title: Colorectal cancer tissue sample (FFPE) 199


title: Colorectal cancer tissue sample (FFPE) 202

status: Public on Nov 14 2014

type: genomic

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

description:
CAIRO arm B: capecitabine and irinotecan first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.

hyb_protocol: Hybridization protocol available via www.agilent.com.

scan_protocol: Slides were scanned using the Agilent microarray scanner, protocol according to Agilent.

data_processing: The profiles were dewaved (van de wiel et al., Bioinformatics. 2009 (PMID 19276148)), median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al., Bioinformatics. 2007 (PMID 17267432)).

molecule: genomic DNA

organism: Homo sapiens

source_name: colorectal cancer, CAIRO arm B

label_protocol: DNA labeling protocol according to Enzo Life Sciences.

extract_protocol: DNA isolation protocol available via www.vumc.nl/microarrays. Also described in Brosens et al., J Pathol. 2010 (PMID 20593488).

tag: tissue

value: colorectal cancer (FFPE)

tag: study

value: CAIRO

tag: study arm

value: B

tag: progression-free survival first line (days)

tag: progression

value: yes

source_name: normal colorectum mucosa

value: normal colon mucosa

tag: patient

value: same patient as in ch1

tag: sample type

value: reference


title: Colorectal cancer tissue sample (FFPE) 196


title: Colorectal cancer tissue sample (FFPE) 190

description:
CAIRO arm A: capecitabine first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.

source_name: colorectal cancer, CAIRO arm A

value: A


title: Colorectal cancer tissue sample (FFPE) 195


title: Colorectal cancer tissue sample (FFPE) 188


title: Colorectal cancer tissue sample (FFPE) 185


title: Colorectal cancer tissue sample (FFPE) 187


title: Colorectal cancer tissue sample (FFPE) 186


title: Colorectal cancer tissue sample (FFPE) 184


title: Colorectal cancer tissue sample (FFPE) 189


title: Colorectal cancer tissue sample (FFPE) 201


title: Control 6

type: RNA

city: Toronto

first: Yidan

last: Zhao

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

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

scan_protocol: GeneChips were scanned using the HuGene-1_0-st-v1 GeneArray Scanner G2500A.

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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: Global profiles were determined in human lung tissue and compared across 11 normal and 12 severe pulmonary arterial hypertension patients.

tag: sample group

value: normal control

value: lung


title: Control 7


title: Colorectal cancer tissue sample (FFPE) 193


title: Control 5


title: Control 4


title: Control 3


title: Control 2


title: Control 1


title: PAH12

value: pulmonary arterial hypertension (PAH) patient


title: PAH11


title: PAH10


title: Colorectal cancer tissue sample (FFPE) 183


title: PAH9


title: PAH7


title: PAH8


title: Colorectal cancer tissue sample (FFPE) 180


title: Colorectal cancer tissue sample (FFPE) 182


title: Colorectal cancer tissue sample (FFPE) 179


title: PAH6


title: PAH5


title: Colorectal cancer tissue sample (FFPE) 175


title: Colorectal cancer tissue sample (FFPE) 178


title: Colorectal cancer tissue sample (FFPE) 218

description:
CAIRO2 arm A: capecitabine, oxaliplatin and bevacizumab
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.

source_name: colorectal cancer, CAIRO2 arm A

value: no


title: Colorectal cancer tissue sample (FFPE) 173


title: Colorectal cancer tissue sample (FFPE) 172


title: Colorectal cancer tissue sample (FFPE) 174


title: PAH4


title: Colorectal cancer tissue sample (FFPE) 223


title: Colorectal cancer tissue sample (FFPE) 171


title: Colorectal cancer tissue sample (FFPE) 176


title: PAH3


title: PAH1


title: PAH2


title: Colorectal cancer tissue sample (FFPE) 164


title: Colorectal cancer tissue sample (FFPE) 167


title: Colorectal cancer tissue sample (FFPE) 169


title: Colorectal cancer tissue sample (FFPE) 168


title: Colorectal cancer tissue sample (FFPE) 170


title: Colorectal cancer tissue sample (FFPE) 166


title: Colorectal cancer tissue sample (FFPE) 165


title: WT rep6

city: Herston

first: Steven

last: Lane

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

description: replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were imported with IDATreader (version 0.2.0, http://www.compbio.group.cam.ac.uk/software/idatreader) to R from Illumina GenomeStudio, after default trimming and collapsing of beads. The data were normalized with lumi (Du et al., 2008). Probes were reannotated and filtered as described previously (Barbosa-Morais et al., 2010)

organism: Mus musculus

source_name: AML LSC

label_protocol: Biotinylated cRNA was prepared using Illumina Total Prep RNA amplification kit (Ambion) according to the manufacturer's recommendations.

growth_protocol: Sublethally irradiated (5.5Gy) 6-8 weeks old C57BL/6J recipients were injected with 10,000 WT or G3 Terc-/- MLLAF9gfp expressing bone marrow derived LKS (lin-, kit+, sca1+). LSC (MLLAF9gfp+, lin-, kit+, Fcgr+) were purified from bone marrow of recipients at individual AML onset.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit including DNAse I treatment according to the manufacturer's recommendations.

tag: strain

tag: cell type

value: purified primary bone marrow - derived LSC (MLLAF9gfp+, lin-, kit+, Fcgr+)


title: Colorectal cancer tissue sample (FFPE) 181


title: Terc-/- rep5

description: replicate 5

tag: terc-/- p53/foxo3a phosphorylation status


title: WT rep4

description: replicate 4


title: Colorectal cancer tissue sample (FFPE) 160


title: Terc-/- rep6

description: replicate 6


title: Terc-/- rep2

description: replicate 2


title: Terc-/- rep4

description: replicate 4

value: p-foxo3a+ (Ser253)


title: Terc-/- rep3

description: replicate 3


title: Colorectal cancer tissue sample (FFPE) 162


title: Colorectal cancer tissue sample (FFPE) 158


title: Colorectal cancer tissue sample (FFPE) 157


title: WT rep2

description: replicate 2


title: Colorectal cancer tissue sample (FFPE) 156


title: Colorectal cancer tissue sample (FFPE) 159


title: Colorectal cancer tissue sample (FFPE) 163


title: Colorectal cancer tissue sample (FFPE) 161


title: WT rep3

description: replicate 3


title: Colorectal cancer tissue sample (FFPE) 155


title: Terc-/- rep1

description: replicate 1


title: Colorectal cancer tissue sample (FFPE) 154


title: WT rep1

description: replicate 1


title: Colorectal cancer tissue sample (FFPE) 153


title: WT rep5

description: replicate 5


title: MCSF derived M2 macrophage, rep2

city: Seoul

first: Yi Rang

address: 101, daehak-ro Jongro-gu

department: Microbiology and Immunology

country: South Korea

institute: Seoul National University College of Medicine

description: gene expression data from murine M2 macrophages

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 1.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: C57BL/6J bone marrow derived cells with M-CSF for 7 days

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Bone marrow cells were differentiated with GM-CSF or M-CSF for 7days in the 10% FBS supplemented RPMI media at 37℃, 5% CO2 ambient.

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

treatment_protocol: Cells were scraped, stained with appropriate antibodies and sorted using BD FACS Aria. Sorted cells were washed with PBS three times and immersed in Trizol reagent.

value: macrophages

value: bone marrow


title: GMCSF derived M1 macrophage, rep2

description: gene expression data from murine M1 macrophages

source_name: C57BL/6J bone marrow derived cells with GM-CSF for 7 days


title: GMCSF derived M1 macrophage, rep1


title: E11.5_serum_free

city: Kyoto

first: Eisuke

last: Nishida

address: Kitashirakawa, Sakyo-ku

department: Department of Cell and Developmental Biology

country: Japan

institute: Graduate School of Biostudies, Kyoto University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner.

data_processing: The data were analyzed with Expression Console (v.1.1). Expression signals of probe sets were calculated using RMA algorithm.

source_name: E11.5_kidneys_serum-free DMEM_48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Kidneys were isolated from C57BL/6 mouse embryos at days 11.5 of gestation and positioned on top of a Transwell filter within an individual well of a 6-well tissue culture dish.

extract_protocol: Total RNA was prepared using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instruction.

treatment_protocol: E11.5 kidneys were cultured for 48 h in 10% FBS DMEM, serum-free DMEM, and serum-free DMEM with retinoic acid.

tag: developmental stage

value: kidney

tag: medium

value: Serum-free DMEM


title: E11.5_serum

source_name: E11.5_kidneys_10% FBS DMEM_48h

value: 10% FBS DMEM


title: Colorectal cancer tissue sample (FFPE) 150

value: colorectal cancer (FFPE)

value: CAIRO


title: MCSF derived M2 macrophage, rep1


title: Colorectal cancer tissue sample (FFPE) 147

value: B

value: yes

value: normal colon mucosa


title: Colorectal cancer tissue sample (FFPE) 148

value: A

value: same patient as in ch1

value: reference


title: Colorectal cancer tissue sample (FFPE) 151


title: Colorectal cancer tissue sample (FFPE) 146


title: Colorectal cancer tissue sample (FFPE) 144


title: Colorectal cancer tissue sample (FFPE) 177


title: Colorectal cancer tissue sample (FFPE) 145


title: Colorectal cancer tissue sample (FFPE) 138


title: Colorectal cancer tissue sample (FFPE) 135


title: Colorectal cancer tissue sample (FFPE) 143


title: Colorectal cancer tissue sample (FFPE) 141


title: Colorectal cancer tissue sample (FFPE) 139


title: Colorectal cancer tissue sample (FFPE) 137


title: Colorectal cancer tissue sample (FFPE) 132


title: Colorectal cancer tissue sample (FFPE) 136


title: Colorectal cancer tissue sample (FFPE) 140


title: Colorectal cancer tissue sample (FFPE) 142


title: Colorectal cancer tissue sample (FFPE) 131


title: Colorectal cancer tissue sample (FFPE) 133


title: Colorectal cancer tissue sample (FFPE) 130


title: Colorectal cancer tissue sample (FFPE) 129


title: Colorectal cancer tissue sample (FFPE) 128


title: Colorectal cancer tissue sample (FFPE) 134


title: Colorectal cancer tissue sample (FFPE) 127


title: Colorectal cancer tissue sample (FFPE) 123


title: Colorectal cancer tissue sample (FFPE) 124


title: Colorectal cancer tissue sample (FFPE) 121


title: Colorectal cancer tissue sample (FFPE) 125


title: Colorectal cancer tissue sample (FFPE) 120


title: Colorectal cancer tissue sample (FFPE) 114


title: Colorectal cancer tissue sample (FFPE) 122


title: Colorectal cancer tissue sample (FFPE) 119


title: Colorectal cancer tissue sample (FFPE) 117


title: Colorectal cancer tissue sample (FFPE) 118


title: Colorectal cancer tissue sample (FFPE) 116


title: Colorectal cancer tissue sample (FFPE) 115


title: Colorectal cancer tissue sample (FFPE) 109


title: Colorectal cancer tissue sample (FFPE) 112


title: Colorectal cancer tissue sample (FFPE) 106


title: Colorectal cancer tissue sample (FFPE) 110


title: Colorectal cancer tissue sample (FFPE) 105


title: Colorectal cancer tissue sample (FFPE) 113


title: Colorectal cancer tissue sample (FFPE) 111


title: Colorectal cancer tissue sample (FFPE) 107


title: Colorectal cancer tissue sample (FFPE) 108


title: Colorectal cancer tissue sample (FFPE) 102


title: Colorectal cancer tissue sample (FFPE) 103


title: Colorectal cancer tissue sample (FFPE) 104


title: Colorectal cancer tissue sample (FFPE) 100


title: Colorectal cancer tissue sample (FFPE) 97


title: Colorectal cancer tissue sample (FFPE) 101


title: Colorectal cancer tissue sample (FFPE) 126


title: Colorectal cancer tissue sample (FFPE) 92


title: Colorectal cancer tissue sample (FFPE) 88


title: Colorectal cancer tissue sample (FFPE) 98


title: Colorectal cancer tissue sample (FFPE) 93


title: Colorectal cancer tissue sample (FFPE) 94


title: Colorectal cancer tissue sample (FFPE) 149


title: E11.5_RA

source_name: E11.5_kidneys_serum-free DMEM with retionic acid_48h

value: Serum-free DMEM with retinoic acid


title: Colorectal cancer tissue sample (FFPE) 91


title: Colorectal cancer tissue sample (FFPE) 96


title: Colorectal cancer tissue sample (FFPE) 152


title: Colorectal cancer tissue sample (FFPE) 87


title: Colorectal cancer tissue sample (FFPE) 86


title: Colorectal cancer tissue sample (FFPE) 89


title: Colorectal cancer tissue sample (FFPE) 84


title: Colorectal cancer tissue sample (FFPE) 82


title: Colorectal cancer tissue sample (FFPE) 90


title: Colorectal cancer tissue sample (FFPE) 95


title: Colorectal cancer tissue sample (FFPE) 83


title: Colorectal cancer tissue sample (FFPE) 80


title: Colorectal cancer tissue sample (FFPE) 85


title: Colorectal cancer tissue sample (FFPE) 81


title: Colorectal cancer tissue sample (FFPE) 76


title: Colorectal cancer tissue sample (FFPE) 73


title: Colorectal cancer tissue sample (FFPE) 78


title: Colorectal cancer tissue sample (FFPE) 99


title: Colorectal cancer tissue sample (FFPE) 74


title: Colorectal cancer tissue sample (FFPE) 67


title: Colorectal cancer tissue sample (FFPE) 71

value: no


title: Colorectal cancer tissue sample (FFPE) 69


title: Colorectal cancer tissue sample (FFPE) 70


title: Colorectal cancer tissue sample (FFPE) 68


title: Colorectal cancer tissue sample (FFPE) 66


title: Colorectal cancer tissue sample (FFPE) 72


title: Colorectal cancer tissue sample (FFPE) 63


title: Colorectal cancer tissue sample (FFPE) 62


title: Colorectal cancer tissue sample (FFPE) 58


title: Colorectal cancer tissue sample (FFPE) 75


title: Colorectal cancer tissue sample (FFPE) 65


title: Colorectal cancer tissue sample (FFPE) 59


title: Colorectal cancer tissue sample (FFPE) 64


title: Colorectal cancer tissue sample (FFPE) 57


title: Colorectal cancer tissue sample (FFPE) 54


title: Colorectal cancer tissue sample (FFPE) 55


title: Colorectal cancer tissue sample (FFPE) 56


title: Colorectal cancer tissue sample (FFPE) 53


title: Colorectal cancer tissue sample (FFPE) 52


title: Colorectal cancer tissue sample (FFPE) 60


title: Colorectal cancer tissue sample (FFPE) 51


title: Colorectal cancer tissue sample (FFPE) 46


title: Colorectal cancer tissue sample (FFPE) 49


title: Colorectal cancer tissue sample (FFPE) 48


title: Colorectal cancer tissue sample (FFPE) 47


title: Colorectal cancer tissue sample (FFPE) 41


title: Colorectal cancer tissue sample (FFPE) 43


title: Colorectal cancer tissue sample (FFPE) 39


title: Colorectal cancer tissue sample (FFPE) 40


title: Colorectal cancer tissue sample (FFPE) 50


title: Colorectal cancer tissue sample (FFPE) 45


title: Colorectal cancer tissue sample (FFPE) 38


title: Colorectal cancer tissue sample (FFPE) 29


title: Colorectal cancer tissue sample (FFPE) 37


title: Colorectal cancer tissue sample (FFPE) 30


title: Colorectal cancer tissue sample (FFPE) 61


title: Colorectal cancer tissue sample (FFPE) 36


title: Colorectal cancer tissue sample (FFPE) 42


title: Colorectal cancer tissue sample (FFPE) 31


title: Colorectal cancer tissue sample (FFPE) 33


title: Colorectal cancer tissue sample (FFPE) 44


title: Colorectal cancer tissue sample (FFPE) 34


title: Colorectal cancer tissue sample (FFPE) 79


title: Colorectal cancer tissue sample (FFPE) 27


title: Colorectal cancer tissue sample (FFPE) 28


title: Colorectal cancer tissue sample (FFPE) 26


title: Colorectal cancer tissue sample (FFPE) 21


title: Colorectal cancer tissue sample (FFPE) 22


title: Colorectal cancer tissue sample (FFPE) 24


title: Colorectal cancer tissue sample (FFPE) 23


title: Colorectal cancer tissue sample (FFPE) 18


title: Colorectal cancer tissue sample (FFPE) 20


title: A/Shanghai/1/2013

type: protein

city: CHICAGO

first: Patrick

middle: C

last: Wilson

state: Illinois

address: 924 E 57th street, Knapp building

department: Medicine, Rheumatology

country: USA

institute: University of Chicago

description:
raw data file: Wilson_11.12.14_array2.xlsx (Block 17)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Shanghai. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.

hyb_protocol: The array was blocked for 1 hour. Then the anti-human IgG-Fc Cy3 was applied on the array for 1hour then washed. 40µg/ml of each biotinylated HA was applied to the array for 1hour then washed and finally the streptavidin-Cy5 was applied and then washed.

scan_protocol: scanned using GenePix 4000B

data_processing: software GenePix Pro 6.0. Ratio of fluorescence (Cy5/Cy3) was used as the anti-human IgG Fc was used to normalize variation in antibody spotting.

molecule: protein

organism: Influenza A virus

source_name: recombinant H7 HA from baculovirus

label_protocol: each recombinant HA was biotinylated overnight prior to incubation on the array

extract_protocol: recombinant HA from baculovirus

tag: protein

value: A recombinant form of the H7 hemagglutinin (HA) protein from influenza virus

tag: labeling

value: biotin then streptavidin-Cy5

organism: Capra hircus

source_name: anti-human IgG Fcγ fragment specific

extract_protocol: anti-human IgG Fc fragment specific generated in goat

value: anti-human IgG antibody Fcγ fragment specific


title: A/Canada/rv444/2004 H7 HA

description:
raw data file: Wilson_11.10.14_array1.xlsx (Block 13)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Canada. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.

tag: to normalize variation in antibody spotting


title: A/Netherlands/219/2003

description:
raw data file: Wilson_11.10.14_array1.xlsx (Block 16)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Netherlands. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.


title: Colorectal cancer tissue sample (FFPE) 77


title: A/chicken/Jalisco/12283/2012 H7 HA

description:
raw data file: Wilson_11.10.14_array1.xlsx (Block 15)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Jalisco. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.

value: A/chicken/Jalisco/12283/2012 H7


title: A/Victoria/316/2011 H3N2 HA

description:
raw data file: Wilson_11.10.14_array1.xlsx (Block 10)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Victoria. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.

source_name: recombinant H3 HA from baculovirus

value: A recombinant form of the H3 hemagglutinin (HA) protein from influenza virus


title: Colorectal cancer tissue sample (FFPE) 13


title: Colorectal cancer tissue sample (FFPE) 12


title: Colorectal cancer tissue sample (FFPE) 16


title: A/Anhui/1/2013

description:
raw data file: Wilson_11.12.14_array2.xlsx (Block 16)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Anhui. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.


title: Colorectal cancer tissue sample (FFPE) 15


title: Colorectal cancer tissue sample (FFPE) 17


title: Colorectal cancer tissue sample (FFPE) 9


title: Colorectal cancer tissue sample (FFPE) 14


title: Colorectal cancer tissue sample (FFPE) 19


title: Colorectal cancer tissue sample (FFPE) 10


title: Colorectal cancer tissue sample (FFPE) 11


title: A/Perth/16/2009 H3N2 HA

description:
raw data file: Wilson_11.10.14_array1.xlsx (Block 7)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Perth. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.


title: Control Untreated Cells 2

city: Hamilton

first: Ali

middle: A

last: Ashkar

address: 1280 Main Street West

department: McMaster Immunology Research Center

institute: McMaster University

description:
Control
SAMPLE 5

data_processing:
The normalization and all data analysis were performed according to manufacturers instructions using the web based software package :  http://sabiosciences.com/pcrarraydataanalysis.php.  Data was normalized to GAPDH. Target gene signals were normalized to housekeeping gene GAPDH(2^n - ΔCt where ΔCt= (Ct(target or GOI) - Ave Ct (HKG)) .  The software package automatically performs all fold change calculations based upon the original raw data submitted.
The matrix normalized worksheet reports the normalized signal against the housekeeping gene.
The fold change worksheet reports the fold change between the treated (500ng/ml)/control(0ng/ml) ratios.

label: SYBR green

label_protocol: PCR Arrays were performed using the RT^2 Profiler PCR Array for Mouse Fatty Acid Metabolism (SABiosciences).  400ng of RNA per sample was used to create cDNA following the procedure outlined in the RT^2 First Strand Kit (3304011,Qiagen).  The plate was run on the Applied Biosystems 7900 RT machine as outlined in the manufacturers instructions.

growth_protocol: Murine preadipocyte 3T3-L1 cells were purchased from ATCC and grown in DMEM with 10% bovine serum, grown to confluency, and treated with adipogenic induction media, defined as day 0, which includes 10% fetal bovine serum, 10ug/ml human insulin, 250nM dexamethasone, and 0.5 mM 30isobutyl-1-methylxanthine (IBMX) in DMEM for 48 hours. The cells were then given 10% FBS DMEM post-induction media for another 12 days. During this time, cells were given fresh media every 2-3 days. Cells were terminally differentiated at day 14.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

treatment_protocol: Once terminally differentiated at day 14, adipocytes were treated with 0ng/ml (control) or 500ng/ml (test) of rmIL-15 for 24 hours

value: Differentiated Adipocytes

tag: activation agent

tag: time

value: 14 days + 1 day


title: Control Untreated Cells 3

description:
Control
SAMPLE 6


title: A/Wisconsin/67/2005 H3N2 HA

description:
raw data file: Wilson_11.10.14_array1.xlsx (Block 4)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Wisconsin. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.

value: A/Wisconsin/67/2005 H3N2


title: 500ng/ml rmIL-15 Treated Cells 1

description:
Test
SAMPLE 1

value: Control


title: Control Untreated Cells 1

description:
Control
SAMPLE 4


title: A/Uruguay/716/2007 H3N2 HA

description:
raw data file: Wilson_11.10.14_array1.xlsx (Block 1)
Channel 1: recombinant HA biotinylated
Reactivity of the antibodies spotted on the array with the HA A/Uruguay. Normalization with the anti-human IgG atibody Fcγ fragment specific.
For the HAs, A/Uruguay, A/Wisconsin, A/Perth, A/Victoria, A/Canada and A/Netherlands have been obtained by BEI ressources. From their website: The H3 hemagglutinin (HA)    protein from influenza virus A/Wisconsin/67/2005 (H3N2) is a full-length    glycosylated recombinant protein that was produced in Sf9 insect cells    using a baculovirus expression vector system. The recombinant H3 HA protein    was purified under conditions that preserve its biological activity and    tertiary structure.    For the HAs A/Anhui et A/Shanghai, they are home made but the same protocol    was used.


title: Colorectal cancer tissue sample (FFPE) 35

tag: tissue

value: colorectal cancer (FFPE)

tag: study

value: CAIRO


title: Colorectal cancer tissue sample (FFPE) 8

tag: study arm

value: B

tag: progression-free survival first line (days)

value: yes

value: normal colon mucosa


title: Colorectal cancer tissue sample (FFPE) 7

value: A

tag: progression

tag: patient

value: same patient as in ch1

value: reference


title: 500ng/ml rmIL-15 Treated Cells 3

description:
Test
SAMPLE 3


title: HGSOC Rep5

city: Jinan

first: Zhaojian

last: Liu

state: Shandong

address: 44# Wenhua xi Road

department: Cell Biology

country: China

institute: Shandong University

description: miRNA profiling data from high-grade serous ovarian carcinoma

hyb_protocol: Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: Slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor.
Expressed data were normalized using the Median normalization.

source_name: high-grade serous ovarian carcinoma

label_protocol: miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3 fluorescent , using T4 RNA ligase

growth_protocol: Tissue transferred into RNAlater within 30 minutes of removal, and frozen at -80C

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

treatment_protocol: Cryopulverization of tissue using the Biopulverizer and then homogenization using the Mini-Bead-Beater-16 before RNA extraction

tag: gender

value: female

value: high-grade serous ovarian carcinoma


title: Colorectal cancer tissue sample (FFPE) 32

tag: sample type


title: 500ng/ml rmIL-15 Treated Cells 2

description:
Test
SAMPLE 2

tag: cell type


title: HGSOC Rep3


title: HGSOC Rep2


title: HGSOC Rep4


title: HGSOC Rep1


title: Normal FT Rep5

description: miRNA profiling data from normal fallopian tube fimbria

source_name: normal fallopian tube fimbria

value: normal fallopian tube fimbria


title: Normal FT Rep4


title: Perfusion 1 pulses 100 nM GnRH D3

city: La Jolla

first: Nick

last: Webster

state: CA

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description: RNA from GnRH pulse perfusion experiment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse MU74Av2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using theAffymetrix GCS3000 scanner.

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

source_name: LbetaT2 gonadotrope cell RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: LbT2 cells were maintained in monolayer cultures in DMEM supplemented with 10% fetal bovine serum and antibiotics in a humidified 10% CO2 atmosphere at 37 °C.  For perfusion studies, cells were plated on cytodex 3 microcarrier beads (GE Healthcare, Buckinghamshire, England) at a density of 1.5 x 107 cells/ml bed volume.  After culture for 5 days, cells were pelleted by spinning at 1000Xg for 1 minute, washed once with Serum-Free DMEM, re-pelleted, and placed in Serum-Free DMEM 16-18h.

extract_protocol: Total RNA was harvested from perifused cells on cytodex 3 microcarriers using Trizol LS and purified on RNeasy spin columns (Qiagen, Valencia, CA).  The mRNA was quantified and its integrity checked by agarose gel electrophoresis.

treatment_protocol: Cells were then loaded into perifusion columns and equilibrated for 1 h in serum-free DMEM supplemented with penicillin and streptomycin at a flow rate of 300 microliters/min.  Subsequently, cells were pulsed for 2 minutes once or at 28, 58, 118 minute intervals or given tonic 10 or 100 nM GnRH for 4 h for the microarray studies, or 6h for the transfection studies.  Perifusion chambers were constructed from C10 chromatography columns (GE Healthcare, Buckinghamshire, England) with modified flow adapters and cells were maintained by perifusion with DMEM equilibrated in an atmosphere of 5% CO2 using a minipulse 3 peristaltic pump (Gilson, Middleton, WI).

tag: #pulses

tag: concentration


title: Colorectal cancer tissue sample (FFPE) 4


title: Colorectal cancer tissue sample (FFPE) 5

description:
CAIRO arm B: capecitabine and irinotecan first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.


title: Perfusion unstimulated D5

value: constant


title: Perfusion 8 pulses 100 nM GnRH D0


title: Perfusion tonic 100 nM GnRH D4


title: Perfusion tonic 10 nM GnRH C4

value: 10 nM


title: Colorectal cancer tissue sample (FFPE) 3


title: Colorectal cancer tissue sample (FFPE) 6

description:
CAIRO arm A: capecitabine first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments.


title: Perfusion 4 pulses 10 nM GnRH C1


title: Colorectal cancer tissue sample (FFPE) 1


title: Perfusion 8 pulses 10 nM GnRH C0


title: Normal FT Rep3


title: Normal FT Rep2


title: Perfusion 1 pulse 10 nM GnRH C3


title: Perfusion 2 pulses 100 nM GnRH D2


title: Normal FT Rep1


title: Colorectal cancer tissue sample (FFPE) 25


title: Perfusion 4 pulses 100 nM GnRH D1


title: Colorectal cancer tissue sample (FFPE) 2


title: Perfusion 4 pulses 10 nM GnRH B1


title: DERL7 24h DMSO

city: Madrid

first: Esperanza

last: Martín-Sánchez

address: Melchor Fernandez Almagro 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: DERL7 cells treated with DMSO for 24h as the control condition for this time point

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent Technologies, Inc.) were added, and samples were applied to microarrays enclosed in Agilent hybridization chambers. After hybridization, slides were sequentially washed.

scan_protocol: Microarray slides were scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Bioconductor's limma package was employed for normalization, thus, background was corrected using normexp method and data were normalized using loess and quantiles method for within-array and inter-array normalization, respectively. GEPAS version 4.0 was used to merge replicates.

source_name: DERL7 cells treated with DMSO for 24h

label_protocol: 500 ng of total RNA were primed with the T7 promoter primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of MMLV RT. Then, the resulting cDNA was transcribed and labeled into cRNA using T7 RNA polymerase, NTPs and a fraction of Cy3-CTP (for the RNA reference) and Cy5-CTP (for the samples) for 2 h at 40ºC (all reagents were obtained from Agilent Technologies, Inc., Santa Clara, CA, USA).

growth_protocol: HuT78, SR786 and MyLa cells were maintained in RPMI 1640 supplemented with 10 % heat-inactivated fetal bovine serum and 1 % penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37 ºC. All reagents were purchased from Life Technologies (Carlsbad, CA, USA). DERL7 cell were additionally supplemented with 20 % heat-inactivated fetal bovine serum and 20 ng/ml human interleukin-2 (PeproTech, Rocky Hill, NJ, USA).

extract_protocol: Total RNA was extracted and purified with the RNeasy Mini Kit (Qiagen, Valencia, CA, USA) following manufacturer's instructions.

treatment_protocol: All cell lines were cultured with 10 μM of the pan-PIM inhibitor ETP-39010 or the vehicle DMSO as a control for 0, 2, 4, 6, 10 and 24 h.

tag: cell line

value: Cell line derived from a patient with hepatosplenic gamma-delta T cell lymphoma

tag: agent

value: control

source_name: Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell ines

tag: reference rna composition

value: RNA from 10 human tumor cell lines


title: DERL7 24h PIM inhibitor

description: DERL7 cells treated with the pan-PIM inhibitor ETP-39010 for 24h

source_name: DERL7 cells treated with PIMi for 24h

value: pan-PIM inhibitor ETP-39010


title: Perfusion tonic 10 nM GnRH B4


title: Pig Sus ileum 016

city: Piacenza

first: Lorenzo

last: Bomba

state: Piacenza

address: via Emilia Parmense, 82

department: Istituto di Zootecnica

country: Italy

institute: Università Cattolica del Sacro Cuore

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)

hyb_protocol: Prehybridization was performed by incubating the arrays with prehybridization solution (6X SSPE, 1% SDS, 0.2% BSA) for 60 minutes at 37 °C.  Hybridization was performed at 37°C for 16 hours in hybridization solution (6X SSPE, 0.8% BSA, 12% DI Formamide, 2.5% SDS). Hybridization washings were performed as following: - wash with 6X SSPET wash solution (6X SSPE, 0.05% Tween-20). - wash with 3X SSPET wash solution (3X SSPE, 0.05% Tween-20). - 2 washes with 0.5X SSPET wash solution (0.5X SSPE, 0.05% Tween-20)

scan_protocol: Scanning was performed using Perkin Elmer ScanArray 4000XL microarray scanner and ScanArray Express 4.0 acquisition software. Laser was set at 60% of power. PMT gain was set at 60%

data_processing: Raw data was extracted using a GenePix 4000B scanner (Molecular Devices, Sunnyvale, USA).

label: Cyanine 5

organism: Sus scrofa

source_name: Ileum tissue_T5_Standard+SorbicAcid

label_protocol: Total RNA (2 μg) was amplified and labeled with Cy5 using RNA Ampulse amplification and labeling kit for Combimatrix one color arrays (Kreatech Diagnostics, The Netherlands), according to manufacturer recommendations. Briefly, the double strand cDNA was obtained by reverse transcribing the total RNA using T7 Oligo (dT) primer. The cDNA was transcribed in vitro to generate an amplified antisense RNA (aRNA). The aRNA was labeled with Cyanine 5 fluorophore using a chemical ligation. After purification, the labeled aRNA was quantified by Varian's Cary spectrophotometer (Agilent Technologies - Life Sciences and Chemical).

growth_protocol: At weaning day (T0, 4wk old), 4 piglets were sacrified and tissue samples collected. The remaining 12 piglets were transported to the experimental farm. There, the piglets were weighted and randomly assigned to different post weaning (T5) diets. One diet (diet A; six piglets) contained 5 g/kg of sorbic acids. In diet B (six piglets) the organic acids were replaced by barley flour. Five days after weaning (T5) all piglets were sacrified and tissue samples collected.

extract_protocol: Total RNA was isolated from ileum samples using the Chomczynski-Sacchi method

treatment_protocol: Piglets were first anaesthetized by i.m. injection of a mixture of Zoletil 100® (Virbac), Rompun (Bayer) and atropine sulfate (6.3 mg/kg of BW + 2.3 mg/kg of BW + 20 µg/kg of BW respectively) and then sacrificed by exsanguination. Before sacrifice, blood samples were obtained from the jugular vein using two vacuum tubes (Vacuette, Kremsmünster, Austria) containing Li-heparin and K-EDTA respectively. The intestine was harvested via midline laparotomy and tissue and digesta samples from the ileum, cecum and colon were collected, weighted and stored at -80°C

value: Ileum

value: Female

tag: age

value: 33 days

tag: diet

value: Standard+SorbicAcid


title: DERL7 6h PIM inhibitor

description: DERL7 cells treated with the pan-PIM inhibitor ETP-39010 for 6h

source_name: DERL7 cells treated with PIMi for 6h

tag: time


title: DERL7 10h DMSO

description: DERL7 cells treated with DMSO for 10h as the control condition for this time point

source_name: DERL7 cells treated with DMSO for 10h


title: Perfusion 1 pulse 100 nM GnRH A3


title: DERL7 4h DMSO

description: DERL7 cells treated with DMSO for 4h as the control condition for this time point

source_name: DERL7 cells treated with DMSO for 4h


title: Perfusion 1 pulse 10 nM GnRH B3


title: DERL7 10h PIM inhibitor

description: DERL7 cells treated with the pan-PIM inhibitor ETP-39010 for 10h

source_name: DERL7 cells treated with PIMi for 10h


title: Perfusion 8 pulses 10 nM GnRH B0


title: Pig Sus ileum 014

tag: tissue


title: Perfusion unstimulated A5


title: Perfusion 4 pulses 100 nM GnRH A1


title: Perfusion 2 pulses 100 nM GnRH A2


title: Pig Sus ileum 010

source_name: Ileum tissue_T5_Standard

value: Standard


title: DERL7 4h PIM inhibitor

description: DERL7 cells treated with the pan-PIM inhibitor ETP-39010 for 4h

source_name: DERL7 cells treated with PIMi for 4h


title: DERL7 0h PIM inhibitor

description: DERL7 cells treated with the pan-PIM inhibitor ETP-39010 for 0h

source_name: DERL7 cells treated with PIMi for 0h


title: DERL7 6h DMSO

description: DERL7 cells treated with DMSO for 6h as the control condition for this time point

source_name: DERL7 cells treated with DMSO for 6h


title: DERL7 0h DMSO

description: DERL7 cells treated with DMSO for 0h as the control condition for this time point

source_name: DERL7 cells treated with DMSO for 0h


title: DERL7 2h PIM inhibitor

description: DERL7 cells treated with the pan-PIM inhibitor ETP-39010 for 2h

source_name: DERL7 cells treated with PIMi for 2h


title: Pig Sus ileum 015


title: Perfusion 8 pulses 100 nM GnRH A0


title: DERL7 2h DMSO

description: DERL7 cells treated with DMSO for 2h as the control condition for this time point

source_name: DERL7 cells treated with DMSO for 2h


title: Pig Sus ileum 013


title: Pig Sus ileum 011


title: Pig Sus ileum 009


title: Perfusion tonic 100 nM GnRH A4


title: Pig Sus ileum 008


title: Pig Sus ileum 012


title: Pig Sus ileum 007


title: Pig Sus ileum 006


title: T5

city: SuZhou

first: Tao

last: Chen

state: JiangSu

address: 199 Ren-Ai-rd

institute: Soochow University

description: Gene expression after 5 days in mouse liver treated with TCE at 1000 mg/kg b.w.

hyb_protocol: Total RNAs were transcribed to double strand cDNA and then, synthesized into cRNA and labeled with Cyanine-3-CTP. The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned by the Agilent Scanner G2505C (Agilent Technologies).

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze microarray images to obtain the raw data and basic analysis was completed using Genesrping.
Differentially expressed genes were then identified through fold change as well as P value obtained from the t-test. The threshold set for up- and down-regulated genes was a fold change of >= 2.0 and a P value<= 0.05.

source_name: liver,TCE, replicate 3

label_protocol: The Agilent Mouse Gene Expression kit (8x60K, Design ID：028005) was used which included 39430 mRNAs.

extract_protocol: Genomic DNA and RNA were purified using AllPrep DNA/RNA Mini Kit (Tiangen, Beijing, China). Turbo DNA-freeTM kit (Life Technologies, Shanghai, China) was used to remove genomic DNA contamination in purified RNA samples.

treatment_protocol: Adult B6C3F1 male mice were oral administrated with either corn oil or TCE for five days. Form each mouse, liver was excised rapidly, frozen in liquid nitrogen, and stored at -80oC.

value: liver

value: male

tag: strain

tag: treatment

value: TCE at 1000mg/kg


title: Pig Sus ileum 005


title: MyLa 10h PIM inhibitor

description: MyLa cells treated with the pan-PIM inhibitor ETP-39010 for 10h

source_name: MyLa cells treated with PIMi for 10h

value: MyLa

value: Cell line derived from a Mycosis Fungoides patient


title: Pig Sus ileum 004

source_name: Ileum tissue_T0_Standard

value: 28  days


title: MyLa 24h PIM inhibitor

description: MyLa cells treated with the pan-PIM inhibitor ETP-39010 for 24h

source_name: MyLa cells treated with PIMi for 24h

source_name: Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell ines


title: MyLa 10h DMSO

description: MyLa cells treated with DMSO for 10h as the control condition for this time point

source_name: MyLa cells treated with DMSO for 10h


title: T4

source_name: liver,TCE, replicate 2


title: T3

source_name: liver,TCE, replicate 1


title: MyLa 4h PIM inhibitor

description: MyLa cells treated with the pan-PIM inhibitor ETP-39010 for 4h

source_name: MyLa cells treated with PIMi for 4h


title: MyLa 24h DMSO

description: MyLa cells treated with DMSO for 24h as the control condition for this time point

source_name: MyLa cells treated with DMSO for 24h


title: MyLa 4h DMSO

description: MyLa cells treated with DMSO for 4h as the control condition for this time point

source_name: MyLa cells treated with DMSO for 4h


title: C4

description: Gene expression after 5 days in mouse liver treated with corn oil

source_name: liver,control, replicate 2

value: corn oil


title: NT_Rep3

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

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

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

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

data_processing: Gene expression data were analyzed through Affymetrix Expression Console using gene-level RMA summarization and sketch-quantile normalization methods; core-gene analysis.

source_name: no treatment

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

growth_protocol: Human lymphoblastoid GM12878 (Coriell Cell Repositories, Camden, NJ), were cultured  in RPMI 1640 medium supplemented with 15% heat-inactivated fetal bovine serum (Invitrogen, Carlsbad, CA) and 1X antibiotics/antimycotics (Gibco, Carlsbad, CA). Cells were incubated at 37 C with 5% CO2.

extract_protocol: Total RNAs were extracted using Qiagen total RNA Miniprep kit (Qiagen, cat #74104 ) with DNase 1 (Invitrogen) digestion according to the manufacturer’s instructions.

treatment_protocol: Lymphoblastoid cells were seeded at 15-cm dish and treated with 0.5 uM doxorubicin or vehicle (water) for up to 18h.

value: control (vehicle)


title: MyLa 0h PIM inhibitor

description: MyLa cells treated with the pan-PIM inhibitor ETP-39010 for 0h

source_name: MyLa cells treated with PIMi for 0h


title: Pig Sus ileum 002

description: All the procedures provided were performed as indicated by Combimatrix protocols available at Combimatrix website (www.combimatrix.com)


title: MyLa 6h PIM inhibitor

description: MyLa cells treated with the pan-PIM inhibitor ETP-39010 for 6h

source_name: MyLa cells treated with PIMi for 6h


title: NT_Rep1


title: NT_Rep2


title: C3

source_name: liver,control, replicate 1


title: Pig Sus ileum 001


title: MyLa 6h DMSO

description: MyLa cells treated with DMSO for 6h as the control condition for this time point

source_name: MyLa cells treated with DMSO for 6h


title: MyLa 2h PIM inhibitor

description: MyLa cells treated with the pan-PIM inhibitor ETP-39010 for 2h

source_name: MyLa cells treated with PIMi for 2h


title: MyLa 2h DMSO

description: MyLa cells treated with DMSO for 2h as the control condition for this time point

source_name: MyLa cells treated with DMSO for 2h


title: Pig Sus ileum 003

source_name: Ileum tissue_T0_Standard


title: C5

source_name: liver,control, replicate 3


title: DOX18h_Rep3

source_name: DOX treated, 18h

value: doxorubicin


title: SR786 24h PIM inhibitor

description: SR786 cells treated with the pan-PIM inhibitor ETP-39010 for 24h

source_name: SR786 cells treated with PIMi for 24h

value: Cell line derived from a patient with anaplastic large cell lymphoma

source_name: Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell ines


title: DOX4h_Rep3

source_name: DOX treated, 4h


title: MyLa 0h DMSO

description: MyLa cells treated with DMSO for 0h as the control condition for this time point

source_name: MyLa cells treated with DMSO for 0h

value: control

value: RNA from 10 human tumor cell lines


title: DOX4h_Rep1


title: SR786 10h PIM inhibitor

description: SR786 cells treated with the pan-PIM inhibitor ETP-39010 for 10h

source_name: SR786 cells treated with PIMi for 10h

value: pan-PIM inhibitor ETP-39010


title: SR786 10h DMSO

description: SR786 cells treated with DMSO for 10h as the control condition for this time point

source_name: SR786 cells treated with DMSO for 10h


title: SR786 6h PIM inhibitor

description: SR786 cells treated with the pan-PIM inhibitor ETP-39010 for 6h

source_name: SR786 cells treated with PIMi for 6h


title: DOX18h_Rep2


title: HuT78 10h PIM inhibitor

description: HuT78 cells treated with the pan-PIM inhibitor ETP-39010 for 10h

source_name: HuT78 cells treated with PIMi for 10h

value: Cell line derived from a Sezary Syndrome patient


title: HuT78 2h PIM inhibitor

description: HuT78 cells treated with the pan-PIM inhibitor ETP-39010 for 2h

source_name: HuT78 cells treated with PIMi for 2h


title: HuT78 6h DMSO

description: HuT78 cells treated with DMSO for 6h as the control condition for this time point

source_name: HuT78 cells treated with DMSO for 6h


title: DOX18h_Rep1


title: SR786 24h DMSO

description: SR786 cells treated with DMSO for 24h as the control condition for this time point

source_name: SR786 cells treated with DMSO for 24h


title: HuT78 2h DMSO

description: HuT78 cells treated with DMSO for 2h as the control condition for this time point

source_name: HuT78 cells treated with DMSO for 2h


title: SR786 6h DMSO

description: SR786 cells treated with DMSO for 6h as the control condition for this time point

source_name: SR786 cells treated with DMSO for 6h


title: SR786 0h DMSO

description: SR786 cells treated with DMSO for 0h as the control condition for this time point

source_name: SR786 cells treated with DMSO for 0h


title: SR786 2h PIM inhibitor

description: SR786 cells treated with the pan-PIM inhibitor ETP-39010 for 2h

source_name: SR786 cells treated with PIMi for 2h


title: HuT78 10h DMSO

description: HuT78 cells treated with DMSO for 10h as the control condition for this time point

source_name: HuT78 cells treated with DMSO for 10h


title: SR786 4h DMSO

description: SR786 cells treated with DMSO for 4h as the control condition for this time point

source_name: SR786 cells treated with DMSO for 4h


title: SR786 2h DMSO

description: SR786 cells treated with DMSO for 2h as the control condition for this time point

source_name: SR786 cells treated with DMSO for 2h


title: SR786 4h PIM inhibitor

description: SR786 cells treated with the pan-PIM inhibitor ETP-39010 for 4h

source_name: SR786 cells treated with PIMi for 4h

source_name: Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell ines


title: SR786 0h PIM inhibitor

description: SR786 cells treated with the pan-PIM inhibitor ETP-39010 for 0h

source_name: SR786 cells treated with PIMi for 0h


title: HuT78 6h PIM inhibitor

description: HuT78 cells treated with the pan-PIM inhibitor ETP-39010 for 6h

source_name: HuT78 cells treated with PIMi for 6h


title: HuT78 24h DMSO

description: HuT78 cells treated with DMSO for 24h as the control condition for this time point

source_name: HuT78 cells treated with DMSO for 24h


title: HuT78 4h DMSO

description: HuT78 cells treated with DMSO for 4h as the control condition for this time point

source_name: HuT78 cells treated with DMSO for 4h


title: HuT78 0h PIM inhibitor

description: HuT78 cells treated with the pan-PIM inhibitor ETP-39010 for 0h

source_name: HuT78 cells treated with PIMi for 0h


title: Secretory ameloblast Replicate 2

city: Chapel Hill

first: Shijia

last: Hu

address: 228 Brauer Hall Campus Box 7450

department: Pediatric Dentistry

institute: University of North Carolina

description:
Sample name: Sec-rep 2
Biological replicate 2 of 4. Microdissected Secretory Ameloblast.

hyb_protocol: Equal amounts of Cy3 and Cy5-labeled cRNA (825 ng) from two different samples were hybridized to Agilent Human Whole Genome Oligonucleotide Microarrays.  The hybridized array was then washed and scanned.

scan_protocol: Scanned on an Agilent G2500 Scanner and data was extracted from the scanned image using Feature Extraction version 9.5 (Agilent Technologies).

source_name: Secretory Ameloblast

label_protocol: The TargetAmp™ 2-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnologies, Madison, WI, USA) was used for the linear amplification process. 5 µg of amplified aRNA from the laser-captured tissue was labeled with the Cy5 dye and hybridized to the arrays with a Cy3-labeled Stratagene Human Universal Reference(Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated from the microdissected cells with the PicoPure RNA Isolation kit (Arcturus Bioscience, Santa Clara, CA, USA).

tag: fetal age

value: 15-20 weeks

value: epithelial

value: Secretory Ameloblast

source_name: Stratagene Human Universal Reference

value: Reference RNA


title: HuT78 4h PIM inhibitor

description: HuT78 cells treated with the pan-PIM inhibitor ETP-39010 for 4h

source_name: HuT78 cells treated with PIMi for 4h


title: DOX4h_Rep2

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

source_name: DOX treated, 4h


title: 20mg/kg_liver_rat3

city: North Chicago

first: Rita

last: Ciurlionis

state: IL

address: 1 North Waukegan Road

institute: Abbvie

description: Gene expression data from liver of rats treated for 3 weeks by IV injection with RGMC Ab at 20 mg/kg/

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230_2 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing:
The data were normalized using with Rosetta Resolver (version 7.2) Error Model
fold_change.txt; all gene expression changes with fold change at least +/-1.5 and p<0.05 in at least one sample; changes not meeting these parameters are considered unchanged (FC=1)

organism: Rattus norvegicus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

treatment_protocol: livers from vehicle and compound treated rats were flash frozen in LN2 at necropsy

value: Sprague Dawley

value: female

tag: weight

tag: treated with

value: RGMC Ab at 20 mg/kg/day by IV injection for 3 wks

value: liver


title: 20mg/kg_liver_rat2

tag: gender


title: 20mg/kg_liver_rat1


title: Secretory ameloblast Replicate 4

description:
Sample name: Sec-rep 4
Biological replicate 4 of 4. Microdissected Secretory Ameloblast.

data_processing: Feature Extraction version 9.5 (Agilent Technologies)

tag: sample type


title: Secretory ameloblast Replicate 3

description:
Sample name: Sec-rep 3
Biological replicate 3 of 4. Microdissected Secretory Ameloblast.

tag: cell type


title: 0.2mg/kg_liver_rat3

description: Gene expression data from liver of rats treated for 3 weeks by IV injection with RGMC Ab at 0.2 mg/kg

value: RGMC Ab at 0.2 mg/kg/day by IV injection for 3 wks


title: Secretory ameloblast Replicate 1

description:
Sample name: Sec-rep 1
Biological replicate 1 of 4. Microdissected Secretory Ameloblast.


title: HuT78 24h PIM inhibitor

description: HuT78 cells treated with the pan-PIM inhibitor ETP-39010 for 24h

source_name: HuT78 cells treated with PIMi for 24h


title: Pre-Secretory ameloblast Replicate 2

description:
Sample name: Pre-rep 2
Biological replicate 2 of 4. Microdissected Pre-secretory Ameloblast.

source_name: Pre-Secretory Ameloblast

value: Pre-Secretory Ameloblast


title: 0.2mg/kg_liver_rat1


title: 0.02mg/kg_liver_rat2

description: Gene expression data from liver of rats treated for 3 weeks by IV injection with RGMC Ab at 0.02 mg/kg

value: RGMC Ab at 0.02 mg/kg/day by IV injection for 3 wks


title: Pre-Secretory ameloblast Replicate 3

description:
Sample name: Pre-rep 3
Biological replicate 3 of 4. Microdissected Pre-secretory Ameloblast.


title: Pre-Secretory ameloblast Replicate 4

description:
Sample name: Pre-rep 4
Biological replicate 4 of 4. Microdissected Pre-secretory Ameloblast.


title: Pre-Secretory ameloblast Replicate 1

description:
Sample name: Pre-rep 1
Biological replicate 1 of 4. Microdissected Pre-secretory Ameloblast.


title: Odontoblast Replicate 3

description:
Sample name: Odo-rep 3
Biological replicate 3 of 4. Microdissected Odontoblast.

source_name: Odontoblast

value: ectomesenchymal

value: Odontoblast


title: 0.2mg/kg_liver_rat2


title: Odontoblast Replicate 2

description:
Sample name: Odo-rep 2
Biological replicate 2 of 4. Microdissected Odontoblast.


title: vehicle_liver_rat3

description: Gene expression data from liver of rats treated for 3 week by IV injection with 0.2% HPMC at 10 ml/kg/day

source_name: vehicle-liver

value: 0.2% HPMC at 10 ml/kg/day by IV injection for 3 wks


title: Odontoblast Replicate 4

description:
Sample name: Odo-rep 4
Biological replicate 4 of 4. Microdissected Odontoblast.


title: 0.02mg/kg_liver_rat1


title: 0.02mg/kg_liver_rat3


title: Colorectal cancer  tissue samples (FFPE) 354

description:
CAIRO arm A: capecitabine first line
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments

data_processing: The profiles were dewaved (van de wiel et al, Bioinformatics. 2009, median normalized and corrected for tumor cell percentage by using the R package CGHcall (van de Wiel et al, Bioinformatics. 2007)

source_name: colorectal cancer, CAIRO arm A

value: colorectal cancer (FFPE)

tag: study

value: CAIRO

tag: study arm

value: A

tag: progression free survival first line (days)

tag: progression

source_name: normal colorectum mucosa

value: normal colon mucosa

tag: patient

value: same patient as in ch1

value: reference


title: Colorectal cancer  tissue samples (FFPE) 355


title: Odontoblast Replicate 1

description:
Sample name: Odo-rep 1
Biological replicate 1 of 4. Microdissected Odontoblast.

value: 15-20 weeks

value: Reference RNA


title: vehicle_liver_rat2

value: Sprague Dawley

value: female


title: Colorectal cancer  tissue samples (FFPE) 356

description:
CAIRO2 arm A: capecitabine, oxaliplatin and bevacizumab
Normal colon mucosa from the same patient as the tumor was used as reference in the aCGH experiments

source_name: colorectal cancer, CAIRO2 arm A


title: vehicle_liver_rat1

description: Gene expression data from liver of rats treated for 3 week by IV injection with 0.2% HPMC at 10 ml/kg/day; necropsy 24 hours after final dose

value: liver


title: Colorectal cancer  tissue samples (FFPE) 353


title: Colorectal cancer  tissue samples (FFPE) 350


title: Colorectal cancer  tissue samples (FFPE) 351


title: Colorectal cancer  tissue samples (FFPE) 352


title: HuT78 0h DMSO

description: HuT78 cells treated with DMSO for 0h as the control condition for this time point

source_name: HuT78 cells treated with DMSO for 0h

tag: cell line

value: Cell line derived from a Sezary Syndrome patient

tag: agent

value: control

source_name: Universal Human Reference RNA (Stratagene, La Jolla, CA): a commercial RNA pooled from human tumor cell ines

tag: reference rna composition

value: RNA from 10 human tumor cell lines


title: prostate_cancer_primary_229 [GBX.VAL.PCA176]

status: Public on Nov 13 2014

city: Vancouver

first: Elai

last: Davicioni

state: British Columbia

address: 1038 Homer st

institute: GenomeDx Biosciences Inc

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using fRMA software package (Bioconductor)
HuEx-1_0-st-v1.r2.pgf

source_name: primary prostate cancer FFPE tissue sample

label_protocol: RNA was amplified, fragmented and biotinylated using the Ovation FFPE system v 3.0 (NuGEN)

extract_protocol: RNA was extracted using the High Pure RNA Paraffin Kit from Roche (Indianapolis, IN).

tag: pathgs

tag: age

tag: pstage


title: prostate_cancer_primary_235 [GBX.VAL.PCA121]


title: prostate_cancer_primary_212 [GBX.VAL.PCA139]

value: TxN+


title: prostate_cancer_primary_231 [GBX.VAL.PCA131]


title: prostate_cancer_primary_233 [GBX.VAL.PCA128]


title: prostate_cancer_primary_221 [GBX.VAL.PCA77]


title: prostate_cancer_primary_214 [GBX.VAL.PCA211]


title: prostate_cancer_primary_223 [GBX.VAL.PCA203]


title: prostate_cancer_primary_225 [GBX.VAL.PCA149]


title: prostate_cancer_primary_215 [GBX.VAL.PCA48]


title: prostate_cancer_primary_228 [GBX.VAL.PCA116]


title: prostate_cancer_primary_208 [GBX.VAL.PCA146]


title: prostate_cancer_primary_218 [GBX.VAL.PCA64]


title: prostate_cancer_primary_220 [GBX.VAL.PCA125]


title: prostate_cancer_primary_209 [GBX.VAL.PCA205]


title: prostate_cancer_primary_207 [GBX.VAL.PCA93]


title: prostate_cancer_primary_230 [GBX.VAL.PCA209]


title: prostate_cancer_primary_232 [GBX.VAL.PCA223]


title: prostate_cancer_primary_226 [GBX.VAL.PCA35]


title: prostate_cancer_primary_219 [GBX.VAL.PCA79]


title: prostate_cancer_primary_234 [GBX.VAL.PCA22]


title: prostate_cancer_primary_211 [GBX.VAL.PCA16]


title: prostate_cancer_primary_222 [GBX.VAL.PCA18]


title: prostate_cancer_primary_217 [GBX.VAL.PCA96]


title: prostate_cancer_primary_224 [GBX.VAL.PCA230]


title: prostate_cancer_primary_206 [GBX.VAL.PCA78]


title: prostate_cancer_primary_216 [GBX.VAL.PCA69]


title: prostate_cancer_primary_210 [GBX.VAL.PCA138]


title: prostate_cancer_primary_227 [GBX.VAL.PCA112]


title: prostate_cancer_primary_205 [GBX.VAL.PCA51]


title: prostate_cancer_primary_213 [GBX.VAL.PCA105]


title: prostate_cancer_primary_203 [GBX.VAL.PCA206]


title: prostate_cancer_primary_195 [GBX.VAL.PCA73]


title: prostate_cancer_primary_184 [GBX.VAL.PCA101]


title: prostate_cancer_primary_196 [GBX.VAL.PCA119]


title: prostate_cancer_primary_191 [GBX.VAL.PCA41]


title: prostate_cancer_primary_193 [GBX.VAL.PCA19]


title: prostate_cancer_primary_204 [GBX.VAL.PCA150]


title: prostate_cancer_primary_198 [GBX.VAL.PCA188]


title: prostate_cancer_primary_186 [GBX.VAL.PCA202]


title: prostate_cancer_primary_201 [GBX.VAL.PCA192]


title: prostate_cancer_primary_197 [GBX.VAL.PCA147]


title: prostate_cancer_primary_192 [GBX.VAL.PCA233]


title: prostate_cancer_primary_190 [GBX.VAL.PCA4]


title: prostate_cancer_primary_194 [GBX.VAL.PCA89]


title: prostate_cancer_primary_189 [GBX.VAL.PCA214]


title: prostate_cancer_primary_187 [GBX.VAL.PCA30]


title: prostate_cancer_primary_199 [GBX.VAL.PCA190]


title: prostate_cancer_primary_200 [GBX.VAL.PCA191]


title: prostate_cancer_primary_188 [GBX.VAL.PCA56]


title: prostate_cancer_primary_185 [GBX.VAL.PCA219]


title: prostate_cancer_primary_182 [GBX.VAL.PCA83]


title: prostate_cancer_primary_183 [GBX.VAL.PCA74]


title: prostate_cancer_primary_181 [GBX.VAL.PCA55]


title: prostate_cancer_primary_180 [GBX.VAL.PCA204]


title: prostate_cancer_primary_202 [GBX.VAL.PCA193]


title: prostate_cancer_primary_177 [GBX.VAL.PCA184]


title: prostate_cancer_primary_176 [GBX.VAL.PCA61]


title: prostate_cancer_primary_179 [GBX.VAL.PCA185]


title: prostate_cancer_primary_173 [GBX.VAL.PCA82]


title: prostate_cancer_primary_175 [GBX.VAL.PCA236]


title: prostate_cancer_primary_166 [GBX.VAL.PCA103]


title: prostate_cancer_primary_171 [GBX.VAL.PCA199]


title: prostate_cancer_primary_170 [GBX.VAL.PCA129]


title: prostate_cancer_primary_161 [GBX.VAL.PCA164]


title: prostate_cancer_primary_158 [GBX.VAL.PCA43]


title: prostate_cancer_primary_159 [GBX.VAL.PCA180]


title: prostate_cancer_primary_165 [GBX.VAL.PCA153]


title: prostate_cancer_primary_162 [GBX.VAL.PCA88]


title: prostate_cancer_primary_169 [GBX.VAL.PCA92]


title: prostate_cancer_primary_164 [GBX.VAL.PCA6]


title: prostate_cancer_primary_163 [GBX.VAL.PCA13]


title: prostate_cancer_primary_168 [GBX.VAL.PCA99]


title: prostate_cancer_primary_153 [GBX.VAL.PCA23]


title: prostate_cancer_primary_174 [GBX.VAL.PCA152]


title: prostate_cancer_primary_155 [GBX.VAL.PCA32]


title: prostate_cancer_primary_157 [GBX.VAL.PCA140]


title: prostate_cancer_primary_167 [GBX.VAL.PCA142]


title: prostate_cancer_primary_178 [GBX.VAL.PCA98]


title: prostate_cancer_primary_151 [GBX.VAL.PCA145]


title: prostate_cancer_primary_152 [GBX.VAL.PCA182]


title: prostate_cancer_primary_150 [GBX.VAL.PCA144]


title: prostate_cancer_primary_160 [GBX.VAL.PCA196]


title: prostate_cancer_primary_144 [GBX.VAL.PCA165]


title: prostate_cancer_primary_147 [GBX.VAL.PCA53]


title: prostate_cancer_primary_145 [GBX.VAL.PCA124]


title: prostate_cancer_primary_146 [GBX.VAL.PCA228]


title: prostate_cancer_primary_148 [GBX.VAL.PCA151]


title: prostate_cancer_primary_149 [GBX.VAL.PCA179]


title: prostate_cancer_primary_156 [GBX.VAL.PCA127]


title: prostate_cancer_primary_135 [GBX.VAL.PCA227]


title: prostate_cancer_primary_154 [GBX.VAL.PCA28]


title: prostate_cancer_primary_137 [GBX.VAL.PCA3]


title: prostate_cancer_primary_143 [GBX.VAL.PCA215]


title: prostate_cancer_primary_142 [GBX.VAL.PCA175]


title: prostate_cancer_primary_172 [GBX.VAL.PCA229]


title: prostate_cancer_primary_140 [GBX.VAL.PCA120]


title: prostate_cancer_primary_138 [GBX.VAL.PCA31]


title: prostate_cancer_primary_128 [GBX.VAL.PCA117]


title: prostate_cancer_primary_136 [GBX.VAL.PCA237]


title: prostate_cancer_primary_129 [GBX.VAL.PCA212]


title: prostate_cancer_primary_134 [GBX.VAL.PCA187]


title: prostate_cancer_primary_130 [GBX.VAL.PCA220]


title: prostate_cancer_primary_133 [GBX.VAL.PCA141]


title: prostate_cancer_primary_127 [GBX.VAL.PCA42]


title: prostate_cancer_primary_131 [GBX.VAL.PCA57]


title: prostate_cancer_primary_139 [GBX.VAL.PCA172]


title: prostate_cancer_primary_141 [GBX.VAL.PCA134]


title: prostate_cancer_primary_126 [GBX.VAL.PCA38]


title: prostate_cancer_primary_125 [GBX.VAL.PCA143]


title: prostate_cancer_primary_132 [GBX.VAL.PCA95]


title: prostate_cancer_primary_123 [GBX.VAL.PCA36]


title: prostate_cancer_primary_121 [GBX.VAL.PCA66]


title: prostate_cancer_primary_122 [GBX.VAL.PCA183]


title: prostate_cancer_primary_119 [GBX.VAL.PCA29]


title: prostate_cancer_primary_117 [GBX.VAL.PCA132]


title: prostate_cancer_primary_120 [GBX.VAL.PCA163]


title: prostate_cancer_primary_124 [GBX.VAL.PCA231]


title: prostate_cancer_primary_112 [GBX.VAL.PCA109]


title: prostate_cancer_primary_116 [GBX.VAL.PCA133]


title: prostate_cancer_primary_115 [GBX.VAL.PCA181]


title: prostate_cancer_primary_113 [GBX.VAL.PCA75]


title: prostate_cancer_primary_104 [GBX.VAL.PCA218]


title: prostate_cancer_primary_111 [GBX.VAL.PCA45]


title: prostate_cancer_primary_118 [GBX.VAL.PCA81]


title: prostate_cancer_primary_110 [GBX.VAL.PCA130]


title: prostate_cancer_primary_114 [GBX.VAL.PCA156]


title: prostate_cancer_primary_108 [GBX.VAL.PCA216]


title: prostate_cancer_primary_102 [GBX.VAL.PCA15]


title: prostate_cancer_primary_109 [GBX.VAL.PCA118]


title: prostate_cancer_primary_103 [GBX.VAL.PCA167]


title: prostate_cancer_primary_107 [GBX.VAL.PCA197]


title: prostate_cancer_primary_106 [GBX.VAL.PCA1]


title: prostate_cancer_primary_99 [GBX.VAL.PCA235]


title: prostate_cancer_primary_97 [GBX.VAL.PCA50]


title: prostate_cancer_primary_100 [GBX.VAL.PCA47]


title: prostate_cancer_primary_98 [GBX.VAL.PCA225]


title: prostate_cancer_primary_105 [GBX.VAL.PCA52]


title: prostate_cancer_primary_95 [GBX.VAL.PCA178]


title: prostate_cancer_primary_91 [GBX.VAL.PCA113]


title: prostate_cancer_primary_96 [GBX.VAL.PCA161]


title: prostate_cancer_primary_84 [GBX.VAL.PCA10]


title: prostate_cancer_primary_94 [GBX.VAL.PCA159]


title: prostate_cancer_primary_90 [GBX.VAL.PCA198]


title: prostate_cancer_primary_92 [GBX.VAL.PCA8]


title: prostate_cancer_primary_82 [GBX.VAL.PCA85]


title: prostate_cancer_primary_88 [GBX.VAL.PCA189]


title: prostate_cancer_primary_85 [GBX.VAL.PCA110]


title: prostate_cancer_primary_86 [GBX.VAL.PCA40]


title: prostate_cancer_primary_77 [GBX.VAL.PCA104]


title: prostate_cancer_primary_79 [GBX.VAL.PCA174]


title: prostate_cancer_primary_78 [GBX.VAL.PCA135]


title: prostate_cancer_primary_89 [GBX.VAL.PCA195]


title: prostate_cancer_primary_70 [GBX.VAL.PCA71]


title: prostate_cancer_primary_74 [GBX.VAL.PCA114]


title: prostate_cancer_primary_83 [GBX.VAL.PCA76]


title: prostate_cancer_primary_72 [GBX.VAL.PCA90]


title: prostate_cancer_primary_101 [GBX.VAL.PCA67]


title: prostate_cancer_primary_73 [GBX.VAL.PCA171]


title: prostate_cancer_primary_75 [GBX.VAL.PCA194]


title: prostate_cancer_primary_71 [GBX.VAL.PCA148]


title: prostate_cancer_primary_93 [GBX.VAL.PCA2]


title: prostate_cancer_primary_62 [GBX.VAL.PCA166]


title: prostate_cancer_primary_66 [GBX.VAL.PCA126]


title: prostate_cancer_primary_65 [GBX.VAL.PCA12]


title: prostate_cancer_primary_67 [GBX.VAL.PCA17]


title: prostate_cancer_primary_68 [GBX.VAL.PCA44]


title: prostate_cancer_primary_64 [GBX.VAL.PCA91]


title: prostate_cancer_primary_60 [GBX.VAL.PCA107]


title: prostate_cancer_primary_61 [GBX.VAL.PCA200]


title: prostate_cancer_primary_80 [GBX.VAL.PCA222]


title: prostate_cancer_primary_59 [GBX.VAL.PCA226]


title: prostate_cancer_primary_55 [GBX.VAL.PCA115]


title: prostate_cancer_primary_57 [GBX.VAL.PCA84]


title: prostate_cancer_primary_58 [GBX.VAL.PCA137]


title: prostate_cancer_primary_54 [GBX.VAL.PCA106]


title: prostate_cancer_primary_81 [GBX.VAL.PCA7]


title: prostate_cancer_primary_87 [GBX.VAL.PCA46]


title: prostate_cancer_primary_63 [GBX.VAL.PCA21]


title: prostate_cancer_primary_52 [GBX.VAL.PCA123]


title: prostate_cancer_primary_76 [GBX.VAL.PCA39]


title: prostate_cancer_primary_49 [GBX.VAL.PCA63]


title: prostate_cancer_primary_47 [GBX.VAL.PCA87]


title: prostate_cancer_primary_51 [GBX.VAL.PCA201]


title: prostate_cancer_primary_46 [GBX.VAL.PCA65]


title: prostate_cancer_primary_56 [GBX.VAL.PCA173]


title: prostate_cancer_primary_45 [GBX.VAL.PCA49]


title: prostate_cancer_primary_53 [GBX.VAL.PCA102]


title: prostate_cancer_primary_50 [GBX.VAL.PCA108]


title: prostate_cancer_primary_42 [GBX.VAL.PCA62]


title: prostate_cancer_primary_37 [GBX.VAL.PCA221]


title: prostate_cancer_primary_38 [GBX.VAL.PCA72]


title: prostate_cancer_primary_44 [GBX.VAL.PCA155]


title: prostate_cancer_primary_43 [GBX.VAL.PCA9]


title: prostate_cancer_primary_41 [GBX.VAL.PCA60]


title: prostate_cancer_primary_34 [GBX.VAL.PCA34]


title: prostate_cancer_primary_36 [GBX.VAL.PCA14]


title: VTA_NONDEP_4

city: New York

first: William

last: Shin

state: NY

address: 1130 St Nicholas Ave

department: Systems Biology

institute: Columbia University

hyb_protocol: Biotin-labeled cRNAs were fragmented, loaded on Affymetrix Rat Genome 230 2.0 GeneChip® microarrays and hybridized at 45°C for 16 h following Affymetrix standard protocol. Washes were performed on a Fluidics Station with the manufacturer’s (Affymetrix) recommended wash solutions, and the chips were stained with a streptavidin–phycoerythrin conjugate for fluorescence detection.

scan_protocol: After staining, chips were scanned with an Affymetrix GeneArray Scanner 2500.

data_processing: The GCRMA package for Bioconductor was used to generate log-2 expression levels for probeset IDs from the original .cel files. R version 3.03 and gcrma version 2.36.0 were used in the analysis.

source_name: nondependent alcohol self-administering rat

label_protocol: Biotin labeling was done using the BioArray High Yield RNA Transcript Labeling Kit T7 (Enzo).

growth_protocol: Rats were trained to orally self-administer alcohol in a concurrent, two-lever, free-choice contingency using a modification of the sweet solution fading procedure (O'Dell et al., 2004; Roberts et al., 2000; Vendruscolo et al., 2012).

extract_protocol: Total RNA was prepared from microdissected rat brain tissue samples with the Picopure RNA Isolation Kit (Arcturus, now Life Technologies). Extracted total RNA was quantified with the NanoDrop ND-1000 spectrophotometer and quality assessed with the Agilent Bioanalyzer. Depending on the brain region, 30 or 50 ng of total RNA was used as a starting template to generate synthetic complementary RNA (cRNA) with the RiboAmp® OA RNA Amplification Kit (Arcturus, now Life Technologies) by in vitro transcription (IVT) of double stranded cDNAs.

treatment_protocol: Following acquisition of self-administration, rats were allowed to self-administer unsweetened alcohol (10%) for 4 weeks and were then assigned to two groups matched by levels of responding: one group (dependent group) was exposed to chronic, intermittent ethanol vapors for 4 weeks to induce dependence; the other group (nondependent group) was not exposed to ethanol vapor. After a month of vapor exposure, rats were again tested during acute withdrawal (6-8 hours after removal from the vapor chambers) until stable levels of alcohol intake were achieved. As expected, alcohol vapor-exposed rats self-administered significantly greater amounts of alcohol than control rats not exposed to alcohol vapor during acute withdrawal. Rats were sacrificed during protracted abstinence (3 weeks after the end of alcohol vapor exposure) along with age-matched alcohol naive rats.

tag: brain region

value: Ventral tegmental area


title: prostate_cancer_primary_29 [GBX.VAL.PCA169]


title: prostate_cancer_primary_39 [GBX.VAL.PCA68]


title: prostate_cancer_primary_28 [GBX.VAL.PCA157]


title: prostate_cancer_primary_48 [GBX.VAL.PCA111]


title: VTA_NONDEP_3


title: prostate_cancer_primary_33 [GBX.VAL.PCA208]


title: VTA_NONDEP_2


title: prostate_cancer_primary_40 [GBX.VAL.PCA154]


title: prostate_cancer_primary_31 [GBX.VAL.PCA33]


title: prostate_cancer_primary_69 [GBX.VAL.PCA5]


title: prostate_cancer_primary_30 [GBX.VAL.PCA217]


title: prostate_cancer_primary_35 [GBX.VAL.PCA86]


title: VTA_DEP_4

source_name: dependent alcohol self-administering rat


title: prostate_cancer_primary_26 [GBX.VAL.PCA186]


title: prostate_cancer_primary_32 [GBX.VAL.PCA94]


title: VTA_DEP_3


title: VTA_CTRL_4

source_name: alcohol naive rat


title: VTA_DEP_1


title: VTA_DEP_2


title: prostate_cancer_primary_20 [GBX.VAL.PCA224]


title: VTA_CTRL_3


title: prostate_cancer_primary_23 [GBX.VAL.PCA170]


title: prostate_cancer_primary_27 [GBX.VAL.PCA97]


title: VTA_CTRL_2


title: VTA_CTRL_1


title: VTA_NONDEP_1


title: prostate_cancer_primary_24 [GBX.VAL.PCA207]


title: prostate_cancer_primary_17 [GBX.VAL.PCA80]


title: V_BNST_NONDEP_4

value: Ventral bed nucleus of the stria terminalis


title: prostate_cancer_primary_21 [GBX.VAL.PCA158]


title: V_BNST_NONDEP_3


title: prostate_cancer_primary_22 [GBX.VAL.PCA168]


title: V_BNST_NONDEP_2


title: prostate_cancer_primary_18 [GBX.VAL.PCA100]


title: V_BNST_NONDEP_1


title: MG12 Imatinib 12h replicate 4

city: Stockholm

first: Maria

last: Genander

address: Tomtebodavägen 16

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Hybridization was done at the Karolinska Core Facility

scan_protocol: Scanning was done at the Karolinska Core Faclity

data_processing: Bioinformatical analysis was done at the Karolinska Core Facility

label: Biotin

source_name: colon 12h after Imatinib injection

label_protocol: Labelling was done at the Karolinska Core Facility (Novum)

growth_protocol: Adult mouse colon was isolated after mice were treated with Imatinib

extract_protocol: RNA was extracted using Trizol according to manufacturers protocol

treatment_protocol: Imatinib was given for either 3 or 12 hours

tag: tissue

value: Colon

tag: developmental stage

value: adult

tag: background strain


title: MG11 Imatinib 12h replicate 3


title: V_BNST_DEP_2


title: V_BNST_DEP_3


title: V_BNST_DEP_4


title: MG09 Imatinib 12h replicate 1


title: MG10 Imatinib 12h replicate 2


title: V_BNST_DEP_1


title: MG08 Imatinib 3h replicate 4

source_name: colon 3h after Imatinib injection


title: prostate_cancer_primary_19 [GBX.VAL.PCA162]


title: MG07 Imatinib 3h replicate 3


title: prostate_cancer_primary_16 [GBX.VAL.PCA70]


title: prostate_cancer_primary_25 [GBX.VAL.PCA210]


title: V_BNST_CTRL_4


title: MG06 Imatinib 3h replicate 2


title: MG05 Imatinib 3h replicate 1


title: V_BNST_CTRL_2


title: V_BNST_CTRL_1


title: Shell_NONDEP_4

value: Shell of the Nucleus Accumbens


title: MG03 control replicate 2

source_name: colon before Imatinib


title: prostate_cancer_primary_14 [GBX.VAL.PCA238]


title: V_BNST_CTRL_3


title: Shell_NONDEP_3


title: MG04 control replicate 3


title: RasV12, U0126 20uM, rep3

city: St. John's

first: Sherri

middle: L

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

institute: Memorial University of Newfoundland

hyb_protocol: Hybridization was performed by The Centre for Applied Genomics (Toronto, Canada) according to the manufacturer's protocol (FS450_0007).

scan_protocol: Scanning was performed with the Affymetrix GeneChip Scanner 3000 by The Centre for Applied Genomics (Toronto, Canada) according to the manufacturer's protocol.

data_processing: Data were processed by Affymetrix GeneChip Command Console software [GCOS v1.4; algorithm: ExpressionStat 5.0] and were further analyzed using GeneSpring v7.3 (Agilent).

source_name: RasV12 cells_U0126 (20uM) treated for 6h

label_protocol: 500 ng of RNA was used for labeling using the Ambion WT kit. Labeling was performed by The Centre for Applied Genomics (Toronto, Canada) according to the manufacturer's protocol.

growth_protocol: Cells were plated 6-well plates the day prior to treatment.

extract_protocol: Total RNA was extracted with TriZOL (Invitrogen) following the manufacturer's protocol. RNA was treated with Turbo DNA-free to remove genomic DNA contamination.

treatment_protocol: Confluent cells were treated with interferon-alpha (500 U/ml), U0126 (20uM) or DMSO (control) for 6h

tag: cell line background

value: NIH/3T3 mouse embryonic fibroblast

tag: transfected with

value: constitutitvely active Ras V12

tag: treated with


title: RasV12, U0126 20uM, rep2


title: MG02 control replicate 1


title: prostate_cancer_primary_15 [GBX.VAL.PCA232]


title: RasV12, U0126 20uM, rep1


title: prostate_cancer_primary_12 [GBX.VAL.PCA24]


title: Shell_NONDEP_1


title: Shell_DEP_4


title: Shell_DEP_3


title: Shell_CTRL_4


title: RasV12, IFN, 6h, rep2

source_name: RasV12 cells_IFN (500U/ml) treated for 6h

value: interferon-alpha (500 U/ml) for 6h


title: Shell_DEP_1


title: RasV12, control 6h, rep2

source_name: RasV12 cells_DMSO treated for 6h

value: DMSO (control) for 6h


title: Shell_DEP_2


title: RasV12, IFN, 6h, rep1


title: Shell_CTRL_3


title: RasV12, IFN, 6h, rep3


title: prostate_cancer_primary_10 [GBX.VAL.PCA213]


title: Shell_CTRL_1


title: Shell_CTRL_2


title: MPF_NONDEP_4

value: Medial Prefrontal Cortex


title: Shell_NONDEP_2


title: prostate_cancer_primary_7 [GBX.VAL.PCA177]


title: RasV12, control 6h, rep1


title: prostate_cancer_primary_13 [GBX.VAL.PCA20]


title: prostate_cancer_primary_8 [GBX.VAL.PCA37]


title: MPF_NONDEP_2


title: prostate_cancer_primary_11 [GBX.VAL.PCA234]


title: MPF_DEP_3


title: MPF_NONDEP_3


title: MPF_CTRL_4


title: prostate_cancer_primary_9 [GBX.VAL.PCA160]


title: MPF_NONDEP_1


title: MPF_DEP_4


title: DL_BNST_NONDEP_3

value: Dorsolateral bed nucleus of the stria terminalis


title: MPF_DEP_2


title: MPF_CTRL_2


title: MPF_CTRL_1


title: MPF_CTRL_3


title: prostate_cancer_primary_5 [GBX.VAL.PCA122]


title: RasV12, control 6h, rep3


title: DL_BNST_CTRL_3


title: DL_BNST_DEP_1


title: prostate_cancer_primary_6 [GBX.VAL.PCA136]


title: DL_BNST_DEP_2


title: DL_BNST_NONDEP_1


title: DL_BNST_DEP_4


title: DL_BNST_NONDEP_2


title: MPF_DEP_1


title: DL_BNST_DEP_3


title: Core_NONDEP_4

value: Core of the Nucleus Accumbens


title: DL_BNST_CTRL_1


title: Core_DEP_4


title: Core_NONDEP_1


title: DL_BNST_CTRL_4


title: CeA_NONDEP_4

value: Central Nucleus of the Amygdala


title: Core_NONDEP_3


title: Core_DEP_2


title: prostate_cancer_primary_3 [GBX.VAL.PCA59]


title: Core_CTRL_3


title: Core_NONDEP_2


title: prostate_cancer_primary_2 [GBX.VAL.PCA58]


title: Core_DEP_1


title: Core_DEP_3


title: Core_CTRL_2


title: DL_BNST_CTRL_2


title: Core_CTRL_1


title: prostate_cancer_primary_1 [GBX.VAL.PCA54]


title: Core_CTRL_4


title: CeA_DEP_3


title: CeA_DEP_4


title: CeA_CTRL_1


title: CeA_NONDEP_1


title: CeA_NONDEP_2


title: CeA_CTRL_4


title: CeA_DEP_1


title: prostate_cancer_primary_4 [GBX.VAL.PCA11]


title: CeA_DEP_2


title: CeA_CTRL_2


title: CeA_CTRL_3


title: BLA_NONDEP_4

value: Basolateral Nucleus of the Amygdala


title: BLA_DEP_4


title: BLA_NONDEP_1


title: DL_BNST_NONDEP_4


title: BLA_NONDEP_3


title: BLA_CTRL_4


title: BLA_NONDEP_2


title: CeA_NONDEP_3


title: BLA_DEP_3


title: BLA_DEP_2


title: BLA_CTRL_2


title: BLA_CTRL_1


title: PrimaryCell1_Nanog_negative

city: Chong qing

first: junjie

last: shen

address: Gaotanyan 30, Shapingba District

institute: Institute of Pathology and Southwest Cancer Center

description: Gene expression from FACS sorted Nanog negative cells

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm,Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Nanog negative cells from patients derive primary HCC cells T1115

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: RNA extraction and purification Total RNA was extracted using TRIZOL Reagent (Cat#15596-018 ， Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

tag: cell type

tag: nanog

value: no

tag: gender

value: male


title: BLA_CTRL_3


title: PrimaryCell2_Nanog_negative

source_name: Nanog negative cells from patients derive primary HCC cells T1224


title: PrimaryCell2_Nanog_positive_rep1

description: Gene expression from FACS sorted Nanog positive cells

source_name: Nanog positive cells from patients derive primary HCC cells T1224, replicate 1

value: yes


title: KY 28d

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater

source_name: in vitro 28-d differentiated tetO:c-myc mBmal1:luc KY1.1 in the absence of dox

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 cell lines were cultured on a feeder layer of mitomycin C-treated primary MEFs in an ES medium containing Glasgow Minimum Essential Medium (G-MEM, Wako, Osaka, Japan) supplemented with 15% fetal bovine serum (FBS, Hyclone, South Logan, UT), 0.1 mM MEM nonessential amino acids (Nacalai Tesque, Kyoto, Japan), 0.1 mM 2-mercaptoethanol (Sigma, St. Louis, U.S.A.), 1,000 units/mL of leukemia inhibitory factor (LIF) and 100 units/mL of penicillin–streptomycin (Nacalai Tesque).

extract_protocol: Total RNAs were isolated using RNeasy (Qiagen).

treatment_protocol: In vitro differentiation of ES cells was performed as described recently (Umemura et al. 2013). Briefly, after ES cells were trypsinized and feeder cells were removed, embryoid bodies (EBs) were generated by harvesting 2,000 cells and seeding them onto low-attachment 96-well plates (Lipidure Coat, NOF, Tokyo, Japan) in a differentiating medium without LIF supplementation (EFM), which was comprised of a high-glucose DMEM (Nacalai Tesque) containing 10% FBS, 1 mM sodium pyruvate (Nacalai Tesque), 0.1 mM nonessential amino acids, GlutaMaxTM-I (Invitrogen), 100 µM β-mercaptoethanol and 100 units/mL penicillin-streptomycin. Two day later, EBs were plated onto gelatin-coated tissue culture 24-well plates and grown for several additional weeks. EFM was changed every 1–2 day. For constitutive expression of c-Myc during in vitro differentiation of ESCs carrying Dox-inducible c-Myc, EFM containing Dox (Invitrogen) was changed every 1–2 days.

tag: es cell line


title: Per2Luc 28d

source_name: in vitro 28-d differentiated tetO:c-myc mPer2Luc ES cells in the absence of dox


title: KY 28d Dox

source_name: in vitro 28-d differentiated tetO:c-myc mBmal1:luc KY1.1 in the presence of 40 ng/ml dox


title: Per2Luc 28d Dox

source_name: in vitro 28-d differentiated tetO:c-myc mPer2Luc ES cells in the presence of 500 ng/ml dox


title: Huh7_Nanog_negative

source_name: Nanog negative cells from Huh7

tag: cell line


title: PrimaryCell1_Nanog_positive_rep1

source_name: Nanog positive cells from patients derive primary HCC cells T1115, replicate 1


title: Huh7_Nanog_positive_rep1

source_name: Nanog positive cells from Huh7, replicate 1


title: Huh7_Nanog_positive_rep2

source_name: Nanog positive cells from Huh7, replicate 2


title: PrimaryCell1_Nanog_positive_rep2

source_name: Nanog positive cells from patients derive primary HCC cells T1115, replicate 2


title: hESC-M Day 5 MC

city: Oeiras

first: Marta

middle: Marques

last: Silva

state: Oeiras

address: Apartado 12

department: Animal Cell Technology Unit

country: Portugal

institute: iBET - Instituto de Biologia Experimental e Tecnológica

description: hESC-M at Day 5 of expansion on synthetic microcarriers in stirred culture system

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Non-normalized data was used for data processing using R. “RNAXXD.AVG_Signal” and “RNAXXD.AVG_Detection Pval” indicates the average signal for the identified probe and the detection p-value for that average detection signal, respectively.
Data was processed using Environment for Statistical Computing (R) 2.7.0 (R Development Core Team 2008) in combination with Bioconductor 2.2 (Gentleman et al. 2004). The Bioconductor lumi package (Du et al. 2008) was used for quality control. Raw data was log2-transformed using the lumiT() function and no background correction was performed (Schmid et al. 2010). Data was transformed using variance-stabilizing transformation (Lin et al. 2008) and quantile normalized (Bolstad et al. 2003). After normalization, the output file retrieves RNAXX_AVG_norm, corresponding to the processed and normalized average values.

source_name: hESC-Monolayer type at Day 5 of expansion on synthetic microcarriers

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

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: hesc line

value: SA181 (single-cell based non-colony monolayer culture)


title: hESC-M Day 8 2D

description: hESC-M at Day 8 of expansion in 2D culture system

source_name: hESC-Monolayer type at Day 8 of expansion in 2D system


title: PrimaryCell2_Nanog_positive_rep2

source_name: Nanog positive cells from patients derive primary HCC cells T1224, replicate 2


title: hESC-M Day 5 2D

description: hESC-M at Day 5 of expansion in 2D culture system

source_name: hESC-Monolayer type at Day 5 of expansion in 2D system


title: BLA_DEP_1

source_name: dependent alcohol self-administering rat


title: hESC-C Day 12 2D (no feeder)

description: hESC-C at Day 12 after expansion on synthetic Synthemax® surface in 2D culture system

source_name: hESC-Colony type at Day 12 of expansion in 2D system on  synthetic Synthemax® surface

value: SCEDTM461 (colony type culture)


title: hESC-M Day 8 2D (replicate)

description: hESC-M at Day 8 of expansion in 2D culture system (replicate)

source_name: hESC-Monolayer type at Day 8 of expansion in 2D system (replicate)


title: hESC-M Day 1 MC

description: hESC-M at Day 1 of expansion on synthetic microcarriers in stirred culture system

source_name: hESC-Monolayer type at Day 1 of expansion on synthetic microcarriers


title: hESC-M Day 0 2D

description: hESC-M at Day 0 of expansion

source_name: hESC-Monolayer type at Day 0 of expansion in 2D system


title: hESC-M Day 8 MC

description: hESC-M at Day 8 of expansion on synthetic microcarriers in stirred culture system

source_name: hESC-Monolayer type at Day 8 of expansion on synthetic microcarriers


title: hESC-M Day 1 2D

description: hESC-M at Day 1 of expansion in 2D culture system

source_name: hESC-Monolayer type at Day 1 of expansion in 2D system


title: GW14.5 human neocortex section 107

city: San Francisco

first: Michael

last: Oldham

address: 35 Medical Center Way #0525

institute: UCSF

description:
Sample name: Hs_107
section 107

data_processing: The data were quantile normalized in R.  Batch effects associated with Array.ID and Extraction.Date were corrected sequentially with ComBat, as described in Supplementary Methods.

source_name: Human neocortex

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser 2100.

tag: section

value: 14.5 gestational weeks

value: neocortex

tag: rin

value: B


title: hESC-C Day 0 2D (with feeder)

description: hESC-C at Day 0 of expansion

source_name: hESC-Colony type at Day 0 of expansion in 2-Dimensional (2D) system


title: GW14.5 human neocortex section 106

description:
Sample name: Hs_106
section 106

tag: age

value: E


title: GW14.5 human neocortex section 103

description:
Sample name: Hs_103
section 103

value: C


title: GW14.5 human neocortex section 105

description:
Sample name: Hs_105
section 105


title: GW14.5 human neocortex section 110

description:
Sample name: Hs_110
section 110

value: J


title: GW14.5 human neocortex section 111

description:
Sample name: Hs_111
section 111

value: D


title: GW14.5 human neocortex section 97

description:
Sample name: Hs_97
section 97

value: I


title: GW14.5 human neocortex section 99

description:
Sample name: Hs_99
section 99

value: G


title: GW14.5 human neocortex section 96

description:
Sample name: Hs_96
section 96

value: A


title: hESC-C Day 12 2D (with feeder)

description: hESC-C at Day 12 after expansion on human foreskin fibroblast feeder  in 2D culture system

source_name: hESC-Colony type at Day 12 of expansion in 2D system


title: GW14.5 human neocortex section 98

description:
Sample name: Hs_98
section 98


title: GW14.5 human neocortex section 89

description:
Sample name: Hs_89
section 89


title: hESC-C Day 12 MC (no feeder)

description: hESC-C at Day 12 after expansion on synthetic microcarriers in stirred culture system

source_name: hESC-Colony type at Day 12 of expansion on synthetic microcarriers


title: GW14.5 human neocortex section 85

description:
Sample name: Hs_85
section 85

value: K


title: GW14.5 human neocortex section 109

description:
Sample name: Hs_109
section 109


title: GW14.5 human neocortex section 95

description:
Sample name: Hs_95
section 95

value: H


title: GW14.5 human neocortex section 93

description:
Sample name: Hs_93
section 93


title: GW14.5 human neocortex section 92

description:
Sample name: Hs_92
section 92


title: GW14.5 human neocortex section 104

description:
Sample name: Hs_104
section 104


title: GW14.5 human neocortex section 91

description:
Sample name: Hs_91
section 91


title: GW14.5 human neocortex section 90

description:
Sample name: Hs_90
section 90


title: GW14.5 human neocortex section 88

description:
Sample name: Hs_88
section 88

value: L


title: GW14.5 human neocortex section 84

description:
Sample name: Hs_84
section 84

value: F


title: GW14.5 human neocortex section 94

description:
Sample name: Hs_94
section 94


title: GW14.5 human neocortex section 83

description:
Sample name: Hs_83
section 83


title: GW14.5 human neocortex section 100

description:
Sample name: Hs_100
section 100


title: GW14.5 human neocortex section 101

description:
Sample name: Hs_101
section 101


title: GW14.5 human neocortex section 112

description:
Sample name: Hs_112
section 112


title: GW14.5 human neocortex section 81

description:
Sample name: Hs_81
section 81


title: GW14.5 human neocortex section 79

description:
Sample name: Hs_79
section 79


title: GW14.5 human neocortex section 77

description:
Sample name: Hs_77
section 77


title: GW14.5 human neocortex section 80

description:
Sample name: Hs_80
section 80


title: GW14.5 human neocortex section 82

description:
Sample name: Hs_82
section 82


title: GW14.5 human neocortex section 72

description:
Sample name: Hs_72
section 72


title: GW14.5 human neocortex section 69

description:
Sample name: Hs_69
section 69


title: GW14.5 human neocortex section 76

description:
Sample name: Hs_76
section 76


title: GW14.5 human neocortex section 56

description:
Sample name: Hs_56
section 56


title: GW14.5 human neocortex section 74

description:
Sample name: Hs_74
section 74


title: GW14.5 human neocortex section 48

description:
Sample name: Hs_48
section 48


title: GW14.5 human neocortex section 54

description:
Sample name: Hs_54
section 54


title: GW14.5 human neocortex section 58

description:
Sample name: Hs_58
section 58


title: GW14.5 human neocortex section 49

description:
Sample name: Hs_49
section 49


title: GW14.5 human neocortex section 70

description:
Sample name: Hs_70
section 70


title: GW14.5 human neocortex section 65

description:
Sample name: Hs_65
section 65