN-B


title: Patient 103Z,sampling 2


title: Patient 104Z,sampling 1


title: Patient 102Z,sampling 4


title: Brain tumor 8622007149_R05C02


title: Brain tumor 8622007149_R04C02

value: PF-EPN-A


title: Patient 103Z,sampling 4


title: Patient 102Z,sampling 2


title: Patient 101Z,sampling 4


title: Patient 102Z,sampling 1


title: Patient 102Z,sampling 3


title: Brain tumor 7310440009_R03C02

value: primary

value: ST-EPN-RELA


title: Brain tumor 6752625133_R04C01


title: Brain tumor 6752625133_R03C01


title: Patient 101Z,sampling 3

value: 1 month after MI


title: Patient 101Z,sampling 2


title: Brain tumor 6752625133_R03C02


title: Patient 100Z,sampling 4

value: 6 months after MI


title: Brain tumor 6285641010_R03C02


title: Brain tumor 6285641012_R06C01


title: Brain tumor 6285641010_R06C02


title: Brain tumor 6752625135_R05C01


title: Patient 100Z,sampling 1

value: PBMC


title: Patient 101Z,sampling 1

value: on the 1st day of MI (admission)


title: Brain tumor 6752625135_R05C02


title: Patient 100Z,sampling 3


title: Patient 99Z,sampling 4

value: non-HF


title: Brain tumor 6285641010_R05C02


title: Brain tumor 6752625133_R01C02


title: Brain tumor 6285641010_R02C02


title: Brain tumor 6285641012_R05C01


title: Brain tumor 6285641010_R04C01


title: Brain tumor 6752625135_R01C02


title: Patient 99Z,sampling 1


title: Brain tumor 6285641010_R04C02


title: Brain tumor 6285641010_R01C01


title: Brain tumor 6752625133_R04C02


title: Patient 99Z,sampling 3


title: Patient 98Z,sampling 3


title: Patient 98Z,sampling 1


title: Brain tumor 6285641012_R04C01


title: Patient 98Z,sampling 2


title: Patient 100Z,sampling 2


title: Brain tumor 6285641012_R04C02


title: Brain tumor 6285641010_R01C02


title: Brain tumor 6285641012_R01C01


title: Patient 96Z,sampling 3

value: HF


title: Brain tumor 6752625133_R06C01


title: Patient 97Z,sampling 1


title: Patient 97Z,sampling 2

value: after 4-6 days of MI (discharge)


title: Patient 96Z,sampling 4


title: Patient 99Z,sampling 2


title: Patient 98Z,sampling 4


title: Brain tumor 6752625135_R03C01


title: Patient 96Z,sampling 1


title: Patient 96Z,sampling 2


title: Patient 95Z,sampling 2


title: Patient 95Z,sampling 3


title: Patient 95Z,sampling 4


title: Patient 95Z,sampling 1


title: Patient 94Z,sampling 2


title: Patient 94Z,sampling 3


title: Brain tumor 6752625133_R05C01

value: relapse 2


title: Patient 93Z,sampling 4


title: Patient 94Z,sampling 1


title: Brain tumor 6752625135_R03C02


title: daf-16(mgDF47) larva at 25, prep3

city: Ann Arbor

first: X.Z Shawn

last: Xu

state: Michigan

address: 210 Washtenaw Ave, Room 6115A

institute: Life Sciences Institute, University of Michigan

description: gene expression data from Late L4 stage daf-16(mgDF47) worms at 25 degree

hyb_protocol: Total RNA was used for hybridization with Affymetrix C.elegans Gene 1.1 ST array strip at the Microarray Core Facility in University of Michigan

scan_protocol: Follow standard Affymetrix protocol

data_processing: gene expression values are processed using RMA methods with R software.

organism: Caenorhabditis elegans

source_name: C.elegans daf-16(mgDF47) mutant larvae at 25 degree

label_protocol: Biotinylated cRNA were prepared according to the standard affymetrix protocol at the Microarray Core Facility in University of Michigan

growth_protocol: worms are growing and ageing on normal NGM plates at different temperature temporally

extract_protocol: Total RNAs are extracted with TRI reagent(Life Technoligies)

treatment_protocol: worms are growing from embryo to late stage L4 worms or aging from late L4 worms to Day3 old adult at 15 and 25 degree

tag: genotype

tag: age

value: Late L4


title: daf-16(mgDF47) larva at 25, prep1


title: Patient 93Z,sampling 2


title: Patient 94Z,sampling 4


title: daf-16(mgDF47) larva at 15, prep1

description: gene expression data from Late L4 stage daf-16(mgDF47) worms at 15 degree

source_name: C.elegans daf-16(mgDF47) mutant larvae at 15 degree


title: daf-16(mgDF47) larva at 15, prep2


title: WT larva at 15, prep3

description: gene expression data from Late L4 stage wild-type worms at 15 degree

source_name: C.elegans Wildtype Late L4 larvae at 15 dgree

value: wild-type


title: WT larva at 15, prep2


title: daf-16(mgDF47) larva at 15, prep3


title: daf-16(mgDF47) larva at 25, prep2


title: WT larva at 25, prep2

description: gene expression data from Late L4 stage wild-type worms at 25 degree

source_name: C.elegans Wildtype Late L4 larvae at 25 dgree


title: Patient 92Z,sampling 4


title: Patient 93Z,sampling 1


title: Patient 93Z,sampling 3


title: Patient 92Z,sampling 3


title: WT larva at 25, prep3


title: daf-16(mgDF47) Adutl at 25, prep2

description: gene expression data from Day3 old daf-16(mgDF47) worms at 25 degree

source_name: C.elegans daf-16(mgDF47) mutant Day3 adults at 25 degree

value: Day3 old


title: WT larva at 15, prep1


title: daf-16(mgDF47) Adutl at 15, prep2

description: gene expression data from Day3 old daf-16(mgDF47) worms at 15 degree

source_name: C.elegans daf-16(mgDF47) mutant Day3 adults at 15 degree


title: Patient 92Z,sampling 2


title: Patient 92Z,sampling 1


title: daf-16(mgDF47) Adutl at 25, prep1


title: daf-16(mgDF47) Adutl at 25, prep3


title: WT Adult at 25, prep3

description: gene expression data from Day3 old wild-type worms at 25 degree

source_name: C.elegans Wildtype Day3 Adults at 25 dgree


title: WT larva at 25, prep1


title: Patient 91Z,sampling 3


title: WT Adult at 25, prep2


title: WT Adult at 25, prep1


title: Patient 91Z,sampling 4


title: daf-16(mgDF47) Adutl at 15, prep3


title: WT Adult at 15, prep3

description: gene expression data from Day3 old wild-type worms at 15 degree

source_name: C.elegans Wildtype Day3 Adults at 15 dgree


title: Patient 91Z,sampling 1

source_name: peripheral blood mononuclear cells


title: WT Adult at 15, prep1


title: Patient 89Z,sampling 1


title: Patient 89Z,sampling 3


title: Patient 87Z,sampling 2


title: Patient 90Z,sampling 1


title: Patient 88Z,sampling 1


title: Patient 90Z,sampling 3


title: WT Adult at 15, prep2


title: Patient 87Z,sampling 3


title: daf-16(mgDF47) Adutl at 15, prep1


title: Patient 89Z,sampling 2


title: Patient 87Z,sampling 4


title: Patient 87Z,sampling 1


title: Patient 90Z,sampling 4


title: Patient 84Z,sampling 4


title: Patient 86Z,sampling 3


title: Patient 90Z,sampling 2


title: Patient 91Z,sampling 2


title: Patient 84Z,sampling 3


title: Patient 84Z,sampling 1


title: Patient 86Z,sampling 4


title: Patient 86Z,sampling 2


title: Patient 83Z,sampling 4


title: Patient 85Z,sampling 1


title: Patient 83Z,sampling 3


title: Patient 83Z,sampling 2


title: Patient 86Z,sampling 1


title: Patient 84Z,sampling 2


title: Patient 83Z,sampling 1


title: Patient 82Z,sampling 2


title: Patient 82Z,sampling 1


title: Patient 80Z,sampling 4


title: Patient 79Z,sampling 4


title: Patient 79Z,sampling 3


title: Patient 76Z,sampling 2


title: Patient 77Z,sampling 3


title: Patient 81Z,sampling 2


title: Patient 81Z,sampling 3


title: Patient 80Z,sampling 3


title: Patient 79Z,sampling 2


title: Patient 79Z,sampling 1


title: Patient 76Z,sampling 3


title: Patient 77Z,sampling 4


title: Patient 77Z,sampling 2


title: Patient 78Z,sampling 1


title: Patient 80Z,sampling 1


title: Patient 76Z,sampling 4


title: Patient 76Z,sampling 1


title: Patient 78Z,sampling 4


title: Patient 75Z,sampling 4


title: Patient 81Z,sampling 4


title: Patient 75Z,sampling 2


title: Patient 74Z,sampling 2


title: Patient 75Z,sampling 1


title: Patient 77Z,sampling 1


title: Patient 81Z,sampling 1


title: Patient 74Z,sampling 4


title: Patient 74Z,sampling 1


title: Patient 75Z,sampling 3


title: Patient 74Z,sampling 3


title: Patient 73Z,sampling 3


title: Patient 73Z,sampling 1


title: Brain tumor 9305216209_R04C02

source_name: brain tumor, SP-MPE, WHO grade 1

value: ependymal tumor

value: SP-MPE


title: Patient 72Z,sampling 3


title: Patient 72Z,sampling 1


title: Patient 71Z,sampling 1


title: Patient 72Z,sampling 2


title: Patient 71Z,sampling 3


title: Patient 71Z,sampling 2


title: Patient 69Z,sampling 4


title: Patient 70Z,sampling 3


title: Patient 73Z,sampling 2


title: Patient 71Z,sampling 4


title: Patient 69Z,sampling 3


title: Patient 69Z,sampling 2


title: Patient 69Z,sampling 1


title: Patient 67Z,sampling 3


title: Patient 70Z,sampling 2


title: Patient 68Z,sampling 2


title: Patient 67Z,sampling 4


title: Patient 68Z,sampling 3


title: Patient 67Z,sampling 1


title: Patient 65Z,sampling 4


title: Patient 70Z,sampling 1


title: Patient 68Z,sampling 4


title: Patient 67Z,sampling 2


title: Patient 68Z,sampling 1


title: Patient 66Z,sampling 1


title: Patient 66Z,sampling 4


title: Patient 63Z,sampling 1


title: Patient 65Z,sampling 1


title: Patient 64Z,sampling 4


title: Patient 66Z,sampling 3


title: Patient 64Z,sampling 3


title: Patient 61Z,sampling 3


title: Patient 62Z,sampling 4


title: Patient 61Z,sampling 1


title: Patient 60Z,sampling 4


title: Brain tumor 6929806038_R03C02

source_name: brain tumor, supratentorial, ST-EPN-YAP1

value: frozen


title: Patient 62Z,sampling 2


title: Patient 63Z,sampling 2


title: Patient 61Z,sampling 4


title: Patient 60Z,sampling 2


title: Patient 64Z,sampling 1


title: Patient 62Z,sampling 3


title: Patient 60Z,sampling 3


title: Patient 64Z,sampling 2


title: Patient 62Z,sampling 1


title: Patient 59Z,sampling 3


title: Patient 65Z,sampling 3


title: Patient 60Z,sampling 1


title: Patient 59Z,sampling 2


title: Patient 59Z,sampling 1


title: Patient 58Z,sampling 1


title: Patient 58Z,sampling 4


title: Patient 57Z,sampling 2


title: Patient 58Z,sampling 3


title: Patient 57Z,sampling 4


title: Patient 58Z,sampling 2


title: Patient 56Z,sampling 4


title: Patient 57Z,sampling 3


title: Patient 56Z,sampling 2


title: Patient 57Z,sampling 1


title: Patient 56Z,sampling 3


title: Patient 53Z,sampling 2


title: Patient 55Z,sampling 2


title: Patient 53Z,sampling 3


title: Patient 56Z,sampling 1


title: Patient 54Z,sampling 2


title: Patient 52Z,sampling 4


title: Patient 55Z,sampling 1


title: Patient 54Z,sampling 3


title: Patient 54Z,sampling 1


title: Patient 52Z,sampling 2


title: Patient 52Z,sampling 1


title: Patient 50Z,sampling 2


title: Patient 50Z,sampling 3


title: Patient 51Z,sampling 3


title: Patient 51Z,sampling 4


title: Patient 54Z,sampling 4


title: Patient 49Z,sampling 4


title: Patient 51Z,sampling 2


title: Patient 55Z,sampling 3


title: Patient 48Z,sampling 4


title: Patient 50Z,sampling 1


title: Patient 49Z,sampling 1


title: Patient 49Z,sampling 2


title: Patient 51Z,sampling 1


title: Patient 53Z,sampling 1


title: Patient 52Z,sampling 3


title: Patient 48Z,sampling 3


title: Patient 48Z,sampling 2


title: Patient 49Z,sampling 3


title: Patient 70Z,sampling 4


title: Patient 47Z,sampling 3


title: Patient 47Z,sampling 4


title: Patient 47Z,sampling 2


title: Patient 47Z,sampling 1


title: Patient 46Z,sampling 2


title: Patient 46Z,sampling 1


title: Patient 45Z,sampling 2


title: Patient 45Z,sampling 1


title: Patient 45Z,sampling 3


title: Patient 46Z,sampling 3


title: Patient 48Z,sampling 1


title: Patient 46Z,sampling 4


title: Patient 44Z,sampling 2


title: Patient 43Z,sampling 4


title: Patient 44Z,sampling 1


title: Patient 43Z,sampling 2


title: Patient 42Z,sampling 1


title: Patient 43Z,sampling 1


title: Patient 45Z,sampling 4


title: Patient 41Z,sampling 4


title: Patient 41Z,sampling 2


title: Patient 42Z,sampling 4


title: Patient 42Z,sampling 2


title: Patient 40Z,sampling 3


title: Patient 41Z,sampling 3


title: Patient 43Z,sampling 3


title: Patient 40Z,sampling 1


title: Patient 42Z,sampling 3


title: Patient 41Z,sampling 1


title: Patient 40Z,sampling 2


title: Patient 39Z,sampling 1


title: Patient 37Z,sampling 4


title: Patient 36Z,sampling 2


title: Patient 37Z,sampling 2


title: Patient 36Z,sampling 1


title: Patient 37Z,sampling 1


title: Patient 36Z,sampling 3


title: Patient 35Z,sampling 4


title: Patient 36Z,sampling 4


title: Patient 38Z,sampling 3


title: Patient 38Z,sampling 4


title: Patient 35Z,sampling 1


title: Patient 37Z,sampling 3


title: Patient 38Z,sampling 2


title: Patient 34Z,sampling 2


title: Patient 38Z,sampling 1


title: Patient 33Z,sampling 3


title: Patient 33Z,sampling 4


title: Patient 34Z,sampling 1


title: LSD1-KD2

city: Kumamoto

first: Akihisa

last: Sakamoto

address: 2-2-1 Honjo, Chuo-ku

department: Institute of Molecular Embryology and Genetics

institute: Kumamoto University

description: LSD1-KD2_(HG-U133_Plus_2) .CEL(normalized)

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit

scan_protocol: GCS3000 Scanner

data_processing: The data were analyzed with Affymetrix Genechip Command Console software (CEL files) using Affymetrix default analysis settings and global scaling, and baseline transformed to the median of control 2 samples. GeneSpring software (v.13.0) was used for summarization by RMA algorithm and baseline transformation (median shift).

source_name: HepG2_siRNA-2 against LSD1

label_protocol: GeneChip  3' IVT Express Kit

growth_protocol: HepG2 cells were cultured in high glucose (25mM D-glucose) Dulbecco-modified eagle’s medium (DMEM) (Sigma) supplemented with 10% (v/v) heat-inactivated fetal bovine serum.

extract_protocol: After cultured for 4 days, semiconfluent cells were harvested RNA extraction using RNeasy kit.

treatment_protocol: For the knockdown experiments, specific siRNAs were introduced to the cells using RNAiMAX reagent (Invitrogen) when they were approximately 50% confluent.

value: human hepatoma cells

tag: transfected with

value: siRNA-2 against LSD1


title: Patient 33Z,sampling 1

tag: samples collection


title: Patient 32Z,sampling 2

tag: hf progression


title: Patient 35Z,sampling 3


title: Patient 32Z,sampling 4


title: Patient 33Z,sampling 2


title: Patient 31Z,sampling 3


title: Cont1

description: Cont1_(HG-U133_Plus_2) .CEL(normalized)

source_name: HepG2_siRNA against GL3

value: siRNA against GL3


title: Patient 30Z,sampling 4


title: Patient 31Z,sampling 2


title: Patient 30Z,sampling 1


title: Patient 32Z,sampling 1


title: 11ep32

first: Marcel

last: Kool

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

description: MAS5.0 normalized data

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

source_name: Frozen ependymal tumor tissue

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumour specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

value: Ependymal tumor

tag: primary/relapse

value: primary

tag: brain location

value: posterior fossa

tag: age at diagnosis (years)

tag: gender

value: f

tag: molecular subgroup


title: 11ep26

description: MAS5.0 normalized data

tag: tissue

value: m


title: Control glioblastoma stem cells

city: Chongqing

first: Yu

last: Shi

state: Chongqing

address: Gao-tan Yan Street

department: Southwest Hospital

country: China

institute: Institute of Pathology and Southwest Cancer Center

description: Control cells with PTPRZ1 knocking-down efficiency confirmed by qRT-PCR

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method, following the manufacture's protocol. Differentially expressed genes were identified when the gene expression ratio between the control group and KD group was more than 2-fold.

source_name: Control glioblastoma stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 20ug total RNA (Cat. AM1792, Ambion).

extract_protocol: The PTPRZ1 knocking-down glioblastoma stem cells and control cells were used for RNA isolatation using  Primescript RT Master Mix (Takara) according to the manufacture's protocol.

tag: cell type

value: glioblastoma stem cells


title: Patient 32Z,sampling 3

value: PBMC

value: 1 month after MI

value: HF


title: LSD1-KD1

description: LSD1-KD1_(HG-U133_Plus_2) .CEL(normalized)

source_name: HepG2_siRNA-1 against LSD1

tag: cell line

value: siRNA-1 against LSD1


title: 11ep22

description: MAS5.0 normalized data

value: supratentorial


title: Cont2

description: Cont2_(HG-U133_Plus_2) .CEL(normalized)


title: 13ep5

description: MAS5.0 normalized data

value: relapse

value: spinal


title: Patient 31Z,sampling 1

value: on the 1st day of MI (admission)


title: PTPRZ1 knocking-down glioblastoma stem cells

description: PTPRZ1 knocking down cells with disrupting efficiency confirmed by qRT-PCR


title: 13ep6

description: MAS5.0 normalized data


title: 11ep25

description: MAS5.0 normalized data


title: Patient 29Z,sampling 4

value: 6 months after MI


title: 11ep21

description: MAS5.0 normalized data


title: Patient 29Z,sampling 3


title: Patient 29Z,sampling 2

value: after 4-6 days of MI (discharge)


title: Patient 28Z,sampling 4


title: Patient 27Z,sampling 2


title: 11ep13

description: MAS5.0 normalized data


title: Patient 28Z,sampling 3


title: Patient 29Z,sampling 1


title: 11ep7

description: MAS5.0 normalized data


title: Patient 28Z,sampling 2


title: 11ep17

description: MAS5.0 normalized data


title: Patient 27Z,sampling 3


title: 11ep6

description: MAS5.0 normalized data


title: 9ep40

description: MAS5.0 normalized data


title: 11ep10

description: MAS5.0 normalized data


title: Patient 26Z,sampling 3


title: 11ep18

description: MAS5.0 normalized data


title: 9ep45

description: MAS5.0 normalized data


title: 9ep44

description: MAS5.0 normalized data


title: 9ep43

description: MAS5.0 normalized data


title: Patient 27Z,sampling 1


title: 9ep47

description: MAS5.0 normalized data


title: Patient 28Z,sampling 1


title: Patient 26Z,sampling 2


title: 11ep19

description: MAS5.0 normalized data


title: Patient 26Z,sampling 1


title: 9ep35

description: MAS5.0 normalized data


title: 9ep38

description: MAS5.0 normalized data


title: Patient 26Z,sampling 4


title: 9ep37

description: MAS5.0 normalized data


title: Patient 25Z,sampling 4


title: Patient 25Z,sampling 3


title: Patient 24Z,sampling 4


title: 9ep34

description: MAS5.0 normalized data


title: Patient 25Z,sampling 2


title: Patient 23Z,sampling 3


title: Patient 25Z,sampling 1


title: 9ep33

description: MAS5.0 normalized data


title: Patient 23Z,sampling 4


title: Patient 23Z,sampling 2


title: 9ep32

description: MAS5.0 normalized data


title: 9ep30

description: MAS5.0 normalized data


title: 9ep22

description: MAS5.0 normalized data


title: 9ep21

description: MAS5.0 normalized data


title: 9ep24

description: MAS5.0 normalized data


title: Patient 24Z,sampling 2


title: Patient 24Z,sampling 1


title: 9ep23

description: MAS5.0 normalized data


title: Patient 22Z,sampling 4


title: 13ep14

description: MAS5.0 normalized data


title: 13ep16

description: MAS5.0 normalized data


title: 9ep15

description: MAS5.0 normalized data


title: Patient 22Z,sampling 2


title: Patient 24Z,sampling 3


title: 9ep20

description: MAS5.0 normalized data


title: Patient 22Z,sampling 1


title: 13ep8

description: MAS5.0 normalized data


title: 9ep9

description: MAS5.0 normalized data


title: Patient 21Z,sampling 4


title: Patient 22Z,sampling 3


title: 9ep19

description: MAS5.0 normalized data


title: 9ep8

description: MAS5.0 normalized data


title: Patient 21Z,sampling 3


title: Patient 20Z,sampling 3


title: Patient 21Z,sampling 1


title: Patient 21Z,sampling 2


title: Patient 20Z,sampling 2


title: Patient 19Z,sampling 3


title: 9ep1

description: MAS5.0 normalized data


title: 9ep7

description: MAS5.0 normalized data


title: 9ep3

description: MAS5.0 normalized data


title: Patient 20Z,sampling 1


title: Patient 19Z,sampling 2


title: 7ep53

description: MAS5.0 normalized data


title: 4ep48

description: MAS5.0 normalized data


title: 7ep41

description: MAS5.0 normalized data


title: 4ep33

description: MAS5.0 normalized data


title: Patient 19Z,sampling 1


title: 4ep28

description: MAS5.0 normalized data


title: Patient 23Z,sampling 1


title: Patient 18Z,sampling 4


title: Patient 18Z,sampling 2


title: Patient 18Z,sampling 1


title: 4ep26

description: MAS5.0 normalized data


title: Patient 17Z,sampling 2


title: Patient 17Z,sampling 1


title: 4ep23

description: MAS5.0 normalized data


title: Patient 18Z,sampling 3


title: 7ep49

description: MAS5.0 normalized data


title: 4ep29

description: MAS5.0 normalized data


title: 4ep35

description: MAS5.0 normalized data


title: 4ep24

description: MAS5.0 normalized data


title: Patient 16Z,sampling 2


title: Patient 16Z,sampling 1


title: 4ep14

description: MAS5.0 normalized data


title: 4ep19

description: MAS5.0 normalized data


title: Patient 15Z,sampling 1


title: 4ep21

description: MAS5.0 normalized data


title: Patient 15Z,sampling 2


title: 13ep10

description: MAS5.0 normalized data


title: 4ep11

description: MAS5.0 normalized data


title: Patient 16Z,sampling 3


title: 4ep12

description: MAS5.0 normalized data


title: Patient 15Z,sampling 3


title: 4ep22

description: MAS5.0 normalized data


title: Patient 13Z,sampling 2


title: 13ep12

description: MAS5.0 normalized data


title: 13ep15

description: MAS5.0 normalized data


title: Patient 14Z,sampling 2


title: 13ep17

description: MAS5.0 normalized data


title: Patient 14Z,sampling 1


title: Patient 14Z,sampling 3


title: 13ep11

description: MAS5.0 normalized data


title: 13ep3

description: MAS5.0 normalized data


title: Patient 12Z,sampling 4


title: Patient 12Z,sampling 2


title: 13ep4

description: MAS5.0 normalized data


title: Patient 12Z,sampling 1


title: 5ep31

description: MAS5.0 normalized data


title: 13ep1

description: MAS5.0 normalized data


title: 9ep12

description: MAS5.0 normalized data


title: Patient 27Z,sampling 4


title: Patient 11Z,sampling 4


title: Patient 11Z,sampling 3


title: Patient 13Z,sampling 1


title: Patient 11Z,sampling 1


title: 5ep30

description: MAS5.0 normalized data


title: 7ep48

description: MAS5.0 normalized data


title: 9ep11

description: MAS5.0 normalized data


title: Patient 10Z,sampling 1


title: Patient 10Z,sampling 3


title: Patient 9Z,sampling 4


title: Patient 10Z,sampling 2


title: Patient 9Z,sampling 3


title: Patient 11Z,sampling 2


title: 5ep27

description: MAS5.0 normalized data


title: Patient 9Z,sampling 2


title: Patient 8Z,sampling 4


title: 5ep29

description: MAS5.0 normalized data


title: 5ep15

description: MAS5.0 normalized data


title: 8ep17

description: MAS5.0 normalized data


title: 8ep3_met

description: MAS5.0 normalized data


title: Patient 9Z,sampling 1


title: Patient 8Z,sampling 2


title: 8ep6

description: MAS5.0 normalized data


title: Patient 8Z,sampling 3


title: 3ep44_2

description: MAS5.0 normalized data


title: 8ep3

description: MAS5.0 normalized data


title: 5ep28

description: MAS5.0 normalized data


title: 2ep28

description: MAS5.0 normalized data


title: 8ep6_met

description: MAS5.0 normalized data


title: Patient 7Z,sampling 3


title: Patient 7Z,sampling 4


title: Patient 8Z,sampling 1


title: 3ep64_2

description: MAS5.0 normalized data


title: 4ep46_2

description: MAS5.0 normalized data


title: Patient 7Z,sampling 1


title: Patient 6Z,sampling 4


title: Patient 6Z,sampling 2


title: 3ep3

description: MAS5.0 normalized data


title: Patient 7Z,sampling 2


title: 1ep6

description: MAS5.0 normalized data


title: 2ep21

description: MAS5.0 normalized data


title: 3ep45

description: MAS5.0 normalized data


title: Patient 5Z,sampling 2


title: 3ep6

description: MAS5.0 normalized data


title: 4ep53

description: MAS5.0 normalized data


title: Patient 6Z,sampling 1


title: 3ep75

description: MAS5.0 normalized data


title: Patient 4Z,sampling 4


title: Patient 6Z,sampling 3


title: Patient 4Z,sampling 2


title: Patient 4Z,sampling 3


title: Patient 3Z,sampling 3


title: Patient 3Z,sampling 4


title: Patient 4Z,sampling 1


title: 3ep28

description: MAS5.0 normalized data


title: 7ep9

description: MAS5.0 normalized data


title: 3ep19

description: MAS5.0 normalized data


title: Patient 3Z,sampling 2


title: Brain tumor 9426020064_R03C01

source_name: brain tumor, infratentorial, PF-EPN-A, WHO grade 3

value: ependymal tumor

tag: tumor type

tag: molecular subtype

value: PF-EPN-A

value: frozen


title: Patient 5Z,sampling 1


title: 7ep35

description: MAS5.0 normalized data

value: Ependymal tumor

value: primary


title: 3ep50

description: MAS5.0 normalized data

value: m


title: Patient 2Z,sampling 4


title: 3ep11

description: MAS5.0 normalized data

value: f


title: 3ep72

description: MAS5.0 normalized data


title: 3ep61

description: MAS5.0 normalized data


title: 3ep30

description: MAS5.0 normalized data


title: 3ep8

description: MAS5.0 normalized data


title: 4ep54

description: MAS5.0 normalized data


title: Patient 2Z,sampling 1

value: PBMC


title: Patient 2Z,sampling 2


title: 4ep47

description: MAS5.0 normalized data


title: 4ep45

description: MAS5.0 normalized data


title: Patient 1Z,sampling 3

value: 1 month after MI


title: Patient 1Z,sampling 1


title: Patient 1Z,sampling 2


title: 4ep37

description: MAS5.0 normalized data


title: 7ep1

description: MAS5.0 normalized data


title: Patient 2Z,sampling 3


title: Patient 3Z,sampling 1


title: hsc2429300

description: MAS5.0 normalized data

value: posterior fossa


title: bt2009042

description: MAS5.0 normalized data


title: 69a98

description: MAS5.0 normalized data


title: MDA-MB-231 control sample, biological rep2

city: University Park

first: Yanming

last: Wang

state: Pennsylvania

address: 454 North Frear Building

institute: The Penn State University

hyb_protocol: Prepare hybridization cocktail using the GeneChip Hybridization Wash and Stain Kit (#702232) and hybridize arrays at 45°C for 16 hours  in the Affymetrix GeneChip Hybridization Oven 640.

scan_protocol: Stained arrays were scanned using the GeneChip Scanner 3000 7G.

data_processing: Data from Affymetix GeneChips were normalized using the Robust Multichip Average (RMA) method with Bioconductor’s affy package.

source_name: MDA-MB-231 cells treat with DMSO vehicle

label_protocol: Label the resulting fragmented cDNA using the Affymetrix GeneChip WT Terminal Labeling Kit (#900671) according to the manufacturer’s protocol. DNA is labeled by TdT with the affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium (Gibco) supplemented with 10% FBS and 1% penicillin-streptomycin in a 5% CO2 incubator at 37 °C.

extract_protocol: Extraction of total RNA was performed using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions.

treatment_protocol: DMSO and YW3-56 were added when cells reached around 70% confluence. Cells were then treated with 10μM YW3-56  for 8hr.

tag: treatment

value: DMSO


title: ept500

description: MAS5.0 normalized data


title: hsc2366617

description: MAS5.0 normalized data


title: MDA-MB-231 YW3-56 treated sample, biological rep3

source_name: MDA-MB-231 cells treat with 10μM YW3-56  for 8hr


title: MDA-MB-231 YW3-56 treated sample, biological rep2


title: hsc2068011-2

description: MAS5.0 normalized data


title: CCR6 ILC3 2

description: Array was performed at the University of Pennsylvania Microarray core

source_name: mesenteric lymph node

tag: strain

value: mesenteric lymph node

value: CCR6+ innate lymphoid cells

tag: cell markers


title: bt2011080

description: MAS5.0 normalized data


title: MDA-MB-231 control sample, biological rep3


title: bt2013017

description: MAS5.0 normalized data

value: supratentorial


title: MDA-MB-231 control sample, biological rep1


title: MDA-MB-231 YW3-56 treated sample, biological rep1


title: CCR6 ILC3 1

scan_protocol: Array was performed at the University of Pennsylvania Microarray core


title: IL2 knockout GM-DCs treated with curdlan for 6 hours, replicate 1

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: Fragmented samples were hybridized according to Affymetrix guidelines for 17hr in 45°C on GeneChip Mouse Gene 1.0 ST Array; The arrays were then washed and stained using the standard fluidics protocol (FS450_0007) for gene arrays on the GeneChip Fluidics Station 450.

scan_protocol: The mouse gene chips were scanned using GeneChip Scanner 3000. The images were analyzed using Expression Console and standard array quality controls analyses were carried out according to the instructions provided by Affymetrix.

data_processing: CEL files were processed in Bioconductor using the xps package. Expression data was summarized at the transcript level and normalized using RMA. Log2 transformation was applied to the expression data.

source_name: GM-DC derived from bone marrow and selected using CD11c microbeads

label_protocol: Single-stranded DNA were prepared according to the Ambion WT Expression Kit from 100ng of total RNA. 5.5ug of ssDNA were fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: Bone marrow was flushed with IMDM medium with GM-CSF (200ng/ml), 1% Penicillin-Streptomycin, 10% Serum, 1% L-Glutamine and 0.1% β-Mercaptoethanol and cells were cultured for 7d  The suspension cells were harvested on d7 and purified by positive selection using CD11c microbeads (Miltenyi Biotec) according to the manufacturer’s protocol. GM-DC (CD11c+, MHCII aI-A/I-E +) purity determined by FACS was routinely >95%.

extract_protocol: Total RNA was extracted following the double extraction protocol using Trizol and Qiagen RNeasy Micro Extraction Kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: Wt and IL-2-/- GM-DCs were treated or not with curdlan for 6h and processed for microarray

value: GM-CSF myeloid dendritic cells

tag: genotype

value: IL2 knockout


title: 4ep13

description: MAS5.0 normalized data


title: IL2 knockout GM-DCs treated with curdlan for 6 hours, replicate 3


title: hsc2068011-1

description: MAS5.0 normalized data


title: Wild type GM-DCs, replicate 3

value: wild type


title: 7ep6

description: MAS5.0 normalized data


title: 4ep32

description: MAS5.0 normalized data


title: 7ep5

description: MAS5.0 normalized data


title: IL2 knockout GM-DCs treated with curdlan for 6 hours, replicate 2


title: IL2 knockout GM-DCs, replicate 1


title: Wild type GM-DCs treated with curdlan for 6 hours, replicate 1


title: Wild type GM-DCs treated with curdlan for 6 hours, replicate 3


title: 7ep31

description: MAS5.0 normalized data


title: 7ep30

description: MAS5.0 normalized data


title: 7ep3

description: MAS5.0 normalized data


title: 7ep17

description: MAS5.0 normalized data


title: Wild type GM-DCs, replicate 2


title: 7ep2

description: MAS5.0 normalized data


title: Cr 20 mg/kg Day 7, Biological rep 4

city: Fort Detrick

first: Michael

middle: Scott

last: Madejczyk

state: MD

address: 568 Doughten Dr

department: Environmental Health Program

institute: US Army Center for Environmental Health Research

hyb_protocol: Samples were hybridized on the GeneChip Rat Genome 230 2.0 Array using Affymetrix instrumentation according to the manufacturer’s instructions

data_processing: Microarray data was processed for background adjustment, normalization, and summarization using the Robust Multi-Array Averaging method (RMA) using Partek Genomic Suite (GS) software (Version 6.6 Copyright 2012, St. Louis, MO)

organism: Rattus norvegicus

source_name: Liver tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Rats were exposed via a single intraperitoneal injection to three concentrations of CdCl2, Na2Cr2O7, or vehicle control.

value: liver

value: Cr 20 mg/kg Day 7


title: IL2 knockout GM-DCs, replicate 2


title: 7ep4

description: MAS5.0 normalized data


title: Wild type GM-DCs treated with curdlan for 6 hours, replicate 2


title: 7ep32

description: MAS5.0 normalized data


title: Cr 20 mg/kg Day 7, Biological rep 3


title: IL2 knockout GM-DCs, replicate 3


title: 7ep15

description: MAS5.0 normalized data


title: 7ep16

description: MAS5.0 normalized data


title: 7ep10

description: MAS5.0 normalized data


title: 4ep60

description: MAS5.0 normalized data


title: Cr 20 mg/kg Day 7, Biological rep 2


title: Cr 20 mg/kg Day 7, Biological rep 5


title: Cr Control Day 7, Biological rep 5

value: Cr Control Day 7


title: Cr 20 mg/kg Day 7, Biological rep 1


title: 7ep18

description: MAS5.0 normalized data

value: Ependymal tumor


title: Cr Control Day 7, Biological rep 4


title: 4ep61

description: MAS5.0 normalized data


title: Wild type GM-DCs, replicate 1


title: 7ep11

description: MAS5.0 normalized data

value: primary


title: 6ep9

description: MAS5.0 normalized data

value: relapse


title: 5ep16

description: MAS5.0 normalized data

value: spinal

value: m


title: 4ep30

description: MAS5.0 normalized data

value: f


title: pnet155

description: MAS5.0 normalized data


title: Cr Control Day 3, Biological rep 4

value: Cr Control Day 3


title: Cr Control Day 7, Biological rep 1


title: Cr 20 mg/kg Day 3, Biological rep 3

value: Cr 20 mg/kg Day 3


title: 5ep12

description: MAS5.0 normalized data

value: posterior fossa


title: pnet159

description: MAS5.0 normalized data


title: 5ep10

description: MAS5.0 normalized data


title: Cr Control Day 7, Biological rep 3


title: Cr Control Day 7, Biological rep 2


title: Cr Control Day 3, Biological rep 3


title: Cr 20 mg/kg Day 3, Biological rep 4


title: 5ep5

description: MAS5.0 normalized data


title: Cr Control Day 3, Biological rep 1


title: Cr 20 mg/kg Day 3, Biological rep 2


title: pnet153

description: MAS5.0 normalized data


title: Cr 20 mg/kg Day 1, Biological rep 5

value: Cr 20 mg/kg Day 1


title: Cr 20 mg/kg Day 1, Biological rep 4


title: pnet150

description: MAS5.0 normalized data

value: supratentorial


title: Cr 20 mg/kg Day 3, Biological rep 5


title: Cr 20 mg/kg Day 1, Biological rep 3


title: Cr Control Day 3, Biological rep 2


title: pnet156

description: MAS5.0 normalized data


title: 5ep4

description: MAS5.0 normalized data


title: pnet151

description: MAS5.0 normalized data


title: 5ep9

description: MAS5.0 normalized data


title: Cr 20 mg/kg Day 3, Biological rep 1


title: pnet98

description: MAS5.0 normalized data


title: pnet9

description: MAS5.0 normalized data


title: Cr 20 mg/kg Day 1, Biological rep 1


title: Cr Control Day 1, Biological rep 3

value: Cr Control Day 1


title: Cr Control Day 1, Biological rep 4


title: glio 1.1

description: MAS5.0 normalized data


title: 3ep67

description: MAS5.0 normalized data


title: ak #654

description: MAS5.0 normalized data


title: 3ep7

description: MAS5.0 normalized data


title: Cd 1.25 mg/kg Day 7, Biological rep 3

value: Cd 1.25 mg/kg Day 7


title: Cr Control Day 1, Biological rep 2


title: Cd 1.25 mg/kg Day 7, Biological rep 5


title: Cd 1.25 mg/kg Day 7, Biological rep 2


title: Cd 1.25 mg/kg Day 7, Biological rep 1


title: Cr Control Day 1, Biological rep 5


title: Cr 20 mg/kg Day 1, Biological rep 2


title: Cr Control Day 1, Biological rep 1


title: 3ep29

description: MAS5.0 normalized data


title: Cd 1.25 mg/kg Day 7, Biological rep 4


title: 3ep25

description: MAS5.0 normalized data


title: 3ep54

description: MAS5.0 normalized data


title: 2ep9

description: MAS5.0 normalized data


title: 3ep55

description: MAS5.0 normalized data


title: 3ep65

description: MAS5.0 normalized data


title: Cd Control Day 7, Biological rep 5

value: Cd Control Day 7


title: 3ep49

description: MAS5.0 normalized data


title: 3ep48

description: MAS5.0 normalized data


title: 3ep18

description: MAS5.0 normalized data


title: 3ep15

description: MAS5.0 normalized data


title: Cd Control Day 7, Biological rep 3

value: liver


title: Cd Control Day 7, Biological rep 4


title: 2ep7

description: MAS5.0 normalized data


title: 2ep6

description: MAS5.0 normalized data


title: Cd Control Day 7, Biological rep 2


title: 2ep4

description: MAS5.0 normalized data


title: Cd Control Day 7, Biological rep 1


title: Cd 1.25 mg/kg Day 3, Biological rep 5

value: Cd 1.25 mg/kg Day 3


title: 2ep36

description: MAS5.0 normalized data


title: Cd 1.25 mg/kg Day 3, Biological rep 4


title: Cd 1.25 mg/kg Day 3, Biological rep 1


title: 2ep31

description: MAS5.0 normalized data


title: 2ep33

description: MAS5.0 normalized data


title: 2ep35

description: MAS5.0 normalized data


title: Cd Control Day 3, Biological rep 4

value: Cd Control Day 3


title: 2ep3

description: MAS5.0 normalized data

value: Ependymal tumor


title: Cd 1.25 mg/kg Day 3, Biological rep 3


title: Cd Control Day 3, Biological rep 3


title: Cd Control Day 3, Biological rep 5


title: 2ep23

description: MAS5.0 normalized data

value: primary


title: Cd 1.25 mg/kg Day 3, Biological rep 2


title: 2ep25

description: MAS5.0 normalized data


title: 2ep27

description: MAS5.0 normalized data


title: Cd Control Day 3, Biological rep 2


title: 2ep20

description: MAS5.0 normalized data


title: 2ep2

description: MAS5.0 normalized data


title: 2ep22

description: MAS5.0 normalized data


title: Cd 1.25 mg/kg Day 1, Biological rep 5

value: Cd 1.25 mg/kg Day 1


title: Cd Control Day 3, Biological rep 1


title: Cd 1.25 mg/kg Day 1, Biological rep 4


title: Cd 1.25 mg/kg Day 1, Biological rep 2


title: 2ep14

description: MAS5.0 normalized data

value: spinal


title: 2ep16

description: MAS5.0 normalized data


title: 2ep11

description: MAS5.0 normalized data

value: m


title: 2ep10

description: MAS5.0 normalized data

value: f


title: Cd Control Day 1, Biological rep 5

value: Cd Control Day 1


title: Cd 1.25 mg/kg Day 1, Biological rep 1


title: Cd Control Day 1, Biological rep 3


title: Cd Control Day 1, Biological rep 4


title: 1ep8

description: MAS5.0 normalized data


title: 1ep7

description: MAS5.0 normalized data


title: Cd Control Day 1, Biological rep 2


title: Cd Control Day 1, Biological rep 1


title: 1ep4

description: MAS5.0 normalized data


title: PBD-ZSD patient hepatocyte-like cell culture [PBD_PEX1fs1_HLC]

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: Gene expression data of PBD-ZSD patient hepatocyte-like cells

hyb_protocol: followed affymetrix protocol

scan_protocol: followed affymetrix protocol

data_processing: WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

source_name: hepatocyte-like cells from PBD-ZSD patient

label_protocol: followed affymetrix protocol

growth_protocol: Patient and control-dervied iPSCs cultured on matrigel-coated plates with MEF-conditioned medium were induced into definitive endoderm by switching to serum-free RPMI 1640 medium supplemented with 100ng/ml of Activin A, 2mM L-glutamine, and 1% antibiotic-antimycotic for 48 hours. This medium was supplemented with 1×B27 supplement and 0.5mM sodium butyrate for the next 3-6 days. To initiate differentiation, we treated definitive endodermal cells with 20 ng/ml of FGF4, 20 ng/ml of BMP2 and 20 ng/ml of HGF in Iscove’s modified Dulbecco’s medium with 20% FBS, 2 mM L-glutamine, 0.3 mM monothioglycerol, 1% antibiotic-antimycotic, 1 uM insulin, 0.5% DMSO and 100 nM dexamethosome for 10 days. For maturation, we cultured these cells in hepatocyte culture medium supplemented with SingleQuots with 2% FBS, 20 ng/ml of FGF4, 20 ng/ml of HGF, 50 ng/ml of oncostatin M, 100 nM dexamethasone and 0.5% DMSO for 6 to 10 days.

extract_protocol: as recommended by affymetrix

treatment_protocol: Candidate hepatocyte-like cells were subject to flow cytometry and ASGPR-positive cells were collected and subject to RNA isolation.

value: hepatocyte-like cells

tag: age

value: unknown


title: 1ep38

description: MAS5.0 normalized data

value: posterior fossa


title: 1ep37

description: MAS5.0 normalized data


title: PBD-ZSD patient hepatocyte-like cell culture [PBD_PEX1ms1]


title: KM_107T

city: Houston

first: Sangbae

last: Kim

address: 1 Baylor plaza

department: HGSC

institute: Baylor Colleage of Medicine

hyb_protocol: Labeled, amplified material (750 ng per array) was hybridized to the Illumina HumanHT-12 V4.0 expression BeadChip according to the manufacturer's instructions (Illumina, Inc., San Diego, CA).

scan_protocol: Arrays were scanned with an Illumina BeadArray Reader confocal scanner (BeadStation 500GXDW; Illumina, Inc., San Diego, CA) according to the manufacturer's instructions.

data_processing: Array data processing was performed on Illumina BeadStudio software. We normalized gene expression data using quantile normalization and log2 transformation. To export to a data matrix, the Sample Gene Profile option of this software was used.

source_name: HCC tumor

label_protocol: Biotin-labeled cRNA samples for hybridization were prepared according to Illumina's recommended sample labeling procedure: 500 ng of total RNA was used for cDNA synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion Inc., Austin, TX). cRNA concentrations were determined using a spectrophotometer (Nanodrop, ND-1000).

extract_protocol: Total RNA was isolated from tissues with the mirVana RNA Isolation labeling kit (Ambion, Inc.) according to the manufacturer's protocol. RNA quality and integrity were confirmed by the ExperionTM Automated Electrophoresis System (BIO-RAD).

tag: disease state

value: hepatocellular carcinoma (HCC)

value: HCC tumor


title: 1ep36

description: MAS5.0 normalized data


title: KM_113T


title: KM_110T


title: Cr Control Day 3, Biological rep 5

value: Cr Control Day 3


title: 1ep34

description: MAS5.0 normalized data


title: 1ep31

description: MAS5.0 normalized data


title: pnet157

description: MAS5.0 normalized data

value: supratentorial


title: 1ep30

description: MAS5.0 normalized data


title: KM_070T


title: 1ep29

description: MAS5.0 normalized data


title: KM_088T


title: 2ep1

description: MAS5.0 normalized data


title: 1ep25

description: MAS5.0 normalized data


title: 1ep32

description: MAS5.0 normalized data


title: KM_048T


title: healthy control hepatocyte-like cell culture

description: Gene expression data of healthy control hepatocyte-like cells

source_name: dermal fibroblast from healthy control

value: healthy control


title: KM_046T


title: 1ep26

description: MAS5.0 normalized data


title: 1ep24

description: MAS5.0 normalized data


title: 1ep27

description: MAS5.0 normalized data


title: KM_059T


title: KM_052T


title: 1ep23

description: MAS5.0 normalized data


title: 1ep19

description: MAS5.0 normalized data


title: KM_043T


title: 1ep17

description: MAS5.0 normalized data


title: KM_020T


title: 1ep16

description: MAS5.0 normalized data


title: 1ep5

description: MAS5.0 normalized data


title: KM_031T


title: KM_005T


title: KM_002T


title: KM_042T


title: 1ep15

description: MAS5.0 normalized data


title: KM_018T


title: 1ep1

description: MAS5.0 normalized data


title: 1ep12

description: MAS5.0 normalized data


title: 1ep14

description: MAS5.0 normalized data


title: Brain tumor 9533774107_R04C01

source_name: brain tumor, infratentorial, PF-EPN-A, WHO grade 2

value: ependymal tumor

value: PF-EPN-A

tag: material

tag: location

tag: who grade


title: 35C2_Resistant_A498

city: Boston

first: Manoj

last: Bhasin

state: MA

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

description: Frozen A498 Resistant Sorafenib

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332).

data_processing: The data was normalised using Robust Multichip Average (RMA), Dchip and MAS5 algorithms

source_name: Frozen A498 Xenograft Tumors

label_protocol: Standard Affymetrix Protocol

growth_protocol: Female athymic nude/beige mice (Charles River Laboratories, MA) were used for subcutaneous xenograft tumor models. All experiments were approved by the Beth Israel Deaconess Medical Center Institutional Animal Care and Use Committee. To establish RCC tumor xenografts, 1 x 10^7 786-O or A498 tumor cells were prepared and injected subcutaneously into the flanks of 6-8 week old mice. To ensure a consistent size at the outset of treatment, tumors were measured with calipers daily once they reached a diameter of 3-5 mm. Sunitinib (additive-free, 53.6 mg/kg) was administered 6 out of 7 days per week by gavage beginning when the tumors had grown to a diameter of 12 mm. Sorafenib (80 mg/kg, Bayer) was administered 6 out of 7 days per week by gavage beginning when the tumors had grown to a diameter of 12 mm. Treated and control tumors were again measured daily during therapy.

extract_protocol: Trizol extraction was performed after tumor were excised and frozen

treatment_protocol: biopsy specimens were snap frozen at time of mouse surgery, then stored at -80C until time of total RNA extraction

value: Frozen A498 Resistant Sorafenib

tag: host organism

value: Mus musculus

value: renal cell carcinoma


title: 35C1_Resistant_A498

description: Frozen A498 Resistant Sorafenib


title: Vec-3_3

city: Bethesda

first: WeiPing

last: Chen

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

department: GCL

institute: NIDDK/NIH

description:
gene expression upon stable Vector transfection
The sorted cell subpopulations

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

data_processing: RMA by software Partek

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

growth_protocol: MIN6-4N stable cell lines cells were cultured in DMEM low glucose medium supplemented with 15% FBS, 1X antibiotic and antimycotic, and 500 µg/ml G418 at 37˚C and 5% CO2.

extract_protocol: Total RNA was isolated using the RNAeasy kit according to the manufacturer's instructions (Qiagen) from 3 independent cultures of a vector transfected clone (Vec-3), and a Meg3 transfected clone (Meg-5).

treatment_protocol: MIN6-4N cells were transfected with Vector or Meg3 plasmid using the nucleofection method with  Solution -T (Amaxa/Lonza) and selected for 5 weeks in 750 µg/ml G418. Stable clones were picked by using cloning cylinders and expanded, and tested for Meg3 expression by RT-PCR.

value: pancreatic beta cell


title: Meg-3_3

description:
gene expression upon stable mouse Meg3 expression
The sorted cell subpopulations


title: Meg-3_2


title: Vec-3_2


title: 35B9_Resistant_A498

description: Frozen A498 Resistant Sorafenib


title: 1ep11

description: MAS5.0 normalized data

value: Ependymal tumor

tag: primary/relapse

value: primary

tag: brain location

tag: age at diagnosis (years)

tag: gender


title: Meg-3_1

tag: cell line

tag: cell type


title: 1ep18

description: MAS5.0 normalized data

tag: tissue

value: m

tag: molecular subgroup


title: 35A8_Untreated_A498

description: Frozen A498 Untreated

tag: treatment

value: Frozen A498 Untreated Sorafenib


title: 35D5_Resistant_786-O

description: Frozen 786-O Resistant Sunitinb

source_name: Frozen 786-O Xenograft Tumors

value: Frozen 786-O Resistant Sunitinb


title: 35B8_Resistant_A498

description: Frozen A498 Resistant Sorafenib


title: 35D8_Resistant_786-O

description: Frozen 786-O Resistant Sunitinb


title: 35A4_Untreated_786-O

description: Frozen 786-O Untreated

value: Frozen 786-O Untreated Sunitinb


title: 35D4_Resistant_786-O

description: Frozen 786-O Resistant Sunitinb


title: 35A5_Untreated_786-O

description: Frozen 786-O Untreated


title: 35D7_Resistant_786-O

description: Frozen 786-O Resistant Sunitinb


title: Brain tumor 9533774107_R05C02

description:
Methylation data from ependymal tumor sample.
Location: 1: infratentorial; 2: spinal; 3: supratentorial.

tag: tumor type

tag: molecular subtype


title: Vec-3_1


title: 35A2_Untreated_786-O

description: Frozen 786-O Untreated


title: 35B7_Resistant_A498

description: Frozen A498 Resistant Sorafenib


title: 33C3_Resistant_786-O

description: Frozen 786-O Resistant Sorafenib

value: Frozen 786-O Resistant Sorafenib


title: 33C9_Resistant_786-O

description: Frozen 786-O Resistant Sorafenib


title: 33D6_Resistant_786-O

description: Frozen 786-O Resistant Sorafenib


title: 35A1_Untreated_786-O

description: Frozen 786-O Untreated


title: 33E3_Resistant_786-O

description: Frozen 786-O Resistant Sorafenib


title: 33D3_Untreated_786-O

description: Frozen 786-O Untreated

value: Frozen 786-O Untreated Sorafenib


title: Brain tumor 9297949078_R02C02


title: Repl.3_Area19 Ventricular Zone

city: San Juan de Alicante

first: Victor

last: Borrell

state: Alicante

address: Av Ramon y Cajal s/n

department: Institute of Neuroscience

country: Spain

institute: CSIC

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-036832 Ferret_44K_v3 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mustela putorius furo

source_name: Repl.3_Area19 Ventricular Zone

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy  Mini  RNA Purification kit (QUIAGEN, Cat. No. 74104) following the manufacturer's recommendations.  The protocol includes  cell lysis  and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: area

tag: zone

value: ventricular

value: Cerebral cortex

tag: age

value: Postnatal day 2


title: 33C6_Untreated_786-O

description: Frozen 786-O Untreated


title: Repl.3_Area19 Outer Subventricular Zone

source_name: Repl.3_Area19 Outer Subventricular Zone

value: outer subventricular


title: Repl.3_Area19 Inner Subventricular Zone_2

value: inner subventricular


title: Control glioblastoma stem cells

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on PrimeView Affymetrix Human Gene Expression Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

value: glioblastoma stem cells


title: Repl.3_Area17 Ventricular Zone

source_name: Repl.3_Area17 Ventricular Zone


title: 33B3_Untreated_786-O

description: Frozen 786-O Untreated

value: Mus musculus


title: 33B6_Resistant_786-O

description: Frozen 786-O Resistant Sorafenib

value: renal cell carcinoma


title: Repl.3_Area17 Outer Subventricular Zone_2


title: 33D9_Untreated_786-O

description: Frozen 786-O Untreated


title: Empty vector transfected cells, biological  rep1

city: Stanford

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

description: Ctrl #1

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16 hour (overnight) hybridization at 45°C at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using Robust Multichip Average (RMA) Express (v.1.0.4) using Affymetrix default analysis settings and quantile as normalization method.

source_name: Mouse SCLC cells_empty vector control_48 hrs

label_protocol: Affymetrix WT Plus kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Affymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: The mouse SCLC cell line, KP1, was grown and maintained at 37°C and 5% CO2 in RPMI media supplemented with 10% bovine growth serum and 1% penicillin-streptomycin.

extract_protocol: Total RNA was extracted using the Qiagen AllPrep DNA/RNA micro kit.

treatment_protocol: Cells were transfected with either an empty ires-GFP vector control or Notch1-ICD-ires-GFP and GFP+ cells were FACS sorted after 48 hours.

value: small cell lung cancer (SCLC) cell line

tag: cell line info.

value: mouse SCLC cells derived from Rb/p53/p130 triple knockout mouse model

tag: transfected with

value: empty vector; ires-GFP

tag: cell subtype

value: FACS sorted for GFP+ cells

tag: time point

value: 48 hours after transfection


title: Repl.3_Area17 Outer Subventricular Zone

source_name: Repl.3_Area17 Outer Subventricular Zone


title: PTPRZ1 knocking-down glioblastoma stem cells


title: Notch1-ICD transfected cells, biological rep 2

description: N1ICD #2

source_name: Mouse SCLC cells_Notch1-ICD_48 hrs

value: activated Notch1; Notch1-ICD-ires-GFP


title: Notch1-ICD transfected cells, biological rep 3

description: N1ICD #3


title: Repl.2_Area19 Ventricular Zone

source_name: Repl.2_Area19 Ventricular Zone


title: Empty vector transfected cells, biological  rep3

description: Ctrl #3


title: Differentiating Day 5 embryoid bodies, ascorbic acid treated, biological rep2

city: Cologne

first: Dina

last: Ivaniuk

address: Robert Koch Str.39

institute: Istitute for Neurophysiology University of Cologne

description: Gene expression data from day 5 of differentiation of mESC

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using Affymetrix Gene-Chip Scanner-3000-7G

data_processing: Robust Multi-array Analysis algorithm (RMA) did background correction, summarization and normalization.Quantile normalization  method was employed to normalize the raw dataset at probe feature level

source_name: Differentiating murine embryonic stem cells at day 5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: murine embryonic stem cells CGR8 were differentiated in hanging drop method.First cell were dissociated and grown in hanging drop with 500 cells per 25 μL .After Day 2 formed embryoid bodies were transfered to shaker and cultured addtional 3 days upon horizontal agitation. At chosen time points samples were collected

treatment_protocol: samples at different stages of differentiation were collected. Embryoid bodies were collected and washed 1 time in PBS and placed into TRIzol(Gibco)

value: mESC

value: day 5

tag: differentiation medium

value: 20% IMDM+Ascorbic acid(100 μM, Wako Pure Chemicals Industry, Japan)


title: Differentiating Day 5 embryoid bodies, ascorbic acid treated, biological rep3


title: Repl.2_Area19 Outer Subventricular Zone

source_name: Repl.2_Area19 Outer Subventricular Zone


title: Differentiating Day 5 embryoid bodies, ascorbic acid treated, biological rep1


title: 35A9_Untreated_A498

description: Frozen A498 Untreated

value: Frozen A498 Untreated Sorafenib

tag: host organism


title: Differentiating Day 5 embryoid bodies, non treated, biological rep2

value: 20% IMDM


title: Differentiating Day 5 embryoid bodies, non treated, biological rep3


title: Notch1-ICD transfected cells, biological rep 1

description: N1ICD #1


title: 35A6_Untreated_A498

description: Frozen A498 Untreated


title: Repl.2_Area19 Inner Subventricular Zone

source_name: Repl.2_Area19 Inner Subventricular Zone

value: Cerebral cortex

value: Postnatal day 2


title: 33B9_Untreated_786-O

description: Frozen 786-O Untreated

value: Frozen 786-O Untreated Sorafenib


title: Differentiating Day 3 embryoid bodies, ascorbic acid treated, biological rep2

description: Gene expression data from Day 3 of differentiation of mESC

source_name: Differentiating murine embryonic stem cells at day 3

value: day 3


title: Repl.2_Area17 Ventricular Zone

source_name: Repl.2_Area17 Ventricular Zone

value: ventricular


title: Differentiating Day 3 embryoid bodies, ascorbic acid treated, biological rep3


title: Differentiating Day 5 embryoid bodies, non treated, biological rep1


title: Differentiating Day 3 embryoid bodies, ascorbic acid treated, biological rep1


title: Repl.3_Area17 Inner Subventricular Zone

source_name: Repl.3_Area17 Inner Subventricular Zone

value: inner subventricular


title: Repl.2_Area17 Outer Subventricular Zone

source_name: Repl.2_Area17 Outer Subventricular Zone

value: outer subventricular


title: Differentiating Day 3 embryoid bodies, non treated, biological rep3