title: Kn ME cells from larva, biological replicate 3

description: Sorted mCD8:GFP positive cells from UAS-knL:HA/GAL4[21-7], UAS-mCD8:GFP line.

hyb_protocol: Hybridisation performed by Takara Bio Inc..

scan_protocol: Scanning performed by Takara Bio Inc..

data_processing: The data were processed with RMA algorithm in the Bioconductor with default settings.

source_name: Body wall, mCD8:GFP positive cells

label_protocol: Labelling performed by Takara Bio Inc..

growth_protocol: Flies developed at 25oC.

extract_protocol: PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: 80 larval body walls were dissected at wandering third instar, digested with protease, dissociated and mCD8:GFP positive cells were collected.

tag: source

value: body wall

tag: developmental stage

value: wandering third instar larva

value: GAL4[21-7] (all class of da neurons)

value: Kn ME


title: DU315-6-M.r. (K-Raslox), technical rep1

status: Public on Nov 27 2013

type: RNA

city: Salamanca

first: Alicia

middle: Ginel

last: Picardo

state: Select a State or Province

address: Campus Miguel de Unamuno

country: Spain

institute: Cic, Salamanca

description:
02. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)

hyb_protocol: For mRNA expression analysis, labeled cRNAs were fragmented and hybridized to the GeneChip Mouse Genome 430 2.0 (Affymetrix) using the Genechip Fluidics Station 450 (Affymetrix). Hybridized arrays were stained with streptavidin–phycoerythrin, rewashed, treated with biotinylated antistreptavidin–phycoerythrin antibodies and restained with streptavidin–phycoerythrin, according to the manufacturer’s protocols. For miRNA samples, hybridizations were performed using the GeneChip miRNA Array (Affymetrix) according to protocols from Affymetrix.

scan_protocol: The stained mRNA expression microarrays were finally scanned in a GeneArray Scanner (Hewlett Packard). For miRNA hybridizations, washing and scanning were performed using the Affymetrix GeneChip System (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing: The RMA function (Irizarry, Hobbs et al. 2003) provided by the package Affy from R/Bioconductor was applied to both mRNA and miRNA raw expression data. The probes were mapped to GENE LOCi by the CDF built by GATExplorer, which can be found at http://bioinfow.dep.usal.es/xgate/mapping/mapping.php

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: MEFs expressing only K-Ras (H-Ras/N-Ras double knockout); Control

label_protocol: Total RNA was reverse transcribed into double-stranded complementary DNA (cDNA) using an oligo(dT)24 primer containing a T7 polymerase promoterbinding site (Genset). cDNA was then used as a template to synthesize cRNA by in vitro transcription (Ambion T7 Megascript), with incorporation of biotinylated nucleotides (Enzo Diagnostics). For miRNA samples, 1000 ng of total RNA were labeled using the Flash Tag Biotin HSR Labeling kit (Genisphere, P/N HSR10FTA) according to the manufacturer´s instructions.

growth_protocol: Cultures of different cell lines were grown in a humidified CO2 (5%) atmosphere at 37°C, in Dulbecco's modified Eagle's medium (DMEM; Gibco) supplemented with fetal bovine serum (10% FBS; Hyclone, Logan, Utah, USA), glutamine (2mM), penicillin (100 U/ml) and streptomycin (100 mg/ml). Hygromycin (200μg/ml, Sigma-Aldrich) or puromycin (2μg/ml, Sigma-Aldrich) was also added as appropriate to MEF cultures expressing BRAF or MEK1, respectively.

extract_protocol: For mRNA expression analysis, total RNA was isolated using the TRIzol reagent and protocol as described by the manufacturer (Ambion, Life Technologies). RNA samples were purified using the RNeasy® Mini Kit (Qiagen) and their concentration, purity and integrity was measured in an “Agilent 2100 Bioanalyzer” (Agilent Technologies). For microRNA studies, total RNA was extracted from two 10cm culture dishes per individual sample by using mirVana miRNA isolation kit (Ambion) according to the manufacturer’s protocol. RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: For tamoxifen induction, cultures were treated as appropriate with 4-Hydroxy-tamoxifen (4-OHT, H7904, Sigma-Aldrich) for 6 or 12 days at final concentration 0.6μM to promote the K-Ras locus disruption. Subconfluent cultures of untreated or 4-OHT-treated cell lines were used for RNA extraction.

tag: treatment

value: control

tag: cell type

value: Mouse Embryonic Fibroblasts (MEFs)

tag: genotype

tag: age

value: Inmortalized MEFs cultures

tag: cell line


title: DU315-6-S (K-Raslox), biological rep2

description:
03. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)


title: Con BDL 48h rep3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: The Affymetrix GeneChip Mouse Gene 1.1 ST 24-array plate consists of 24 single Gene 1.1 ST peg arrays arranged into the standard 96 well plate format. Array hybridization, washing and scanning were performed on a GeneTitan Instrument according to the manufacturer’s recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

label: biotin

source_name: liver from control [JNK1f/f] mice, 48 hrs after bile duct ligation

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit (Applied Biosystems, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: JNK1-deficient mice were purchased from Harlan Laboratories (Bar Harbor, ME). JNK1f/f (C57BL/6 background) mice were kindly donated by Dr. Roger J. Davis (Howard Hughes Medical Institute, Chevy Chase, MD) and crossed with transgenic animals expressing the Cre transgene under control of a postnatal activated albumin promoter by crossing giving yield to the JNK1Δhepa strain, mice with specific deletion of JNK1 only in hepatocytes. Mice were maintained on standard laboratory chow.

extract_protocol: Total RNA was prepared from the liver using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Induction of liver fibrosis was performed in 7-8 weeks old age-matched male mice (n = 9-10 per group) by ligating the common bile duct (BDL). Control treated animals were opened and immediately closed (sham).  Mice were sacrificed 48h and 28days later.

value: bile duct ligation

tag: time

tag: genetic background

value: JNK1f/f (control)

tag: gender

value: male

tag: tissue

value: liver

value: 8 weeks


title: mild hand,foot and mouth disease

city: Guangzhou

first: Hong-Ling

last: Jia

state: Guangdong

address: Huangpu Road

country: China

institute: Jinan University

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent miRNA Spike- In kit and miRNA Hybridization Kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).
Agilent Feature Extraction Software (version 10.7.1.1) was used for background subtraction and quantile normalization.

organism: Homo sapiens

source_name: serum samples

label_protocol: 100 ng of total RNA(including miRNA) were dephosphorylated and denaturated,then ligated with Cyanine 3-pCp at 16℃ for 2 hours using T4 RNA Ligase.

extract_protocol: We isolated exosomes of sera from all participants by using ExoQuick precipitation following manufacturer′s instructions, Total RNA extracted using Trizol following manufacturer′s instructions

treatment_protocol: Blood samples from five mild  Hand,foot and mouth disease and five extremely severe Hand,foot and mouth disease children according to the ‘hand,foot and mouth disease prevention control guide’(2008 Edition) issued by the Ministry of Health, China(http://www.moh.gov.cn/publicfiles/business/htmlfiles/mohbgt/s9511/200805/34775.htm), were randomly collected for experiments and clinical symptoms and laboratory test(EV71 nucleic acid detection kit) confirmed that the EV71infections caused all these hand,foot and mouth disease cases. In addition to meeting the above symptoms, extremely severe Hand,foot and mouth disease patients all had encephalitis, pulmonary hemorrhage, and mechanical ventilation and other clinical symptoms.They were proven to have no other disease after a systematic check in the hospital.Five blood samples from healthy children were collected as controls

tag: diseaste state

value: mild hand,foot and mouth disease patients


title: JNK1KO BDL 48h rep1

source_name: liver from JNK1 null [JNK1-/-] mice, 48 hrs after bile duct ligation

value: JNK1 null (JNK1-/-)


title: Con sham 28d rep1

source_name: liver from control [JNK1f/f] mice, 28 days after sham (control) treatment

value: sham

value: 12 weeks


title: Kn ME cells from larva, biological replicate 2

city: Kyoto

first: Yukako

last: Hattori

address: Sakyo-ku

department: Graduate School of Biostudies

country: Japan

institute: Kyoto University

organism: Drosophila melanogaster


title: DU315-6-M (K-Raslox), biological rep1

description:
01. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)


title: Con sham 28d rep3


title: JNK1dhepa BDL 28d rep3

source_name: liver from hepatocyte-specifik JNK1 null [JNK1Δhepa] mice, 28 days after bile duct ligation

value: hepatocyte-specific JNK1 null (JNK1Δhepa)


title: HeLa cell line

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description: Analysis of gene expression in human HeLa cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_Plus_2.0 arrays. 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 Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

source_name: HeLa cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual v2, Affymetrix).

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

treatment_protocol: Proliferating cells were grown up to 80% confluence under cell culture conditions

tag: HeLa cell line


title: Kn ME cells from larva, biological replicate 1

value: body wall


title: Ab ME cells from larva, biological replicate 3

description: Sorted mCD8:GFP positive cells from +/GAL4[21-7], UAS-mCD8:GFP; UAS-abL/+ line.

value: wandering third instar larva

value: Ab ME


title: HFK transfected with pLXSN-HPV16E6/E7

description: Analysis of gene expression in human foreskin keratinocytes (HFK) transfected with retroviral vectors harboring the human papillomavirus type 16 (HPV16) oncogenes E6, E7, or E6/E7. Gene expression was compared to HFK containing the empty vector pLXSN to identify cellular genes which are influenced by the expression of HPV16 E6, E7 or E6/E7.

source_name: HFK transfected with pLXSN-HPV16E6/E7

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual v2, Affymetrix).

growth_protocol: subconfluent growing human cells in vitro

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

tag: HFK transfected with pLXSN-HPV16E6/E7


title: 444 cell line

description: Analysis of gene expression in human 444 cells

source_name: 444 cell line

tag: 444 cell line


title: Con sham 28d rep2


title: HFK transfected with pLXSN-HPV16E6

source_name: HFK transfected with pLXSN-HPV16E6

tag: HFK transfected with pLXSN-HPV16E6


title: Ab ME cells from larva, biological replicate 2

value: GAL4[21-7] (all class of da neurons)


title: HFK transfected with pLXSN

source_name: HFK transfected with pLXSN

tag: HFK transfected with pLXSN


title: JNK1dhepa BDL 28d rep2


title: Ab ME cells from larva, biological replicate 1

tag: source


title: JNK1dhepa BDL 28d rep1


title: Control cells from larva, biological replicate 2

description: Sorted mCD8:GFP positive cells from +/GAL4[21-7], UAS-mCD8:GFP  line.

tag: developmental stage

value: control


title: Control cells from larva, biological replicate 3


title: JNK1KO BDL 28d rep1

source_name: liver from JNK1 null [JNK1-/-] mice, 28 days after bile duct ligation

tag: treatment


title: JNK1KO BDL 28d rep3


title: CGL3 cell line

description: Analysis of gene expression in human CGL3 cells

source_name: CGL3 cell line

tag: CGL3 cell line


title: Con BDL 28d rep3

source_name: liver from control [JNK1f/f] mice, 28 days after bile duct ligation

tag: genotype


title: Con BDL 28d rep2

tag: age


title: Control cells from larva, biological replicate 1

tag: cell type


title: JNK1KO BDL 28d rep2

tag: time


title: Con BDL 28d rep1

tag: genetic background


title: HFK transfected with pLXSN-HPV16E7

source_name: HFK transfected with pLXSN-HPV16E7

tag: HFK transfected with pLXSN-HPV16E7


title: max2-3, dehydrated 4h, replicate 3

status: Public on Nov 26 2013

city: Lubbock

first: chien

middle: Van

last: ha

state: TX

address: 1006 Carton Avenue, Box 43135

department: IGCAST

country: USA

institute: texas tech university

description:
max2-3-D4_3
Gene expression data from dehydrated max2-3

hyb_protocol: 1.65 µg of Cy3-labelled cRNA were fragmented at 60°C for 30 minutes following the manufacturer's instructions. Agilent hybridization buffer was then added to the fragmentation mixture and hybridized to Agilent 021169 Arabidopsis Ver.4 Oligo Microarray 4x44K G2519F for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray slides were washed and dried immediately by a brief centrifugation.

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 scanned images were analyzed with GeneSpring GX11.5.1 (Agilent). Percentile normalization (75 percentile) was performed for each chip.

organism: Arabidopsis thaliana

source_name: max2-3_dehydrated 4h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Two-week-old WT and max2-3 mutant plants were transferred from GM plates to soil and grown for 10 additional day (22ºC, 16-h-light/8-h-dark, 60 μmol m-2 sec-1 photon flux density).

extract_protocol: Total RNA was extracted from the rosette leaves using RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: The aerial of 24-d-old plants were detached and exposed to dehydration on KimTowel papers for 0, 2 or 4h.

tag: ecotype

tag: genotype/variation

value: max2-3 mutant

value: 24 day-old

tag: exposed to

value: 4h dehydration

tag: tissue

value: rosette leaves


title: max2-3, dehydrated 2h, replicate 2

description:
max2-3-D2_2
Gene expression data from dehydrated max2-3

source_name: max2-3_dehydrated 2h

value: 2h dehydration


title: max2-3, dehydrated 4h, replicate 1

description:
max2-3-D4_1
Gene expression data from dehydrated max2-3


title: max2-3, well-watered (0h), replicate 1

description:
max2-3-C_1
Gene expression data from well-watered max2-3

value: 0h dehydration (well-watered)


title: max2-3, dehydrated 2h, replicate 1

description:
max2-3-D2_1
Gene expression data from dehydrated max2-3


title: max2-3, dehydrated 2h, replicate 3

description:
max2-3-D2_3
Gene expression data from dehydrated max2-3


title: max2-3, well-watered (0h), replicate 3

description:
max2-3-C_3
Gene expression data from well-watered max2-3


title: max2-3, dehydrated 4h, replicate 2

description:
max2-3-D4_2
Gene expression data from dehydrated max2-3


title: WT, dehydrated 4h, replicate 3

description:
WT-D4_3
Gene expression data from dehydrated WT

source_name: WT_dehydrated 4h

value: wild type


title: max2-3, well-watered (0h), replicate 2

description:
max2-3-C_2
Gene expression data from well-watered max2-3


title: WT, dehydrated 4h, replicate 2

description:
WT-D4_2
Gene expression data from dehydrated WT


title: WT, dehydrated 2h, replicate 3

description:
WT-D2_3
Gene expression data from dehydrated WT

source_name: WT_dehydrated 2h


title: WT, dehydrated 4h, replicate 1

description:
WT-D4_1
Gene expression data from dehydrated WT


title: WT, dehydrated 2h, replicate 2

description:
WT-D2_2
Gene expression data from dehydrated WT


title: MTC Familial with germline C634S RET mutation [MTC2_F_634]

city: Madrid

first: Mercedes

last: Robledo

state: Madrid

address: C/ Melchor Fernández Almagro, 3

department: Human Cancer Genetics Program

institute: Spanish National Cancer Research Centre (CNIO)

description: Pool of 10 cell lines (Adenocarcinoma, mammary gland Hepatoblastoma, liver Adenocarcinoma, cervix Embryonal carcinoma, testis Glioblastoma, brain Melanoma Liposarcoma Histiocytic lymphoma; macrophase; histocyte Lymphoblastic leukemiaPlasmacytoma; myeloma; B lymphocyte )

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to a established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2565BA (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Microarray background substraction was done using the normexp method  (Ritchie, 2007). The data set was normalized using loess within-array normalization and quantile between-array normalization. . Differentially expressed genes were identified by applying linear models using the Bioconductor limma R package (Smyth, 2005) (http://www.bioconductor.org). Normalized data were preprocessed using GEPAS server (Montaner et al., 2006). Inconsistent replicates (SD>1) were discarded, and consistent replicates were averaged. Finally, genes that exhibited flat patterns (SD>0.8) across the set of samples were filtered and omitted in further comparisons.

source_name: Universal Human Reference RNA (Stratagene)

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Universal Human Reference RNA (Stratagene, La Jolla, CA, USA) was used as a control for all samples. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from Universal Human Reference RNA was labeled with cyanine 3 (Cy3)-conjugated dUTP.

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

tag: reference

value: collection of RNA pooled from ten cell lines

tag: test

value: RNA extracted from primary tumors


title: WT, well-watered (0h), replicate 1

description:
WT-C_1
Gene expression data from well-watered WT


title: WT, well-watered (0h), replicate 3

description:
WT-C_3
Gene expression data from well-watered WT


title: MTC Familial with germline C620G RET mutation [MTC76_F_620]


title: WT, well-watered (0h), replicate 2

description:
WT-C_2
Gene expression data from well-watered WT


title: MTC Sporadic wild-type ( no RET mutation) [MTC77_S_WT]


title: MTC Sporadic with somatic M918T RET mutation [MTC3-2_S_918]


title: MTC Sporadic wild-type ( no RET mutation) [MTC78_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC53_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC4_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC74_S_WT]


title: WT, dehydrated 2h, replicate 1

description:
WT-D2_1
Gene expression data from dehydrated WT


title: MTC Sporadic wild-type ( no RET mutation) [MTC73_S_WT]


title: MTC Familial with germline C634S RET mutation [MTC1_F_634]


title: MTC Sporadic with somatic M918T RET mutation [MTC3_S_918]


title: DU315-6-N2 (K-Raslox), technical rep3

description:
06. K-Raslox MEFs, Control
Gene Expression data from K-Raslox sample (Control, proliferating cells expressing only K-Ras)

source_name: MEFs expressing only K-Ras (H-Ras/N-Ras double knockout); Control

value: Mouse Embryonic Fibroblasts (MEFs)

value: Inmortalized MEFs cultures

tag: cell line


title: MTC Familial with germline C620G RET mutation [MTC71_F_620]


title: MTC Familial with germline RET mutation [MTC62_F_NA]

source_name: MTC Familial with germline RET mutation


title: MTC Sporadic wild-type ( no RET mutation) [MTC49_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC48_S_WT]


title: MTC Sporadic with somatic C630G RET mutation [MTC47_S_630]


title: MTC Sporadic with somatic M918T RET mutation [MTC54_S_918]


title: MTC Sporadic with somatic C634R RET mutation [MTC52_S_634]


title: MTC Sporadic with somatic M918T RET mutation [MTC57_S_918]


title: MTC Sporadic wild-type ( no RET mutation) [MTC70_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC33_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC17_S_WT]


title: MTC Sporadic with somatic M918T RET mutation [MTC68_S_918]


title: MTC Sporadic wild-type ( no RET mutation) [MTC31_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC72_S_WT]


title: MTC Sporadic with somatic M918T RET mutation [MTC50_S_918]


title: MTC Sporadic with somatic M918T RET mutation [MTC16_S_918]


title: MTC Sporadic wild-type ( no RET mutation) [MTC30_S_WT]


title: MTC Sporadic with somatic M918T RET mutation [MTC15_S_918]


title: MTC Familial with germline C634R RET mutation [MTC28_F_634]


title: MTC Familial with germline C634R RET mutation [MTC26_F_634]


title: MTC Familial with germline C634Y RET mutation [MTC22-2_F_634]


title: MTC Familial with germline C634Y RET mutation [MTC22_F_634]


title: MTC Familial with germline C634R RET mutation [MTC20_F_634]


title: MTC Familial with germline C618S RET mutation [MTC29_F_618]


title: MTC Familial with germline RET mutation [MTC27_F_NA]


title: MTC Familial with germline C634R RET mutation [MTC23_F_634]


title: MTC Familial with germline RET mutation [MTC21_F_Neg]


title: MDS2 iPSC clone 1

type: genomic

city: Tsukuba

first: Yohei

last: Hayashi

state: Ibaraki

address: 3-1-1 Koyadai

department: BioResource Research Center

institute: RIKEN

description:
6097.9.2
Hybridized to Axiom® Genome-Wide EUR 1 Array Plate

hyb_protocol: As per manufacturer (Affymetrix)

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

data_processing: SNP genotype calls were generated using the “apt-probeset-genotype” function in Affymetrix Power Tools.  Heterozygosity was determined in R36 by counting the number of individuals with homozygous genotypes and the ones with heterozygous genotypes. This has been done on chromosome 17, the chromosome of interest, and chromosome 16, the control chromosome.     For CNV estimation and visualization, we used a similar procedure to previous successful methods, as available CNV calling tools such as PennCNV, QuantiSNP and Birdsuite are not able to handle Axiom data.  First, quantile normalization (QN) transforms the quantiles for each array to have the same distribution (Bolstad, 2001). This was performed using the “apt-probeset-genotype” function in Affymetrix Power Tools on a complete plate of arrays (N=95). Second, to estimate integer copy number, we use the COPy number Polymorphism Evaluation Routine (COPPER), previously developed to call CNVs from SNP array data37. In brief, COPPER uses genotype calls to set the median for 0, 1, and 2 copies of each allele and transform the intensity axes appropriately to derive scaled intensity estimates. This procedure was implemented in R. After QN and COPPER, we sum up the intensities on each axis, which represents a total copy number estimate at each locus for each individual.     After the first iteration of this procedure, genome-wide variability in each individual’s copy number graph is manually assessed and individuals with excess variability are excluded. Typical individuals have variance ~1, so individuals with variance across entire chromosomes >>1 are excluded, leaving 87 samples in this case for the second run of QN and COPPER to perform CNV calling.  To take into account the non-independence of consecutive SNPs, we utilize a 5-SNP median, as the Copy Number (CN) of a locus is estimated more accurately by including information from SNP probes on each side. We then apply a HMM to make the CNV calls, similar to QuantiSNP 38, implemented in Python.

molecule: genomic DNA

source_name: MDS2 iPSC clone 1

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted fromMDS fibroblasts and iPSCs using the Qiagen QIAmp DNA micro Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer.

tag: karyotype

value: Miller-Dieker Syndrome


title: MDS3 iPSC clone 1

description:
9208.4.4
Hybridized to Axiom® Genome-Wide EUR 1 Array Plate

source_name: MDS3 iPSC clone 1


title: MDS1 iPSC clone 2

description:
6047.2.4
Hybridized to Axiom® Genome-Wide EUR 1 Array Plate

source_name: MDS1 iPSC clone 2

value: Uniparental Disomy (Chromosome 17)


title: MTC Sporadic with somatic M918T RET mutation [MTC18_S_918]


title: MDS1 fibro

description:
6047_f
Hybridized to Axiom® Genome-Wide EUR 1 Array Plate

source_name: MDS1 fibroblast


title: MDS1 iPSC clone 1

description:
6047.1.3
Hybridized to Axiom® Genome-Wide EUR 1 Array Plate

source_name: MDS1 iPSC clone 1

value: Uniparenta Disomy (Chromosome 17)


title: miRNA, mouse postnatal day7, biological rep 5

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

description: microRNA expression data from lung tissue of postnatal mice

hyb_protocol: Labeled RNA was hybridized for 20 hr at 55C on Agilent 8X15K microRNA array. Arrays were washed according to the manufacturer's protocol.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15K array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters.

source_name: Lung tissue, mouse postnatal, day7, biological rep 5

label_protocol: Cy3 labeled RNA was prepared according to the standard Agilent protocol from 100ng total RNA

extract_protocol: Total RNA extracted using miRNeasy mini kit (Qiagen) according to the manufacturer's instructions.

tag: strain

value: whole lung

value: 7 days


title: MTC Sporadic wild-type ( no RET mutation) [MTC36_S_UN_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC35_S_UN_WT]


title: MTC Sporadic with somatic M918T RET mutation [MTC44_S_918]


title: MTC Sporadic wild-type ( no RET mutation) [MTC37_S_UN_WT]


title: miRNA, mouse postnatal day7, biological rep 4

source_name: Lung tissue, mouse postnatal, day7, biological rep 4


title: MTC Sporadic with somatic M918T RET mutation [MTC38_S_918]


title: MTC Sporadic wild-type ( no RET mutation) [MTC51_S_WT]


title: MTC Sporadic wild-type ( no RET mutation) [MTC34_S_UN_WT]


title: JNK1,2 KO MEFs_d6_3

city: Heidelberg

first: Peter

last: Angel

address: Im Neuenheimer Feld 280

department: Signal Transduction and Growth Control

institute: German Cancer Research Center

description: JNK1,2-deficient MEFs post triad 3; rep 3; 1 cell culture insert was used for this sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: The arrays were scanned using an iScan array scanner (Illumina Inc.)

data_processing: The data were normalised using quantile normalisation according to Smyth GK, Speed T (2003) Methods 31:265-73.

source_name: JNK1,2-deficient MEFs

label_protocol: 500 ng of total RNA were reverse transcribed into cDNA, which was further amplified to generate biotin-labeled cRNA by in vitro transcription using the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies). Following column-based purification, eluted cRNA was re-assessed for quality and quantity using the RNA 6000 Nano Kit on an Agilent 2100 Bioanalyzer and the NanoDrop ND-1000 spectrophotometer, respectively.

growth_protocol: Cells were cultured at 37°C and 8% CO2 in a humidified atmosphere on cell culture inserts (BD Biosciences) in FAD medium in absence (day 0) or presence (days 2, 4, 6) of NHEK. The FAD medium is composed of DMEM:Ham´s F12  (3:1) without calcium chloride supplemented with 5 % calcium-depleted FBS, 2 mM L-glutamine, 100 U ml-1 penicillin, 0.1 mg ml-1 streptomycin, 5 µg/ml insulin, 0.4 µg/ml hydrocortisone, 10-10 M cholera toxin, 24 ng/ml adenine, 1 ng/ml hEGF, 200 µM CaCl2.

extract_protocol: Total RNA was extracted with RLT buffer provided in the QIAGEN RNeasy mini kit, 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 of all samples was performed by measuring quality and concentration of RNA  with Nanodrop ND-1000 and Agilent 2100 Bioanalyzer.

treatment_protocol: Murine embryonic fibroblasts were isolated from JNK1,2-deficient and wildtype E10.0 embryos and immortalized following the 3T3 protocol. Cells were published previously in Sabapathy et al. (2004) Mol Cell 15:713-25.

tag: strain background

value: mouse embryo

tag: developmental stage

value: immortalized 3T3 murine embryonic fibroblasts (MEFs)


title: wt MEFs_d6_4

description: wildtype MEFs post triad 3; rep 4; three independent cell culture inserts were pooled for this sample

source_name: JNK1,2 wildtype MEFs

value: JNK1,2 wildtype


title: MTC Sporadic with somatic M918T RET mutation [MTC46-2_S_918]


title: Dex-12h 3 replicates

city: UNSW, SYDNEY

first: Kenneth

middle: K

last: Hsu

state: NSW

address: Rm422, 4E, Wallace Wurth Bld,

department: School of Medical Sciences

country: Australia

institute: University of New South Wales

description: Test

data_processing:
Gene expression was calculated with the web-based software package (SABiosciences).
For the normalization it uses the geometric mean of three housekeeping genes: HPRT, b-actin, GAPDH.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)], the cut off value for all Cts was set to 38
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Series supplementary file fold-change2.txt reports test/control (i.e. S100A8 treated vs HBSS saline treated) ratios.

label: SYBR Green

source_name: Lung

label_protocol: PCR assays were performed using varified in-house qPCR array (64 genes) in 384-well plates. Reactions were performed using the LightCycler® 480 system (Roche) under standard cycle conditions. Reactions containing 2´SYBR Green master mixture, 4 ml diluted cDNA template or non-amplified controls and 250 nM of each primer in a final volume of 10 ml.

extract_protocol: Total RNA was extracted from the lung by standard procedures using TRIzol® Reagent (Invitrogen), genomic DNA removed with DNase (Turbo DNase, Ambion) before reverse transcription (1.5 mg) using Super Script® VILO™ Master Mix (Invitrogen).

value: BALB/C

value: lung

tag: activation agent

value: Dexamethasone


title: Dex-6h 3 replicates

description: Test

value: 6 h


title: A8A-20h 3 replicates

description: Test

value: Cys42 to Ala42 mutant S100A8


title: JNK1,2 KO MEFs_d6_4

description: JNK1,2-deficient MEFs post triad 3; rep 4; three independent cell culture inserts were pooled for this sample


title: miRNA, mouse postnatal day7, biological rep 3

source_name: Lung tissue, mouse postnatal, day7, biological rep 3

tag: age


title: MTC Sporadic with somatic M918T RET mutation [MTC39_S_918]

value: collection of RNA pooled from ten cell lines


title: strain AR6 exponential-replica2

city: Daejeon

first: Hyun Uk

last: Kim

state: Republic of Korea

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description: M2 set 2

hyb_protocol: Labeled cDNAs were mixed with hybridization solution (MYcroarray.com), and the hybridization mixtures were heated at 65℃ for 5 min and then immediately cooled on ice for 5 min. Hybridization mixtures were directly loaded onto assembled MYcroarray.com microarray. The arrays hybridized at 50℃ for 16 hr using Agilent Hybridization oven (Agilent Technology, USA).

scan_protocol: The hybridization images were analyzed by GenePix Pro 6.0 (Axon Instruments, CA).

data_processing:
The average fluorescence intensity for each spot was calculated and local background was subtracted.
Gene Pix Pro 6.0 (Axon Instruments, CA) was used for background subtraction and GenoWiz 4.0 (Ocimumbiosolutions, India) was used Global normalization.

organism: Corynebacterium glutamicum ATCC 13032

source_name: AR6 at 24hr (2nd)

label_protocol: Labeling reactions were performed with a Bioprime labeling kit (Invitrogen) in a volume of 50 μl with a modified dNTP pool containing 120 μM each of dATP, dGTP, and dCTP; 60 μM dTTP; and 60 μM Cy5-dUTP (for all)

growth_protocol: Fed-batch cultivations using 5-liter reactor were carried out under aerobic condition at 30 ºC and 500rpm with defined culture medium.

extract_protocol: Samples were prepared for the extraction of total RNA from AR1 and AR6 strains, which were extracted with RNA preparation kit (i.e., RNA Mini Kit) from Qiagen.

treatment_protocol: Cell culture broths were centrifuated for 5 min at 13000 rpm. Their supenatents were removed and cell pellets were frozen by using liquied nitrogen immedietly.


title: miRNA, mouse postnatal day7, biological rep 2

source_name: Lung tissue, mouse postnatal, day7, biological rep 2


title: MTC Sporadic wild-type ( no RET mutation) [MTC41_S_WT]

value: RNA extracted from primary tumors


title: JNK1,2 KO MEFs_d6_2

description: JNK1,2-deficient MEFs post triad 3; rep 2; 1 cell culture insert was used for this sample

tag: cell type


title: MTC Sporadic with somatic M918T RET mutation [MTC46_S_918]


title: MTC Sporadic with somatic M918T RET mutation [MTC19_S_918]


title: wt MEFs_d6_3

description: wildtype MEFs post triad 3; rep 3; 1 cell culture insert was used for this sample


title: JNK1,2 KO MEFs_d6_1

description: JNK1,2-deficient MEFs post triad 3; rep 1; two independent cell culture inserts were pooled for this sample


title: wt MEFs_d6_1

description: wildtype MEFs post triad 3; rep 1; two independent cell culture inserts were pooled for this sample


title: wt MEFs_d6_2

description: wildtype MEFs post triad 3; rep 2; 1 cell culture insert was used for this sample


title: JNK1,2 KO MEFs_d4_2

description: JNK1,2-deficient MEFs post triad 2; rep 2; 1 cell culture insert was used for this sample


title: JNK1,2 KO MEFs_d4_1

description: JNK1,2-deficient MEFs post triad 2; rep 1; two independent cell culture inserts were pooled for this sample


title: strain AR6 exponential-replica1

description: M2 set 1

source_name: AR6 at 24hr (1st)


title: A8-20h 3 replicates

description: Test

tag: time


title: A8A-12h 3 replicates

description: Test


title: strain AR1 exponential-replica2

description: M1 set 2

source_name: AR2 at 24hr (2nd)


title: miRNA, mouse postnatal day7, biological rep 1

source_name: Lung tissue, mouse postnatal, day7, biological rep 1


title: miRNA, mouse postnatal day4, biological rep 3

source_name: Lung tissue, mouse postnatal, day4, biological rep 3

value: 4 days


title: miRNA, mouse postnatal day4, biological rep 5

source_name: Lung tissue, mouse postnatal, day4, biological rep 5


title: miRNA, mouse postnatal day4, biological rep 4

source_name: Lung tissue, mouse postnatal, day4, biological rep 4


title: strain AR1 exponential-replica1

description: M1 set 1

source_name: AR2 at 24hr (1st)


title: A8-6h 5 replicates

description: Test


title: A8-12h 4 replicates

description: Test


title: MTC Familial with germline M918T RET mutation [MTC32_F_918]

description: Pool of 10 cell lines (Adenocarcinoma, mammary gland Hepatoblastoma, liver Adenocarcinoma, cervix Embryonal carcinoma, testis Glioblastoma, brain Melanoma Liposarcoma Histiocytic lymphoma; macrophase; histocyte Lymphoblastic leukemiaPlasmacytoma; myeloma; B lymphocyte )

source_name: Universal Human Reference RNA (Stratagene)


title: miRNA, mouse postnatal day4, biological rep 2

source_name: Lung tissue, mouse postnatal, day4, biological rep 2


title: wt MEFs_d4_2

description: wildtype MEFs post triad 2; rep 2; 1 cell culture insert was used for this sample


title: miRNA, mouse postnatal day4, biological rep 1

source_name: Lung tissue, mouse postnatal, day4, biological rep 1


title: ccdB_replicate_B4 vs. AAAE13_replicate_A4

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

hyb_protocol: The paired and balanced cDNAs are suspended in Agilent 2X Gene Expression buffer (25ul), Agilent 10X Blocking agent (5ul), and water to a total volume of 50ul.  This hybridization solution is applied to Agilent Yeast v2 8x15K microarrays (Design ID 016322).  Hybridization is carried out at 65C for 20 hours.  Washing procedures are carried out according to Agilent gene expression protocols.

scan_protocol: Slides are scanned on a Axon 4000B scanner to detect Cy3 and Cy5 fluorescence.  Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence.

data_processing: Gridding and analysis of images is performed using Genepix v6.1 (Axon). From raw data file generated by Genepix v6.1, log2 ratio of Cy5/Cy3 (F635/F532) median intensities was used in expression analysis.

organism: Saccharomyces cerevisiae

source_name: Control yeast (pAG305GPD-ccdB replicate B4)

label_protocol: First strand cDNA is generated by oligo-dT primed reverse transcription utilizing the Superscript Plus Indirect labeling system (Invitrogen).  For cDNA synthesis, 2ul of anchored oligo-dT primer is added to 10ug of total RNA and the solution is incubated at 70C for 5 minutes then cooled on ice for 1 minute.  To each sample are added RNase inhibitor (RNaseOUT; Invitrogen) (1ul), 5X first strand buffer (6ul), dNTP mix (dATP, dCTP, dGTP, dTTP, one aminoallyl-modified nucleotide, and one aminohexyl-modified nucleotide) (1.5ul), 0.1M DTT (1.5ul), and Superscript III RNase H- Reverse Transcriptase (2ul).  Reverse transcription is carried out at 46C for 3 hours.  After purification of cDNA, 2X coupling buffer (5ul) and either DMSO resuspended Alexa Fluor  555 or Alexa Fluor 647 reactive dye (2ul) are then added to each appropriate cDNA sample.  Sample/dyes are then incubated at room temperature in the dark for 2 hours.  Coupling reactions are then quenched with 3M sodium acetate (20ul).  Fluorescently labeled cDNAs are purified with Zymo Research Clean and Concentrator 5 clean-up columns according to manufacturer’s instructions.  The cDNAs are quantitated via spectrophotometry to confirm recovery.  Samples are then paired and balanced by mass.

growth_protocol: The transgenic and control yeast cells were cultured in SD-drop out medium at 30 °C under shaken conditions.

extract_protocol: The cells were harvested at mid-log phase. Yeast total RNA was isolated from yeast cells using a Master-Pure yeast RNA purification kit (EPICENTRE Biotechnologies) according to the manufacturer’s instructions. Total RNA quality was determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations.

treatment_protocol: Malonate was fed into cells at final concentration 0.2 mM when the value of OD600 reached at 0.1.

tag: transfection

value: Control yeast (pAG305GPD-ccdB)

tag: growth

value: mid-log phase

source_name: Transgenic yeast (pAG305GPD-AAE13 replicate A4)

value: Transgenic yeast (pAG305GPD-AAE13)


title: miRNA, mouse postnatal day1, biological rep 5

source_name: Lung tissue, mouse postnatal, day1, biological rep 5

value: 1 day


title: HBSS 5 replicates

description: Control

source_name: Lung

value: control

value: 4 h


title: A8-1h 4 replicates

description: Test

value: 1 h


title: A8-4h 4 replicates

description: Test


title: miRNA, mouse postnatal day1, biological rep 4

source_name: Lung tissue, mouse postnatal, day1, biological rep 4

value: whole lung


title: AAAE13_replicate_A1_ccdB_replicate_B1

source_name: Transgenic yeast (pAG305GPD-AAE13  replicate A1)

source_name: Control yeast (pAG305GPD-ccdB  replicate B1)


title: JNK1,2 KO MEFs_d2_1

description: JNK1,2-deficient MEFs post triad 1; rep 1; two independent cell culture inserts were pooled for this sample

source_name: JNK1,2-deficient MEFs

value: mouse embryo

value: immortalized 3T3 murine embryonic fibroblasts (MEFs)


title: wt MEFs_d4_1

description: wildtype MEFs post triad 2; rep 1; two independent cell culture inserts were pooled for this sample

source_name: JNK1,2 wildtype MEFs

value: JNK1,2 wildtype


title: ccdB_replicate_B2 vs. AAAE13_replicate_A2

source_name: Control yeast (pAG305GPD-ccdB replicate B2)

source_name: Transgenic yeast (pAG305GPD-AAE13 replicate A2)


title: wt MEFs_d2_1

description: wildtype MEFs post triad 1; rep 1; two independent cell culture inserts were pooled for this sample


title: JNK1,2 KO MEFs_d2_2

description: JNK1,2-deficient MEFs post triad 1; rep 2; 1 cell culture insert was used for this sample


title: NHEK_JNK1,2 KO MEF_d8_2

description: NHEK_after 8 days in co-culture with JNK1,2-deficient MEFs (day 8)_rep 2_ two independent wells were pooled for this sample

data_processing: Cross-platform (Sentrix, HumanHT) probe matching was performed for raw data using probe sequences and resulted in the removal of approximately 8700 non-matching probes. The raw data were normalised using quantile normalisation according to Rafael A.I. et al. (2003) Nucl. Acids Res. (2003) 31 (4): e15.

source_name: NHEK, with JNK1,2-deficient MEFs, day 8

growth_protocol: Cells were cultured at 37°C in a humidified atmosphere on 6well plates (Nunc) at 5%CO2 in absence (day 0)  or at 8%CO2 in presence (days 2, 4, and 6) of JNK1,2-deficient or wildtype mouse embryonic fibroblasts (MEFs). NHEK in absence of MEFs were cultured in Keratinocyte Growth Medium 2 (KGM2; PromoCell, Germany) and NHEK in presence of MEFs were cultured in FAD medium. The FAD medium is composed of DMEM:Ham´s F12  (3:1) without calcium chloride supplemented with 5 % calcium-depleted FBS, 2 mM L-glutamine, 100 U ml-1 penicillin, 0.1 mg ml-1 streptomycin, 5 µg/ml insulin, 0.4 µg/ml hydrocortisone, 10-10 M cholera toxin, 24 ng/ml adenine, 1 ng/ml hEGF, 200 µM CaCl2. Total RNA was isolated from confluent NHEK droplets prior to application of MEFs (day 0) and every second day during the co-culture with MEFs (days 2, 4, 6).

treatment_protocol: Primary normal human epidermal keratinocytes (NHEK) were isolated from human foreskin and cells  of passage 1 were stored in liquid nitrogen. Passage 2-3 keratinocytes were used for the experiments.

tag: variation

value: primary cells

value: foreskin


title: JNK1,2 KO MEFs_d0_1

description: JNK1,2-deficient MEFs before co-cultivation with NHEK (day 0); rep 1; two independent cell culture inserts were pooled for this sample

tag: genotype/variation


title: miRNA, mouse postnatal day1, biological rep 3

description: microRNA expression data from lung tissue of postnatal mice

source_name: Lung tissue, mouse postnatal, day1, biological rep 3


title: NHEK_JNK1,2 KO MEF_d8_1

description: NHEK_after 8 days in co-culture with JNK1,2-deficient MEFs (day 8)_rep 1_ two independent wells were pooled for this sample

value: normal human epidermal keratinocytes (NHEK)


title: wt MEFs_d0_1

description: wildtype MEFs before co-cultivation with NHEK (day 0); rep 1; two independent cell culture inserts were pooled for this sample


title: wt MEFs_d2_2

description: wildtype MEFs post triad 1; rep 2; 1 cell culture insert was used for this sample


title: NHEK_wt MEF_d8_2

description: NHEK_after 8 days in co-culture with wt MEFs (day 8)_rep 2_ two independent wells were pooled for this sample

source_name: NHEK, with wt MEFs, day 8


title: AAAE13_replicate_A3_ccdB_replicate_B3

source_name: Transgenic yeast (pAG305GPD-AAE13 replicate A3)

source_name: Control yeast (pAG305GPD-ccdB  replicate B3)


title: miRNA, mouse postnatal 2 week, biological rep 5

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 5

value: 2 weeks


title: NHEK_wt MEF_d8_1

description: NHEK_after 8 days in co-culture with wt MEFs (day 8)_rep 1_ two independent wells were pooled for this sample


title: NHEK_JNK1,2 KO MEF_d6_2

description: NHEK_after 6 days in co-culture with JNK1,2-deficient MEFs (day 6)_rep 2_ 1 well was used for this sample

source_name: NHEK, with JNK1,2-deficient MEFs, day 6


title: NHEK_JNK1,2 KO MEF_d6_4

description: NHEK_after 6 days in co-culture with JNK1,2-deficient MEFs (day 6)_rep 4_ 1 well was used for this sample


title: NHEK_JNK1,2 KO MEF_d6_3

description: NHEK_after 6 days in co-culture with JNK1,2-deficient MEFs (day 6)_rep 3_ 1 well was used for this sample


title: NHEK_JNK1,2 KO MEF_d6_5

description: NHEK_after 6 days in co-culture with JNK1,2-deficient MEFs (day 6)_rep 5_ 1 well was used for this sample


title: NHEK_JNK1,2 KO MEF_d6_1

description: NHEK_after 6 days in co-culture with JNK1,2-deficient MEFs (day 6)_rep 1_ two independent wells were pooled for this sample


title: miRNA, mouse postnatal 2 week, biological rep 4

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 4


title: NHEK_wt MEF_d6_5

description: NHEK_after 6 days in co-culture with wt MEFs (day 6)_rep 5_ 1 well was used for this sample

source_name: NHEK, with wt MEFs, day 6


title: miRNA, mouse postnatal 2 week, biological rep 3

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 3


title: NHEK_wt MEF_d6_4

description: NHEK_after 6 days in co-culture with wt MEFs (day 6)_rep 4_ 1 well was used for this sample


title: NHEK_wt MEF_d6_1

description: NHEK_after 6 days in co-culture with wt MEFs (day 6)_rep 1_ two independent wells were pooled for this sample


title: NHEK_wt MEF_d6_3

description: NHEK_after 6 days in co-culture with wt MEFs (day 6)_rep 3_ 1 well was used for this sample


title: miRNA, mouse postnatal day1, biological rep 1

source_name: Lung tissue, mouse postnatal, day1, biological rep 1


title: miRNA, mouse postnatal day1, biological rep 2

source_name: Lung tissue, mouse postnatal, day1, biological rep 2


title: NHEK_JNK1,2 KO MEF_d4_2

description: NHEK_after 4 days in co-culture with JNK1,2-deficient MEFs (day 4)_rep 2_ 1 well was used for this sample

source_name: NHEK, with JNK1,2-deficient MEFs, day 4


title: miRNA, mouse postnatal 2 week, biological rep 1

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 1


title: miRNA, mouse postnatal 6 week, biological rep 4

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 4

value: 6 weeks


title: miRNA, mouse postnatal 2 week, biological rep 2

source_name: Lung tissue, mouse postnatal, 2 week, biological rep 2


title: miRNA, mouse postnatal 6 week, biological rep 2

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 2


title: NHEK_wt MEF_d6_2

description: NHEK_after 6 days in co-culture with wt MEFs (day 6)_rep 2_ 1 well was used for this sample


title: miRNA, mouse postnatal 6 week, biological rep 3

description: microRNA expression data from lung tissue of postnatal mice

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 3


title: NHEK_JNK1,2 KO MEF_d2_1

description: NHEK_after 2 days in co-culture with JNK1,2-deficient MEFs (day 2)_rep 1_ two independent wells were pooled for this sample

source_name: NHEK, with JNK1,2-deficient MEFs, day 2


title: NHEK_wt MEF_d2_2

description: NHEK_after 2 days in co-culture with wt MEFs (day 2)_rep 2_ 1 well was used for this sample

source_name: NHEK, with wt MEFs, day 2


title: NHEK_wt MEF_d4_2

description: NHEK_after 4 days in co-culture with wt MEFs (day 4)_rep 2_ 1 well was used for this sample

source_name: NHEK, with wt MEFs, day 4


title: NHEK_JNK1,2 KO MEF_d4_1

description: NHEK_after 4 days in co-culture with JNK1,2-deficient MEFs (day 4)_rep 1_ two independent wells were pooled for this sample


title: NHEK_wt MEF_d4_1

description: NHEK_after 4 days in co-culture with wt MEFs (day 4)_rep 1_ two independent wells were pooled for this sample


title: A8A-2h+L 9 replicates

description: Test

data_processing:
Gene expression was calculated with the web-based software package (SABiosciences).
For the normalization it uses the geometric mean of three housekeeping genes: HPRT, b-actin, GAPDH.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)], the cut off value for all Cts was set to 38
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Series file fold-change1.txt reports test/control (i.e. S100A8 treated vs HBSS saline treated) ratios.

source_name: Lung

value: BALB/C

value: lung


title: Dex-2h+L 5 replicates

description: Test

value: Dexamethasone+LPS

value: Dexamethasone(-2 h)+LPS 4 h


title: LPS 7 replicates

description: Test

value: HBSS+LPS

value: HBSS(-2 h)+LPS 4 h


title: L+A8+15m 4 replicates

description: Test

value: LPS+S100A8(+15 min):Total 4 h


title: miRNA, mouse postnatal 6 week, biological rep 1

source_name: Lung tissue, mouse postnatal, 6 week, biological rep 1


title: NHEK_d0_1

description: NHEK_before application of MEFs (day 0)_rep 1_ two independent wells were pooled for this sample

source_name: NHEK, day 0


title: NHEK_JNK1,2 KO MEF_d2_2

description: NHEK_after 2 days in co-culture with JNK1,2-deficient MEFs (day 2)_rep 2_ 1 well was used for this sample


title: NHEK_wt MEF_d2_1

description: NHEK_after 2 days in co-culture with wt MEFs (day 2)_rep 1_ two independent wells were pooled for this sample


title: NHEK_d0_2

description: NHEK_before application of MEFs (day 0)_rep 2_ 1 well was used for this sample


title: A8-2h+L 9 replicates

description: Test


title: LoV oxaliplatin 10 fold resistant

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Cells were cultured at 37ºC in an atmosphere of 5% (v/v) CO2, in DMEM-HAM’s F12 medium supplemented with 20% (w/v) fetal bovine serum, 100U/penicillin and 100µg/l streptomycin (Invitrogen, Carlsbad,CA).

extract_protocol: genomic DNA was extracted and purified from cell lines using DNAzol Kit according to standard instructions.

tag: gender

value: male

value: colon, derived from left supraclavicular region metastasis.

tag: disease

value: Dukes' type C, grade IV,colorectal adenocarcinoma

tag: morphology

value: epithelial

tag: culture properties

value: adherent


title: LoVo oxaliplatin sensitive

tag: cell line

tag: tissue


title: PBS 8 replicates

description: Control

tag: strain

value: HBSS+PBS

value: HBSS(-2 h)+PBS 4 h


title: Lichen_wetted_15min_rep3

status: Public on Nov 25 2013

city: Turku

first: Sini

last: Junttila

address: Tykistökatu 6 A

department: Centre for Biotechnology

country: Finland

institute: University of Turku

hyb_protocol: 1.65 μg of Cy3-labelled sample was hybridized to the array at 65°C overnight using Agilent’s Gene Expression Hybridization kit. The arrays were washed using Agilent’s Gene Expression Wash Pack and Stabilization and Drying solutions.

scan_protocol: The arrays were scanned with Agilent Technologies’ Scanner model G2565CA. The numerical data was produced with Agilent’s Feature Extraction software, version 10.5.1.1, using grid 024161_D_F_20090605, protocol GE1_105_Dec08 and QC metric set GE1_QCMT_Dec08.

data_processing: Data were quantile normalized with limma package in R.

organism: Cladonia rangiferina

source_name: Lichen thallus tissue, wetted, 15 min

label_protocol: 600 ng of total RNA was amplified and labelled with Cy3 using Agilent’s Quick Amp Labelling kit.

growth_protocol: None, collected from nature

extract_protocol: Spectrum Plant Kit (Sigma Aldrich, Germany)

treatment_protocol: After collection the lichen material was stored at -20C in desiccated state. Prior to treatment, the material was brought back to room temperature. The desiccated lichen tissue was rewetted by spraiyng with tap water and placing the tissue on a wet dish cloth. Samples were collected at 15 minutes, 30 minutes, 1 hour and 3 hours after rewetting. After three hours of wetting the lichen tissue was left to dry in room temperature on a dry cloth and samples were collected at one, three, six and 24 hours of drying. The samples were immediately placed in liquid notrogen and ground with mortar and pestle and stored at -80C.

value: thallus


title: Lichen_wetted_15min_rep1


title: Lichen_drying_6hours_rep3

source_name: Lichen thallus tissue, drying, 6 hours


title: Lichen_drying_3hours_rep3

source_name: Lichen thallus tissue, drying, 3 hours


title: Lichen_wetted_1hour_rep3

source_name: Lichen thallus tissue, wetted, 1 hour


title: Lichen_drying_3hours_rep2


title: Lichen_drying_3hours_rep1


title: Lichen_wetted_30min_rep2

source_name: Lichen thallus tissue, wetted, 30 min


title: Lichen_drying_1hour_rep1

source_name: Lichen thallus tissue, drying, 1 hour


title: Lichen_wetted_15min_rep2


title: Lichen_wetted_1hour_rep1


title: Lichen_wetted_1hour_rep2


title: Lichen_drying_6hours_rep1


title: Lichen_wetted_30min_rep3


title: Lichen_dry_rep3

source_name: Lichen thallus tissue, dry, 24 hours


title: Lichen_wetted_30min_rep1


title: Lichen_drying_1hour_rep3


title: Lichen_wet_rep1

source_name: Lichen thallus tissue, wet, 3 hours


title: Lichen_drying_6hours_rep2


title: Lichen_dry_rep1


title: Lichen_dry_rep2


title: Lichen_wet_rep3


title: Lichen_wet_rep2


title: Lichen_drying_1hour_rep2


title: xylose pulse, replicate 1

city: Göteborg

first: Magnus

last: Ask

address: Kemivägen 10

country: Sweden

institute: Chalmers University of Technology

hyb_protocol: Samples hybridized for 16 h

scan_protocol: Scanning performed with a GeneChip Scanner 3000 7G

data_processing: R/Bioconductor RMA. Statistical analysis using limma package

source_name: Saccharomyces cerevisiae, VTT C-10883

label_protocol: 3'IVT expression kit (Affymetrix)

growth_protocol: Anaerobic batch culivations

extract_protocol: Qiagen RNeasy

treatment_protocol: pulse of 3.9 g/L HMF and 1.2 g/L furfural in either the glucose or the xylose consumption phase

tag: treatment

value: xylose pulse


title: xylose control, replicate 3

value: xylose control


title: xylose control, replicate 2


title: xylose pulse, replicate 2


title: glucose pulse, replicate 1

value: glucose pulse


title: glucose pulse, replicate 3


title: xylose pulse, replicate 3


title: glucose pulse, replicate 2


title: glucose control, replicate 3

value: glucose control


title: KON_24H_B

city: London

first: Vladimir

last: Zhurov

state: ON

address: 1151 Richmond Street

department: Biology

country: Canada

institute: University of Western Ontario

description: Gene expression of Kon plants after 24 h 10 mite treatment

hyb_protocol: Hybridization and washing were done following Affymetrix guidelines using a Hybridization Oven 640 and a Fluidics Station 450 (Affymetrix, Santa Clara, CA).

scan_protocol: Scanning was done following Affymetrix guidelines on a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: CEL files were processed in Bioconductor using RMA workflow with standard settings and custom CDF (ATH1121501_At_TAIRG) file from http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp

source_name: Kon plants, 24 h 10 mite treatment, bio rep 2

label_protocol: Probes for microarrays were labeled using the Message Amp II Biotin kit (Ambion, Life Technologies, Carlsbad, CA).

growth_protocol: Plants were grown under 100-150 µmol m-2 s-1 cool-white fluorescent light at 24°C with a 16:8 h (light/dark) photoperiod in controlled growth chambers.

extract_protocol: RNA samples were processed in duplicate from pooled samples of six plants per treatment. Whole rosettes were used. Total RNA was prepared using the RNeasy Plant RNA extraction kit (Qiagen, Venlo, Netherlands).

treatment_protocol: In timecourse scenario 10 adult female spider mites were applied per plant and allowed to feed for 1, 3, 6, 12 or 24 h. In feeding site scenario rosettes were covered with hundreds of mites that were allowed to feed for 1 h.

value: rosette

tag: genotype

value: Kon

value: 3 weeks old

value: after 24 h 10 mite treatment


title: KON_FS_B

description: Gene expression of Kon plants after feeding site mite treatment

source_name: Kon plants, feeding site mite treatment, bio rep 2

value: after feeding site mite treatment


title: glucose control, replicate 2


title: KON_12H_A

description: Gene expression of Kon plants after 12 h 10 mite treatment

source_name: Kon plants, 12 h 10 mite treatment, bio rep 1

value: after 12 h 10 mite treatment


title: KON_FS_A

source_name: Kon plants, feeding site mite treatment, bio rep 1


title: KON_06H_A

description: Gene expression of Kon plants after 6 h 10 mite treatment

source_name: Kon plants, 6 h 10 mite treatment, bio rep 1

value: after 6 h 10 mite treatment


title: KON_24H_A

source_name: Kon plants, 24 h 10 mite treatment, bio rep 1


title: KON_03H_B

description: Gene expression of Kon plants after 3 h 10 mite treatment

source_name: Kon plants, 3 h 10 mite treatment, bio rep 2

value: after 3 h 10 mite treatment


title: xylose control, replicate 1


title: KON_06H_B

source_name: Kon plants, 6 h 10 mite treatment, bio rep 2


title: KON_12H_B

source_name: Kon plants, 12 h 10 mite treatment, bio rep 2


title: glucose control, replicate 1


title: KON_01H_A

description: Gene expression of Kon plants after 1 h 10 mite treatment

source_name: Kon plants, 1 h 10 mite treatment, bio rep 1

value: after 1 h 10 mite treatment


title: KON_03H_A

source_name: Kon plants, 3 h 10 mite treatment, bio rep 1


title: BLA_24H_B

description: Gene expression of Bla-2 plants after 24 h 10 mite treatment

source_name: Bla-2 plants, 24 h 10 mite treatment, bio rep 2


title: KON_CNTRL_24H_A

description: Gene expression of Kon control plants

source_name: Kon control plants, bio rep 1

value: control plants


title: BLA_FS_B

description: Gene expression of Bla-2 plants after feeding site mite treatment

source_name: Bla-2 plants, feeding site mite treatment, bio rep 2


title: BLA_FS_A

source_name: Bla-2 plants, feeding site mite treatment, bio rep 1


title: BLA_12H_A

description: Gene expression of Bla-2 plants after 12 h 10 mite treatment

source_name: Bla-2 plants, 12 h 10 mite treatment, bio rep 1


title: BLA_12H_B

source_name: Bla-2 plants, 12 h 10 mite treatment, bio rep 2


title: KON_01H_B

source_name: Kon plants, 1 h 10 mite treatment, bio rep 2


title: BLA_03H_B

description: Gene expression of Bla-2 plants after 3 h 10 mite treatment

source_name: Bla-2 plants, 3 h 10 mite treatment, bio rep 2


title: KON_CNTRL_24H_B

description: Gene expression of Kon control plants

source_name: Kon control plants, bio rep 2


title: BLA_06H_A

description: Gene expression of Bla-2 plants after 6 h 10 mite treatment

source_name: Bla-2 plants, 6 h 10 mite treatment, bio rep 1


title: BLA_24H_A

source_name: Bla-2 plants, 24 h 10 mite treatment, bio rep 1


title: BLA_01H_B

description: Gene expression of Bla-2 plants after 1 h 10 mite treatment

source_name: Bla-2 plants, 1 h 10 mite treatment, bio rep 2


title: BLA_CNTRL_24H_B

description: Gene expression of Bla-2 control plants

source_name: Bla-2 control plants, bio rep 2


title: BLA_CNTRL_24H_A

description: Gene expression of Bla-2 control plants

source_name: Bla-2 control plants, bio rep 1


title: BLA_06H_B

source_name: Bla-2 plants, 6 h 10 mite treatment, bio rep 2


title: BLA_01H_A

source_name: Bla-2 plants, 1 h 10 mite treatment, bio rep 1


title: RNA_pcr1D

city: Salamanca

first: Luis

last: Quintales

address: Calle Zacarías González, 2

department: Universidad de Salamanca / CSIC

institute: Instituto de Biología Funcional y Genómica (IBFG)

description: RNA Mitosis_pcr1D

hyb_protocol: 220 ml 1x hybridization mixture containing 5.5 mg of fragmented and labeled DNA target, 7% DMSO, 1.5, 5, 25 and 100 pM of Eukaryotic Hibridization Controls (bioB, bioC, bioD, cre) respectively, and 50 pM control oligonucleotide B2 were prepared using the Affymetrix GeneChip Hybridization Kit as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Assay Labeling Manual. The final DNA target mixture was hybridized to Affymetrix S. pombe Tiling 1.0FR arrays and incubated in a hybridization oven at 45 °C and 60 rpm for 17 h ±1h.

scan_protocol: Affymetrix standard protocol using Affymetrix Fluidics 450 and Scanner 3000

data_processing:
The eight RNA_*.CEL  were quantile normalized (PMID:12538238). After this, individual raw signals were reported in WIG files.
All the results files are in Wiggle Track Format (WIG) containing: RNA log2 raw signal for RNA* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

organism: Schizosaccharomyces pombe

source_name: RNA Mitosis_pcr1D

label_protocol: 5.5 mg of the fragmented single-stranded DNA samples resuspended in 45 ml were incubated with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ul) and 1× Terminal Deoxynucleotidyl Transferase Buffer in a thermal cycler as described in the Affymetrix GeneChip Whole Transcript (WT) Sense Target Assay Labeling Manual.

growth_protocol: Rich medium (YES) at 32ºC until OD595=0.8

extract_protocol: Total RNA was prepared by resuspending the cell pellets in 20 μl extraction buffer (100 mM EDTA, pH 8.0, 100 mM NaCl, 50 mM Tris-HCl, pH 8.0), 20 μl phenol/chloroform, 2 μl 10% SDS, 200 μl glass beads (425-600 μm, SIGMA G-8772). Cells were mechanically disrupted in a Fast-Prep device (Savant BIO 101) and the cell lysate was extracted with phenol, phenol/chloroform and chloroform/isoamyl alcohol before precipitation with 0.3 M sodium acetate and ethanol. RNA was resuspended in 50 μl of sterile water with diethyl pyrocarbonate (SIGMA D-5758) and was further purified with the RNeasy mini kit (Quiagen) following the supplier's specifications.

value: h+ ura4.d18 leu1.32 ade6M210 pcr1D::kanMX4

tag: culture type

value: Asynchronous mitosis


title: RNA_Mit_pat1.114

description: RNA Mitosis_pat1.114

source_name: RNA Mitosis pat1.114

growth_protocol: Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC until OD595=0.8


title: RNA_atf1D

description: RNA Mitosis_atf1D

source_name: RNA Mitosis_atf1D

value: h+ ura4.d18 leu1.32 ade6M210 atf1D::kanMX4


title: RNA_Mit

description: RNA Mitosis

source_name: RNA Mitosis


title: RNA_Mei5h

description: RNA Meiosis 5h

source_name: RNA Meiosis 5h

growth_protocol: Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen and 0,05 g/l leucine for 14 h after which NH4Cl was added to 0.5 g/l and leucine concentration was increased to 0,1 g/l.  Sample was taken 5h after transfer to 34 ºC to induce synchronous meiosis

value: Synchronous meiosis


title: mES Bright Knockout rep6

city: Austin

first: Bum-Kyu

last: Lee

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description: Day 15 differentiation of Bright null mouse embryonic stem cells

hyb_protocol: Array hyb was performed according to Nimblegen protocol

scan_protocol: Scanning was done with Genepix 4000B microarry scanner following instruction provided by Nimblegen array protocal

data_processing: After background correction using theNimbleScan software package, raw data were normalized by RMA (Robust Multi-Array Analysis) method using Bioconductor tool

source_name: mES Bright KO

label_protocol: Sample was labelled with cy3 random nonamers

growth_protocol: Pluripotent conditions; cells were grown on a mitotically inactivated MEF line in the presence of LIF

extract_protocol: Total RNA was harvested using Qiagen Rneasy kit, DNA was removed on-column using Rnase free Dnase (Qiagen)

treatment_protocol: Cells were untreated or allowed to differentiate by removal of LIFand suspension in hanging drops, encouraging embryoid formation

value: mES

value: Bright KO


title: mES Bright Knockout rep2

description: Bright null mouse embryonic stem cells


title: BLA_03H_A

source_name: Bla-2 plants, 3 h 10 mite treatment, bio rep 1

tag: age


title: mES Bright Knockout rep8

tag: cell type


title: mES Bright Knockout rep5

description: Day 6 differentiation of Bright null mouse embryonic stem cells


title: MEF Bright Knockout rep1

description: Bright null mouse embryonic fibroblast

source_name: MEF Bright KO

value: MEF Bright KO


title: iPSC Bright Knockout rep1

description: Spontaneously reprogrammed Bright null clone

source_name: IPSC induced from Bright KO MEF

value: iPSC


title: RNA_Mei0h

description: RNA Meiosis 0h

data_processing:
The eigth RNA_*.CEL  were quantile normalized (PMID:12538238). After this, individual raw signals were reported in WIG files.
All the results files are in Wiggle Track Format (WIG) containing: RNA log2 raw signal for RNA* samples (transcription mapping). The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.

source_name: RNA Meiosis 0h

growth_protocol: Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen and 0,05 g/l leucine for 14 h after which NH4Cl was added to 0.5 g/l and leucine concentration was increased to 0,1 g/l.  Sample was taken immediately after transfer to 34 ºC to induce synchronous meiosis


title: mES Bright Knockout rep4


title: mES Bright Knockout rep7


title: mES wild type rep2

description: Wild type mouse ES cells

source_name: mES wild type

value: wild type


title: RNA_Mei3h

description: RNA Meiosis 3h

source_name: RNA Meiosis 3h

growth_protocol: Minimal Medium (MM) with 0,1 g/l leucine at 25 ºC (asynchronous) until OD595=0.8 followed by transfer to MM without nitrogen and 0,05 g/l leucine for 14 h after which NH4Cl was added to 0.5 g/l and leucine concentration was increased to 0,1 g/l.  Sample was taken 3h after transfer to 34 ºC to induce synchronous meiosis


title: MN_atf1D

description:
Control CEL: DNA_naked.CEL
Mononucleosomal DNA_atf1D

hyb_protocol: 200 ml 1x hybridization mixture containing 4.5 mg of fragmented and labeled DNA target, 7% DMSO and 50 pM control oligonucleotide B2 (Affymetrix P/N 900720) were prepared according to the Affymetrix hibridization  protocol for single tiling arrays described in the Affymetrix GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual. The final DNA target mixture was hybridized onto Affymetrix S. pombe Tiling 1.0FR arrays and incubated in a hybridization oven at 45 °C and 60 rpm for 16 h.

data_processing:
The test and ctrl CEL files were quantile normalized (PMID:12538238). After this, individual log2(test/control) fold changes were reported in WIG files.
All the results files are in Wiggle Track Format (WIG) containing: log2(mononucleosomal fraction/input fraction) for MN* samples. The WIG file coordinates are mapped against the Sanger September 2008 Schizosaccharomyces pombe genome version.
For all the genomic analyses, we have used as a reference the S. pombe genome version of 23/08/07 (http://www.pombase.org/ , ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/).

source_name: Mononucleosomal DNA_atf1D

label_protocol: 4.5 mg of the fragmented double-stranded DNA samples resuspended in 45 mg were incubated with a labeling master mix containing DNA Labeling Reagent (5 mM), terminal deoxynucleotidyl transferase (30 U/ml) and 1× Terminal Deoxynucleotidyl Transferase Buffer in a thermal cycler as described in the Affymetrix GeneChip Whole Transcript (WT) Double-Stranded Target Assay Manual.

extract_protocol: Chromatin was prepared from formaldehyde crosslinked log phase cells and digested with micrococcal nuclease (Fermentas #ENO181) to a final concentration of 180 units/ml for 40 minutes at 37 ºC to yield about 90% mononucleosomes. DNA of mononucleosomal size was purified from agarose gels, fragmented to an average size of about 50 bp with DNaseI. DNAseI fragmented genomic DNA from S. pombe was used as hybridization control.

source_name: Naked DNA


title: MN_Mit

description:
Control CEL: DNA_naked.CEL
Mononucleosomal DNA_Mit

source_name: Mononucleosomal DNA_Mit


title: MN_pcr1D

description:
Control CEL: DNA_naked.CEL
Mononucleosomal DNA_pcr1D

source_name: Mononucleosomal DNA_pcr1D


title: mES Bright Knockout rep1

description: Bright null mouse embryonic stem cells


title: mES Bright Knockout rep3


title: mES wild type rep1

description: Wild type mouse ES cells


title: dDP eye discs, irradiated, biological replicate 2

city: Chicago

first: Aaron

last: Ambrus

state: IL

address: 900 S. Ashland Ave.

institute: University of Illinois at Chicago

description: Gene expression data from irradiated dDP mutant eye discs

hyb_protocol: RNA was fragmented and then hybridized for 16h at 45°C on an Affymetrix GeneChip Drosophila Genome 2.0 Array. GeneChips were then washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned with a Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Affymatrix CEL files were background corrected and normalized using RMA method in Bioconductor package “affy”.

source_name: dDP eye discs, irradiated

label_protocol: Biotinylated RNA were prepared according to standard Affymetrix protocol from 50ng of total RNA per sample (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: All larva were kept in a 25°C incubator on standard fly food until 3rd instar when they were either untreated or irradiated.

extract_protocol: RNA was extracted with a combination Trizol and Rneasy Mini Kit (Qiagen).

treatment_protocol: Biological triplicates of wild type, dDP mutant and de2f1, deleted in the posterior, eye discs were untreated or irradiated with 40Gy of gamma radiation. After 4h, eye discs were dissected and RNA was extracted.

value: 3rd instar larval eye imaginal disc

value: dDP

value: irradiated with 40Gy of gamma radiation


title: dDP eye discs, irradiated, biological replicate 1


title: de2f1 eye discs, irradiated, biological replicate 2

description: Gene expression data from irradiated e2f1 posterior deleted eye discs

source_name: de2f1 eye discs, irradiated


title: dDP eye discs, untreated, biological replicate 1

description: Gene expression data from untreated dDP mutant eye discs

source_name: dDP eye discs, untreated


title: dDP eye discs, untreated, biological replicate 3


title: de2f1 eye discs, irradiated, biological replicate 3


title: dDP eye discs, irradiated, biological replicate 3


title: de2f1 eye discs, untreated, biological replicate 2

description: Gene expression data from untreated e2f1 posterior deleted eye discs

source_name: de2f1 eye discs, untreated


title: de2f1 eye discs, untreated, biological replicate 3


title: Leaves_by MU_48h_rep3

city: Gainesville

first: Jeffrey

middle: B.

last: Jones

state: FL

address: 1453 Fifield Hall

department: Plant Pathology

institute: University of Florida

description:
Sweet orange (C. Sinensis) Valencia
Gene expression data of sweet orange at 48 h post infiltration of Xcc306 mutant strain with pthA4 gene deletion

hyb_protocol: A total of 300 ng of labeled cDNA for each sample was hybridized with rotation at 45°C for 16 hours to the Affymetrix GeneChip Citrus Genome Array. The arrays were washed and stained using a GeneChip® Hybridization Wash and Stain kit (Affymetrix, Inc) on an Affymetrix Fluidics Station 450 accroding to user's manual.

scan_protocol: The arrays were scanned using a a GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: Statistical tests were performed using BioConductor statistical software, open source software based on the R programming language (http://www.bioconductor.org/). Robust Multichip Analysis (RMA) approach was used for normalizing the raw data. Differential expression analysis was carried out using a linear modeling approach and the empirical Bayes statistics as implemented in the Limma package.

organism: Citrus sinensis

source_name: Sweet orange leaves inoculated with Xcc306 mutant with pthA4 gene deleted  (MU) at 48 hpi

label_protocol: Labeling was performed using a GeneChip 3'IVT Express kit (Affymetrix, Inc). Brifely, cDNA was generated from 250 ng of the total RNA through in vitro transcription; the modified cDNA was labeled with biotin and labeled cDNA was purified and fragmented following the manufacturer’s instructions.

growth_protocol: The plants were kept in a quarantine glasshouse with temperature of 28 ± 2 °C,16 h light and 40-60% humidity. Strains of Xanthomonas were grown at 28 °C in nutrient agar (NA). The leaf samples were wrapped with aluminum foil and put in liquid nitrogen immediately, then were kept in -80°C freezer.

extract_protocol: RNA extraction was performed by using RNeasy Plant Mini Kit (Qiagen, Valencia, CA). Brifely, the leaf tissue was ground in liquid nitrogen, buffer RLT was added  to the powder and mixed, suspension was centrifuged with the spin column, clear lysate was collected, ethanol was added to precipitate RNA, suspension was centrifuged in RNeasy spin column, pellet was saved and washed with buffer RW1 and buffer RPE, then pellet was dissolved in RNase-free water

treatment_protocol: The plants were inoculated at the concentration of 5 X 108 cfu/ml using syringe with needle

value: Young leaves

tag: time

value: 48 hours post inoculation

tag: infection

value: Xcc306 with pthA4 gene deletion


title: dDP eye discs, untreated, biological replicate 2


title: wild type eye discs, irradiated, biological replicate 3

description: Gene expression data from irradiated wild type eye discs

source_name: wild type eye discs, irradiated


title: Leaves_by MU_6h_rep2

description:
Sweet orange (C. Sinensis) Valencia
Gene expression data of sweet orange at 6 h post infiltration of Xcc306 mutant strain with pthA4 gene deletion

source_name: Sweet orange leaves inoculated with Xcc306 mutant with pthA4 gene deleted  (MU) at 6 hpi

value: 6 hours post inoculation


title: de2f1 eye discs, untreated, biological replicate 1


title: wild type eye discs, untreated, biological replicate 3

description: Gene expression data from untreated wild type eye discs

source_name: wild type eye discs, untreated


title: COL-0, rep3

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description: Replicate 3 of 4, Col-0 vs. bean

hyb_protocol: Cy3 and Cy5 labeled cRNAs were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65°C. Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing:
Data were extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for gene expression two-color microarrays (GE2_107_Sep09).
Two-color data processed using limma with the following parameters:
Background correction: normexp with offset=50
Within array normalization: loess
Between array normalization: Aquantile

organism: Tetranychus urticae

source_name: spider mites fed Arabidopsis line Col-0

label_protocol: 100 ng of total RNA (+ RNA-spike in control) was used to generate Cy3 or Cy5 labeled cRNAs, using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies).

extract_protocol: Total RNA was extracted from about 100 adult female spider mites using RNeasy Mini Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Adult female spider mites were transferred to the three Arabidopsis lines (Col-0, qKo, atr1D) or bean, and after 24 hours, the gene expression levels were analyzed.

tag: developmental stage

value: adult

value: female

value: Arabidopsis line Col-0

source_name: spider mites fed bean

value: bean


title: Leaves_by WT_48h_rep2

description:
Sweet orange (C. Sinensis) Valencia
Gene expression data of sweet orange at 48 h post infiltration of Xcc306 wild type strain

source_name: Sweet orange leaves inoculated with Xcc306 wild type (WT) at 48 hpi

value: Xcc306 wild type


title: COL-0, rep4

description: Replicate 4 of 4, Col-0 vs. bean


title: SUM159 sphere

city: FuZhou

first: Haiwei

last: Wang

state: FuJian

address: Daoshan road 180

institute: Fujian Maternity and Child Health Hospital

description: Gene expression data from SUM159 sphere cells

hyb_protocol: Fragmented and biotin-labeled cRNA was hybridized to affymetrix human U133 plus 2.0 array chip using the Affymetrix hybridization kit. Arrays were incubated in 45°C hybridization oven for 16 hours,rotating at 60 rpm.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 .

source_name: sphere cells from SUM159

label_protocol: 5 ug of total RNA was used to prepare double-stranded cDNA with the one-cycle cDNA synthesis kit (Affymetrix, USA). The cDNA was used to synthesize biotin-labeled cRNA with the IVT kit (Affymetrix, USA). Biotin-labeled cRNA was fragmented according to affymetrix protocol.

growth_protocol: Ovarian caner cells A2780, breast caner cells MCF7 and SUM159 were cultured on adhered plates in 10% FBS.

extract_protocol: Cellular RNA was isolated by Tri-Reagent using the manufacturer’s instructions. Qualified total RNA was further purified by RNeasy micro kit and RNase-Free DNase Set.

treatment_protocol: A2780, MCF7 and SUM159 cells were cultured in sphere formation media on non-adhered plates. The sphere formation media was DMEM-F12  supplemented with 2% B-27，20ng/mL epidermal growth factor, 5μg/mL insulin , and 0.4% bovine serum albumin.

value: breast cancer


title: Leaves_by MU_48h_rep2


title: wild type eye discs, untreated, biological replicate 2


title: de2f1 eye discs, irradiated, biological replicate 1


title: Leaves_by MU_48h_rep1


title: Leaves_by WT_48h_rep3


title: Leaves_by MU_6h_rep3


title: Leaves_by WT_48h_rep1


title: wild type eye discs, untreated, biological replicate 1


title: SUM159 cell line

description: Gene expression data from SUM159 adhered cells

source_name: SUM159 adhered cells


title: wild type eye discs, irradiated, biological replicate 1


title: Leaves_by WT_6h_rep3

description:
Sweet orange (C. Sinensis) Valencia
Gene expression data of sweet orange at 6 h post infiltration of Xcc306 wild type strain

source_name: Sweet orange leaves inoculated with Xcc306 wild type (WT) at 6 hpi


title: Leaves_by WT_6h_rep2


title: COL-0, rep1

description: Replicate 1 of 4, Col-0 vs. bean


title: COL-0, rep2

description: Replicate 2 of 4, Col-0 vs. bean


title: Leaves_by WT_6h_rep1


title: QKO, rep2

description:
Replicate 2 of 4, qKO vs. Col-0
The Arabidopsis line has previously been characterized: Differential effects of indole and aliphatic glucosinolates on lepidopteran herbivores. Muller R, de Vos M, Sun JY, Sonderby IE, Halkier BA, Wittstock U, Jander G. J Chem Ecol. 2010 Aug;36(8):905-13. PMID 20617455.

source_name: spider mites fed Arabidopsis line qKo

value: Arabidopsis line qKo


title: ATR1D, rep3

description:
Replicate 3 of 4, atr1D vs. Col-0
The Arabidopsis line has previously been characterized: The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis. Celenza JL, Quiel JA, Smolen GA, Merrikh H, Silvestro AR, Normanly J, Bender J. Plant Physiol. 2005 Jan;137(1):253-62. PMID 15579661.

source_name: spider mites fed Arabidopsis line atr1D

value: Arabidopsis line atr1D


title: A2780 cell line

description: Gene expression data from A2780 adhered cells

source_name: A2780 adhered cells

value: ovarian cancer


title: QKO, rep4

description:
Replicate 4 of 4, qKO vs. Col-0
The Arabidopsis line has previously been characterized: Differential effects of indole and aliphatic glucosinolates on lepidopteran herbivores. Muller R, de Vos M, Sun JY, Sonderby IE, Halkier BA, Wittstock U, Jander G. J Chem Ecol. 2010 Aug;36(8):905-13. PMID 20617455.


title: MCF7 sphere

description: Gene expression data from MCF7 sphere cells

source_name: sphere cells from MCF7


title: ATR1D, rep4

description:
Replicate 4 of 4, atr1D vs. Col-0
The Arabidopsis line has previously been characterized: The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis. Celenza JL, Quiel JA, Smolen GA, Merrikh H, Silvestro AR, Normanly J, Bender J. Plant Physiol. 2005 Jan;137(1):253-62. PMID 15579661.


title: A2780 sphere

description: Gene expression data from A2780 sphere cells

source_name: sphere cells from A2780


title: ATR1D, rep1

description:
Replicate 1 of 4, atr1D vs. Col-0
The Arabidopsis line has previously been characterized: The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis. Celenza JL, Quiel JA, Smolen GA, Merrikh H, Silvestro AR, Normanly J, Bender J. Plant Physiol. 2005 Jan;137(1):253-62. PMID 15579661.


title: patient2_ovary_rep3

city: Boston

first: Melissa

middle: Amy

last: Merritt

state: MA

address: 450 Brookline Ave

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were normalized using the vsnrma function in the package vsn.

source_name: patient 2, ovarian epithelial cells, cultured, hTERT-immortalized

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

growth_protocol: Cells were grown in newly developed WIT-fo medium (described in the associated publication)

extract_protocol: Total RNA was extracted using Qiagen RNA Mini kits according to the manufacturer's instructions.

tag: patient

tag: origin

value: ovarian epithelium

tag: cell passage


title: MCF7 cell line

description: Gene expression data from MCF7 adhered cells

source_name: MCF7 adhered cells


title: QKO, rep1

description:
Replicate 1 of 4, qKO vs. Col-0
The Arabidopsis line has previously been characterized: Differential effects of indole and aliphatic glucosinolates on lepidopteran herbivores. Muller R, de Vos M, Sun JY, Sonderby IE, Halkier BA, Wittstock U, Jander G. J Chem Ecol. 2010 Aug;36(8):905-13. PMID 20617455.

tag: gender


title: Leaves_by MU_6h_rep1


title: ATR1D, rep2

description:
Replicate 2 of 4, atr1D vs. Col-0
The Arabidopsis line has previously been characterized: The Arabidopsis ATR1 Myb transcription factor controls indolic glucosinolate homeostasis. Celenza JL, Quiel JA, Smolen GA, Merrikh H, Silvestro AR, Normanly J, Bender J. Plant Physiol. 2005 Jan;137(1):253-62. PMID 15579661.


title: QKO, rep3

description:
Replicate 3 of 4, qKO vs. Col-0
The Arabidopsis line has previously been characterized: Differential effects of indole and aliphatic glucosinolates on lepidopteran herbivores. Muller R, de Vos M, Sun JY, Sonderby IE, Halkier BA, Wittstock U, Jander G. J Chem Ecol. 2010 Aug;36(8):905-13. PMID 20617455.


title: patient2_fallopian_tube_rep1

source_name: patient 2, fallopian tube epithelial cells, cultured, hTERT-immortalized

value: fallopian tube epithelium


title: patient2_fallopian_tube_rep3


title: patient2_ovary_rep1


title: NCOR KO liver, biological rep4

city: Houston

first: Zheng

last: Sun

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: knockout (AAV-Cre)

hyb_protocol: RNA were hybridized to the Mouse Gene 2.0 ST Array (Affymetrix).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.

data_processing: Microarray image analysis was carried out using Partek Genomics Suite software. Subsequent analysis was carried out using BioConductor. Data from the 8 samples were subjected to background subtraction, quantile normalization, log2 transformation and probeset summarization using the RMA (Robust Multichip Average) algorithm. Only the probe sets that interrogate genes were retained and those meant for QC and normalization purposes were excluded from further analysis. The SAM procedure was then used to obtain multiple test corrected q-values for differential expression of genes between the hearts from MCH3-KO mice and control.

source_name: Liver, knockout (AAV-Cre)

label_protocol: GeneChip WT Terminal Labeling and Control Kit (Affymetrix)

growth_protocol: Mice were maintained on normal chow and the normal 24-hr light/dark cycle

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

treatment_protocol: Livers were put into liquid nitrogen immediately after mice euthanization

value: NCOR knockout

value: 3-month old


title: NCOR KO liver, biological rep2

description: knockout (AAV-Cre)


title: NCOR KO liver, biological rep3

description: knockout (AAV-Cre)


title: patient2_fallopian_tube_rep2


title: WT liver, biological rep3

description: AAV-Cre + AAV-HDAC3 WT

source_name: Liver, AAV-Cre + AAV-HDAC3 WT

value: male

value: HDAC3 rescued wild-type

value: 4-month old


title: patient2_ovary_rep2


title: WT liver, biological rep4

description: AAV-Cre + AAV-HDAC3 WT


title: WT liver, biological rep2

description: AAV-Cre + AAV-HDAC3 WT


title: WT liver, biological rep4

description: wild-type (AAV-GFP)

source_name: Liver, wild-type (AAV-GFP)

value: wild-type


title: WT liver, biological rep1

description: AAV-Cre + AAV-HDAC3 WT


title: patient1_fallopian_tube_rep4

source_name: patient 1, fallopian tube epithelial cells, cultured, hTERT-immortalized


title: HDAC3 KO liver, biological rep3

description: AAV-Cre

source_name: Liver, AAV-Cre

value: HDAC3 knockout


title: WT liver, biological rep3

description: wild-type (AAV-GFP)


title: NCOR KO liver, biological rep1

description: knockout (AAV-Cre)


title: patient1_ovary_rep2

source_name: patient 1, ovarian epithelial cells, cultured, hTERT-immortalized


title: patient1_fallopian_tube_rep3


title: patient1_fallopian_tube_rep2


title: patient1_ovary_rep3


title: rat bladder, 10d deobstruction_4A, mRNA

status: Public on Nov 24 2013

city: Lund

first: Mari

last: Ekman

state: Sverige

address: BMC D12

institute: Lund University

description: rat bladder, 10d deobstruction_4A

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed using expression console software version 1.1.2 using default analysis settings and RMA as normalization method.

organism: Rattus norvegicus

source_name: deobstructed bladders

extract_protocol: unknown

value: Urinary bladders

tag: related mirna sample


title: rat bladder, 6w obstruction_11, mRNA

description: rat bladder, 6w obstruction_11

source_name: long time obstructed bladders


title: rat bladder, 10d deobstruction_6A, mRNA

description: rat bladder, 10d deobstruction_6A


title: patient1_ovary_rep1


title: HDAC3 KO liver, biological rep1

description: AAV-Cre


title: WT liver, biological rep1

description: wild-type (AAV-GFP)


title: rat bladder, 6w obstruction_6A, mRNA

description: rat bladder, 6w obstruction_6A


title: WT liver, biological rep2

description: wild-type (AAV-GFP)


title: HDAC3 KO liver, biological rep2

description: AAV-Cre


title: rat bladder, 6w obstruction_8, mRNA

description: rat bladder, 6w obstruction_8


title: rat bladder, 10d deobstruction_5A, mRNA

description: rat bladder, 10d deobstruction_5A


title: rat bladder, 6w obstruction_4A, mRNA

description: rat bladder, 6w obstruction_4A


title: rat bladder, 10d obstruction_6A, mRNA

description: rat bladder, 10d obstruction_6A

source_name: short time obstructed bladders


title: rat bladder, no obstruction_5A, mRNA

description: rat bladder, no obstruction_5A

source_name: control bladders


title: rat bladder, 10d obstruction_4A, mRNA

description: rat bladder, 10d obstruction_4A


title: rat bladder, no obstruction_4A, mRNA

description: rat bladder, no obstruction_4A


title: rat bladder, 6w obstruction_5A, mRNA

description: rat bladder, 6w obstruction_5A


title: rat bladder, 10d obstruction_5A, mRNA

description: rat bladder, 10d obstruction_5A


title: rat bladder, 10d deobstruction_3A, mRNA

description: rat bladder, 10d deobstruction_3A


title: rat bladder, 6w obstruction_6A

description:
21_6 w obstruc 6A
miRNA profiling

source_name: urinary bladder, 6w obstruction

extract_protocol: Total RNA from urianry bladder tissue was prepared using the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's recommendations

value: Sprague-Dawley

tag: protocol

value: obstruction

value: urinary bladder


title: rat bladder, no obstruction_6A, mRNA

description: rat bladder, no obstruction_6A


title: rat bladder, 10d deobstruction_4A

description:
24_10d deobstruc 4A
miRNA profiling

source_name: urinary bladder, 10d deobstruction

value: deobstruction


title: rat bladder, 6w obstruction_11

description:
23_6 w obstruc 11
miRNA profiling


title: rat bladder, 10d deobstruction_6A

description:
26_10 d deobstruc 6A
miRNA profiling


title: rat bladder, 6w obstruction_8

description:
22_6 w obstruc 8
miRNA profiling


title: rat bladder, 10d deobstruction_5A

description:
25_10 d deobstruc 5A
miRNA profiling


title: rat bladder, 6w obstruction_3A, mRNA

description: rat bladder, 6w obstruction_3A


title: rat bladder, 10d obstruction_5A

description:
17_10d obstruc 5A
miRNA profiling

source_name: urinary bladder, 10d obstruction


title: rat bladder, 10d deobstruction_2A, mRNA

description: rat bladder, 10d deobstruction_2A


title: rat bladder, 10d deobstruction_1A, mRNA

description: rat bladder, 10d deobstruction_1A


title: rat bladder, 6w obstruction_4A

description:
19_6 w obstruc 4A
miRNA profiling


title: rat bladder, 10d obstruction_4A

description:
16_10d obstruc 4A
miRNA profiling


title: rat bladder, 10d obstruction_6A

description:
18_10d obstruc 6A
miRNA profiling


title: rat bladder, 6w obstruction_5A

description:
20_6 w obstruc 5A
miRNA profiling


title: rat bladder, 6w obstruction_2A, mRNA

description: rat bladder, 6w obstruction_2A


title: rat bladder, no obstruction_6A

description:
15_Sham op 6A
miRNA profiling

source_name: urinary bladder, no obstruction

value: sham-operated

value: control


title: miR126KO_rep1

city: New York

first: Brian

last: Brown

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: Values were generated through the data generation and quality control pipeline of the Immunological Genome Project (www.immgen.org). Raw data were background-corrected and normalized using the RMA algorithm. 4000 probesets recognizing un-annotated genes, noisy probes (high CV) and probes with SNPs were excluded, following Immgen's SOP.

source_name: pDC spleen miR126KO

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: Trizol

value: miR-126 KO

value: FACS-sorted pDCs from spleen

value: 2 months


title: rat bladder, no obstruction_5A

description:
14_Sham op 5A
miRNA profiling


title: miR126KO_rep2


title: rat bladder, 10d deobstruction_2A

description:
11_10 d deobstruc 2A
miRNA profiling


title: rat bladder, 10d deobstruction_3A

description:
12_10 d deobstruc 3A
miRNA profiling


title: rat bladder, 10d obstruction_3A, mRNA

description: rat bladder, 10d obstruction_3A


title: rat bladder, no obstruction_4A

description:
13_Sham op 4A
miRNA profiling


title: rat bladder, 6w obstruction_1A, mRNA

description: rat bladder, 6w obstruction_1A


title: miR126KO_rep3


title: rat bladder, 10d deobstruction_1A

description:
10_10d deobstruc 1A
miRNA profiling


title: rat bladder, 6w obstruction_3A

description:
9_6 w obstruc 3A
miRNA profiling


title: WT_rep3

source_name: pDC spleen WT

value: wild type


title: rat bladder, 10d obstruction_2A, mRNA

description: rat bladder, 10d obstruction_2A


title: WT_rep1


title: WT_rep2


title: rat bladder, 6w obstruction_2A

description:
8_6 w obstruc 2A
miRNA profiling


title: rat bladder, 6w obstruction_1A

description:
7_6 w obstruc 1A
miRNA profiling


title: rat bladder, 10d obstruction_3A

description:
6_10d obstruc 3A
miRNA profiling


title: rat bladder, no obstruction_3A, mRNA

description: rat bladder, no obstruction_3A


title: rat bladder, no obstruction_2A, mRNA

description: rat bladder, no obstruction_2A


title: JH-AF-5 5

status: Public on Nov 23 2013

city: San Francisco

first: Joseph

middle: Leo

last: Wiemels

state: California

address: 1450 3rd Street, MC 0520

department: Epidemiology and Biostastics

institute: UCSF

description: Acute leukemia with t(1;19) translocation

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:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
The array image was processed using CNAG copy number software for estimating copy number changes (results reported in .CFN files).   SNP data is not reported or assessed.

source_name: leukemia patient tumor DNA

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was isolated from leukemia cells with SDS-proteinase K methods.  DNA was quantified using Pico-green fluirimetry and gel leectrophoresis

value: acute leukemia


title: JH-AF-5 6


title: JH-AF-5 7


title: rat bladder, no obstruction_1A, mRNA

description: rat bladder, no obstruction_1A


title: rat bladder, 10d obstruction_1A

description:
4_10d obstruc 1A
miRNA profiling


title: JH-AF-5 8


title: rat bladder, no obstruction_3A

description:
3_Sham op 3A
miRNA profiling


title: rat bladder, 10d obstruction_2A

description:
5_10d obstruc 2A
miRNA profiling


title: JH-AF-5 4


title: rat bladder, no obstruction_2A

description:
2_Sham op 2A
miRNA profiling


title: rat bladder, no obstruction_1A

description:
1_Sham op 1A
miRNA profiling


title: JH-AF-5 2


title: JH-AF-5 3


title: rat bladder, 10d obstruction_1A, mRNA

description: rat bladder, 10d obstruction_1A


title: JH-AF-5 1


title: JH-AF-4 5


title: JH-AF-3 6


title: JH-AF-3 4


title: JH-AF-4 8


title: JH-AF-3 5