title: WP3ΔlexA-4℃-rep6

description:
8190 WP3cy5-lexAcy3.LSR
WP3ΔlexA cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) shaking at  220 rpm at 4°C

value: WP3 cells were cultured at 4℃ in 2216E medium


title: WP3ΔlexA-4℃-rep5

status: Public on Dec 01 2014

type: RNA

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model
2 raw data files, each with 3 spots per probe/gene, each spot is a techinical replicate for a total of 6 replicates

molecule: total RNA

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

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

tag: treatment

tag: genotype

value: delta lexA

value: wild type


title: sieIF4AI.sub [I A-S]

city: Cambridge

first: Roslin

last: Russell

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

description: I A-S

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol

data_processing: The bead-level data were preprocessed using BASH (Cairns et al. (2008) Bioinformatics 24(24):2921-2), a function from the beadarray package (Dunning et al (2007) Bioinformatics 23(16):2183-4) in Bioconductor, and also log base 2 transformed and lowess normalised.

label: biotin

organism: Homo sapiens

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

growth_protocol: MCF7 cells were grown in DMEM 10% FBS under standard cell culture conditions.

extract_protocol: Total RNA was extracted using TRIAZOL reagent. Subpolysomal and polysomal RNA was extracted using Guanidine HCl-ethanol precipitation, followed by LiCl precipitation. All samples were then repurified using miRNeasy kit (Qiagen).

treatment_protocol: Control ON-TARGETplus Non-targeting Pool and ON-TARGETplus SMART pool siRNAs targeting eIF4A1 were transfected into cells according to manufacturer's instructions (Thermo Scientific). DharmaFECT1 Transfection Reagent was used.

tag: cell line


title: PA080_16982_090407

type: genomic

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

description: Hybridized to SNP6.0 array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: BioDiscovery Nexus Copy Number 6.0 and default settings and SNP Rank segmentation, human genome version GRCh37/hg19 and default HAPMAP-based reference file.

label: Biotin

molecule: genomic DNA

source_name: colon cancer primary tumour tissue

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: QIAamp DNA mini kit.

tag: tissue

value: colon cancer

tag: Stage

value: MSS


title: WP3ΔlexA-20℃-rep4

description:
8211 WP3cy5-lexAcy3.LSR
WP3ΔlexA cDNA was labled with Cy3 and WP3 wild-type cDNA was labled with Cy5

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1 M DTT, 1 μl 10 mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40 mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl) shaking at  220 rpm at 20°C

value: WP3 cells were cultured at 20℃ in 2216E medium


title: Adult control substantia nigra, 028/09 (gene level)

city: London

first: Mina

last: Ryten

address: Queen Square

department: Department of Molecular Neuroscience

institute: UCL Institute of Neurology

description:
A653_534
Adult control substantia nigra.

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 95° for 5 minutes, then 45° for 5 minutes. Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Data were processed using Partek Genomics Suite v6.6. Arrays were preprocessed using RMA quantile normalization with GC background correction. Gene-level summary signals were generated by calculating the Winsorized mean of expression values of all probe sets annotated to a transcript.

Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.na30.hg19.probeset_core.mps
Core exons were used in the analysis.
Transcript assignments were based on genome build hg19.

source_name: Control adult substantia nigra

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix).

growth_protocol:
hESCs: CDM+FGF2(10ng/ml) + Insulin (10ng/ml) + Activin (10ng/ml).
Neural precursors: CDM (Day0-8), FGF2(10ng/ml; Day 8-16), FGF8(200ng/ml) + puromorphamine (1µM) from Day 16-24.
hESC-derived neurons: DMEM(HG)+ B27(2%)+BDNF(10ng/ml)+GDNF(10ng/ml).

extract_protocol: Total RNA was extracted from all cell samples using the RNeasy kit (Qiagen), from fetal samples using TRIzol (Invitrogen) and from adult substantia nigra using the miRNeasy kit (Qiagen). cDNA synthesis and amplification was performed using the Ambion®WT Expression Kit (Ambion).

value: substantia nigra

tag: developmental stage

value: adult


title: WP3ΔlexA-4℃-rep4


title: Adult control substantia nigra, 030/09 (gene level)

description:
A653_522
Adult control substantia nigra.


title: siControl.total [II C-tot]

description: II C-tot


title: PA080_163_111214

description: Hybridized to SNP6.0 array


title: sieIF4AI.sub [IV A-S]

description: IV A-S


title: PA080_163_090621

description: Hybridized to SNP6.0 array

value: MSI-H


title: Adult control substantia nigra, 025/05 (gene level)

description:
A653_381
Adult control substantia nigra.


title: PA080_16266_090213

description: Hybridized to SNP6.0 array


title: WP3ΔlexA-4℃-rep3

description:
8188 WP3cy3-lexAcy5.LSR
WP3ΔlexA cDNA was labled with Cy5 and WP3 wild-type cDNA was labled with Cy3


title: sieIF4AI.poly [III A-P]

description: III A-P


title: WP3ΔlexA-4℃-rep2


title: WP3ΔlexA-4℃-rep1


title: PA080_157_111106

description: Hybridized to SNP6.0 array


title: siControl.sub [III C-S]

description: III C-S


title: Adult control substantia nigra, 022/09 (gene level)

description:
A653_380
Adult control substantia nigra.


title: Adult control substantia nigra, 025/09 (gene level)

description:
A653_297
Adult control substantia nigra.


title: FAT-M12-b

city: Singapore

first: Caroline

last: Lee

address: 14 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using PARTEK software

source_name: FAT10 overexpressed mutants with mutation at left and right region

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

growth_protocol: wild type HCT116 cells were grown in McCoy's Dulbecco medium, stable cells were selected and grown in McCoy's Dulbecco medium with Geneticin

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: colorectal cancer

value: HCT116 cells (ATCC)


title: PA080_167_111209

description: Hybridized to SNP6.0 array


title: PA080_155_111123

description: Hybridized to SNP6.0 array


title: P.falciparum culture control rep2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: gene expression in mock treated P.falciparum culture

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).  The hybridized, washed microarray slides were then scanned on a G2565C scanner (Agilent Technologies)

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C

data_processing: Data extraction from Images was done using Feature Extraction software Version 11.5 and Percentile shift normalization Normalization of the data was done in GeneSpring GX V 12

organism: Plasmodium falciparum

source_name: P.falciparum culture control replicate2

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop

growth_protocol: P. falciparum was cultured in RPMI medium supplemented with 0.5% Albumax II in human O+ erythroctes and incubated in humified incubators with 5% CO2 with a replacement of spent medium with new medium every 24h

extract_protocol: RNA isolation was performed using Qiagen Mini Kit with Dnase treatment as per the manufacturer’s instructions

treatment_protocol: Asynchronous cultures were treated with 10mM DTT or mock treated for 1 h. Following incubation, the parasites isolated from the erythrocytes by lysing with saponin detergent were used for RNA preparation and microarray analysis

tag: sample type

value: culture

value: control


title: PA080_1612_090814

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 018/06 (gene level)

description:
A653_286
Adult control substantia nigra.


title: P.falciparum culture 1 h DTT treatment rep2

description: gene expression after 1 h DTT treatment to P.falciparum culture

source_name: P.falciparum culture 1 h DTT treatment replicate2

value: 1 h 10mM DTT treatment


title: PA080_159_111206

description: Hybridized to SNP6.0 array


title: FAT-M2-b

source_name: FAT10 overexpressed mutants with mutation at right region


title: P.falciparum culture control rep1

source_name: P.falciparum culture control replicate1


title: Adult control substantia nigra, 016/07 (gene level)

description:
A653_248
Adult control substantia nigra.


title: FAT-M12-a


title: Adult control substantia nigra, 017/09 (gene level)

description:
A653_283
Adult control substantia nigra.


title: FAT-M2-a


title: Adult control substantia nigra, 021/09 (gene level)

description:
A653_243
Adult control substantia nigra.


title: PA080_159_090621

description: Hybridized to SNP6.0 array


title: P.falciparum culture 1 h DTT treatment rep1

source_name: P.falciparum culture 1 h DTT treatment replicate1


title: Adult control substantia nigra, 037/08 (gene level)

description:
A653_239
Adult control substantia nigra.


title: PA080_153_111220

description: Hybridized to SNP6.0 array


title: revertant-iPSCs (P21)

city: New York

first: Jane

middle: E.

last: Cerise

state: NY

address: 1150 St. Nicholas Avenue

country: USA

institute: Columbia University

description: revertant mosacism

hyb_protocol: Following fragmentation, 5 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array (HTA) 2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G3000.

data_processing: The data were analyzed with Expression Console version 1.3 using Affymetrix default analysis settings and RMA as normalization method.

source_name: revertant-iPSCs from patient EB026-01

label_protocol: Extracted total RNA of each samples were reverse transcribed and amplified using the GeneChip WT PLUS Reagent Kit (WT PLUS Kit) (Affymetrix).

growth_protocol: iPSCs were cultured in the human ES cell medium. Normal FB and revertant-iPSC-FB were cultured in the 10% FBS-DMEM. Revertant-iPSC-KC and the original revertant keratinocytes were cultured in the CnT-57 (CELLnTEC).

extract_protocol: Qiagen RNeasy with on-column DNase digestion

tag: cell type

value: revertant-iPSCs


title: Adult control substantia nigra, 033/08 (gene level)

description:
A653_238
Adult control substantia nigra.


title: FAT-M1-b

source_name: FAT10 overexpressed mutants with mutation at left region


title: Adult control substantia nigra, 032/08 (gene level)

description:
A653_234
Adult control substantia nigra.


title: Adult control substantia nigra, 038/08 (gene level)

description:
A653_223
Adult control substantia nigra.


title: PA080_143_111220

description: Hybridized to SNP6.0 array


title: FAT10-2

source_name: FAT10-overexpressed stable cells


title: original revertant keratinocytes (P3)

description: revertant mosacism

source_name: original revertant keratinocytes from patient EB026-01

value: revertant keratinocytes


title: FAT10-1


title: revertant-iPS-KC (P1)

description: revertant mosacism

source_name: revertant-iPSC-KC from patient EB026-01

value: revertant-iPSC-KC


title: PA080_147_120816

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 014/09 (gene level)

description:
A653_219
Adult control substantia nigra.


title: PA080_141_111206

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 039/06 (gene level)

description:
A653_165
Adult control substantia nigra.


title: PA080_153_090618

description: Hybridized to SNP6.0 array


title: normal FB (P4), technical rep 2

description: normal human fibroblasts

source_name: normal fibroblasts from healthy control

value: normal human fibroblasts


title: FAT-M1-a


title: revertant-iPSC-FB (P9), technical rep 3

description: revertant mosacism

source_name: revertant-iPSC-FB from patient EB026-01

value: revertant-iPSC-FB


title: WT-2

source_name: wild type HCT116 cells


title: I-48-M (E)

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

institute: Singapore Immunology Network

hyb_protocol: 750ng of labelled cRNAs were hybridized to the Illumina Human HT12 arrays for 16 hours at 58°C and the arrays were washed and stained according to the Illumina Wash Protocol

scan_protocol: The human chips were scanned using BeadArray Scanner 500GX and the images were analyzed using GenomeStudio Gene Expression v 1.9.0

data_processing: Raw data was extracted with Illumina's Genomestudio without background correction. Data was quantile normalized using R v 2.15.2 and bioconductor

source_name: THP-1 cells

label_protocol: Biotinylated cRNA was prepared according to the Epicentre TargetAmp Nano-g Biotin-aRNA Labelling kit for Illumina system.

growth_protocol: THP-1 cells were maintained in RPMI1640 medium with 10% FCS.

extract_protocol: RNA extraction was performed according to the miRVana miRNA isolation kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: M. bovis BCG infected THP-1 cells were treated with 2mM of metformin.

tag: infection

value: M. bovis BCG

tag: timepoint

value: 48 hours

value: 2mM Metaformin


title: PA080_13327_090423

description: Hybridized to SNP6.0 array

source_name: colon cancer primary tumour tissue

value: colon cancer

value: MSI-L


title: WT-1


title: normal FB (P4), technical rep 1

description: normal human fibroblasts


title: Adult control substantia nigra, 016/09 (gene level)

description:
A653_157
Adult control substantia nigra.

source_name: Control adult substantia nigra

value: substantia nigra

value: adult


title: PA080_135_111209

description: Hybridized to SNP6.0 array

value: MSI-H


title: PA080_133_111106

description: Hybridized to SNP6.0 array

value: MSS


title: revertant-iPSC-FB (P9), technical rep 2

description: revertant mosacism


title: I-48-M (C)


title: Adult control substantia nigra, 035/06 (gene level)

description:
A653_149
Adult control substantia nigra.


title: PA080_137_111123

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 009/09 (gene level)

description:
A653_147
Adult control substantia nigra.


title: Adult control substantia nigra, 024/08 (gene level)

description:
A653_146
Adult control substantia nigra.


title: PA080_132_090621

description: Hybridized to SNP6.0 array


title: I-48-M (A)


title: I-48-M (B)


title: mouse_hippocampus_63weeks_Transgenic_rep3

city: Huddinge

first: Jean-Ha

last: Baek

address: 7 Halsovagen

department: Biosciences and Nutrition

institute: Karolinska Institute

hyb_protocol: The hybridization cocktail containing the fragmented and Biotin labeled cDNAs were hybridized to The Affymetrix GeneChip® Mouse Exon 1.0 ST Array according to standard Affymetrix protocol.

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

data_processing:
RMA
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

organism: Mus musculus

source_name: HGPS Transgenic hippocampus

label_protocol: Amplification and labeling were performed according to standard Affymetrix protocol.

growth_protocol: Mouse hippocampus dissected from 63 week old mouse

extract_protocol: 63 week old transgenic and wild-type animals (n = 3 in each group) were sacrificed by cervical dislocation, then the hippocampus was dissected and snapped frozen in liquid nitrogen as described in previous section. Total RNA was extracted using mirVANA miRNA isolation kit (Ambion), which was then quantified using a spectrophotometer (BioPhotometer, Eppendorf), followed by a quality check with the Agilent Tapestation 2200.

tag: age

value: 63 weeks


title: revertant-iPSC-FB (P9), technical rep 1

description: revertant mosacism


title: I-48-M (D)


title: P2 plus IFNa

first: Dusan

last: Bogunovic

state: New York

address: 1468 Madison Avenue,

department: Microbiology

institute: Icahn School of Medicine at Mount Siani

description: P2 plus IFNa

hyb_protocol: Standard Affymetrix protocol was perfomed

scan_protocol: GeneChips were scanned using standard GeneArray Scanner.

data_processing: Affymetrix Console and TAC

source_name: ISG15 deficient patient plus IFNa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA.

extract_protocol: RNAeasy kits from Qiagen

treatment_protocol: HTert-immortalized fibroblasts from C1, C6, C16,  P1, P2 and P3 were treated with 1000U of IFN-α2b for 12 h, washed with PBS and left to rest for 36 h, after which relative mRNA levels were assessed

value: H tert Fibroblasts


title: P3 plus IFNa

description: P3 plus IFNa


title: PA080_129_111206

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 031/08 (gene level)

description:
A653_145
Adult control substantia nigra.


title: Adult control substantia nigra, 010/09 (gene level)

description:
A653_142
Adult control substantia nigra.


title: PA080_131_111220

description: Hybridized to SNP6.0 array


title: P1 plus IFNa

description: P1 plus IFNa


title: Adult control substantia nigra, 020/08 (gene level)

description:
A653_141
Adult control substantia nigra.


title: C16 plus IFNa

description: C16 plus IFNa

source_name: control plus IFNa


title: I-48-NT (D)


title: mouse_hippocampus_63weeks_Transgenic_rep1


title: C6 plus IFNa

description: C6 plus IFNa


title: mouse_hippocampus_63weeks_Wildtype_rep3

source_name: Wildtype, hippocampus


title: Adult control substantia nigra, 021/08 (gene level)

description:
A653_140
Adult control substantia nigra.


title: PA080_127_111206

description: Hybridized to SNP6.0 array


title: mouse_hippocampus_63weeks_Wildtype_rep2


title: I-48-NT (B)


title: mouse_hippocampus_63weeks_Wildtype_rep1


title: I-48-NT (C)


title: Adult control substantia nigra, 017/07 (gene level)

description:
A653_115
Adult control substantia nigra.


title: mouse_hippocampus_63weeks_Transgenic_rep2


title: PA080_123_111206

description: Hybridized to SNP6.0 array


title: I-4-M (E)

value: 4 hours


title: PA080_12792_090304

description: Hybridized to SNP6.0 array


title: C1 plus IFNa

description: C1 plus IFNa


title: P3

source_name: ISG15 deficient patient


title: Brain_fructose_rep8

city: Copenhagen N

first: Ole

middle: Hartvig

last: Mortensen

address: Panum 6.5.28, Blegdamsvej 3

department: Department of Biomedical Sciences

country: Denmark

institute: University of Copenhagen

description: Gene expression data from brain without cerebellum, 15 month old maternal fructose diet offspring

hyb_protocol: 5.5 ug of fragmented cRNA wae hybridized for 16 hr at 45C on GeneChip Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with Bioconductor 2.12 and R 3.0.1 using built-in RMA with default settings

organism: Rattus norvegicus

source_name: Rat brain, 15 month old male, maternal fructose diet offspring

label_protocol: Biotinylated cRNA was prepared from 100 ng RNA using the Ambion WT Expression Kit (Life Technologies) and the Affymetrix Whole Transcription (WT) Expression kit (Affymetrix) according to the manufacturer's instructions

extract_protocol: Total RNA was isolated by Qiazol (Qiagen) as described by the manufacturer and further purified using the RNeasy kit (Qiagen) as described by the manufacturer. Quality of RNA was assured using a Bioanalyzer (Agilent, Santa Clara, CA, USA) as described by the manufacturer

treatment_protocol: Pregnant Fischer F344 rats were subjected to either a control or a high fructose diet during gestation and lactation. Offspring were weaned on day 20 onto a chow diet and sacrificed at 15 months of age after which the brain was removed for RNA isolation.

value: Brain without cerebellum

tag: strain

value: Fischer F344

tag: gender

value: Male

value: 15 months

tag: diet

value: high fructose


title: PA080_121_111106

description: Hybridized to SNP6.0 array


title: P2


title: I-48-NT (A)

value: M. bovis BCG


title: I-4-M (D)


title: Adult control substantia nigra, 022/06 (gene level)

description:
A653_111
Adult control substantia nigra.


title: PA080_13_111123

description: Hybridized to SNP6.0 array


title: PA080_121_090618

description: Hybridized to SNP6.0 array


title: Brain_fructose_rep7


title: PA080_119_111214

description: Hybridized to SNP6.0 array


title: C16

source_name: control


title: Adult control substantia nigra, 016/08 (gene level)

description:
A653_102
Adult control substantia nigra.


title: P1


title: Brain_fructose_rep4


title: Adult control substantia nigra, 023/09 (gene level)

description:
A653_121
Adult control substantia nigra.


title: Adult control substantia nigra, 004/08 (gene level)

description:
A653_093
Adult control substantia nigra.


title: I-48-NT (E)

value: 48 hours


title: I-4-M (C)

value: 2mM Metaformin


title: I-4-M (A)


title: PA080_12_090621

description: Hybridized to SNP6.0 array

value: colon cancer


title: Adult control substantia nigra, 036/08 (gene level)

description:
A653_092
Adult control substantia nigra.


title: PA080_110_090618

description: Hybridized to SNP6.0 array


title: Brain_fructose_rep3


title: Brain_fructose_rep2


title: Adult control substantia nigra, 005/09 (gene level)

description:
A653_112
Adult control substantia nigra.


title: Adult control substantia nigra, 025/08 (gene level)

description:
A653_072
Adult control substantia nigra.


title: S10 vs S10D-rep3

city: Chennai

first: Alamelu

last: Raja

state: Tamil Nadu

address: No,1 Mayor sathyamoorthy Road, Chetpet

department: Department of Immunology

institute: National Institute for Research in Tuberculosis

description: Sample 9

hyb_protocol: Samples with higher labelling efficiency (Specific activity >= 15) was selected for competitive hybridization as per the Agilent protocol. A 60mer oligonucleotide based custom array chip was used from Agilent Technologies in 8x15K format. 300ng of Cy5 labelled cRNA from anaerobic cultures of H37Rv, S7 and S10 was hybridized against Cy3 labelled cRNA from aerobic cultures of H37Rv, S7 and S10. Hybridization was done for 17 hrs, 10 rpm at 650C. The image analysis was done using Feature extraction tool version 9.5.3.1 (Agilent Technologies, USA).

scan_protocol: The Typhoon 9210 scanner (GE Life Sciences).

data_processing: Microarray data analysis was done using Bioconductor LIMMA package. The background-corrected raw intensity values were used for analysis. LOWESS algorithm was used to normalize the data and fold change (Fc) was further calculated based on the ratio of Cy5/Cy3 (anaerobic/aerobic) intensities. For statistical analysis, student’s t-test against zero was performed using Benjamini Hochberg multiple testing correction. Genes showing > 1.5 fold change in the test sample compared to the reference pool were compiled as differentially regulated genes.

organism: Mycobacterium tuberculosis

label_protocol: Agilent Two-Color Microarray-Based Exon Analysis, Low Input Quick Amp WT Labeling, cy3 for aerobic and cy 5 for hypoxic

growth_protocol: Aerated cultures of Mycobacterium tuberculosis lab strain H37Rv (ATCC 27294), clinical isolates S7 and S10 were obtained by growing them in Middlebrook 7H9 media supplemented with 2% (v/v) glycerol, 10% albumin-dextrose-catalase (ADC) and 0.05% (v/v) Tween 80 at 37°C, 200rpm.

extract_protocol: Total RNA was isolated from M. tuberculosis H37Rv,S7 and S10 cultures grown in Middlebrook 7H9 media under aerobic (200 rpm) and hypoxic (120rpm) RNA was extracted by RNeasy columns (Qiagen,USA) according to the manufacturer instruction.

treatment_protocol: Laboratory strain H37Rv and clinical isolates S7 and S10 were inoculated in screw capped test tubes (20 by 125mm, with a total fluid capacity of 25.5 ml) containing supplemented MB7H9.  Stirring was achieved with 8-mm Teflon-coated magnetic stirring bars in the tubes (120 rpm) and incubated at 37°C. Methylene blue indicator was added in the media to yield a final concentration of 1.5µg/ml. Reduction and decolorization of this dye served as a visual indication of oxygen depletion.

tag: oxygen condition

value: aerobic

value: Bacterial culture cell pellet

value: hypoxic


title: I-4-M (B)


title: C6


title: Brain_control_rep8

description: Gene expression data from brain without cerebellum, 15 month old maternal control diet offspring

source_name: Rat brain, 15 month old male, maternal control diet offspring

value: control


title: Brain_fructose_rep1


title: I-4-NT (E)


title: I-4-NT (D)


title: PA080_1_090621

description: Hybridized to SNP6.0 array

value: MSS


title: PA080_11_111206

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 015/09 (gene level)

description:
A653_058
Adult control substantia nigra.

value: substantia nigra

value: adult


title: S7 vs S7D-rep3

description: Sample 6


title: Adult control substantia nigra, 018/08 (gene level)

description:
A653_055
Adult control substantia nigra.


title: I-4-NT (B)

value: 4 hours


title: Brain_control_rep7

value: Brain without cerebellum


title: Rv vs RvD-rep3

description: Sample 3


title: C1

value: H tert Fibroblasts


title: Brain_control_rep5

value: Fischer F344

value: Male


title: Adult control substantia nigra, 023/08 (gene level)

description:
A653_003
Adult control substantia nigra.


title: S7 vs S7D-rep2

description: Sample 5


title: Adult control substantia nigra, 018/09 (gene level)

description:
A653_034
Adult control substantia nigra.


title: S10 vs S10D-rep1

description: Sample 7


title: I-4-NT (C)


title: Adult control substantia nigra, 004/06 (gene level)

description:
A653_043
Adult control substantia nigra.


title: S10 vs S10D-rep2

description: Sample 8


title: U-4-NT (D)


title: PA080_125_111123

description: Hybridized to SNP6.0 array


title: Adult control substantia nigra, 013/09 (gene level)

description:
A653_040
Adult control substantia nigra.


title: I-4-NT (A)


title: Rv vs RvD-rep2

description: Sample 2


title: Brain_control_rep1

value: 15 months


title: S7 vs S7D-rep1

description: Sample 4


title: Brain_control_rep4


title: U-4-NT (B)


title: U-4-NT (C)


title: Brain_control_rep3


title: PA080_1_111123

description: Hybridized to SNP6.0 array


title: Rv vs RvD-rep1

description: Sample 1


title: Adult control substantia nigra, 006/09 (gene level)

description:
A653_002
Adult control substantia nigra.


title: 69_cx_28_bx2 none

status: Public on Nov 21 2014

city: San Francisco

first: Linda

last: Giudice

state: CA

address: 513 Parnassus Ave. HSE 1619

department: OBGYN and RS

institute: University of California, San Francisco

hyb_protocol: Microarrays were hybridized, washed, and stained according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

scan_protocol: Microarrays were scanned according to the protocol described in WT Sense Target Labeling Assay Manual from Affymetrix (Version 4; FS450_0007) at the UCSF Gladstone Genomics Core Facility.

data_processing: For each sample, intensity values for all probe sets in the GeneChip operating software (Affymetrix) were imported into GeneSpring GX version 12.6 (Agilent Technologies, Santa Clara, CA) and processed using the robust multiarray analysis algorithm for background adjustment, normalization, and log2 transformation of perfect-match values. The intensity values in each condition and tissue type were normalized to the median of all samples. Genes lists were generated using two-way ANOVA and Benjamini-Hochberg multiple testing correction for false discovery rate, and filtered with a ≥1.5 fold change cut-off and P≥0.05.

source_name: Cervical transformation zone, control

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN Ovation Pico WTA V2 kit, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

growth_protocol: Tissue biopsies were flash frozen immediately following procedure and stored at -80C until TRIzol extraction.

extract_protocol: RNA was extracted from frozen tissues using TRIzol Reagent (Life Technologies, Grand Island, NY) and purified using the NucleoSpin RNA II kit (Macherey-Nagel, Bethlehem, PA) as described. Total RNA as well as protein (abs260/abs280) and organic compound (abs260/abs230) contamination were measured using the Nanodrop (Thermo Fisher Scientific Inc., Waltham, MA, USA).

treatment_protocol: Cervical transformation zone and endometrial biopsies were obtained from 3 groups of volunteers: those using no hormonal contraceptives, DMPA users, or LNG-IUS users. DMPA and LNG-IUS groups had used these contraceptives for at least 6 months.

value: cervical transformation zone

tag: hormonal contraceptive treatment

value: no treatment (mid-secretory phase)


title: 47_endo_30_bx1 none

source_name: Endometrium, control

value: endometrium


title: 35_endo_16_bx1 none


title: 19_Cx_2_bx3 none


title: 59_cx_20_bx1 none


title: 10_Endo_7_bx3 none


title: IPCRR 233 involved vs IPCRR 233 uninvolved (merged dyeswaps)

status: Public on Nov 16 2014

city: Santa Cruz

first: Yuan

last: Cao

address: 2161 Delaware Ave., Suite D

institute: Transderm Inc

description:
K16 R127G
dyeswap

hyb_protocol: 627 to 825 ng of each cRNA sample was hybridized to Agilent 4X44K Human Whole Genome Gene Expression microarrays (part # G4112F) Slides were washed in four successive buffers: a high salt SSPE buffer, a low salt SSPE buffer, an acetonitrile dip, and finally, a Stabilization and Drying Solution (Agilent). All buffers were pre-warmed to 25°C.

scan_protocol: Slides were scanned on an Agilent Microarray Scanner (model G2505B or G2565CA) at 5-mm resolution with the XDR setting

data_processing:
Data were extracted from the scanned images using Agilent Feature Extraction (v9.7.3 or v10.7.3) and imported into Rosetta (Kirkland, WA) Resolver (v7.2.2.0) For the differential expression analysis, fold changes and p-values were computed for each two-channel experiment using Rosetta's standard ratio experiment pipeline. Rosetta performs a two-sided, two-sample t-test on the means of the probe intensities corresponding to a single gene in each channel. The null hypothesis is that there is no fold change between the genes in the two channels. The p-values were corrected using Benjamini-Hochberg Multiple Test Correction (Benjamini and Hochberg, 1995)
The calculation in Rosetta for fold change is: Larger true intensity/smaller true intesity, then multiplied by -1 if the Cy3 true intensity (Channel 1) is the larger value.

label: Cy3, Cy5

source_name: IPCRR 233 involved

label_protocol: Total RNA (100 to 200 ng  of 50 ng/µl per sample) was processed following Agilent’s (Santa Clara, CA) Two-Color Microarray-Based Gene Expression Analysis Protocol (Version 5.7)

extract_protocol: Total RNA was isolated using the RNeasy Mini Plus kit (Qiagen), according to manufacturer’s instructions

tag: individual

value: IPCRR 233

value: plantar skin

tag: tissue status

value: involved

source_name: IPCRR 233 uninvolved

value: un-involved


title: 49_cx_11_bx3 none


title: 56_cx_18_bx1 none


title: IPCRR 1015 involved Cy3 vs IPCRR 1015 uninvolved Cy5

description: K16 R127C

source_name: IPCRR 1015 involved Cy3

value: IPCRR 1015

source_name: IPCRR 1015 uninvolved Cy5


title: 70_cx_29_bx1 none


title: 09_Endo_6_bx3 none


title: U-4-NT (A)

source_name: THP-1 cells

tag: treatment


title: 34_endo_15_bx2 none


title: 16_Cx_1_bx3 none


title: 05_Endo_4_bx3 none


title: 43_endo_22_bx1 none


title: IPCRR 10 involved plantar biopsy Cy3 vs IPCRR 10 uninvolved plantar biopsy Cy5

description: K6a N171K

source_name: IPCRR 10 involved plantar biopsy Cy3

value: IPCRR 10

source_name: IPCRR 10 uninvolved plantar biopsy Cy5


title: IPCRR 394 involved Cy3 vs IPCRR 394 uninvolved Cy5

description: K17 N92S

source_name: IPCRR 394 involved Cy3

value: IPCRR 394

source_name: IPCRR 394 uninvolved Cy5


title: IPCRR 661 involved Cy3 vs IPCRR 661 uninvolved Cy5

description: K6b E472K

source_name: IPCRR 661 involved Cy3

value: IPCRR 661

source_name: IPCRR 661 uninvolved Cy5


title: IPCRR 1009 involved Cy3 vs IPCRR 1009 uninvolved Cy5

description: K16 R127C

source_name: IPCRR 1009 involved Cy3

value: IPCRR 1009

source_name: IPCRR 1009 uninvolved Cy5


title: Bronchial Epithelial Cells severe biological rep56

status: Public on Nov 14 2014

city: Pittsburgh

first: Jadranka

last: Milosevic

state: PA - Pennsylvania

address: 2330 Tilbury Avenue

institute: University of Pittsburgh

description:
Sample name: GSK052V4_SA
Freshly isolated  Bronchial Epithelial Cells

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4X44K array slides

data_processing:
The data was extracted using the Agilent Feature Extraction software 10.7.3.1 (Agilent Technologies)
The data set was normalized by cyclic-LOESS with use of Bioconductor package as described previously (Wu W et. al. 2005). Probes which did not map to an Entrez ID were excluded

source_name: Human Fresh Bronchial Epithelial cells

label_protocol: Cy3-CTP  labeled RNA was prepared according to the standard Agilent protocol from 50ng total RNA.  Labeled RNA   was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays.

extract_protocol:
[Isolation protocol] Bronchoscopy with endobronchial epithelial brushing was performed as previously described (Chu et al., 2002; Zhao et al., 2011). The bronchial brushings generally comprised >90% epithelial cells and were placed into Trizol for mRNA analysis.
Total RNA was extracted from the fresh bronchial epithelial brushings suspended in Trizol solution using the QIACube system (Qiagen, Valencia, CA). RNA quality was determined using the Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), and only samples with an RIN higher than 7 used for microarray experiments.

value: severe asthmatic

value: Fresh Bronchial Epithelial Cells


title: 42_endo_21_bx2 none


title: HPR (control non-PC) involved Cy3 vs HPR (control non-PC) uninvolved Cy5

description: non-PC Control

source_name: HPR (control non-PC) involved Cy3

value: HPR

source_name: HPR (control non-PC) uninvolved Cy5


title: 11_Endo_10_bx3 none

source_name: Endometrium, control


title: Bronchial Epithelial Cells severe biological rep54

description:
Sample name: 2314H_SA
Freshly isolated  Bronchial Epithelial Cells

hyb_protocol: RNA  was hybridized to Agilent Human GE 4 × 44 Kv2 whole human genome microarrays


title: IPCRR 8 involved Cy3 vs HPR (control non-PC) involved Cy5

description: K6a N171K

source_name: IPCRR 8 involved Cy3

value: IPCRR 8

source_name: HPR (control non-PC) involved Cy5


title: Bronchial Epithelial Cells severe biological rep55

description:
Sample name: GSK047V4_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep49

description:
Sample name: 2276Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep51

description:
Sample name: 2280Q_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep50

description:
Sample name: 2278D_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep52

description:
Sample name: 2288G_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep40

description:
Sample name: 2111T_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep44

description:
Sample name: 2166S_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep43

description:
Sample name: 2147O_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep38

description:
Sample name: 2047K_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep36

description:
Sample name: 2040W_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep47

description:
Sample name: 2254P_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep32

description:
Sample name: 1997E_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep31

description:
Sample name: 1989F_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep45

description:
Sample name: 2177X_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep53

description:
Sample name: 2293Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep46

description:
Sample name: 2184U_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep41

description:
Sample name: 2118H_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep42

description:
Sample name: 2136J_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep48

description:
Sample name: 2261M_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep33

description:
Sample name: 1998G_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep37

description:
Sample name: 2042A_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep35

description:
Sample name: 2030T_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep30

description:
Sample name: 1986Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep39

description:
Sample name: 2102S_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep34

description:
Sample name: 2016Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep28

description:
Sample name: 1969Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep29

description:
Sample name: 1970K_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep23

description:
Sample name: 1918I_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep24

description:
Sample name: 1921X_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep25

description:
Sample name: 1929N_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep27

description:
Sample name: 1964P_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep26

description:
Sample name: 1941D_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep21

description:
Sample name: 1841Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep19

description:
Sample name: 1744B_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep18

description:
Sample name: 1743Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep16

description:
Sample name: 1695O_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep20

description:
Sample name: 1771E_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep13

description:
Sample name: 1661X_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep12

description:
Sample name: 1628Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep22

description:
Sample name: 1870G_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep8

description:
Sample name: 1566D_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep9

description:
Sample name: 1568H_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep6

description:
Sample name: 1224B_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep2

description:
Sample name: 0658D_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep3

description:
Sample name: 0667E_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep15

description:
Sample name: 1683H_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep72

description:
Sample name: GSK082_notSA
Freshly isolated  Bronchial Epithelial Cells

value: not severe asthmatic


title: Bronchial Epithelial Cells severe biological rep1

description:
Sample name: 0497F_SA
Freshly isolated  Bronchial Epithelial Cells


title: Brain_control_rep2

description: Gene expression data from brain without cerebellum, 15 month old maternal control diet offspring

source_name: Rat brain, 15 month old male, maternal control diet offspring

value: Brain without cerebellum

value: Fischer F344

value: Male

value: 15 months

value: control


title: Bronchial Epithelial Cells severe biological rep4

description:
Sample name: 0828C_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep14

description:
Sample name: 1682F_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep17

description:
Sample name: 1726Z_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep11

description:
Sample name: 1623P_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep7

description:
Sample name: 1389H_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep10

description:
Sample name: 1578K_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells severe biological rep5

description:
Sample name: 1036A_SA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep71

description:
Sample name: GSK079_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep70

description:
Sample name: GSK068V4_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep65

description:
Sample name: 2303C_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep54

description:
Sample name: 2198F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep59

description:
Sample name: 2237P_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep49

description:
Sample name: 2154L_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep69

description:
Sample name: GSK067V4_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep53

description:
Sample name: 2183S_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep50

description:
Sample name: 2156P_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep52

description:
Sample name: 2168W_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep64

description:
Sample name: 2301Y_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep66

description:
Sample name: 2305G_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep63

description:
Sample name: 2292X_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep61

description:
Sample name: 2284Y_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep47

description:
Sample name: 2139P_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep56

description:
Sample name: 2224G_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep67

description:
Sample name: 2306I_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep58

description:
Sample name: 2232F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep51

description:
Sample name: 2163M_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep68

description:
Sample name: GSK053V4_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep62

description:
Sample name: 2291J_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep46

description:
Sample name: 2134F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep57

description:
Sample name: 2230B_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep45

description:
Sample name: 2131Z_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep43

description:
Sample name: 2128K_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep55

description:
Sample name: 2223E_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep48

description:
Sample name: 2143G_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep41

description:
Sample name: 2119J_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep40

description:
Sample name: 2079X_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep44

description:
Sample name: 2130X_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep42

description:
Sample name: 2122Y_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep39

description:
Sample name: 2073L_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep35

description:
Sample name: 2014V_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep38

description:
Sample name: 2065M_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep37

description:
Sample name: 2063I_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep34

description:
Sample name: 2012R_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep22

description:
Sample name: 1784N_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep26

description:
Sample name: 1863J_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep36

description:
Sample name: 2048M_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep25

description:
Sample name: 1821T_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep27

description:
Sample name: 1908F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep19

description:
Sample name: 1774K_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep17

description:
Sample name: 1752A_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep30

description:
Sample name: 1958U_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep33

description:
Sample name: 2003Q_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep21

description:
Sample name: 1781H_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep32

description:
Sample name: 2001M_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep14

description:
Sample name: 1691G_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep60

description:
Sample name: 2253N_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep12

description:
Sample name: 1341F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep11

description:
Sample name: 1273O_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep16

description:
Sample name: 1751Y_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep18

description:
Sample name: 1765J_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep29

description:
Sample name: 1945L_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep28

description:
Sample name: 1926H_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep23

description:
Sample name: 1790I_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep10

description:
Sample name: 1142Z_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep31

description:
Sample name: 1973Q_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep24

description:
Sample name: 1815Y_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep20

description:
Sample name: 1780F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep15

description:
Sample name: 1708X_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep13

description:
Sample name: 1397G_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep8

description:
Sample name: 0423C_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep7

description:
Sample name: 0311B_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep9

description:
Sample name: 1005P_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep6

description:
Sample name: 0308V_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep3

description:
Sample name: 0154V_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep5

description:
Sample name: 0211F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep1

description:
Sample name: 0112F_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep20

description:
Sample name: 2129M_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep13

description:
Sample name: 1878H_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep4

description:
Sample name: 0168R_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep15

description:
Sample name: 1925F_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep23

description:
Sample name: 2252L_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep27

description:
Sample name: 2310Z_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep26

description:
Sample name: 2309O_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep10

description:
Sample name: 1733W_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep19

description:
Sample name: 2096X_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep8

description:
Sample name: 1701J_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep11

description:
Sample name: 1734Y_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep21

description:
Sample name: 2170J_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep14

description:
Sample name: 1902T_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep18

description:
Sample name: 2052D_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep22

description:
Sample name: 2244M_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep25

description:
Sample name: 2295D_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep9

description:
Sample name: 1705R_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep17

description:
Sample name: 2034B_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep24

description:
Sample name: 2287E_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep16

description:
Sample name: 1943H_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells not severe biological rep2

description:
Sample name: 0114X_notSA
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep5

description:
Sample name: 1619Y_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep4

description:
Sample name: 1579M_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep12

description:
Sample name: 1818E_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep6

description:
Sample name: 1624R_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep3

description:
Sample name: 1546X_NC
Freshly isolated  Bronchial Epithelial Cells


title: 12_pRCC1

status: Public on Nov 06 2014

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was hybridized with the CGX Nimblegen protocol

scan_protocol: We used ScanRI software to control a ScanRI scanner

data_processing: the image data was processed by DEVA software provided by Perkin Elmer to obtain a .txt file. This file is transform by a soft tool ngpackager supplied by Nimblegen to obtain a .ggx file compiling log Ratio Cy3/Cy5 average for every probe (unknown/default parameters).

label_protocol: DNA was labeled with the CGX Nimblegen protocol

extract_protocol: DNA was extracted from fresh or frozen fragments using Qiamp DNA mini kit.

value: Papillary renal cell carcinoma (pRCC)

tag: rcc type

value: type 1

source_name: Promega Human Genomic DNA (G1471/G1521)

value: reference


title: 39_uRCC

value: unclassified renal cell carcinoma (uRCC)

value: unclassified


title: Bronchial Epithelial Cells control biological rep7

description:
Sample name: 1656E_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep1

description:
Sample name: 1070A_NC
Freshly isolated  Bronchial Epithelial Cells


title: Bronchial Epithelial Cells control biological rep2

description:
Sample name: 1225D_NC
Freshly isolated  Bronchial Epithelial Cells


title: 7_pRCC1


title: Pituitary low endophyte animal #4

status: Public on Oct 23 2014

city: Lexington

first: James

middle: C

last: Matthews

state: Ky

address: 207 W.P. Garrigus Buidling

department: Animal and Food Sciences

institute: University of Kentucky

hyb_protocol: Following fragmentation, 10 µg of labeled cRNA was hybridized to Affymetrix Bovine Genome Array for 16 hr at 45°C using the gene chips in the GeneChip Hybridization Oven 640, using 1 chip per RNA sample. GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were stained with R-Phycoerythrin Streotavidin, followed by an antibody solution and a second R-Physcoerythrin Streptavidin solution, with all lquid handling performed by a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 7G GeneChip Scanner (GCS) with AGCC software (Command Console).

data_processing: The raw data were collected with the GeneChip Operating Software (GCOS, version 1.2). The expression intensity values from the software (i.e., the .cel files) were imported into Partek Genomics Suite software (version 6.4; Partek Inc., St. Louis, MO, USA). The algorithm of Robust Multichip Averaging data were further converted into expression values via the algorithms of Quantile normalization of different chips and then Median Polish summarization of multiple probes.

organism: Bos taurus

source_name: Pituitary

label_protocol: Biotinylated cRNA were prepared from 3 µg of total RNA according to Affymetrix protocol. Double-stranded cDNA was synthesized using SuperScriptII (Invitrogen, Carlsbad, CA, USA) and oligo(dT)24 primers. Bio-labeled cRNA was prepared by cDNA in vitro transcription biotinylated UTP.

growth_protocol: The growth protocol has been described in the overall design section above.

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

treatment_protocol: The treatment protocol (i.e. endophyte level) has been described in the overall design section above.

tag: tissue

value: Pituitary

value: Steer

tag: food group

value: low toxic endophyte tall fescue-mixed grass


title: Pituitary high endophyte animal #2

value: high toxic endophyte infected tall fescue


title: Pituitary low endophyte animal #8


title: Pituitary high endophyte animal #6


title: Pituitary high endophyte animal #3


title: Pituitary low endophyte animal #7


title: Pituitary high endophyte animal #8


title: Pituitary low endophyte animal #1


title: Pituitary high endophyte animal #7


title: Pituitary low endophyte animal #5


title: Pituitary low endophyte animal #2


title: Pituitary low endophyte animal #6


title: Pituitary high endophyte animal #4


title: Fibroblast from 6-month wild-type thymus, replicate 2

status: Public on Sep 12 2014

city: Austin

first: Lauren

last: Ehrlich

state: TX

address: 2506 Speedway A5000

department: Molecular Biosciences

institute: The University of Texas at Austin

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 7G with GCOS version 1.4.0.036

data_processing: The data were normalized using the GC-RMA method on Gene Expression Commons (http://gexc.stanford.edu/)

source_name: Fibroblast from a 6-month wild-type C57BL/6J mouse

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

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

value: thymus

value: Fibroblasts

tag: strain/background

value: 6 months

value: male


title: Pituitary high endophyte animal #1


title: Sirpa+ dendritic cells from 6-month wild-type thymus, replicate 2

description:
DCS_6m_B6_2
FACS-sorted thymic dendritic cells

source_name: Sirpa+ dendritic cells from a 6-month wild-type C57BL/6J mouse

value: Sirpa+ dendritic cells

tag: disease state

value: normal


title: Fibroblast from 3-month wild-type thymus, replicate 1

source_name: Fibroblast from a 3-month wild-type C57BL/6J mouse

tag: cell type

value: 3 months


title: Pituitary low endophyte animal #3


title: Fibroblast from 6-month wild-type thymus, replicate 1


title: Fibroblast from 1-month wild-type thymus, replicate 1

source_name: Fibroblast from a 1-month wild-type C57BL/6J mouse

value: 1 month


title: Pituitary high endophyte animal #5


title: Fibroblast from 3-month wild-type thymus, replicate 2


title: Fibroblast from 1-month wild-type thymus, replicate 2


title: Sirpa+ dendritic cells from 3-month wild-type thymus, replicate 2

source_name: Sirpa+ dendritic cells from a 3-month wild-type C57BL/6J mouse


title: Sirpa+ dendritic cells from 6-month wild-type thymus, replicate 1

description:
DCS_6m_B6_1
FACS-sorted thymic dendritic cells


title: Sirpa+ dendritic cells from 1-month wild-type thymus, replicate 2

source_name: Sirpa+ dendritic cells from a 1-month wild-type C57BL/6J mouse


title: Sirpa+ dendritic cells from 3-month wild-type thymus, replicate 1


title: Sirpa+ dendritic cells from 1-month wild-type thymus, replicate 1


title: Sirpa- dendritic cells from 6-month wild-type thymus, replicate 2

description:
DC_6m_B6_2
FACS-sorted thymic dendritic cells

source_name: Sirpa- dendritic cells from a 6-month wild-type C57BL/6J mouse

value: Sirpa- dendritic cells


title: Sirpa- dendritic cells from 3-month wild-type thymus, replicate 2

source_name: Sirpa- dendritic cells from a 3-month wild-type C57BL/6J mouse


title: medullary thymic epithelial cells (CD80 hi and MHC-II hi) from 3-month wild-type thymus, replicate 1

source_name: mTEChi from a 3-month wild-type C57BL/6J mouse


title: medullary thymic epithelial cells (CD80 hi and MHC-II hi) from 1-month wild-type thymus, replicate 2

source_name: mTEChi from a 1-month wild-type C57BL/6J mouse


title: Sirpa- dendritic cells from 3-month wild-type thymus, replicate 1


title: medullary thymic epithelial cells (CD80 lo and MHC-II lo) from 6-month wild-type thymus, replicate 2

source_name: mTEClo from a 6-month wild-type C57BL/6J mouse


title: medullary thymic epithelial cells (CD80 hi and MHC-II hi) from 3-month wild-type thymus, replicate 2


title: medullary thymic epithelial cells (CD80 hi and MHC-II hi) from 6-month wild-type thymus, replicate 1

source_name: mTEChi from a 6-month wild-type C57BL/6J mouse


title: Sirpa- dendritic cells from 1-month wild-type thymus, replicate 2

source_name: Sirpa- dendritic cells from a 1-month wild-type C57BL/6J mouse


title: medullary thymic epithelial cells (CD80 lo and MHC-II lo) from 1-month wild-type thymus, replicate 1

source_name: mTEClo from a 1-month wild-type C57BL/6J mouse


title: medullary thymic epithelial cells (CD80 lo and MHC-II lo) from 3-month wild-type thymus, replicate 1

source_name: mTEClo from a 3-month wild-type C57BL/6J mouse


title: medullary thymic epithelial cells (CD80 lo and MHC-II lo) from 3-month wild-type thymus, replicate 2


title: Sirpa- dendritic cells from 1-month wild-type thymus, replicate 1


title: medullary thymic epithelial cells (CD80 lo and MHC-II lo) from 1-month wild-type thymus, replicate 2


title: medullary thymic epithelial cells (CD80 lo and MHC-II lo) from 6-month wild-type thymus, replicate 1


title: cortical thymic epithelial cells from 3-month wild-type thymus, replicate 1

source_name: cTEC from a 3-month wild-type C57BL/6J mouse

value: cortical thymic epithelial cells


title: Sirpa- dendritic cells from 6-month wild-type thymus, replicate 1

description:
DC_6m_B6_1
FACS-sorted thymic dendritic cells


title: medullary thymic epithelial cells (CD80 hi and MHC-II hi) from 1-month wild-type thymus, replicate 1


title: cortical thymic epithelial cells from 6-month wild-type thymus, replicate 1

source_name: cTEC from a 6-month wild-type C57BL/6J mouse


title: cortical thymic epithelial cells from 6-month wild-type thymus, replicate 2


title: medullary thymic epithelial cells (CD80 hi and MHC-II hi) from 6-month wild-type thymus, replicate 2


title: cortical thymic epithelial cells from 1-month wild-type thymus, replicate 2

source_name: cTEC from a 1-month wild-type C57BL/6J mouse


title: RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-664

status: Public on Jul 26 2014

city: Notre Dame

first: Mary

middle: Ann

last: McDowell

state: Indiana

address: 210 Galvin Life Science Center

department: Biological Sciences

institute: University of Notre Dame

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the second of four biological replicates
664_UI

hyb_protocol: Labeled cDNAs were hybridized to 12-plex NimbleGen Homo sapiens Expression Arrays (platform accession number GPL16025), featuring 45,033 probes representing 23,752 gene transcripts, using Hybridization Kit, LS (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations.

scan_protocol: Image acquisition of arrays was performed using a NimbleGen MS 200 Microarray Scanner, at a 2 micron resolution.

data_processing:
NimbleGen array image data were processed using NimbleScan (version 2.5) to extract intensity values for each gene. NimbleScan software automates the pre-processing of NimbleGen microarray image data, including identifying the location of each probe, extraction of intensity data from the image, background correction, and obtaining expression summary values for each gene using a probe-level summarization method RMA (Robust Multi-Array Average).
Values are hybridization fluorescence intensity averages of RMA normalized gene transcript probesets (consisting of three probes per gene transcript). All sample values are reported for any probeset with an intensity value in at least one of the 24 samples which was two times greater than that of the corresponding sample array background. Such values were subsequently used in downstream analysis. All values for any probeset that did not pass this filter are listed as "NULL".

label_protocol: 25ng of high quality RNA was converted to double stranded cDNA using Sigma TransPlex Complete Whole Transcriptome Amplification Kit (Sigma). RNA degradation, double stranded cDNA purification, and cDNA precipitation was conducted following NimbleGen Gene Expression Array user’s guide protocols (Roche NimbleGen). A Nanodrop ND-2000 (ThermoScientific) was used to determine total RNA and double stranded cDNA concentrations. Sample cDNAs were Cy3-labeled using NimbleGen Single Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations.

growth_protocol: CD14+ monocytes of four anonymous healthy adult female human donors (Central Indiana Regional Blood Center, Indianapolis, IN) were isolated from peripheral blood mononuclear cells by positive selection using an AutoMACS separator (Miltenyi Biotec) after isolation using lymphocyte separating media (Cellgro) following manufacturer protocols. The purity of separated monocytes was determined by flow cytometry analysis on a MCL500 flow cytometer (Beckman Coulter) using fluorescent antibody staining for CD14, CD19, CD45, and CD3 (Biolegend). Enriched monocytes were differentiated into dendritic cells (MDDC) by treatment with granulocyte-macrophage colony-stimulating factor (GM-CSF; 2,000 U/mL) and interleukin-4 (IL-4; 800 U/mL) recombinant cytokines (Peprotech) on days 0, 3, and 6 after plating in six-well plates at 2.5 × 106 cells/mL in complete RPMI medium (10% fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine). Immature MDDC were harvested on day 7 and plated in 6-well plates at 2 × 106 cells in 2 mL complete RPMI medium per well in the absence of exogenous cytokine. The phenotype puritiess of DCs was determined by flow cytometry analysis of CD1a, CD14, HLA-DR, CD40, CD80, and CD86 expression. All infections were performed with Leishmania major Friedlin V1 strain (NIH) and gene knockout and add-back mutants for LPG1 [encoding a galactofuranosyl transferase] or LPG2 [encoding a golgi GDP-Man transporter] genes. All parasites were cultured at 26°C without CO2 in complete medium 199 (20% heat-inactivated fetal bovine serum, 100 U/mL penicillin, 100 μg/mL streptomycin, 2 mM L-glutamine, 40 mM HEPES, 0.1 mM adenine in 50 mM HEPES, 5 mg/mL hemin in 50% triethanolamine, and 1 mg/mL biotin). Parasites tested negative for mycoplasma using a Mycoplasma PCR detection set (Takara) and tested below the detection limits for endotoxin using a Limulus Amoebocyte Lysate kit (Charles River Laboratories). Infective-stage metacyclic promastigotes were isolated by use of a Ficoll gradient as previously described (PMID: 11748963) and opsonized with 5% normal human serum prior to infection at a concentration of ten parasites to one host cell. Infection rates were determined at the end of each experiment by DiffQuick staining of cytospin whole cell preparations and visualization by light microscopy.

extract_protocol: Total RNA from uninfected or Leishmania-infected human MDDCs was isolated using an RNEasy kit (Qiagen). Bioanalyzer 2100 (Agilent Technologies) and RNA 6000 Nano kits (Agilent Technologies) were used to determine total RNA integrity.

treatment_protocol: After 8 hours post-infection, MDDCs were harvested washing in medium and application of 0.5 mM EDTA (Gibco) in 1X PBS (Cellgro). Cell harvests were spun down, washed, and pellets resuspended in RNAlater RNA Stabilization Solution (Applied Biosystems).

tag: host cell type

value: Monocyte derived dendritic cells (MDDCs)

tag: donor id number

tag: infecting parasite species

value: Uninfected

tag: background


title: cortical thymic epithelial cells from 3-month wild-type thymus, replicate 2

tag: age

tag: gender


title: RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-686

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the fourth of four biological replicates
686_UI


title: RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-665

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the third of four biological replicates
665_UI


title: RNA_human-monocyte-derived-dendritic-cell_uninfected_donor-170

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells which are uninfected and is the first of four biological replicates
170_UI


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-knockout-mutant-infected_8hpi_donor-686

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout Leishmania major (FV1 strain) parasites and is the fourth of four biological replicates
686_LPG2_KO

value: Leishmania major

tag: parasite strain

tag: parasite genotype/variation

value: lpg2 gene knockout

tag: hours post-infection (hpi)

value: 8 hours


title: cortical thymic epithelial cells from 1-month wild-type thymus, replicate 1


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-addback-mutant-infected_8hpi_donor-686

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the fourth of four biological replicates
686_LPG2_AB

value: lpg2 gene knockout add-back


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-addback-mutant-infected_8hpi_donor-686

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the fourth of four biological replicates
686_LPG1_AB

value: lpg1 gene knockout add-back


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-knockout-mutant-infected_8hpi_donor-665

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout Leishmania major (FV1 strain) parasites and is the third of four biological replicates
665_LPG2_KO


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-knockout-mutant-infected_8hpi_donor-170

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout Leishmania major (FV1 strain) parasites and is the first of four biological replicates
170_LPG2_KO


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-knockout-mutant-infected_8hpi_donor-686

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout Leishmania major (FV1 strain) parasites and is the fourth of four biological replicates
686_LPG1_KO

value: lpg1 gene knockout


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-knockout-mutant-infected_8hpi_donor-664

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout Leishmania major (FV1 strain) parasites and is the second of four biological replicates
664_LPG2_KO


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-knockout-mutant-infected_8hpi_donor-664

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout Leishmania major (FV1 strain) parasites and is the second of four biological replicates
664_LPG1_KO


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-addback-mutant-infected_8hpi_donor-665

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the third of four biological replicates
665_LPG2_AB


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8hpi_donor-665

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with wild type Leishmania major (FV1 strain) parasites and is the third of four biological replicates
665_FV1

value: Wild Type


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-addback-mutant-infected_8hpi_donor-170

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the first of four biological replicates
170_LPG2_AB


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg2-addback-mutant-infected_8hpi_donor-664

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg2 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the second of four biological replicates
664_LPG2_AB


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-addback-mutant-infected_8hpi_donor-664

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the second of four biological replicates
664_LPG1_AB


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-knockout-mutant-infected_8hpi_donor-170

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout Leishmania major (FV1 strain) parasites and is the first of four biological replicates
170_LPG1_KO


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-addback-mutant-infected_8hpi_donor-170

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the first of four biological replicates
170_LPG1_AB


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-addback-mutant-infected_8hpi_donor-665

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout add-backs Leishmania major (FV1 strain) parasites and is the third of four biological replicates
665_LPG1_AB


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-lpg1-knockout-mutant-infected_8hpi_donor-665

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with lpg1 gene knockout Leishmania major (FV1 strain) parasites and is the third of four biological replicates
665_LPG1_KO


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8hpi_donor-664

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with wild type Leishmania major (FV1 strain) parasites and is the second of four biological replicates
664_FV1


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8hpi_donor-170

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with wild type Leishmania major (FV1 strain) parasites and is the first of four biological replicates
170_FV1


title: RNA_human-monocyte-derived-dendritic-cell_Leishmania-major-strain-FV1-infected_8hpi_donor-686

description:
This sample is expression values of total mRNA taken from cytokine stimulated human monocyte derived dendritic cells infected with wild type Leishmania major (FV1 strain) parasites and is the fourth of four biological replicates
686_FV1


title: MMTV-PyVT/HdhQ7/Q7 rep1

status: Public on Apr 14 2014

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

description:
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

hyb_protocol: Affymetrix GeneChip Mouse Exon 1.0 ST Array were hybridized with 4,7µg of labelled DNA according Affymetrix protocols, for 17h at 45°C and 60rpm

scan_protocol: An Affymetrix GCS3000 7G scanner was used to scan microarrays, following mouse exon array requirements and specifications

data_processing: Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), exon level expression were summarized from the corrected intensities and then quantile normalized.

source_name: MMTV-PyVT/HdhQ7/Q7 breast tumour

label_protocol: 100ng of total RNA was used to prepare biotinilated DNA, according Affymetrix recomandations (http://media.affymetrix.com/support/downloads/manuals/wt_expressionkit_manual.pdf). Whole transcript targets were produced using the Ambion WT kit and the Affymetrix kit (The Affymetrix GeneChip® WT Terminal Labeling Kit) to fragment and labelled DNA.

growth_protocol: Animals were kept in standard conditions, water and food ad libium

extract_protocol: Samples were dissected and snap-frozen in liquid nitrogen, RNA extraction with mRNeasy mini kit (Quiagen)

treatment_protocol: Tumors were not treated - genetic modifications

tag: htt polyq

tag: strain


title: MMTV-PyVT/HdhQ111/Q111 rep4

source_name: MMTV-PyVT/HdhQ111/Q111 breast tumour


title: MMTV-PyVT/HdhQ111/Q111 rep1


title: MMTV-PyVT/HdhQ111/Q111 rep3


title: MMTV-PyVT/HdhQ7/Q7 rep3


title: MMTV-PyVT/HdhQ7/Q7 rep2


title: MMTV-PyVT/HdhQ111/Q111 rep2


title: MMTV-PyVT/HdhQ7/Q7 rep4


title: Diffuse Intrinsic Pontine Glioma 7 - Normal-6.0

status: Public on Mar 31 2014

city: Toronto

first: Pawel

last: Buczkowicz

state: Ontario

address: 686 Bay Street

department: Paediatric Laboratory Medicine

country: Canada

institute: Hospital for Sick Children

description:
Dx: diagnosis, OS: overral survival
Hybridized to 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files  were processed using Partek Genome Suite V6.6 and Genotyping Console V4.1 using Segmentation and Hidden-Markov Model Analysis. Tumour samples were normalized to their matched normal. Tumour samples with no corresponding matched normal were normalized using HapMap.
CHP files for samples analyzed on the 6.0 platform were normalized using Birdseed V2 algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Diffuse Intrinsic Pontine Glioma 6 - Normal

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from snap frozen biopsy and autopsy samples from DIPG patients using the acidic phenol-chloroform method. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: normal brain

value: M

tag: age at dx (years)

tag: os (years)


title: Diffuse Intrinsic Pontine Glioma 9 - Normal-6.0

source_name: Diffuse Intrinsic Pontine Glioma 8 - Normal

tag: tissue


title: Diffuse Intrinsic Pontine Glioma 57 - Normal-6.0

value: F


title: Diffuse Intrinsic Pontine Glioma 9 - Tumour-6.0

source_name: Diffuse Intrinsic Pontine Glioma 8 - Tumour

value: Diffuse Intrinsic Pontine Glioma

value: DIPG


title: Diffuse Intrinsic Pontine Glioma 30 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 8 - Tumour-6.0

source_name: Diffuse Intrinsic Pontine Glioma 7 - Tumour


title: Diffuse Intrinsic Pontine Glioma 18 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 25 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 39 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 55 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 27 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 56 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 28 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 37 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 19 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 60 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 19 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 26 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 45 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 24 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 62 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 6 - Normal-6.0

source_name: Diffuse Intrinsic Pontine Glioma 5 - Normal


title: Diffuse Intrinsic Pontine Glioma 58 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 4 - Normal-6.0

source_name: Diffuse Intrinsic Pontine Glioma 3 - Normal


title: Diffuse Intrinsic Pontine Glioma 18 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 7 - Tumour-6.0

source_name: Diffuse Intrinsic Pontine Glioma 6 - Tumour


title: Diffuse Intrinsic Pontine Glioma 41 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 61 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 5 - Normal-6.0

source_name: Diffuse Intrinsic Pontine Glioma 4 - Normal


title: Diffuse Intrinsic Pontine Glioma 29 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 1 - Normal-6.0


title: Diffuse Intrinsic Pontine Glioma 79 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 63 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 62 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 80 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 58 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 60 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 67 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 50 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 47 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 3 - Normal-6.0

source_name: Diffuse Intrinsic Pontine Glioma 2 - Normal


title: Diffuse Intrinsic Pontine Glioma 66 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 61 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 55 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 48 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 64 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 57 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 71 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 51 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 56 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 49 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 78 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 46 - Tumour-6.0


title: Diffuse Intrinsic Pontine Glioma 41 - Tumour-6.0


title: Csnk1a1 knockdown (Csnk1a1-97 shRNA) in LSCs rep6

status: Public on Feb 23 2014

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

hyb_protocol: Standard Illumina hybridzation protocol

scan_protocol: BeadArrays were scanned with a BeadArray Reader (Illumina) and expression intensities were calculated with Beadstudio software (Illumina).

data_processing: The samples were analyzed by MouseWG-6 v2.0 Expression beadchip (Illumina). The quality of probe intensities was determined using the beadarray R package from Bioconductor (Dunning et al., 2007)

label_protocol: Standard Illumina protocol

extract_protocol: RNA was isolated using Trizol (Invitrogen).

tag: strain background

tag: genotype/variation

value: Actin-dsRed

value: bone marrow

value: Leukemia stem cells (LSCs)

tag: cell type info

value: [Hoechst low dsRed+ c-kit hi CD34+ FcyRII hi] driven by the MLL-AF9 oncogene were isolated from the bone marrow of quaternary transplant leukemic mice


title: w30tM2

status: Public on Dec 30 2013

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description: mut male 30 weeks old

hyb_protocol: ssDNAs were hybridized to the Mouse Exon 1.0 ST arrays for 17 hours at 45°C.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Gene-level calculation was performed by RMA (RobustMultichip Average) [Irizarry et al., 2003] and normalization by quantile sketch [Bolstad et al., 2003] by mean of APT tools 1.12.0 integrated in oneChannelGUI bioconductor package 1.18.1
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: mutant

label_protocol: standard affymetrix exon array kit

extract_protocol: trizol

value: 30 weeks

value: mutant

value: male


title: Csnk1a1 knockdown (Csnk1a1-97 shRNA) in LSCs rep4

tag: cell type


title: w30cM3

description: wt male 30 weeks old

source_name: wt

value: wild type


title: w30tF2

description: mut female 30 weeks old

value: female


title: w30cM2

description: wt male 30 weeks old


title: Diffuse Intrinsic Pontine Glioma 39 - Tumour-6.0


title: w30tM1

description: mut male 30 weeks old


title: Diffuse Intrinsic Pontine Glioma 38 - Tumour-6.0


title: w30tF1

description: mut female 30 weeks old


title: w30cF2

description: wt female 30 weeks old


title: Diffuse Intrinsic Pontine Glioma 45 - Tumour-6.0


title: w30cF3

description: wt female 30 weeks old


title: w20tM1

description: mut male 20 weeks old

value: 20 weeks


title: Diffuse Intrinsic Pontine Glioma 52 - Tumour-6.0


title: w20tM2

description: mut male 20 weeks old


title: w20cM3

description: wt male 20 weeks old


title: w30cM1

description: wt male 30 weeks old


title: w20cM2

description: wt male 20 weeks old


title: w20cF2

description: wt female 20 weeks old


title: w10tM2

description: mut male 10 weeks old

value: 10 weeks


title: w20cF1

description: wt female 20 weeks old


title: w20tF2

description: mut female 20 weeks old


title: w20tF1

description: mut female 20 weeks old


title: w10tM1

description: mut male 10 weeks old


title: w20cM1

description: wt male 20 weeks old


title: w20cF3

description: wt female 20 weeks old


title: Csnk1a1 knockdown (Csnk1a1-97 shRNA) in LSCs rep5


title: w10tF2

description: mut female 10 weeks old


title: w10tM3

description: mut male 10 weeks old


title: w30cF1

description: wt female 30 weeks old


title: w10tF1

description: mut female 10 weeks old


title: w10tF3

description: mut female 10 weeks old


title: w10cM2

description: wt male 10 weeks old


title: Diffuse Intrinsic Pontine Glioma 44 - Tumour-6.0


title: w10cF2

description: wt female 10 weeks old


title: w10cM1

description: wt male 10 weeks old


title: w10cF1

description: wt female 10 weeks old


title: placenta mnr female rep1

status: Public on Dec 06 2013

city: San Antonio

first: Laura

middle: L

last: Cox

state: Texas

department: Genetics

institute: Texas Biomedical Research Institute

description: 25680 MNR Female

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were all median normalised and log2 transformed in Genesifter Analysis Edition (http://www.geospiza.com/Products/AnalysisEdition.shtml)

organism: Papio hamadryas

source_name: placenta mnr

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Tissue samples were flash frozen immediately at collection and stored at -80 degrees C.

tag: nutrient availability

value: nutrient restricted

tag: developmental stage (days of gestation)

value: 165 dGa

value: placenta


title: placenta control female rep2

description: 27049 Con Female

source_name: placenta control

value: normal (control)


title: placenta mnr male rep3

description: 26990 MNR Male


title: placenta control female rep3

description: 27133 Con Female


title: placenta mnr male rep2

description: 26699 MNR Male


title: placenta mnr male rep1

description: 25679 MNR Male