title: FoxO6 +/+ (WT) After Learning biological replicate 1

value: male

value: C57BL/6J-129sv mixed background

tag: genotype/variation

value: Wild Type FoxO6

value: After learning


title: FoxO6 -/- (Mutant) After Learning biological replicate 3

status: Public on Nov 08 2012

type: RNA

city: Stanford

first: Anne

last: Brunet

state: California

address: 300 Pasteur Drive,

department: Genetics

country: USA

institute: Stanford University

description: Gene expression data from adult hippocampus from FoxO6 mutant mice after learning task

hyb_protocol: Followed the 169 Format array requirements. GeneChip Hybridization Oven 640, GeneChip Fluidics station 450.

scan_protocol: GeneChip Scanner 3000 7G.

data_processing: The data were adjusted for background and then normalized using Robust Multiarray Analysis (RMA).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: adult hippocampus, FoxO6 mutant, object learning task

label_protocol: Biotinylated single-stranded DNA was prepared according to Affymetrix Whole Transcript Sense Targeting Labeling Assay protocol.

extract_protocol: RNAqueous (Ambion) using the manufacturer's protocol.

treatment_protocol: The cohort of basal mice were housed individually for at least 3 days prior to tissue harvesting. The mice used to collect hippocampal samples after the object learning task were handled daily  in the procedure room, prior to the object learning task. 24 hours before the object learning task, each mouse was individually habituated to the empty novel object arena for 10 min. On the days of the novel object learning task and the empty arena habituation, the mice were transferred to the procedure room and acclimatized for 60 min. For the novel object learning task, the mice were allowed to explore two identical and novel objects for 10 min in a 70 x 70 x 70 cm black plastic arena with a white PVC vinyl material on the base. After the object exploration, mice were transferred to an empty cage, and were euthanized after 60 min. The brains were dissected and incubated in ice-cold RNAlater (Ambion) for 24 hours at 4ºC. The brains were then rapidly frozen in O.C.T. Tissue-Tek (Sakura) at -80ºC. Coronal brain sections (300 µm) were made using a microtome (Microm), the hippocampus was finely dissected and collected into ‘RNA lysis buffer’ (Ambion), and homogenized for 30 sec using a rotar-stat homogenizer.

tag: age

tag: gender

tag: strain

value: FoxO6 null

tag: time point


title: Minnesota

type: genomic

city: Atlanta

first: Brian

middle: H

last: Raphael

state: GA

address: 1600 Clifton Road

department: Enteric Diseases Laboratory Branch

institute: Centers for Disease Control and Prevention

hyb_protocol: Labeled DNA was hybridized with microarrays at 42 degrees C for 16 hours.

scan_protocol: Arrays were scanned with a GenePix 4000B.

data_processing: The log10 (average 635 nm median signal intensity for triplicate probes/average signal intensity for all empty spots on the array) was determined. Normalization was not performed.

molecule: genomic DNA

organism: Clostridium botulinum

source_name: Minnesota, type E

label_protocol: Genomic DNA was labeled with Klenow fragment and Cy5-labeled random primers at 37 degrees C for 2 hours.

growth_protocol: Bacteria were grown under anaerobic conditions at 35 degrees C for 24-48 hours prior to genomic DNA extraction.

extract_protocol: DNA was isolated using the PureLink Genomic DNA kit (Life Technologies, Grand Island, NY).

value: Minnesota

tag: group

value: II

tag: strain type

value: E

tag: source

value: unknown

tag: geographical location


title: FoxO6 -/- (Mutant) After Learning biological replicate 2


title: VH

source_name: VH, type E

value: VH


title: CDC40329

source_name: CDC40329, type E

value: fish

value: Alaska


title: CDC42861

source_name: CDC42861, type E

value: seal flipper


title: FACS isolated adult murine prostate basal cells, cultured in vitro and DAPT-treated 1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: FACS isolated adult murine prostate basal cells, cultured in vitro and DAPT-treated, compared to universal reference RNA

hyb_protocol: The sample and reference probes were mixed with GEx hybridization buffer and blocking solution (Agilent, Santa Clara, CA) and denatured by a 2-minute incubation at 95 degC. Probes were hybridized to Agilent 4x44K Whole Mouse Genome arrays and rotating over night at 65 degC.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent and Bioconductor software was used.

label: Alexa Fluor 647

source_name: FACS isolated adult murine prostate basal cells, cultured in vitro.

label_protocol: Complementary DNA (cDNA) reverse transcription and fluorescent labeling reactions were carried out using SuperScript Plus Direct cDNA Labeling system (Invitrogen, Carlsbad, CA).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.  Microarray analysis was performed using 2.5 micrograms of total RNA.

treatment_protocol: The γ-Secretase inhibitor N-[(3,5-Difluorophenyl)acetyl]-L-alanyl-2-phenyl]glycine-1,1-dimethylethyl ester (DAPT) (Tocris Bioscience, Ellisville, MO) was used at a concentration of 5µM. Cell culture media containing DAPT or DMSO was replaced every 24 hours.

tag: cell type

value: prostate basal cells

tag: treatment

value: DAPT

label: Alexa Fluor 555

source_name: mouse, universal reference RNA

tag: reference

value: Stratagene, Universal Mouse Reference RNA Catalog #740100


title: FACS isolated adult murine prostate basal cells, cultured in vitro and vehicle-treated 2

description: FACS isolated adult murine prostate basal cells, cultured in vitro and vehicle-treated, compared to universal reference RNA

value: vehicle


title: FACS isolated adult murine prostate basal cells, cultured in vitro and DAPT-treated 2


title: liver, Wt females_4956

city: St. Louis

first: Nancy

last: Marcus

state: Missouri

address: 1100 S. Grand,Doisy Research Center

department: Pediatrics

institute: St. Louis University

description: Wt females_4956

hyb_protocol: Biotinylated cRNA was hybridized for 16h at 45°C to gene chips of the MOE430A series for each category of pooled RNA: 4953,4954,4955,4956. Biotinylated cRNA was hybridized for 16 h at 45°C to gene chips of the MOE430B series.

scan_protocol: Samples were scanned with the Affymetrix Gene Chip Scanner 3000

data_processing: The Affymetrix Gene Chip Operating Software and the MAS 5 algorithm were used for processing.  The .txt file outputs are linear and scaled to an array-mean of 1500.

label: biotin

source_name: Wt female liver

label_protocol: Biotinylated cRNA was prepared using instructions from the Affymetrix protocol.

extract_protocol: Rneasy Qiagen RNA was extracted according to the manufacturer's protocol.

treatment_protocol: Livers were flash-frozen in liquid nitrogen

value: female

value: wild type

tag: tissue

value: liver


title: CDC59471

source_name: CDC59471, type E

value: stool


title: liver, PiZ males_4953

description: PiZ males_4953

source_name: PiZ male liver

value: male

value: Transgenic mouse, human ATZ hepatocyte expression


title: FoxO6 +/+ (WT) After Learning biological replicate 2

description: Gene expression data from adult hippocampus from Wild Type mice after learning task

source_name: adult hippocampus, Wild Type, object learning task

value: C57BL/6J-129sv mixed background

value: Wild Type FoxO6

value: After learning


title: liver, Wt males_4955

description: Wt males_4955

source_name: Wt male liver


title: CDC59470

source_name: CDC59470, type E

value: II

value: E

value: stink eggs


title: Human Dendritic Cell L. major 24hrs biological rep2

city: Notre Dame

first: Michelle

middle: A

last: Favila

state: IN

address: 210 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

description: Gene expression data from human monocyte derived dendritic cells, L. major infected, 24hrs

hyb_protocol: Purified cRNA was fragmented in 5X fragmentation buffer (200mM Tris-Acetate, pH8.1, 500mM potassium acetate, 150mM magnesium acetate) at 94ºC for 35 min prior to cRNA chip hybridization.  Gene chips were washed and stained utilizing the Affymetrix Fluidics Station 400

scan_protocol: Gene chips were scanned with the Gene Chip Scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: The Affymetrix data files (.cel) were processed using Bioconductor software package (http://www.bioconductor.org/, Seattle, WA) [13].  Probe set signal intensities were subjected to background correction by GCRMA (Genespring GX 7.0) normalization across all 15 chips.  The mean fluorescence intensity was derived from a log2 transformation of the raw data.  Probe sets with “present” call in at least 7 of the 15 chips were retained, which filtered our list of 54,000 probe sets down to ~14,000.  Statistical significance was determined using a one-way ANOVA and Benjamini-Yekutieli multiple correction test to control false discovery rates.  A final set of 848 candidate probe set were identified as significantly expressed in at least one time point compared to non-infected samples (p<0.05).

organism: Homo sapiens

source_name: Human Dendritic Cell L. major 24hrs

label_protocol: Biotinylated cRNAs were prepared according to standard Affymetrix protocol from 2μg of total RNA according to manufacturer's protocols (Affymetrix, Santa Clara, CA)

growth_protocol: Monocyte-derived human dendritic cells were maintained in RPMI-complete media (10% FBS, 2mM l-glutamine 100U/ml, 1% penicillin/streptomycin) at 37°C

extract_protocol: Uninfected and L. major infected samples were harvested at 2, 4, 8, or 24hrs post infection.  Total RNA was extracted from each sample utilzing an RNEasy kit according to manufacturer's protocols (Qiagen, Valencia, CA)

treatment_protocol: L. major parasites were maintained in complete M199 media (supplemented with 20% FBS).  Metacyclic promastigotes were isolated using a ficol density gradient protocol and opsonized by treatment with 5% human serum for 30 min at 37°C.  Metacyclic promastigotes were utilized for infection of the monocyte-derived human dendritic cells

value: monocyte-derived dendritic cells

tag: leishmania major infected

value: yes

value: 24 hrs


title: liver, PiZ females_4954

description: PiZ females_4954

source_name: PiZ female liver


title: liver, Wt females_4966

description: Wt females_4966


title: CDC52256

source_name: CDC52256, type E

value: Illinois


title: Human Dendritic Cell L. major 24hrs biological rep3


title: FoxO6 -/- (Mutant) After Learning biological replicate 1

value: FoxO6 null


title: liver, Wt males_4965

description: Wt males_4965


title: Human Dendritic Cell L. major 24hrs biological rep1


title: Human Dendritic Cell L. major 8hrs biological rep2

description: Gene expression data from human monocyte derived dendritic cells, L. major infected, 8hrs

source_name: Human Dendritic Cell L. major 8hrs

value: 8 hrs


title: Alaska

source_name: Alaska, type E

value: Alaska

value: unknown


title: liver, PiZ females_4964

description: PiZ females_4964

value: female

value: liver


title: liver, PiZ males_4963

description: PiZ males_4963

value: male

value: Transgenic mouse, human ATZ hepatocyte expression


title: Human Dendritic Cell L. major 8hrs biological rep1


title: FACS isolated adult murine prostate basal cells, cultured in vitro and vehicle-treated 1

value: prostate basal cells

value: vehicle

value: Stratagene, Universal Mouse Reference RNA Catalog #740100


title: CDC59498

source_name: CDC59498, type E

value: II

value: E

value: stink head


title: Human Dendritic Cell L. major 4hrs biological rep2

description: Gene expression data from human monocyte derived dendritic cells, L. major infected, 4hrs

source_name: Human Dendritic Cell L. major 4hrs

value: monocyte-derived dendritic cells

value: yes

value: 4 hrs


title: Human Dendritic Cell L. major 4hrs biological rep3


title: Human Dendritic Cell L. major 8hrs biological rep3


title: Human Dendritic Cell L. major 4hrs biological rep1


title: CDC47437

source_name: CDC47437, type E

value: stool


title: CDC42840

source_name: CDC42840, type E


title: Human Dendritic Cell L. major 2hrs biological rep3

description: Gene expression data from human monocyte derived dendritic cells, L. major infected, 2hrs

source_name: Human Dendritic Cell L. major 2hrs

value: 2 hrs


title: CDC42747

source_name: CDC42747, type E

value: Alaska


title: Human Dendritic Cell L. major 2hrs biological rep2


title: CDC41648

source_name: CDC41648, type E

value: seal flipper


title: CDC5247

source_name: CDC5247, type E

value: fermented seal flipper


title: Promyelocyte_310511_hm450

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

description: Healthy donor cells

scan_protocol: Arrays were imaged using HiScan instrument (Illumina Inc.) using standard recommended Illumina scanner setting

data_processing: Data preprocessing and methylation level extraction was performed using the Genome Studio software v2011.1 (Illumina Inc.) including the  Methylation module v1.9.0 and the Illumina Genome Viewer module v1.9.0.

label: Cy5 and Cy3

source_name: Generated in vitro from CD34+ above

label_protocol: Standard Illumina Protocol

extract_protocol: Bisulfite conversion of genomic DNA was performed using using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA). Bisulphite converted DNA was amplified, fragmented and 500 ng converted DNA was hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

tag: sample type

value: Healthy donor cells


title: CD34_260511_hm450

description: Healthy donor cells

hyb_protocol: DNA was hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

source_name: Density centrifuged bone marrow


title: Human Dendritic Cell uninfected 2hrs biological rep3

description: Gene expression data from human monocyte derived dendritic cells, uninfected

source_name: Human Dendritic Cell uninfected 2hrs

value: no


title: Human Dendritic Cell L. major 2hrs biological rep1


title: Beluga

source_name: Beluga, type E

value: Beluga

value: fermented whale


title: Soil gene expression study_DasR (+chitin) rep2-2

status: Public on Nov 07 2012

city: Tsukuba

first: Behnam

last: Nazari

state: Ibaraki

address: 3-1-3 Kannondai

department: Environmental Biofunction Division

country: Japan

institute: National Institute for Agro-Environmental Sciences

description: This sample is Streptomyces coelicolor A3(2)[M145] delta-dasR mutant. It is the second of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from chitin-amended soil cultures

hyb_protocol: The cDNA was labeled with Cy3-random nonamers using a NimbleGen One-Color DNA Labeling Kit (Roche NimbleGen) and hybridized to the microarrays for 16 h at 42°C on a NimbleGen Hybridization System. The cDNA labeling, hybridization and washing were carried out according to manufacturer’s instruction of Roche NimbleGen (http://www.Nimblegen.com/products/lit/ expression_userguide_v5p0.pdf).

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.The washed arrays were scanned at 5 mm resolutions using a Genepix 4000B microarray scanner (Molecular Devices, Sunnyvale,CA).

data_processing: NIMBLESCAN v2.5 software (http://www.nimblegen.com/ products/software/index.html) was used to extract raw data from scanned images and perform normalization using the quantile normalization method and Robust Multiarray Average (RMA) algorithm across arrays to generate gene expression values as described in the NIMBLESCAN’s manual

organism: Streptomyces coelicolor A3(2)

growth_protocol: Brown forest soil obtained from a field at the Ehime Agricultural Experiment Station, Japan (FAO classification, Gleyic Cambisols), was used in experiment. The autoclaved soil samples were adjusted to 60% of the maximum water-holding capacity with sterilized water (as a control) or a sterilized solution of colloidal chitin to give a final 0.2% (w/w) of colloidal chitin, and then distributed in 2 g portions into 15 ml sterile disposable plastic tubes. Spores wild type of S. coelicolor A3(2)or dasR-disrupted mutant (YU1)(final 106 CFU/g soil for each) were inoculated into the soil, followed by incubation at 30°C for 48 h

extract_protocol: RNA samples for microarray analysis were extracted from the soil cultures incubated at 30˚C for 48 h.total RNA was extracted from 2 g soil cultures using an RNA PowerSoil Total RNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA) according to the manufacturer’s instructions. To obtain enough RNA (at least 20 μg) from soil cultures for microarray analysis, the RNA samples prepared from each of 2 g of soil cultures were mixed. Total 16 g of chitin amended soil cultures and 20 g of control soil cultures were used for the preparation of RNA. The mixed RNA samples were purified using a MicroSpin S-400 HR spin column (GE Healthcare, Little Chalfont, UK), subjected to DNase digestion using a TURBO DNA-Free Kit (Ambion, Austin, TX), and then concentrated with an RNA Clean-up & Concentration Kit column (Zymo Research, Orange, CA). The concentrations of RNA were determined using a Nanodrop system (Nanodrop, Wilmington, DE).

treatment_protocol: For analysis of wild type strain, the autoclaved soil samples were adjusted to 60% of the maximum water-holding capacity with sterilized water (as a control) or a sterilized solution of colloidal chitin to give a final 0.2% (w/w) of colloidal chitin. For analysis of wild type and dasR-disrupted mutant, the autoclaved soil samples were adjusted to 60% of the maximum water-holding capacity with sterilized solution of colloidal chitin to give a final 0.2% (w/w) of colloidal chitin.

tag: taxid

value: 100226_disruption dasR mutant

tag: phenotype

value: Deficient in aerial mycelium and spore formation

tag: growth condition

value: plus chitin


title: Soil gene expression study_DasR (+chitin) rep3-1

description: This sample is Streptomyces coelicolor A3(2)[M145] delta-dasR mutant. It is the third of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from chitin-amended soil cultures

label_protocol: The cDNA was labeled with Cy3-random nonamers using a NimbleGen One-Color DNA Labeling Kit (Roche NimbleGen) and hybridized to the microarrays for 16 h at 42°C on a NimbleGen Hybridization System. The cDNA labeling, hybridization and washing were carried out according to manufacturer’s instruction of Roche NimbleGen (http://www.Nimblegen.com/products/lit/ expression_userguide_v5p0.pdf).


title: Soil gene expression study_DasR (+chitin) rep3-2

source_name: Streptomyces coelicolor A3(2)[M145] delta-dasR


title: Soil gene expression study_DasR (+chitin) rep1-2

description: This sample is Streptomyces coelicolor A3(2)[M145] delta-dasR mutant. It is the first of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from chitin-amended soil cultures


title: Soil gene expression study_DasR (+chitin) rep1-1


title: Soil gene expression study_wild-type (+chitin) rep3-2

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the third of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from soil cultures.

source_name: Streptomyces coelicolor A3(2)[M145] wild type

value: 100226_wild type

value: normal


title: Soil gene expression study_DasR (+chitin) rep2-1


title: APL_8503_hm450

description: Primary diagnosis

value: Primary diagnosis


title: Soil gene expression study_wild-type (+chitin) rep3-1


title: Soil gene expression study_wild-type (+chitin) rep2-1

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the second of three wild-type biological replicates used in this experiment,each from separate pooled RNA samples excracted from soil cultures.


title: Human Dendritic Cell uninfected 2hrs biological rep2

value: monocyte-derived dendritic cells


title: Soil gene expression study_wild-type (+chitin) rep1-1

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the first of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from soil cultures.


title: Soil gene expression study_S. coelicolor (+chitin) rep3-2

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the third of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from chitin-amended soil cultures


title: APL_9882_hm450

description: Primary diagnosis


title: Human Dendritic Cell uninfected 2hrs biological rep1


title: APL_8452_hm450

description: Primary diagnosis


title: Soil gene expression study_wild-type (+chitin) rep2-2

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the second of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from soil cultures.


title: Soil gene expression study_S. coelicolor (+chitin) rep3-1


title: APL_11428_hm450

description: Remission bone marrow

value: Remission bone marrow


title: APL_10545_hm450

description: Primary diagnosis


title: APL_10325_hm450

description: Remission bone marrow


title: Soil gene expression study_S. coelicolor (+chitin) rep1-2

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the first of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from chitin-amended soil cultures


title: Soil gene expression study_S. coelicolor (+chitin) rep2-1

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the second of three wild-type biological replicates used in this experiment,each from separate pooled RNA samples excracted from chitin-amended soil cultures


title: Soil gene expression study_S. coelicolor (+chitin) rep2-2

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the second of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from chitin-amended soil cultures


title: Soil gene expression study_S. coelicolor (-chitin) rep3-2

value: minus chitin


title: Soil gene expression study_wild-type (+chitin) rep1-2


title: Soil gene expression study_S. coelicolor (-chitin) rep2-2


title: Soil gene expression study_S. coelicolor (-chitin) rep3-1


title: Soil gene expression study_S. coelicolor (+chitin) rep1-1

description: This sample is of wild-type of Streptomyces coelicolor A3(2)[M145]. It is the first of three wild-type biological replicates used in this experiment, each from separate pooled RNA samples excracted from chitin-amended soil cultures.


title: Soil gene expression study_S. coelicolor (-chitin) rep1-2


title: Soil gene expression study_S. coelicolor (-chitin) rep1-1


title: APL_11523_hm450

description: Remission bone marrow


title: Soil gene expression study_S. coelicolor (-chitin) rep2-1


title: CM501 replicate 3

city: Cambridge

first: Sean

middle: Michael

last: Carroll

state: MA

address: Biological Laboratories, Room 3084, 16 Divinity Ave

department: Organismic and Evolutionary Biology

institute: Harvard University

description:
Wild-type C1-metabolism
Marx lab 2012, Harvard University, custom Agilent 60-mer array with 15K features for Methylobacterium extorquens AM1 based on GPL6262

hyb_protocol: standard Agilent protocol by MOgene, LC

scan_protocol: standard Agilent protocol by MOgene, LC

data_processing: standard Agilent protocol by MOgene, LC

organism: Methylorubrum extorquens AM1

source_name: Mid-exponential phase batch cultures grown on 15 mM methanol

label_protocol: standard Agilent protocol by MOgene, LC

growth_protocol: Growth experiments were initiated by inoculating 10 μL of freezer stock into 9.6 mL Hypho in a 50 mL Erlenmeyer flask containing 10 mM methanol and 1.75 mM succinate plus 50 mg/mL kanamycin. Flasks were grown at 225 rpm in a 30 °C shaker-incubator until reaching stationary phase (2-4 days). A second acclimation cycle was accomplished by transferring 150 μL of saturated culture into 9.45 mL fresh medium with 0.5x kanamycin plus the carbon substrate to be tested; then transferred again into the same conditions for experimental (measured) growth. A 1:64 dilution of cultures with the given substrate concentrations allowed for ~ 26 doublings per growth cycle.

extract_protocol: Total RNA extraction was performed using the RNeasy kit (Qiagen, Valencia, CA), genomic DNA was removed using the TURBO DNA-free kit (Ambion, Austin, TX), and the RNA samples were concentrated using Amicon Ultra centrifugal filters (Millipore, Billerica, MA).

treatment_protocol: Triplicate cultures of strains were grown to half-maximal OD600 in 15 mM methanol before harvesting and RNA

tag: isolate

value: wild-type (WT)

value: Wild-type C1-metabolism


title: 100% OCI-Ly8_0% HEK293

city: Aalborg

first: Maria

middle: Bro

last: Kloster

address: Sdr. Skovvej 15

department: Department of Haematology

country: Denmark

institute: Aalborg Hospital

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

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned using GeneChip Scanner 7G (Affymetrix) at the Department of Haematology Core Facility.

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

data_processing:
The .CEL-files were imported into Bioconductor using the aroma.affymetrix package. The .CEL-files were background corrected and normalized by the RMABackgroundCorrection and QuantialeNormalization functions from the aroma.affymetrix package. Core probe intensities were summarized to gene expression levels by means of the ExonRMAPlm(, mergeGroups=TRUE) function using the customized cdf-file for core transcripts downloaded from http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
probe group file: HuEx-1_0-st-v2.pgf
meta-probeset file: HuEx-1_0-st HuEx-1_0-stv2, A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.csv

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

growth_protocol: OCI-Ly8 was maintained in RPMI-1640 medium including 10% foetal bovine serum. HEK293 was maintained in Eagle’s Minimum Essential Medium including 10% foetal bovine serum. Both cell lines were in a CO2 incubater at 37°C and 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated from 5 million cells with the Trizol reagent and mirVana miRNA isolation kit (Ambion), according to the manufacturer’s instructions.

treatment_protocol: Cell lines were harvest in the exponential phase. Cells were sorted directly into RNAlater in different cellular concentrations using the FACSAria II cell sorter.

tag: cell line


title: 30% OCI-Ly8_70% HEK293


title: 10% OCI-Ly8_90% HEK293


title: 20% OCI-Ly8_80% HEK293


title: 0.5% OCI-Ly8_99.5% HEK293


title: 1% OCI-Ly8_99% HEK293


title: APL_11364_hm450

description: Remission bone marrow


title: 11d_virgin_heterozygote_SBSb_colony_MN17_2008

city: Lausanne

first: Mingkwan

last: Nipitwattanaphon

address: Biophore Building, UNIL-Sorge

department: Department of Ecology and Evolution

country: Switzerland

institute: University of Lausanne

description: RNA from the whole body of a single queen of specific genotype and age

hyb_protocol: Hybridization buffer (3x SSC, 0.18% SDS, 200 ng/μl yeast tRNA, 200 ng/µl polyA DNA; final concentration) was added to samples; samples were denatured, applied to microarrays, and hybridized overnight at 64°C. After hybridization, slides were washed sequential.

scan_protocol: Scanner: Agilent Technologies microarray scanner. Image quantification GenePix 5.1

data_processing: printTipLoess normalization and between-array normalization with limma (Bioconductor)

organism: Solenopsis invicta

source_name: Reference RNA batch 2006

label_protocol: Total RNA was amplified using the Ambion Message Amp II kit. Amplified RNA plus Alien spike control RNAs (Stratagene) were labeled using the indirect aa-dUTP labeling method. Reverse transcription primers: random 9mers.

extract_protocol: Total RNA extracted using Qiagen RNeasy Kit following manufacturer's instructions

value: whole organism

tag: batch

value: year 2006

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

source_name: 11-day-old virgin heterozygote SB/Sb

value: Genotype - SB/Sb, Age - 11-day-old virgin, Year - 2008, Social form - polygyne

tag: genotype

value: SB/Sb

value: year 2008

tag: age

value: 11-day-old virgin

tag: state

value: virgin

tag: social form

value: polygyne


title: 0% OCI-Ly8_100% HEK293


title: 5% OCI-Ly8_95% HEK293


title: 11d_virgin_heterozygote_SBSb_colony_MN10_2008


title: 11d_virgin_heterozygote_SBSb_colony_MN5_2008


title: 11d_virgin_heterozygote_SBSb_colony_MN18_2008


title: 11d_virgin_heterozygote_SBSb_colony_MN9_2008


title: 11d_virgin_heterozygote_SBSb_colony_MN8_2008


title: 11d_virgin_heterozygote_SBSb_colony_MN3_2008


title: 11d_virgin_homozygote_SBSB_colony_MN17_2008

source_name: 11-day-old virgin homozygote SB/SB

value: Genotype - SB/SB, Age - 11-day-old virgin, Year - 2008, Social form - polygyne

value: SB/SB


title: 1d_virgin_heterozygote_SBSb_colony_MN2_2008

source_name: 1-day-old virgin heterozygote SB/Sb

value: Genotype - SB/Sb, Age - 1-day-old virgin, Year - 2008, Social form - polygyne

value: 1-day-old virgin


title: 11d_virgin_homozygote_SBSB_colony_MN3_2008


title: 1d_virgin_heterozygote_SBSb_colony_MN11_2008


title: 1d_virgin_heterozygote_SBSb_colony_MN17_2008


title: 1d_virgin_heterozygote_SBSb_colony_MN6_2008


title: 11d_virgin_homozygote_SBSB_colony_MN5_2008


title: 11d_virgin_homozygote_SBSB_colony_MN8_2008


title: 1d_virgin_heterozygote_SBSb_colony_MN12_2008


title: 1d_virgin_heterozygote_SBSb_colony_MN22_2008


title: 11d_virgin_homozygote_SBSB_colony_MN18_2008


title: 11d_virgin_homozygote_SBSB_colony_MN9_2008


title: 11d_virgin_homozygote_SBSB_colony_MN10_2008


title: 1d_virgin_heterozygote_SBSb_colony_MN15_2008


title: 1d_virgin_homozygote_SBSB_colony_MN11_2008

source_name: 1-day-old virgin homozygote SB/SB

value: Genotype - SB/SB, Age - 1-day-old virgin, Year - 2008, Social form - polygyne


title: 1d_virgin_homozygote_SBSB_colony_MN15_2008


title: 1d_virgin_homozygote_SBSB_colony_MN8_2008


title: 1d_virgin_homozygote_SBSB_colony_MN17_2008


title: 1d_virgin_homozygote_SBSB_colony_MN6_2008


title: 1d_virgin_homozygote_SBSB_colony_MN22_2008


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ4_2009

source_name: reproductive queen heterozygote SB/Sb

value: Genotype - SB/Sb, Age - reproductive queen, Year - 2009, Social form - polygyne

value: year 2009

value: reproductive queen


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ6_2009

value: whole organism


title: 1d_virgin_homozygote_SBSB_colony_MN2_2008

value: year 2006


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ8_2009

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)


title: 1d_virgin_homozygote_SBSB_colony_MN12_2008


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ2_2009


title: 1d_virgin_heterozygote_SBSb_colony_MN8_2008


title: reproductive_queen_homozygote_SBSB_colony_Mg371_2009

source_name: reproductive queen homozygote SB/SB

value: Genotype - SB/SB, Age - reproductive queen, Year - 2009, Social form - monogyne

value: monogyne


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ7_2009

value: SB/Sb


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ3_2009


title: wild type, biological rep3

city: Beijing

first: Dong

last: Liu

address: School of Life Sciences

country: China

institute: Tsinghua University

description: Gene expression data from 8-day-old wild type seedlings.

hyb_protocol: Array hybridization and wash were performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in a Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA US) following the manufacturer’s instructions.

scan_protocol: Hybridized slides were scanned by GeneChip©Scanner 3000 (Cat00-00212, Affimetrix, Santa Clara, CA US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA US) with default settings.

data_processing: Raw data were normalized by the MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). Microarray data analysis was performed using the SBC Analysis system, which is available on the website: http://sas.ebioservice.com/index.jsp. The username and password to access to this website are available upon request.

organism: Arabidopsis thaliana

source_name: 8-day-old wild type seedling

label_protocol: Total RNA was amplified, labeled, and purified with the GeneChip 3’IVT Express Kit (Cat#901229, Afftnetrix, Santa Clara, CA, US) following the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The sterilized Arabidopsis seeds were sown on Petri dishes containing a medium of 1/2 Murashige & Skoog (MS) basal salts with 1% sucrose, 0.1% MES (adjusted to pH 5.7 with 1 N NaOH), and 1.2% agar. After 2 days of stratification at 4℃, the agar plates were placed vertically in the growth room with a photoperiod of 16 h light : 8 h dark at 22–24℃.The light intensity was 100 µmol m-2 s-1. At day 8 after seed germination, whole seedlings were collected for RNA isolation.

extract_protocol: Trizol extraction of total RNA was performed using RNA extraction kit (Cat#15596-018，Life technologies, Carlsbad, CA, US) according to the manufacturer's instructions.

treatment_protocol: No treatment is applied.

tag: ecotype

tag: genotype/variation

value: wild type

value: whole seedling

tag: developmental stage

value: 8-day-old (after germination)


title: reproductive_queen_homozygote_SBSB_colony_Mg380_2009


title: reproductive_queen_homozygote_SBSB_colony_Mg374_2009


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ1_2009

value: polygyne


title: reproductive_queen_homozygote_SBSB_colony_Mg367_2009

value: SB/SB


title: 11d_virgin_heterozygote_SBSb_colony_Pg342_2009

value: Genotype - SB/Sb, Age - 11-day-old virgin, Year - 2009, Social form - polygyne

value: 11-day-old virgin

value: virgin


title: wild type, biological rep1


title: 11d_virgin_heterozygote_SBSb_colony_Pg356_2009


title: reproductive_queen_homozygote_SBSB_colony_Mg379_2009


title: reproductive_queen_homozygote_SBSB_colony_Mg366_2009


title: reproductive_queen_homozygote_SBSB_colony_Mg378_2009


title: lib mutant, biological rep2

description: Gene expression data from 8-day-old lib mutant seedlings.

source_name: 8-day-old lib mutant seedling

value: lib mutant


title: lib mutant, biological rep1


title: wild type, biological rep2


title: lib mutant, biological rep3


title: 11d_virgin_homozygote_SBSB_colony_Pg342_2009

value: Genotype - SB/SB, Age - 11-day-old virgin, Year - 2009, Social form - polygyne

value: year 2009


title: 11d_virgin_homozygote_SBSB_colony_Pg356_2009

value: whole organism


title: 11d_virgin_homozygote_SBSB_colony_Pg352_2009

value: year 2006


title: Wnt 3a + 5a treated 1

city: Dublin

first: Patricia

last: Maguire

address: Belfield

department: Conway Institute

country: United Kingdom

institute: University College Dublin

description:
3a5a1
4743194088_A

hyb_protocol: The biotinylated cRNA (1500 ng per sample) was applied to Illumina HumanWG-6 v3 Expression BeadChips and hybridized overnight at 58˚C. Chips were washed, detected and scanned according to the manufacturer’s instructions and the scanner output imported into BeadStudio software (Illumina, Cambridge, UK)

scan_protocol: Chips were scanned according to the manufacturer’s instructions and the scanner output imported into BeadStudio software (Illumina, Cambridge, UK)

data_processing: Statistical analysis of the data was performed using the lumi package for Bioconductor/R (www.r-project.org)

source_name: CHRF 288-11 cells

label_protocol: Total RNA (500 ng) was amplified using the Illumina Total Prep RNA Amplification Kit (Applied Biosystems, Warrington, UK) according to the manufacturer’s instructions.

growth_protocol: CHRF288-11 cells were cultured in RPMI 1640, 10% fetal calf serum, 2 mM l-glutamine in a humidified incubator with 5% CO2

extract_protocol: Cells were collected as described above, lysed in 200 μL Trizol reagent (Invitrogen, Paisley, UK) and prepared according to the manufacturer’s instructions.

treatment_protocol: For RNA preparation, cells (106/mL) were cultured in serum free medium for 16 hours before treatment with recombinant Wnt3a (150 ng/mL), Wnt5a (1200 ng/mL) or both Wnt3a and 5a in combination

tag: treatment

value: Wnt 3a + 5a treated

tag: time

value: 8 hours

value: CHRF 288-11 cells


title: Wnt3a treated 1

description:
3a1
4743194088_C

value: Wnt3a treated


title: 11d_virgin_heterozygote_SBSb_colony_Pg352_2009

tag: tissue

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

value: SB/Sb


title: Wnt5a treated 2

description:
5a2
4743194088_E

value: Wnt5a treated


title: 1d_virgin_heterozygote_SBSb_colony_Pg352_2009

tag: sample type

value: Genotype - SB/Sb, Age - 1-day-old virgin, Year - 2009, Social form - polygyne

value: 1-day-old virgin

value: polygyne


title: Untreated 1

description:
untreated1
4743194088_D

value: Untreated


title: Wnt 3a + 5a treated 2

description:
3a5a2
4743194088_F


title: Wnt 3a + 5a treated 3

description:
3a5a3
4743194088_B


title: reproductive_queen_homozygote_SBSB_colony_Mg375_2009

value: Genotype - SB/SB, Age - reproductive queen, Year - 2009, Social form - monogyne

value: SB/SB

value: reproductive queen

value: monogyne


title: 1d_virgin_heterozygote_SBSb_colony_Pg356_2009

value: whole organism

value: year 2009

value: virgin


title: 1d_virgin_homozygote_SBSB_colony_Pg352_2009

value: year 2006

value: Genotype - SB/SB, Age - 1-day-old virgin, Year - 2009, Social form - polygyne


title: Wnt3a treated 3

description:
3a3
4743194086_F

value: Wnt3a treated

value: 8 hours

value: CHRF 288-11 cells


title: 1d_virgin_heterozygote_SBSb_colony_Pg342_2009

value: Amplified total RNA isolated en masse from hundreds of adult workers collected from the foraging area of 30 colonies (eight and seven of each social form from Georgia and Louisiana, respectively)

value: SB/Sb


title: Untreated 2

description:
untreated2
4743194086_C


title: Wnt5a treated 1

description:
5a1
4743194086_E

value: Wnt5a treated


title: Wnt3a treated 2

description:
3a2
4743194086_A


title: Wnt5a treated 3

description:
5a3
4743194086_B


title: 1d_virgin_homozygote_SBSB_colony_Pg356_2009

value: 1-day-old virgin

value: polygyne


title: Untreated 3

description:
untreated3
4743194086_D

value: Untreated


title: 1d_virgin_homozygote_SBSB_colony_Pg342_2009

value: SB/SB


title: CGNs, Temporal 1.5 DIV, biological rep3

city: Worcester

first: Baojin

last: Ding

address: 55 Lake AVE. N.

department: Microbiology and Physiological Systems

institute: UMASS Medical School

description:
Day1.5_REP3
cerebellar granule neurons pooled litter

hyb_protocol: Samples were hybridized using the Affymetrix Hybridization Cocktail recipe consisting of components (BSA 50mg/ml from Invitrogen and Herring Sperm DNA from Promega) and lab prepared 2X Hybridization Buffer • Pre-hybridize arrays at 450C for 10 minutes with 1X Hybridization Buffer Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes and centrifuge at max speed for ~3 minute (N.B. this deviates from Affy SOP)• Transfer 200 μl of hybridization solution to each array, then cover holes with Tough Spots • Hybridize ~16 hours at 45°C at 60rpm• Fluidics wash protocol used was EukGE-WS2v5.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: NFI-EnR data were processed using RMA. Gene expression values in the Affymetrix cel files were first background corrected and normalized together using RMA algorithm (Bioconductor R package).  Low expression probes (i.e., expression value below 40th percentile in at least 7 out of 8 arrays) were removed.  For multiple probes mapping to the same gene, only the probe showing the highest expression change for each gene was retained.  Finally, moderated t-statistics and FDR correction (limma R package v.2.15.1.) were used to assess the significance of differential expression. Identical steps for signal normalization, background noise correction and statistical testing were applied to temporal arrays. NFI differentially regulated genes were defined as probes with FDR P-value<0.15 and fold change>1.5. Differentially expressed temporal genes were defined as having probes with FDR P-value<0.1 and fold change>2.

label_protocol: Samples were prepared using an Affymetrix GeneChip 3’IVT Express Kit, in which total RNA undergoes reverse transcription to synthesize first strand cDNA and is then converted into double-stranded DNA template for transcription. IVT synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified and fragmented.

growth_protocol: Mouse CGN progenitors were purified from P6 mice cerebellum and cultured  in complete Neurobasal medium until 1.5 or 6 days.

extract_protocol: RNA was extracted from cultured cells using Tri reagent (Sigma) and purified with an RNeasy Plus Micro Kit (QIAGEN).

treatment_protocol: For NFI group, CGNs were transduced on the day of plating with lentiviruses expressing either NFI-EnR or EnR alone. Fresh medium was added on 3DIV (days in vitro).

tag: strain background

value: wild-type

tag: tissue origin

value: P6 mice cerebellum

value: cerebellar granule neurons

tag: day in vitro (div)

value: 1.5 days


title: CGNs, Temporal 6 DIV, biological rep2

description:
Day6_REP2
cerebellar granule neurons pooled litter

value: 6 days


title: reproductive_queen_heterozygote_SBSb_colony_PgXXQ5_2009

value: whole organism

value: year 2006

value: Genotype - SB/Sb, Age - reproductive queen, Year - 2009, Social form - polygyne

value: year 2009

value: reproductive queen


title: (B6xBALB/C)F1 juvenile testes 6

city: Prague

first: Petr

last: Simecek

state: Not Applicable

address: Vídeňská 1083

department: Department of Mouse Molecular Genetics

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR, v. v. i.

description: Gene expression data from 14.5d B6 x BALB/C testes

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours at 45°C on GeneChip Gene 1.0 ST array according to the standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix GeneChip 450 Fluidics Station.

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

data_processing: The data were analyzed with R / Bioconductor using xps package.

source_name: pool of four juvenile testes of B6 x BALB/C mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual).

growth_protocol: The mice had ad libitum access to a standard rodent diet (VELAS, ST-1, 3.4% fat) and acidified water.

extract_protocol: Total RNA was isolated using the miRNeasy Mini Kit according to the manufacturer’s protocol.

treatment_protocol: Testes of 14.5days old mice were dissected, testicular tunica was removed, spermatogenic populations were isolated and the cells were placed into RLT buffer of the miRNeasy Mini isolation kit (QIAGEN) and homogenized using syringe and needle.

value: B6 x BALB/C

value: testes


title: CGNs, Temporal 1.5 DIV, biological rep2

description:
Day1.5_REP2
cerebellar granule neurons pooled litter


title: CGNs, Temporal 6 DIV, biological rep1

description:
Day6_REP1
cerebellar granule neurons pooled litter


title: CGNs, Temporal 6 DIV, biological rep3

description:
Day6_REP3
cerebellar granule neurons pooled litter


title: (BALB/CxB6)F1 juvenile testes 3

description: Gene expression data from 14.5d BALB/C x B6 testes

source_name: pool of four juvenile testes of BALB/C x B6 mice

value: BALB/C x B6


title: CGNs, Temporal 1.5 DIV, biological rep1

description:
Day1.5_REP1
cerebellar granule neurons pooled litter


title: (B6xBALB/C)F1 juvenile testes 4


title: (BALB/CxB6)F1 juvenile testes 2


title: (B6xPWD)F1 juvenile testes 3

description: Gene expression data from 14.5d B6 x PWD testes

source_name: pool of four juvenile testes of B6 x PWD mice

value: B6 x PWD


title: CGNs, NFI-EnR , biological rep4

description:
NFI-EnR_REP4
cerebellar granule neurons pooled litter
B#2_(Mouse430_2).CEL

source_name: NFI suppressor

tag: tranduced with


title: (BALB/CxB6)F1 juvenile testes 1


title: CGNs, NFI-EnR , biological rep2

description:
NFI-EnR_REP2
cerebellar granule neurons pooled litter
E2.CEL


title: CGNs, NFI-EnR , biological rep1

description:
NFI-EnR_REP1
cerebellar granule neurons pooled litter
E1.CEL


title: (B6xBALB/C)F1 juvenile testes 5


title: CGNs, NFI-EnR , biological rep3

description:
NFI-EnR_REP3
cerebellar granule neurons pooled litter
A2_(Mouse430_2).CEL


title: CGNs, EnR control, biological rep4

description:
EnR_REP4
cerebellar granule neurons pooled litter
A_(Mouse430_2).CEL

source_name: EnR control


title: CGNs, EnR control, biological rep3

description:
EnR_REP3
cerebellar granule neurons pooled litter
A1_(Mouse430_2).CEL


title: (B6xPWD)F1 juvenile testes 2


title: CGNs, EnR control, biological rep2

description:
EnR_REP2
cerebellar granule neurons pooled litter
D2.CEL


title: CGNs, EnR control, biological rep1

description:
EnR_REP1
cerebellar granule neurons pooled litter
D1.CEL


title: Macrophages_normallipid_Pg_rep3

city: Fuzhou

first: Lang

last: Lei

state: Fujian

address: 246# Yangqiaozhong Road, Gulou District

institute: Fujian Medical University

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 and Command Console Software 3.1 with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software (Agilent technologies, Santa Clara, CA, US).

label_protocol: Using Affymetrix GeneChip 3’IVT Express Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) to obtain biotin labeled cRNA according to manufacturer's instruction.

growth_protocol: Macrophages from peritoneal fluid after Percoll isolation was cultured in RPMI 1640

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: PBS washing

tag: strain

tag: Sex

value: male

value: wild type

value: peritoneal fluid

value: 20wk of age


title: Macrophages_normallipid_Pg_rep2

tag: genotype


title: (B6xPWD)F1 juvenile testes 1

tag: age


title: Definitive endoderm derived from HSF1

city: Los Angeles

first: David

last: Chan

state: CA

address: 621 Charles E Young Drive South

department: MCDB

institute: UCLA

description:
Gene expression data from HSF1 definitive endoderm
HSF1-endo d5

hyb_protocol: Affymetrix GeneChip Hybridization oven 645; overnight 16 hours

scan_protocol: Affymetrix G7 scanner

data_processing:
Affymetrix Expression Console version 1.2 with TGT=500
The data were processed and normalized in GeneSpring and 3 separate normalizations were performed (for FFH9 ES PTK7- and FFH9 ES PTK7+; XFiPSC2 ES PTK7- and XFiPSC2 ES PTK7+; HSF1-undiff d0 and HSF1-endo d5).  We made use of the raw RMA signals after the normalization.

source_name: Definitive enoderm derived from HSF1

label_protocol: Ambion MessageAmp(tm) Premier RNA Amplification Protocol or Nugen Ovation(r) Pico WTA System V2

growth_protocol: Pluripotent stem cells were cultured in standard conditions as described

extract_protocol: Total RNA was extracted with Qiagen RNeasy micro kit or mini kit according to manufacturer's protocol

treatment_protocol: Spontaneous differentiation by culturing in low bFGF conditions, Definitive endoderm derivation by culturing in 100ng/mL ActivinA

tag: differentiation

value: Induced by ActivinA

tag: length of differentiation

value: 5 days

tag: cell population

value: Definitive endoderm derived from HSF1


title: B6 juvenile testes 3

description: Gene expression data from 14.5d B6 testes

source_name: pool of four juvenile testes of B6 mice


title: PTK7+ cells from XFiPSC2

description:
Gene expression data from XFiPSC2 PTK7+ population
XFiPSC2 ES PTK7+

source_name: PTK7+ FACS population from differentiated XFiPSC2

value: Spontaneous

value: 2 days

value: differentiated XFiPSC2

tag: facs population


title: B6 juvenile testes 2


title: Macrophages_normallipid_Pg_rep1


title: PTK7+ cells from Feeder-free H9

description:
Gene expression data from H9 PTK7+ population
FFH9 ES PTK7+

source_name: PTK7+ FACS population from differentiated H9

value: differentiated H9


title: PTK7- cells from XFiPSC2

description:
Gene expression data from XFiPSC2 PTK7- population
XFiPSC2 ES PTK7-

source_name: PTK7- FACS population from differentiated XFiPSC2


title: Undifferentiated HSF1

description:
Gene expression data from undifferentiated HSF1
HSF1-undiff d0

source_name: Undifferentiated HSF1

value: 0 days

value: Undifferentiated HSF1


title: B6 juvenile testes 1


title: Bone marrow mononuclear cells, 08_930

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

country: Spain

institute: IDIBELL

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using the standard recommended Illumina scanner setting.

data_processing: Genome Studio V2011.2. The methylation score of each CpG is represented as an average beta value (AVG_Beta).

label: Cy3, Cy5

source_name: bone marrow mononuclear cells, leukemia

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Mononuclear cells and B cells were selected by Lymphoprep or CD19 microbeads protocols, and total DNA was isolated by standard procedures.

tag: cell type

value: bone marrow mononuclear cells

tag: gender

tag: disease state

value: leukemia

tag: recurrence

value: no


title: Macrophages_normallipid_blank_rep3

tag: tissue


title: (PWDxB6)F1 juvenile testes 3

description: Gene expression data from 14.5d PWD x B6 testes

source_name: pool of four juvenile testes of PWD x B6 mice

value: PWD x B6

value: testes


title: PWD juvenile testes 3

description: Gene expression data from 14.5d PWD testes

source_name: pool of four juvenile testes of PWD mice

value: PWD


title: (PWDxB6)F1 juvenile testes 2


title: B cells, CD19_C

source_name: B cells, healthy

value: B cells from whole blood

value: male

value: healthy


title: Macrophages_normallipid_blank_rep2

value: wild type

value: peritoneal fluid

value: 20wk of age


title: (PWDxB6)F1 juvenile testes 1


title: Macrophages_normallipid_blank_rep1


title: HIV infected mDC_232

city: Davis

first: Lauren

last: Nagy

address: 451 Health Sciences

department: Medical Microbiology and Immunology

institute: University of California-Davis

description: 232 PBMC CD11c

hyb_protocol: Following fragmentation, 15ug of cRNA were hybridized for 16 hrs at 45C on U133 2.0 Human GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Data was analyzed with Genespring 9.0 software using default analysis settings. No minumium fluorescence cut-off was used for data analysis.

source_name: HIV infected blood CD11c+ cells

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

extract_protocol: Quiagen Rneasy kit for isolated cells was used as per manufacturer's protocol

treatment_protocol: Whole PBMCs were isolated from blood and then CD11c+ cells were sorted using magnetic beads bound to human anti-CD11c+ antibody.

value: blood

value: whole peripheral blood mononuclear cells (PBMCs)

tag: cell subtype

value: CD11c+ Myeloid Dendritic Cells (mDCs)

tag: cd4 count

tag: viral load


title: B cells, CD19_D


title: B cells, CD19_A

value: female


title: PTK7- cells from Feeder-free H9

description:
Gene expression data from H9 PTK7- population
FFH9 ES PTK7-

source_name: PTK7- FACS population from differentiated H9

value: Spontaneous

value: 2 days

value: differentiated H9


title: B cells, CD19_B


title: HIV infected mDC_1010

description: 1010 PBMC CD11c


title: Macrophages_hyperlipid_Pg_rep3

value: ApoE-/-


title: (PWDxPWK)F1 juvenile testes 2

description: Gene expression data from 14.5d PWD x PWK testes

source_name: pool of four juvenile testes of PWD x PWK mice

value: PWD x PWK


title: Macrophages_hyperlipid_Pg_rep2


title: HIV uninfected mDC_215

description: 215 PBMC CD11c

source_name: HIV uninfected blood CD11c+ cells


title: HIV infected mDC_1009

description: 1009 PBMC CD11c


title: (B6xBALB/C)F1 juvenile testes 3

description: Gene expression data from 14.5d B6 x BALB/C testes

source_name: pool of four juvenile testes of B6 x BALB/C mice

value: B6 x BALB/C

value: testes


title: Bone marrow mononuclear cells, 02_1522

value: bone marrow mononuclear cells

value: leukemia

tag: treatment

value: no


title: HIV infected mDC_1011

description: 1011 PBMC CD11c


title: Bone marrow mononuclear cells, 02_723


title: Macrophages_hyperlipid_blank_rep3

tag: strain

value: male


title: (B6xBALB/C)F1 juvenile testes 2


title: HIV uninfected mDC_213

description: 213 PBMC CD11c


title: (B6xBALB/C)F1 juvenile testes 1


title: Macrophages_hyperlipid_blank_rep2

tag: Sex

value: peritoneal fluid


title: Macrophages_hyperlipid_Pg_rep1

tag: genotype

value: 20wk of age


title: Bone marrow mononuclear cells, 08_785


title: HIV uninfected mDC_204

description: 204 PBMC CD11c

tag: age

value: blood


title: HIV uninfected mDC_214

description: 214 PBMC CD11c

value: whole peripheral blood mononuclear cells (PBMCs)


title: Bone marrow mononuclear cells, 04_6


title: Macrophages_hyperlipid_blank_rep1


title: Bone marrow mononuclear cells, 03_106


title: PWD juvenile testes 1

value: PWD


title: PWD juvenile testes 2


title: Bone marrow mononuclear cells, 08_151

value: female


title: Bone marrow mononuclear cells, 07_1962


title: Inner Cell Mass 2 (Rat)

city: Zurich

first: Michal

middle: J

last: Okoniewski

state: Zurich

address: Binzmühlestrasse 130

institute: ETH Zurich

description: Inner Cell Mass

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

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

data_processing: RMA summaries using Brainarray CDFs Version 13.0.0 ENSG

organism: Rattus norvegicus

source_name: Inner Cell Mass

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: 6 to 12 weeks old Wistar females were check for estrus by using the Estrus Cycle Monitor EC40 (Fine Science Tools, Foster City, CA). All the positive females were breaded with Wistar males for 24 h and then housed separately to the males. At day E4 of pregnancy Wistar females were sacrificed and morula embryos were isolated and stored for later RNA extraction. Blastocyst embryos were isolated at E4.5 and either collected for further RNA extraction or processed for immunosurgery.

extract_protocol: Total RNA was extracted by using RNeasy Micro Kit (QIAGEN) according to the manufacture’s recommended protocols. All RNA samples were kept at -80°C till they were processed for microarray hybridization.

treatment_protocol: Immunosurgery for inner cell mass isolation: After removal of the zona pellucida, blastocysts were incubated for 3 hours (37°C, 5% CO2) in rabbit anti-rat serum (Sigma). Afterwards, embryos were washed several times with DMEM medium (GIBCO) supplemented with 10% of fetal bovine serum and incubated with rat serum (made in-house) for 20 min (37°C,  5% CO2). Rabbit anti-rat serum was used 1:5 diluted in DMEM medium; rat serum was diluted 1:5 in DMEM.

value: Inner Cell Mass

value: 6 to 12 weeks old

value: Wistar

value: females


title: shRNA6-16-plusDox-rep2

city: South San Francisco

first: Jinfeng

address: 1 DNA Way, MS93

department: Bioinformatics and Computational Biology

institute: Genentech Inc.

hyb_protocol: HGU 133 plus 2.0 arrays were hybridized according to the Affymetrix protocol

scan_protocol: HGU 133 plus 2.0 arrays were scanned according to the Affymetrix protocol

data_processing: Affymetrix HGU 133 plus 2.0 intensity signal CEL files were processed using the RMA algorithm as implemented in the 'affy' package from Bioconductor.

source_name: bladder cancer cells treated 48 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: RT112 cells expressing doxycline-inducible shRNAs targeting FGFR3 or EGFP were grown in 1%FBS medium with or without doxycycline (1 μg/ml) for 48 hr.

extract_protocol: Total cellular RNA was prepared with a RNeasy Plus kit (Qiagen) and subject to DNAse I digestion.

treatment_protocol: After overnight seeding, cells were treated with or without doxycycline (1 μg/ml) for 48 hr before RNA extraction.

tag: cell line

tag: transduced

value: FGFR3 shRNA 6-16

tag: doxycycline treatment

value: yes


title: (PWDxPWK)F1 juvenile testes 1

value: PWD x PWK

value: testes


title: Inner Cell Mass 1 (Rat)

description: Inner Cell Mass


title: shRNA6-16-noDox-rep3


title: Bone marrow mononuclear cells, 10_1789

value: bone marrow mononuclear cells

value: leukemia


title: Bone marrow mononuclear cells, 06_518

value: male

value: no


title: Inner Cell Mass 2 (Mouse)

description: Inner Cell Mass

growth_protocol: 3 to 5 weeks old B6D2F1 females were superovulated with 5IU pregnant mare’s serum gonadotropin (PMSG) (FolligonH Intervet) and 48 h later, with 5IU human chronicle gonadotropin (hCG) (ChorulonH Intervet). Superovulated females were mated with B6D2F1 males for 24 h and then housed separately to the males. Upon isolation morula and blastocyst stage embryos were either stored at -80°C for further RNA extraction or immunosurgery was performed for the isolation of the inner cell masses (ICMs).

treatment_protocol: Immunosurgery for inner cell mass isolation: Zona pellucida was removed by shortly incubating the blastocysts with Tyrode’s solution (Sigma). Consequently zona-free blastocysts were washed several times with M2 medium (Sigma) and immunosurgery was performed, by incubating the embryos 30 min with rabbit anti-mouse serum (Sigma). Afterwards, embryos were washed several times with DMEM medium (GIBCO) supplemented with 10% of fetal bovine serum. The embryos were then incubated (37°C, 5% CO2) with guinea pig complement serum (Sigma) for another 30 min. Rabbit anti-mouse serum was used 1:30 diluted in DMEM medium; guinea pig complement serum was diluted 1:3 in DMEM.

value: 3 to 5 weeks old


title: Blastocyst 1 (Rat)

description: Blastocyst

source_name: Blastocyst

value: Blastocyst


title: Bone marrow mononuclear cells, 02_1550


title: Bone marrow mononuclear cells, 11_834


title: shRNA6-16-noDox-rep1


title: Blastocyst 2 (Mouse)

description: Blastocyst


title: Blastocyst 2 (Rat)

description: Blastocyst


title: shRNA4-1-plusDox-rep2

value: FGFR3 shRNA 4-1


title: Inner Cell Mass 1 (Mouse)

description: Inner Cell Mass


title: shRNA4-1-noDox-rep3


title: Morula 2 (Rat)

description: Morula

source_name: Morula

value: Morula


title: Bone marrow mononuclear cells, 07_1768

value: female


title: Bone marrow mononuclear cells, 06_2096


title: Morula 2 (Mouse)

description: Morula


title: Morula 1 (Rat)

description: Morula


title: shRNA2-4-plusDox-rep2

value: FGFR3 shRNA 2-4


title: Bone marrow mononuclear cells, 05_1464


title: Morula 1 (Mouse)

description: Morula


title: shRNA2-4-noDox-rep3


title: Blastocyst 1 (Mouse)

description: Blastocyst


title: shRNA4-1-noDox-rep1


title: shRNA2-4-noDox-rep1


title: Mouse6_WT_rep2

hyb_protocol: Fragmented aRNA was hybridized at 42°C overnight using the HybBag mixing system with 1X OneArray® Hybridization Buffer (Phalanx Biotech), 10 mg/ml sheared salmon sperm DNA (Promega), at a concentration of 25 mg/ml labeled target. After hybridization, the arrays were washed according to the OneArray® protocol.

scan_protocol: Raw intensity signals for each microarray were captured using a Molecular Dynamics™ Axon 4100A scanner, measured using GenePixPro™ Software, and stored in GPR format.

data_processing: Expression summary values for all probes were obtained by doing background correction and quantile normalization with the 'limma' package from Bioconductor. Statistical analyses of differentially expressed genes were performed using linear models and empirical Bayes moderated statistics as implemented in the 'limma' package. Significant genes were defined as those with Benjamini-Hochberg adjusted p-values < 0.1 and fold changes > 2.

source_name: primary cells from bone marrow, myeloid progenitor, WT

label_protocol: RNA was converted to double-stranded cDNA and amplified using in vitro transcription that included amino-allyl UTP. The aRNA product was subsequently conjugated with Cy5™ NHS ester (GEH Lifesciences).

growth_protocol: These data were collected with only primary cells isolated from BAP1 WT and KO mice. The mice were injected with tamoxifen to induce systemic deletion of BAP1.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Mini Kit as per the manufacturer's instructions.

tag: strain/background

value: BAP1 WT

value: myeloid progenitor lineage-ScaI-Kit+ cells

tag: mouse identifier


title: Liver_WildType_NormalDiet_5

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >12.8 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min) and Stabilization and Drying Solution (Agilent Technologies, 30 sec).

scan_protocol: Slides were scanned immediately after washing on a GenePix™ 4000B array scanner.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014868_D_20070207). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):
myfunw<-function(x)
{okType<-x$ControlType==0
okFoundGreen<-x$gIsFound==1
okPos=x$gIsPosAndSignif==1
okWellAbove<- x$gIsWellAboveBG==1
as.numeric(okType & okFoundGreen & okPos & okWellAbove)}
We selected the spots with a weight of 1 for 16 out of 20 microarrays or with a weight of 1 in all 5 microarrays from at least one experimental group. At this step, 26057 spots out of 45018 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 24493 rows, each corresponding to a unique ProbeName.

source_name: Liver, wild-type control, normal diet

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 1 µg of total RNA using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions,  followed by RNeasy column purification (QIAGEN, Courtaboeuf, France).  Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 28-week-old wild-type and LXR-/- mice were housed at 22+2°C on a 12 hour light/dark cycle and allowed free access to water and food. The in vivo study was conducted under the European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.

extract_protocol: Immediately following euthanasia, the liver was removed, weighed, dissected (~100 mg fragments from the large lobe), snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with TRIzol reagent (Invitrogen) following the manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific).

treatment_protocol: Groups of mice were fed ad libitum for 7 weeks a normal chow (2016 Teklad Global 16% Protein Rodent Diet, Harlan, France) or a Western Diet (TD.88051 Cocoa Butter Diet and Purina Mouse Chow, Harlan, France).

value: mixed Sv129/C57Bl6J

value: wild-type

tag: gender

value: 28 weeks

value: liver

value: normal diet


title: Mouse5_WT_rep3

tag: cell type


title: control-plusDox-rep2

value: EGFP shRNA

value: yes


title: Mouse5_WT_rep2


title: control-noDox-rep2


title: Bone marrow mononuclear cells, 12_254

value: bone marrow mononuclear cells

tag: disease state

value: leukemia

tag: recurrence


title: Bone marrow mononuclear cells, 00_751

value: male


title: Liver_WildType_NormalDiet_4

tag: tissue


title: Mouse6_WT_rep3


title: Mouse5_WT_rep1


title: Bone marrow mononuclear cells, 08_774

value: no


title: Mouse3_WT_rep3

source_name: primary cells from bone marrow, HSC-enriched, WT

value: HSC-enriched lineage-ScaI+Kit+ cells


title: Mouse3_WT_rep2


title: control-noDox-rep1


title: shRNA6-16-plusDox-rep3

value: FGFR3 shRNA 6-16


title: Mouse6_WT_rep1


title: shRNA6-16-noDox-rep2


title: Bone marrow mononuclear cells, 08_723

value: yes (at relapse)


title: Liver_WildType_NormalDiet_1


title: control-noDox-rep3


title: Liver_WildType_NormalDiet_3


title: Liver_WildType_NormalDiet_2


title: Mouse3_WT_rep1


title: shRNA6-16-plusDox-rep1


title: Liver_WildType_WesternDiet_5

source_name: Liver, wild-type control, Western diet

value: Western diet


title: Liver_WildType_WesternDiet_4


title: shRNA4-1-plusDox-rep3

value: FGFR3 shRNA 4-1


title: Liver_WildType_WesternDiet_3


title: Mouse1_WT_rep2

value: BAP1 WT


title: shRNA4-1-plusDox-rep1


title: Mouse8_KO_rep3

source_name: primary cells from bone marrow, myeloid progenitor, BAP1 KO

value: BAP1 KO

value: myeloid progenitor lineage-ScaI-Kit+ cells


title: shRNA4-1-noDox-rep2


title: Bone marrow mononuclear cells, 01_1808

source_name: bone marrow mononuclear cells, leukemia

value: female


title: Liver_WildType_WesternDiet_1

value: mixed Sv129/C57Bl6J

value: wild-type

value: 28 weeks

value: liver


title: Mouse1_WT_rep1


title: shRNA2-4-plusDox-rep3

value: FGFR3 shRNA 2-4

value: yes


title: Mouse1_WT_rep3


title: Mouse8_KO_rep1


title: Bone marrow mononuclear cells, 06_758

value: bone marrow mononuclear cells

value: male

value: leukemia

value: SHOP/LAL-RECURRENCE


title: Liver_LXRko_NormalDiet_5

source_name: Liver, LXR alpha/beta double knockout, normal diet

value: LXR alpha/beta double knockout

value: normal diet


title: shRNA2-4-plusDox-rep1


title: Liver_WildType_WesternDiet_2

value: Western diet


title: Bone marrow mononuclear cells, 04_126

value: no


title: Mouse7_KO_rep3

value: BAP1 KO


title: Mouse8_KO_rep2

value: myeloid progenitor lineage-ScaI-Kit+ cells


title: Mouse7_KO_rep2


title: control-plusDox-rep3

value: EGFP shRNA


title: shRNA2-4-noDox-rep2


title: Bone marrow mononuclear cells, 05_579

value: yes (at relapse)


title: Liver_LXRko_NormalDiet_2

value: mixed Sv129/C57Bl6J


title: Bone marrow mononuclear cells, 03_1310


title: Liver_LXRko_NormalDiet_4

value: 28 weeks


title: control-plusDox-rep1


title: Mouse7_KO_rep1


title: Mouse4_KO_rep2

source_name: primary cells from bone marrow, HSC-enriched, BAP1 KO

value: HSC-enriched lineage-ScaI+Kit+ cells


title: Mouse4_KO_rep1


title: Liver_LXRko_NormalDiet_3

value: liver


title: Bone marrow mononuclear cells, 03_1380

value: female


title: Liver_LXRko_NormalDiet_1


title: Bone marrow mononuclear cells, 10_1420

value: bone marrow mononuclear cells


title: Mouse2_KO_rep3


title: Liver_LXRko_WesternDiet_2

source_name: Liver, LXR alpha/beta double knockout, Western diet

value: male


title: Liver_LXRko_WesternDiet_3


title: Bone marrow mononuclear cells, 05_170

value: leukemia


title: Bone marrow mononuclear cells, 07_2252


title: Bone marrow mononuclear cells, 02_1505


title: Mouse4_KO_rep3


title: Stump_rep3 [Exiqon]

status: Public on Nov 06 2012

city: New Haven

first: Edna

middle: C

last: Holman

state: CT

address: 266 Whitney Ave. KBT-442

department: Molecular, Cellular and Developmental Biology

institute: Yale University

description:
378st
Biological Replicate 3 of 3
Slide6
Cy3: 1_Exiqon_13768593_S01_Cropped.txt
Cy5: 0_Exiqon_13768593_S01_Cropped.txt

hyb_protocol: The samples were hybridized on the miRCURY™ LNA Array (v.9.2) as per Exiqons protocols.

scan_protocol: Arrays were scanned as per Exiqons protocols.

data_processing: Log ratios between the Hy3/Hy5 have been provided along with the normalized independent Hy3 and Hy5 signals. The quantified signals (background correction) were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

organism: Ambystoma mexicanum

source_name: Non-regenerating stump

label_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ power labeling kit (Outsourced to Exiqon)

extract_protocol: Total RNA extracted using mirVana miRNA Isolation Kit (Ambion) manufacturer's instructions

tag: days post amputation

value: Non-regenerating stump

source_name: Common Reference

tag: sample type

value: Common Reference (made by pooling all the samples)


title: Blastema_17dpa_rep2 [Exiqon]

description:
369bl
Biological Replicate 2 of 3
Slide3
Cy3: 1_Exiqon_13768590_S01_Cropped.txt
Cy5: 0_Exiqon_13768590_S01_Cropped.txt

source_name: Mid-bud regenerating blastema

value: Mid-bud regenerating blastema


title: Stump_rep2 [Exiqon]

description:
369st
Biological Replicate 2 of 3
Slide4
Cy3: 1_Exiqon_13768591_S01_Cropped.txt
Cy5: 0_Exiqon_13768591_S01_Cropped.txt


title: Liver_LXRko_WesternDiet_1

value: LXR alpha/beta double knockout

tag: treatment

value: Western diet


title: Blastema_17dpa_rep3 [Exiqon]

description:
378bl
Biological Replicate 3 of 3
Slide5
Cy3: 1_Exiqon_13768592_S01_Cropped.txt
Cy5: 0_Exiqon_13768592_S01_Cropped.txt


title: YWHAZ overexpressed CL1-0, biological rep3

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profiles from vector control transfectants and YWHAZ overexpressed transfectants were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

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

scan_protocol: GeneChips from the hybridization experiments were read by the Affymetrix GeneChip scanner 3000.

data_processing: The data were processed by GeneSpring GX software version 7.3.1 GC-RMA preprocessor to use on the CEL files

source_name: Human lung adenocarcinoma cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms purified cRNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Human lung adenocarcinoma cell lines of CL1-0 YWHAZ-transfected and CL1-0 vector control were grown in DMEM with 10% fetal bovine serum at 37¢XC, 20% O2, 5% CO2 and 1000 £gg/ml G418.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNAs extracted using TRIZOL reagent were quantified spectrophotometrically. The cDNA synthesis was carried out by using SUPERSCRIPTTM one-step RT-PCR kit (Invitrogen). For the reverse transcription step, the whole 5 ul of the resuspended RNAs were incubated for 60 min at 42oC, then 15 min at 72oC in 50 ul of reaction mixture containing 25 ul of 2x Reaction Mix (Invitrogen) and 1 ul of RT/PLANTINUM Taq Mix (Invitrogen). 28.5 ul of the cDNAs present in the 50 ul RT reaction mixture purified by Microarray Target Purification Kit (Roche Applied Science, Indianapolis, ID, USA, http://www.roche-applies-science.com) were used as templates to amplify cDNA by Microarray Target Amplification Kit. The amplified cDNAs were purified by Microarray Target Purification Kit, and complementary RNAs (cRNAs) were synthesized from 200 ng cDNA with Microarray RNA Target Synthesis Kit (Roche Applied Science).

tag: transfection

value: YWHAZ vector


title: CL1-0 mock control, biological rep1

value: vector control


title: Liver_LXRko_WesternDiet_5


title: YWHAZ overexpressed CL1-0, biological rep1


title: Blastema_17dpa_rep1 [Exiqon]

description:
368bl
Biological Replicate 1 of 3
Slide1
Cy3: 1_Exiqon_13768588_S01_Cropped.txt
Cy5: 0_Exiqon_13768588_S01_Cropped.txt


title: CL1-0 mock control, biological rep2


title: Mouse2_KO_rep1

value: BAP1 KO


title: Stump_rep1 [Exiqon]

description:
368st
Biological Replicate 1 of 3
Slide2
Cy3: 1_Exiqon_13768589_S01_Cropped.txt
Cy5: 0_Exiqon_13768589_S01_Cropped.txt


title: YWHAZ overexpressed CL1-0, biological rep2


title: CL1-0 mock control, biological rep3


title: Platelet-ET-27

city: Stony Brook

first: Xiao

last: Xu

state: NY

address: Stony Brook University

institute: Stony Brook University BME

description: US84103569_252182713284_S01_miRNA_107_Sep09_1_4

hyb_protocol: For hybridization, the samples were resuspended in 17 microliters of DEPC-treated water.  To each sample, 1 microliter of diluted Hybridization Spike Control, 4.5 mkl of 10X GE Blocking Agent (Agilent Technologies) and 22.5 microliters of 2X HiRPM Hybridization Buffer (Agilent Technologies) were added.  The samples were heated to 100oC for 5 minutes and transferred immediately to an ice water bath for 5 minutes.  The samples were then loaded onto Human miRNA Microarray (V3, 8x15K array). Hybridization was performed at 55oC for 20 hours. The arrays were then washed for 5 minutes at room temperature in GE Wash Buffer 1 (Agilent Technologies).  A second wash was performed in pre-warmed, 37oC GE Wash Buffer 2 (Agilent Technologies) for 5 minutes.  Each array was then dipped for 10 seconds into Acetonitrile (Fisher Scientific) and scanned using an Agilent High-Resolution C Scanner.  The scanned image was analyzed using Agilent Feature Extraction software v 10.7.3.1

scan_protocol: Agilent High-Resolution C scanner was used with default settings

data_processing: Data are 75th percentile shifted and normalized with RMA method, a filtering procedure was applied to keep miRNAs with >70% presence in at least one group using bioconductor (v 2.6) limma package on R (v 2.11). KNN method was used to impute missing values

source_name: Platelets

label_protocol: Total RNA was labeled with Cyanine 3-Cytidine biphosphate (pCp) using the Agilent’s miRNA Complete Labeling and Hybridization Kit (Agilent Technologies).Briefly, 100 ng of total RNA was combined with diluted Labeling Spike In controls.  The samples were dephosphorylated using Calf Intestinal Phosphatase at 37oC for 30 minutes, followed by denaturation with 10% DMSO at 100oC for 10 minutes and incubation in an ice water bath.  The Cyanine 3-pCp was then ligated onto the miRNA molecule using T4 RNA Ligase at 16oC for 2 hr. The labeled samples were immediately purified using Micro Bio-Spin 6 columns (BioRad). The columns were prepared according to manufacturer’s protocol.  TE was added to the labeled samples to a final volume of 50 microliters.  The samples were applied to the column, centrifuged for 4 minutes at 1000 g and then dried in a speedvac.

extract_protocol: RNA was isolated using Trizol

treatment_protocol: Leukocytes were isolated by density-gradient centrifugation from sodium citrate-treated blood (0.4% v/v final concentration) while platelet-rich plasma (PRP) served as the source of platelet mRNA.  Leukocyte contamination of PRP was < 1×10-5, and the isolation, quantification and quality control of both leukocyte and platelet RNAs was established using an Agilent 2100 Bioanalyzer

value: Platelets

tag: phenotype

value: ET


title: Platelet-NO-29

description: US84103569_252182713285_S01_miRNA_107_Sep09_1_3

value: NO


title: Platelet-NO-30

description: US84103569_252182713285_S01_miRNA_107_Sep09_1_4


title: Platelet-RT-21

description: US84103569_252182713285_S01_miRNA_107_Sep09_2_3

value: RT


title: Platelet-RT-22

description: US84103569_252182713285_S01_miRNA_107_Sep09_2_4


title: Platelet-ET-25

description: US84103569_252182713285_S01_miRNA_107_Sep09_2_1


title: Platelet-NO-27

description: US84103569_252182713285_S01_miRNA_107_Sep09_1_1


title: Platelet-RT-19

description: US84103569_252182713284_S01_miRNA_107_Sep09_2_3


title: Platelet-ET-24

description: US84103569_252182713284_S01_miRNA_107_Sep09_2_2


title: Platelet-RT-20

description: US84103569_252182713284_S01_miRNA_107_Sep09_2_4


title: Platelet-ET-23

description: US84103569_252182713284_S01_miRNA_107_Sep09_2_1


title: Platelet-NO-26

description: US84103569_252182713284_S01_miRNA_107_Sep09_1_3


title: Platelet-NO-23

description: US84103569_252182713014_S01_miRNA_107_Sep09_2_4


title: Platelet-NO-25

description: US84103569_252182713284_S01_miRNA_107_Sep09_1_2


title: Platelet-ET-26

description: US84103569_252182713285_S01_miRNA_107_Sep09_2_2


title: Platelet-NO-28

description: US84103569_252182713285_S01_miRNA_107_Sep09_1_2


title: Platelet-ET-22

description: US84103569_252182713014_S01_miRNA_107_Sep09_2_3


title: Platelet-RT-18

description: US84103569_252182713014_S01_miRNA_107_Sep09_2_1


title: Platelet-NO-24

description: US84103569_252182713284_S01_miRNA_107_Sep09_1_1


title: Liver_LXRko_WesternDiet_4

value: mixed Sv129/C57Bl6J

tag: genotype

value: 28 weeks

value: liver


title: Platelet-ET-21

description: US84103569_252182713014_S01_miRNA_107_Sep09_2_2


title: Mouse2_KO_rep2

value: HSC-enriched lineage-ScaI+Kit+ cells


title: Platelet-ET-20

description: US84103569_252182713014_S01_miRNA_107_Sep09_1_4


title: Platelet-NO-22

description: US84103569_252182713014_S01_miRNA_107_Sep09_1_3


title: Platelet-NO-17

description: US84103569_252182713011_S01_miRNA_107_Sep09_1_2


title: Platelet-NO-19

description: US84103569_252182713013_S01_miRNA_107_Sep09_1_3


title: Platelet-NO-21

description: US84103569_252182713014_S01_miRNA_107_Sep09_1_1


title: Platelet-ET-15

description: US84103569_252182713011_S01_miRNA_107_Sep09_2_1


title: Platelet-RT-14

description: US84103569_252182713011_S01_miRNA_107_Sep09_1_3


title: Platelet-RT-15

description: US84103569_252182713011_S01_miRNA_107_Sep09_2_2


title: Platelet-ET-18

description: US84103569_252182713013_S01_miRNA_107_Sep09_2_1


title: Platelet-RT-17

description: US84103569_252182713014_S01_miRNA_107_Sep09_1_2


title: Platelet-RT-16

description: US84103569_252182713013_S01_miRNA_107_Sep09_1_2


title: Platelet-ET-14

description: US84103569_252182713011_S01_miRNA_107_Sep09_1_4


title: Platelet-NO-20

description: US84103569_252182713013_S01_miRNA_107_Sep09_2_2


title: Platelet-NO-14

description: US84103569_252182712805_S01_miRNA_107_Sep09_2_2


title: Platelet-ET-17

description: US84103569_252182713013_S01_miRNA_107_Sep09_1_4


title: Platelet-NO-18

description: US84103569_252182713011_S01_miRNA_107_Sep09_2_4


title: Platelet-ET-16

description: US84103569_252182713011_S01_miRNA_107_Sep09_2_3


title: Platelet-RT-12

description: US84103569_252182712805_S01_miRNA_107_Sep09_2_1


title: Platelet-ET-13

description: US84103569_252182712806_S01_miRNA_107_Sep09_1_3


title: Platelet-ET-12

description: US84103569_252182712805_S01_miRNA_107_Sep09_2_3


title: Platelet-NO-16

description: US84103569_252182713011_S01_miRNA_107_Sep09_1_1


title: Platelet-ET-19

description: US84103569_252182713013_S01_miRNA_107_Sep09_2_4


title: Platelet-NO-13

description: US84103569_252182712805_S01_miRNA_107_Sep09_1_3


title: Platelet-ET-11

description: US84103569_252182712805_S01_miRNA_107_Sep09_1_4


title: Platelet-NO-15

description: US84103569_252182712806_S01_miRNA_107_Sep09_1_1


title: Platelet-RT-11

description: US84103569_252182712805_S01_miRNA_107_Sep09_1_2


title: Platelet-RT-13

description: US84103569_252182712805_S01_miRNA_107_Sep09_2_4


title: Platelet-ET-10

description: US84103569_252182712804_S01_miRNA_107_Sep09_2_4


title: Platelet-NO-12

description: US84103569_252182712805_S01_miRNA_107_Sep09_1_1


title: Platelet-ET-9

description: US84103569_252182712804_S01_miRNA_107_Sep09_2_2


title: Platelet-RT-9

description: US84103569_252182712804_S01_miRNA_107_Sep09_2_1


title: Platelet-RT-10

description: US84103569_252182712804_S01_miRNA_107_Sep09_2_3


title: Platelet-RT-3

description: US84103569_252182711958_S01_miRNA_107_Sep09_1_3


title: Platelet-RT-4

description: US84103569_252182711958_S01_miRNA_107_Sep09_1_4


title: Platelet-RT-5

description: US84103569_252182711958_S01_miRNA_107_Sep09_2_1


title: Platelet-ET-8

description: US84103569_252182712804_S01_miRNA_107_Sep09_1_4


title: Platelet-RT-6

description: US84103569_252182711958_S01_miRNA_107_Sep09_2_2


title: Platelet-RT-8

description: US84103569_252182711958_S01_miRNA_107_Sep09_2_4


title: Platelet-RT-7

description: US84103569_252182711958_S01_miRNA_107_Sep09_2_3


title: Platelet-NO-9

description: US84103569_252182712804_S01_miRNA_107_Sep09_1_1


title: Platelet-NO-11

description: US84103569_252182712804_S01_miRNA_107_Sep09_1_3


title: Platelet-NO-10

description: US84103569_252182712804_S01_miRNA_107_Sep09_1_2


title: zfs1∆582_Rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
Gene expression data of PolyA+ specific RNA
10357_582_zfs_Rep_3_(Yeast_2).mas5.CHP
10357_582_zfs_Rep_3_(Yeast_2).CEL

hyb_protocol: 5 μg of amplified biotin-aRNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0003.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: MAS5.0 data was obtained using the GeneChip® Command Console Software (AGCC; Version 1.1).

molecule: polyA RNA

organism: Schizosaccharomyces pombe

source_name: yeast

label_protocol: Twenty five ng of total RNA was amplified as directed in the NuGEN Ovation Pico WTA System protocol and labeled using the NuGEN Encore Biotin Module.

growth_protocol: Cultures were grown to mid-log phase in yeast extract with supplements medium (YES; MP Biomedicals, Solon, OH) at 30˚C

extract_protocol: Total cellular RNA was isolated from cells growing at mid-log phase using the RiboPure Yeast RNA Purification kit (Life Technologies, Grand Island, NY) following the manufacturer’s protocol.  PolyA+ specific RNA was isolated from the total RNA samples using the Oligotex Direct mRNA kit (Qiagen, Valencia, CA).  Total and polyA+ RNA samples were reverse transcribed into cDNAs using the High Capacity cDNA Kit protocol (Life Technologies, Grand Island, NY).

treatment_protocol: No treatment

tag: project

tag: strain

value: zfs1 null mutant


title: zfs1∆cbf12∆582_Rep2

description:
Gene expression data of PolyA+ specific RNA
10362_582_zfs_cbf_Rep_2_(Yeast_2).mas5.CHP
10362_582_zfs_cbf_Rep_2_(Yeast_2).CEL

value: zfs1cbf12 null mutant


title: zfs1∆cbf12∆582_Rep1

description:
Gene expression data of PolyA+ specific RNA
10361_582_zfs_cbf_Rep_1_(Yeast_2).mas5.CHP
10361_582_zfs_cbf_Rep_1_(Yeast_2).CEL


title: zfs1∆cbf12∆582_Rep3

description:
Gene expression data of PolyA+ specific RNA
10363_582_zfs_cbf_Rep_3_(Yeast_2).mas5.CHP
10363_582_zfs_cbf_Rep_3_(Yeast_2).CEL


title: cbf12∆582_Rep2

description:
Gene expression data of PolyA+ specific RNA
10359_582_cbf_Rep_2_(Yeast_2).mas5.CHP
10359_582_cbf_Rep_2_(Yeast_2).CEL

value: cbf12 null mutant


title: zfs1∆582_Rep2

description:
Gene expression data of PolyA+ specific RNA
10356_582_zfs_Rep_2_(Yeast_2).mas5.CHP
10356_582_zfs_Rep_2_(Yeast_2).CEL


title: cbf12∆582_Rep3

description:
Gene expression data of PolyA+ specific RNA
10360_582_cbf_Rep_3_(Yeast_2).mas5.CHP
10360_582_cbf_Rep_3_(Yeast_2).CEL


title: Platelet-RT-1

description: US84103569_252182711958_S01_miRNA_107_Sep09_1_1


title: Platelet-ET-7

description: US84103569_252182711957_S01_miRNA_105_Jan09_2_3


title: Platelet-RT-2

description: US84103569_252182711958_S01_miRNA_107_Sep09_1_2


title: Platelet-ET-6

description: US84103569_252182711957_S01_miRNA_105_Jan09_2_2


title: cbf12∆582_Rep1

description:
Gene expression data of PolyA+ specific RNA
10358_582_cbf_Rep_1_(Yeast_2).mas5.CHP
10358_582_cbf_Rep_1_(Yeast_2).CEL


title: Platelet-ET-5

description: US84103569_252182711957_S01_miRNA_105_Jan09_2_1


title: WT582_Rep2

description:
Gene expression data of PolyA+ specific RNA
10353_582_WT_Rep_2_(Yeast_2).mas5.CHP
10353_582_WT_Rep_2_(Yeast_2).CEL

value: WT


title: zfs1∆529_Rep4

description:
Gene expression data of PolyA+ specific RNA
9288_529_zfs_Rep_4_(Yeast_2).mas5.CHP
9288_529_zfs_Rep_4_(Yeast_2).CEL


title: zfs1∆529_Rep5

description:
Gene expression data of PolyA+ specific RNA
9289_529_zfs_Rep_5_(Yeast_2).mas5.CHP
9289_529_zfs_Rep_5_(Yeast_2).CEL


title: zfs1∆529_Rep3

description:
Gene expression data of PolyA+ specific RNA
9287_529_zfs_Rep_3_(Yeast_2).mas5.CHP
9287_529_zfs_Rep_3_(Yeast_2).CEL


title: zfs1∆582_Rep1

description:
Gene expression data of PolyA+ specific RNA
10355_582_zfs_Rep_1_(Yeast_2).mas5.CHP
10355_582_zfs_Rep_1_(Yeast_2).CEL


title: Platelet-ET-4

description: US84103569_252182711957_S01_miRNA_105_Jan09_1_4


title: WT582_Rep1

description:
Gene expression data of PolyA+ specific RNA
10352_582_WT_Rep_1_(Yeast_2).mas5.CHP
10352_582_WT_Rep_1_(Yeast_2).CEL


title: Platelet-NO-8

description: US84103569_252182711959_S01_miRNA_105_Dec08_2_4


title: Platelet-ET-2

description: US84103569_252182711957_S01_miRNA_105_Jan09_1_2


title: Platelet-ET-1

description: US84103569_252182711957_S01_miRNA_105_Jan09_1_1


title: Platelet-ET-3

description: US84103569_252182711957_S01_miRNA_105_Jan09_1_3


title: WT582_Rep3

description:
Gene expression data of PolyA+ specific RNA
10354_582_WT_Rep_3_(Yeast_2).mas5.CHP
10354_582_WT_Rep_3_(Yeast_2).CEL


title: Platelet-NO-5

description: US84103569_252182711959_S01_miRNA_105_Dec08_2_1


title: Platelet-NO-7

description: US84103569_252182711959_S01_miRNA_105_Dec08_2_3


title: Platelet-NO-6

description: US84103569_252182711959_S01_miRNA_105_Dec08_2_2


title: Platelet-NO-4

description: US84103569_252182711959_S01_miRNA_105_Dec08_1_4


title: zfs1∆529_Rep2

description:
Gene expression data of PolyA+ specific RNA
9286_529_zfs_Rep_2_(Yeast_2).mas5.CHP
9286_529_zfs_Rep_2_(Yeast_2).CEL


title: Platelet-NO-3

description: US84103569_252182711959_S01_miRNA_105_Dec08_1_3


title: zfs1∆529_Rep1

description:
Gene expression data of PolyA+ specific RNA
9285_529_zfs_Rep_1_(Yeast_2).mas5.CHP
9285_529_zfs_Rep_1_(Yeast_2).CEL


title: WT529_Rep3

description:
Gene expression data of PolyA+ specific RNA
9282_529_WT_Rep_3_(Yeast_2).mas5.CHP
9282_529_WT_Rep_3_(Yeast_2).CEL


title: Platelet-NO-2

description: US84103569_252182711959_S01_miRNA_105_Dec08_1_2


title: WT529_Rep2

description:
Gene expression data of PolyA+ specific RNA
9281_529_WT_Rep_2_(Yeast_2).mas5.CHP
9281_529_WT_Rep_2_(Yeast_2).CEL


title: WT529_Rep1

description:
Gene expression data of PolyA+ specific RNA
9280_529_WT_Rep_1_(Yeast_2).mas5.CHP
9280_529_WT_Rep_1_(Yeast_2).CEL


title: zfs1∆488_Rep1

description:
Gene expression data of PolyA+ specific RNA
8966_zfs1PolyA+_Rep1_(Yeast_2).mas5.CHP
8966_zfs1PolyA+_Rep1_(Yeast_2).CEL


title: WT529_Rep4

description:
Gene expression data of PolyA+ specific RNA
9283_529_WT_Rep_4_(Yeast_2).mas5.CHP
9283_529_WT_Rep_4_(Yeast_2).CEL


title: WT529_Rep5

description:
Gene expression data of PolyA+ specific RNA
9284_529_WT_Rep_5_(Yeast_2).mas5.CHP
9284_529_WT_Rep_5_(Yeast_2).CEL


title: WT488_Rep2

description:
Gene expression data of PolyA+ specific RNA
8964_WTPolyA+_Rep2_(Yeast_2).mas5.CHP
8964_WTPolyA+_Rep2_(Yeast_2).CEL


title: zfs1∆488_Rep2

description:
Gene expression data of PolyA+ specific RNA
8967_zfs1PolyA+_Rep2_(Yeast_2).mas5.CHP
8967_zfs1PolyA+_Rep2_(Yeast_2).CEL


title: zfs1∆488_Rep3

description:
Gene expression data of PolyA+ specific RNA
8968_zfs1PolyA+_Rep3_(Yeast_2).mas5.CHP
8968_zfs1PolyA+_Rep3_(Yeast_2).CEL


title: Platelet-NO-1

description: US84103569_252182711959_S01_miRNA_105_Dec08_1_1


title: WT488_Rep3

description:
Gene expression data of PolyA+ specific RNA
8965_WTPolyA+_Rep3_(Yeast_2).mas5.CHP
8965_WTPolyA+_Rep3_(Yeast_2).CEL


title: WT488_Rep1

description:
Gene expression data of PolyA+ specific RNA
8963_WTPolyA+_Rep1_(Yeast_2).mas5.CHP
8963_WTPolyA+_Rep1_(Yeast_2).CEL


title: Med20_vs_WT

city: Gothenburg

first: Claes

middle: M

last: Gustafsson

address: Medcinaregatan 9A

department: Department of Medical biochemistry and cell biology

country: Sweden

institute: Gothenburg University

description:
Med20_A
Med20_B
cDNA from WT Biological Rep 1-2, chip A
cDNA from WT mutnat Biological Rep 1-2, chip B

hyb_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

data_processing: Raw data (CEL files) was analyzed in affymetrix tilling array analysis software,The raw cel data were imported into TAS as two analysis treatment group -- mutant Vs WTcontrol.  two side test, bandwidth 150 . Probe match chosen was PM/MM(perfect match/mismatch). Finally, we analyzed the intensity to get the Bar format signal files.

source_name: med20 mutant fission yeast cells

label_protocol: Labeling was performed according to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

growth_protocol: Yeast cells were grown to mid-log phase in YEA rich medium

extract_protocol: RNA was isolated from mid-log phase cultures according to Xuefeng zhu et al. 2006 .  cDNA converted from RNA.

tag: genotype/variation

value: med20 mutant

source_name: WT fission yeast cells

value: wild type


title: Med20_Dcr1_vs_Dcr1

description:
Med20_Dcr1_A
Med20_Dcr1_B
cDNA from Dcr1  mutnat Biological Rep 1-2, chip A
cDNA from Dcr1 mutnat Biological Rep 1-2, chip B

scan_protocol: According to the GeneChip expression analysis technical manual that is available for download at www.affymetrix.com.

data_processing: Raw data (CEL files) was analyzed in affymetrix tilling array analysis software,The raw cel data were imported into TAS as two analysis treatment group -- dblmutant Vs mutant.  two side test, bandwidth 150 . Probe match chosen was PM/MM(perfect match/mismatch). Finally, we analyzed the intensity to get the Bar format signal files.

source_name: med20 and dcr1 double mutant fission yeast cells

value: med20 and dcr1 double mutant

source_name: Dcr1 mutant yeast cells

value: Dcr1 mutant


title: TMAO vs. O2

city: Baltimore

first: Priya

last: DasSarma

state: MD

address: 701 East Pratt Street, Suite 236

department: Microbiology

institute: UMB

description: O2vsTMAO_left20PMT.txt: Cy3=O2, Cy5=TMAO

hyb_protocol: Labeled cDNA targets were mixed with hybridization buffer (Agilent) and hybridized to microarray slides, which were assembled into a hybridization chamber (Agilent) for 17 h at 65°C in the dark.

scan_protocol: Slides were scanned for the Cy3 and Cy5 fluorescent signals using an Agilent DNA microarray scanner.

data_processing: Image processing was carried out using Agilent Feature Extraction software. Data from replicate arrays were analyzed using the Agilent microarray data analyzing software GeneSpring version 11.5.1.  Green and red signal intensities of the probes were imported using a custom-created single-color technology.

organism: Halobacterium salinarum NRC-1

source_name: wild type grown under standard conditions

label_protocol: Total RNA was combined with 500 ng of random hexamers (Qiagen) and reverse transcribed to Cy3- or Cy5-dCTP (Amersham Pharmacia)-labeled cDNA using SuperScript II RNase H_ reverse transcriptase (Invitrogen).

growth_protocol: Cells were grown to early log phase for all samples except the bat cultures, which were grown to log phase, in CM+ or modified CM+ media (see DasSarma, S., and E. M. Fleischmann. 1995. Halophiles. Cold Spring Harbor Laboratory Press, Plainview, N.Y.)

extract_protocol: RNA was isolated immediately after cell harvest using spin columns (Agilent, Palo Alto, Calif.).

treatment_protocol: Cells were chilled prior to nucleic acid extraction.

tag: growth condition

value: standard (O2)

source_name: wild type grown with TMAO

value: TMAO


title: DdmsR vs. dmsR+

description:
This Sample represents 2 merged dye-swap samples.

dmsr_30_PMT_left.txt: Cy3=dmsR knockout, Cy5=wild type
dmsr_30_PMT_right.txt: Cy3=wild type, Cy5=dmsR knockout

source_name: knockout of dmsR gene

value: dmsR knockout

label: Cy5, Cy3

source_name: wild type


title: Arg vs. O2

description:
This Sample represents 2 replicate samples.

ArgO2_left.txt: Cy3=arginine, Cy5=O2
10_15_right_ArgO2.txt: Cy3=arginine, Cy5=O2

source_name: wild type grown with arginine

value: arginine


title: Dbat vs. bat+

description:
This Sample represents 2 replicate samples.

bat1.txt: Cy3=wild type, Cy5=bat knockout
bat2.txt: Cy3=wild type, Cy5=bat knockout

source_name: knockout of bat gene

value: bat knockout


title: Arg vs. TMAO

description:
This Sample represents 2 replicate samples.

arg_TMAO_2_2_1_1.txt: Cy3=arginine, Cy5=TMAO
arg_TMAO_2_2_1_2.txt: Cy3=arginine, Cy5=TMAO


title: PCNSL patient 34

city: Kyoto

first: Ryuya

last: Yamanaka

address: 465 Kajii-cho, Kamigyoku

institute: Kyoto Prefectural University of Medicine

description: Tumor tissue from female patient, 68 years old, KPS 60, HD-MTX chemotherapy treated.

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The data were log2-transformed.

source_name: Human brain tumor tissue from PCNSL patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: brain tumor

value: primary central nervous system lymphoma (PCNSL)

value: female

tag: age

value: 68 years

tag: karnofsky performance status (kps)

tag: therapy

value: HD-MTX chemotherapy

tag: outcome

value: alive

tag: survival time

value: less than 1 year