title: PAO1planktonic_0mMCalcium_rep2

description: Exponential phase planktonic cells grown in BMM

hyb_protocol: For each Pseudomonas genome array (#900339, Affymetrix), labeled fragmented cDNA was hybridized to the arrays at 50oC for 16 h with constant rotational mixing at 60 rpm.  Washing and staining of the arrays was performed using the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Affymetrix CEL files were imported into FlexArray v1.6.1 for quality control, normalization, and data analysis. Microarray data was background corrected and normalized using the GC-RMA algorithm. ANOVA was used to compare expression levels with and without 10 mM calcium in planktonic cells.

source_name: Stationary phase planktonic cells

label_protocol: Biotinylated fragmented cDNA was prepared from 10 micrograms of total RNA according to Affymetrix's Prokaryotic Target Labeling Protocol  (GeneChip Expression Analysis Technical Manual; November, 2004).

growth_protocol: Cells were cultured planktonically for 18 hours in BMM at 37°C with shaking.

extract_protocol: Total RNA was extracted using a hot phenol method. Pelleted cells were suspended in 1.5 mls lysis buffer (0.15 M sucrose, 0.01 M sodium acetate, pH 4.5) and 1.5 mls 2% sodium dodecyl sulfate.  Following the addition of 3 mls of water-saturated phenol, the mixture was incubated for 5 minutes at 65°C with frequent vortexing. The mixture was centrifuged for 30 minutes at 4°C. The aqueous phase was precipitated overnight, washed, and resuspended in RNase-free water.  The RNA was treated with DNase1 and cleaned on an RNeasy column (Qiagen) following the manufacturer’s mini cleanup protocol.

tag: calcium level

value: 0 mM


title: PAO1planktonic_10mMCalcium_rep2

status: Public on Dec 02 2015

type: RNA

city: Bozeman

first: Kerry

middle: S

last: Williamson

state: Montana

address: 109 Lewis Hall

department: Microbiology and Immunology

country: USA

institute: Montana State University

label: Biotin

molecule: total RNA

organism: Pseudomonas aeruginosa

treatment_protocol: Cells were cultured in BMM with no added calcium, or with 10 mM added calcium.

value: 10 mM


title: PAO1planktonic_10mMCalcium_rep1


title: THP-1 infected with Mtb  R5 48 Hrs

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation using GeneSpring Gx v12.5

organism: Homo sapiens

source_name: THP-1 infected with Mtb

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

growth_protocol: Human THP-1 monocytic cells (ATCC TIB 202) were grown in RPMI-1640 supplemented with 10% FBS, L-glutamine, sodium carbonate and HEPES.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance to manufacturer's instructions. Quality control was performed with BioRad Bioanalyser EXPERION.

treatment_protocol: 6 million THP-1 monocytic cells were seeded in 6-well plates. Cells were allowed to differentiate with 20 ng/mL phorbol myristate acetate and were allowed to rest for 3 days. After 3 days, differentiated THP-1 were infected with Mtb and Mtb∆whiB3 mutant at an MOI of 10 for 4 h, followed by amikacin treatment for 2 h. After 2 h, cells were washed to remove any extracellular bacteria. For 0 h time point, cells were lysed and RNA was isolated. Cells of 12 h, 24 h, 36 h, 48 h time points were kept in fresh RPMI with 10% FBS till time point.

tag: infected strain

value: WT Mtb strain H37Rv

tag: time

value: 48 hrs

tag: cell line


title: dye260

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics suite 6.6 and  in STATA/SE 11.2.

organism: Mus musculus

source_name: retinae

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

extract_protocol: Trizol

tag: background strain

value: mixed breed

tag: age

tag: genotype/variation

value: wt

tag: tissue

value: retina


title: 5°C liver-BORN-replicate2

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

country: Germany

institute: Research Institute for Farm Animal Biology

description: Pool of 5 individual RNAs

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA (0.6 µg) in hybridization buffer was hybridized at 65 °C for 17 h to 8×60 K Whole Salmon Genome Oligo Microarrays (AMADID 049158; Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 10.7.3.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Oncorhynchus mykiss

source_name: 5°C liver-BORN

label_protocol: Five individual RNA samples from the same tissue (liver, gills, kidney), strain (Born or TCO) and temperature (5°C, 0°C) were pooled. 100 ng of each total RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Fish were grown under standard aquauculture conditions in brackish water. When a temperature of 5°C was reached the treatment was performed.

extract_protocol: Liver, kidney and gill were taken from BORN and TCO. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations and quantitative real-time PCR (qPCR) assays.

treatment_protocol: Fish were put in basins containing either 5°C or 0°C cold water and incubated for 30 minutes. Fish were randomly sampled using hand nets. Anaesthetization of fish with was done using phenoxyethanol prior to tissue sampling.

value: liver

tag: strain

value: BORN

tag: gender

value: mixed

value: 8 months


title: GS biological rep1 (array)

city: New York

first: Sebastian

last: Poliak

state: NY

address: 701 West 168st

department: Neuroscience and Biochemistry and Molecular Biophysics

institute: Columbia University

hyb_protocol: The Affymetrix GeneChip Hybridization control kit and GeneChip Hybridization, Wash, and Stain kit were used to hybridize samples to Affymetrix 430 2.0 GeneChip arrays, with fluidics performed on the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data analysis was performed in Partek Genomics Suite version 6.6 using the GC Robust Multi-array Average (GCRMA) normalization algorithm, followed by one-way ANOVA to analyze relative fold-enrichment in TA vs GS proprioceptors.  TAvsGS_affy_PartekAnalysis.txt is linked as a supplementary file on the Series record.

label: biotin

source_name: proprioceptors supplying GS muscle

label_protocol: cDNA was prepared from 5 µg of total RNA using the WT-Ovation One-Direct RNA Amplification system (Nugen)

growth_protocol: Dissection and purification of individual proprioceptors, following TA or GS ctb-555 muscle injections,  were done following Malin et al., 2007; and Hempel et al., 2007

extract_protocol: total RNA was extracted using a PicoPure RNA isolation kit (Arcturus).

value: GS muscle

tag: cell type

value: neuron


title: GS biological rep3 (array)


title: GS biological rep2 (array)


title: THP-1 Infected with MtbΔwhiB3  W1 48 Hrs

description: replicate 1

scan_protocol: Standard Illumina hybridization protocol

source_name: THP-1 Infected with MtbΔwhiB3

value: WhiB3 mutant of strain H37Rv


title: THP-1 Infected with MtbΔwhiB3  W2 48 Hrs

description: replicate 2


title: 0°C liver-BORN-replicate1

description: Pool of 5 individual RNAs

source_name: 0°C liver-BORN


title: PAO1planktonic_0mMCalcium_rep1


title: THP-1 infected with Mtb  R2 48 Hrs

description: replicate 1


title: THP-1 infected with Mtb  R5 24 Hrs

description: replicate 3

value: 24 hrs


title: 5°C liver-BORN-replicate1

description: Pool of 5 individual RNAs


title: dye259


title: THP- infected with Mtb  R4 24 Hrs

description: replicate 2

source_name: THP- infected with Mtb


title: THP- infected with Mtb  R3 48 Hrs

description: replicate 2


title: HOL7899

first: Klaus

last: Wimmers

department: Genome Biology

institute: FBN Dummerstorf

description: Tissue response to high energy diet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42°C on Affymetrix GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and Affymetrix Expression Console 1.1

organism: Bos taurus

source_name: Holstein steer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Energy rich feeding (Gotoh et al. 2009)

value: male

tag: breed

value: Holstein

value: Musculus longissimus dorsi


title: Cryopreserved 8 days differentiated cells,  1 day differentiation after thawing (sample 1)

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

hyb_protocol: 12.5μg of fragmented aRNA was hybridized to the Human Genome U133 plus 2.0 microarrays in the Genechip Hybridisation Oven-645 (Affymetrix, United Kingdom) for 16 h at 45º C.

scan_protocol: Arrays were washed and stained with phycoerythrin with Fluidics Station 450 and scanned using the Gene-Chip Scanner 3000 7G (Affymetrix, United Kingdom) according to the manufacturer's instructions.

data_processing: The quality control (QC) matrices were confirmed with expression console software  from Affymertix, USA. QC passed CEL files were further analyzed as described.

source_name: H9 hESC line (WA09 line)

label_protocol: 100ng total RNA was used for aRNA amplification with GeneChip® 3’ IVT Express Kit (Affymetrix, United Kingdom) according to the manufacturer’s instructions. After 16 h of biotinylated in vitro transcription, aRNA was purified using magnetic beads and 15μg of purified aRNA was fragmented with fragmentation buffer.

growth_protocol: hESCs were cultured in undifferentiated state according to  Thomson JA, Itskovitz-Eldor J, Shapiro SS, et al. Embryonic stem cell lines derived from human blastocysts. Science. 1998;282:1145-1147.

extract_protocol: Total RNA from 6 days differentiated hESCs in the presence and absence of benchmark concentration (BMC) of toxicants has been isolated with Trizol reagent (Invitrogen) and purified with the RNeasy Plus kit from Qiagen.

treatment_protocol: Immature dorsal root ganglia neurons have been generated as described in Chambers SM, Qi Y, Mica Y, et al. Combined small-molecule inhibition accelerates developmental timing and converts human pluripotent stem cells into nociceptors. Nat Biotechnol. 2012;30:715-720, with slide modifications.

value: female

value: cryopreserved 8 days differentiated cells, 1 days differentiaton after thawing


title: Cryopreserved 8 days differentiated cells,  1 day differentiation after thawing (sample 2)


title: THP-1 infected with Mtb  R3 24 Hrs

description: replicate 1

value: WT Mtb strain H37Rv


title: THP-1 infected with Mtb  R3 12 hrs

description: replicate 3

value: 12 hrs


title: Cryopreserved 8 days differentiated cells,  1 day differentiation after thawing (sample 3)


title: THP-1 infected with Mtb  R1 12  Hrs

description: replicate 1


title: Cryopreserved 8 days differentiated cells,  4 days differentiation after thawing (sample 1)

value: cryopreserved 8 days differentiated cells, 4 days differentiaton after thawing


title: THP- infected with Mtb  R2 12 Hrs

description: replicate 2


title: THP-1 infected with Mtb  R3 0 Hrs

description: replicate 3

value: 0 hrs


title: IB278

description: Tissue response to high energy diet

source_name: Japanese Black steer

value: Japanese Black


title: HOL7814

description: Tissue response to high energy diet


title: IB279

description: Tissue response to high energy diet


title: Cryopreserved 8 days differentiated cells,  4 days differentiation after thawing (sample 2)


title: HOL7620

description: Tissue response to high energy diet


title: Cryopreserved 8 days differentiated cells,  4 days differentiation after thawing (sample 3)


title: THP-1 infected with Mtb  R1 0 Hrs

description: replicate 1


title: Cryopreserved 8 days differentiated cells,  4 days differentiation after thawing (sample 4)


title: IB283

description: Tissue response to high energy diet


title: Cryopreserved 8 days differentiated cells, 7 days differentiaton after thawing (sample 1)

value: cryopreserved 8 days differentiated cells, 7 days differentiaton after thawing


title: THP- infected with Mtb  R2 0 Hrs

description: replicate 2


title: Cryopreserved 8 days differentiated cells,  1 day differentiation after thawing (sample 4)


title: 8 days differentiated hESCs (sample 1)

value: 8 days differentiated hESCs


title: 8 days differentiated hESCs (sample 4)


title: Cryopreserved 8 days differentiated cells, 7 days differentiaton after thawing (sample 3)


title: Cryopreserved 8 days differentiated cells, 7 days differentiaton after thawing (sample 4)


title: Muskel Rind S201

description: M. longissimus dorsi mRNA expression related to IMF content

source_name: M. longissimus dorsi

value: Holstein x Charolais F2

tag: imf content

value: high


title: Muskel Rind S192


title: undifferentiated hESCs (sample 1)

value: undifferentiated hESCs


title: 8 days differentiated hESCs (sample 3)


title: Muskel Rind S82

value: low


title: Muskel Rind S98


title: Muskel Rind S138


title: Muskel Rind S113


title: 8 days differentiated hESCs (sample 2)


title: Muskel Rind S134


title: Muskel Rind S84


title: Muskel Rind S141


title: undifferentiated hESCs (sample 4)


title: Muskel Rind 3


title: Muskel Rind 77


title: Muskel Rind S136


title: Mtb_2hr_pH 4.5 1

first: Amit

last: Singh

address: CV Raman Road

department: MCBL

institute: Indian Institute of Science

description: Gene expression of Mtb early log phase cultures after 2 hr treatment with 7H9-ADS medium of pH 4.5

hyb_protocol: The Gene Expression Hybridization Kit (Agilent Technologies, 5188-5279) and associated protocols were used (G4140-90040).  The purified cRNA (600ng) was fragmented with fragmentation blocking mix by incubating samples at 60°C for 30 minutes. Microarrays were prepared in Agilent Technologies Hybridization Chamber according to manufacturers instructions (G2534-90001). Once loaded into thehybridization chamber, samples were placed in thehybridization oven (Agilent Technologies, G2505-80085) and incubated for 17 hours at 65°C while rotating at setting 10. Following hybridization, samples were washed according to procedure described by Agilent Technologies.

scan_protocol: Microarray slides were scanned at the resolution of 5µm using Agilent Microarray scanner (G2565CA) with scan control software as per manufacturer's instructions (G2505-90020). Settings included Agilent HD_GX_1colour (61X21.6mm), TIFF 20 bit, and Photomultiplier tube (PMT) gain 100%. Scanned image displays were analyzed by quantifying the pixel density of each hybridization spot using the Agilent Feature Extraction software (v10.5). Local background signals were subtracted from the data automatically by this software and raw data was obtained.

data_processing: Normalization was done to 50th percentile of each sample and data transformation was done to median of all samples using GeneSpring Gx V 12.0 from Agilent Technologies

organism: Mycobacterium tuberculosis H37Rv

source_name: Mtb H37Rv, 2hrs, pH 4.5, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low RNA Input Quick Amplification Labelling kit (Agilent Technologies, G4140-90040) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mtb and MtbΔwhiB3 were seeded at 0.05 OD600 in 7H9-ADS medium and grown till early log phase of ~0.3.

extract_protocol: Gene expression from Treated cultures were fixed using Guanidine thiocyanate, pelleted and total RNA was isolated using FastRNA PRO blue kit (according to manufacturer's instructions). RNA was purified using Qiagen RNeasy plus kit according to manufacturer's instructions. DNAse treatment was done using Ambion TURBO DNA-free kit according to manufacturer's instructions. RNA quality was measured using Agilent Bioanalyzer.

treatment_protocol: Early log phase culture cells were taken. Mtb and MtbΔwhiB3 were treated with 7H9-Ty--ADS medium of pH 4.5. Control Mtb cultures were treated with 7H9-Ty-ADS medium

tag: treatment

value: Wild type strain of Mtb H37Rv

tag: growth phase

value: early log phase


title: Mtb_2hr_pH 4.5 2

source_name: Mtb H37Rv, 2hrs, pH 4.5, replicate 2


title: undifferentiated hESCs (sample 2)


title: Muskel Rind 222


title: Cryopreserved 8 days differentiated cells, 7 days differentiaton after thawing (sample 2)


title: undifferentiated hESCs (sample 3)


title: Gag-specific_CD8_T_cells_week20_rep2

city: Lincoln

first: Wuxun

last: Lu

state: NE

address: 4240 Fair ST

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

description:
R142W20
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 20 weeks after SIVΔnef vaccination

hyb_protocol: Labeled cDNA samples were hybridized in Affymetrix GeneChip Hybridization Oven 640 on GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 7G scanner.

data_processing: Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using RMA.

organism: Macaca mulatta

label_protocol: The cDNA samples were purified with QIAquick PCR Purification Kit (Cat# 28104, QIAGEN), and labeled with biotin using Encore Biotin Module (Cat# 4200-12, NuGEN).

growth_protocol: Rhesus macaques were vaccinated intravenously with SIVΔnef virus. At 3 (n=5) and 20 WPV (n=3), SIV Gag-specific CD8+ T cells were isolated from peripheral blood samples using tetramer staining and flow cytometry.

extract_protocol: Total RNAs were extracted from sorted cells using TRIzol (Life Technologies), followed by cDNA synthesis using Ovation Pico WTA System (Cat# 3300-12, NuGEN).

tag: protocol

value: SIVΔnef vaccination

value: 20 weeks post-vaccination

value: peripheral blood

value: Gag-specific CD8+ T cell

tag: genotype

value: adult


title: Muskel Rind 217

value: Musculus longissimus dorsi


title: MtbΔwhiB3_2hr_pH 4.5_2

description: Gene expression of MtbΔwhiB3 early log phase cultures after 2 hr treatment with 7H9-ADS medium of pH 4.5

source_name: MtbΔwhiB3, 2hrs, pH 4.5,  replicate 2

value: WhiB3 mutant strain of Mtb H37Rv


title: Gag-specific_CD8_T_cells_week20_rep3

description:
R434W20
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 20 weeks after SIVΔnef vaccination

value: female


title: Muskel Rind 196


title: Muskel Rind 176


title: Gag-specific_CD8_T_cells_week20_rep1

description:
R140W20
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 20 weeks after SIVΔnef vaccination


title: Mtb_2hr_normal pH_2

description: Gene expression of Mtb early log phase cultures in 7H9-ADS medium

source_name: Mtb H37Rv,2hrs,normal pH, replicate 2

value: normal pH


title: Muskel Rind 164


title: Muskel Rind 215


title: MtbΔwhiB3_2hr_pH 4.5_1

source_name: MtbΔwhiB3, 2hrs, pH 4.5,  replicate 1


title: Mtb_2hr_normal pH_3

source_name: Mtb H37Rv, 2hrs, normal pH, replicate 3


title: Muskel Rind 142


title: Mtb_2hr_normal pH_1

source_name: Mtb H37Rv,2hrs,normal pH, replicate 1


title: Gag-specific_CD8_T_cells_week3_rep5

description:
R434W3
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 3 weeks after SIVΔnef vaccination

value: 3 weeks post-vaccination


title: Gag-specific_CD8_T_cells_week3_rep2

description:
R137W3
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 3 weeks after SIVΔnef vaccination


title: Gag-specific_CD8_T_cells_week3_rep3

description:
R140W3
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 3 weeks after SIVΔnef vaccination


title: Gag-specific_CD8_T_cells_week3_rep4

description:
R142W3
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 3 weeks after SIVΔnef vaccination


title: Gag-specific_CD8_T_cells_week3_rep1

description:
R134W3
Gene expression data from peripheral blood SIV Gag-specific CD8+ T cells 3 weeks after SIVΔnef vaccination


title: R108_1 with array type Medgene -1.0stv1 from Affymetrix

status: Public on Dec 01 2015

city: evry

first: labrune

last: cecile

address: 2 rue gaston cremieux

country: France

institute: INRA

description: The experiment is designed to detect transcriptome differences between wild type and two fix minus (NF737 and MS240) mutant lines.

hyb_protocol: labelled extract quantity: 5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Medicago truncatula

label_protocol: labelling Biotin direct, amplification=yes, total RNA 50 ng.

growth_protocol: roots - In vitro in 12cm square plates using the BN medium. 16h day light, 24 °C

treatment_protocol: no treatment

value: wild type

value: 14 days

tag: dev. stage (boyes et al. plant cell 2001)

value: nodule


title: MS240_3 with array type Medgene -1.0stv1 from Affymetrix

value: mutant (ms240)


title: MS240_1 with array type Medgene -1.0stv1 from Affymetrix


title: MS240_2 with array type Medgene -1.0stv1 from Affymetrix


title: NF737_3 with array type Medgene -1.0stv1 from Affymetrix

value: mutant (nf737)


title: NF737_1 with array type Medgene -1.0stv1 from Affymetrix


title: HBL1 shFOXP1 26 - day 4 - mAdbID:98419

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description:
mAdb experiment ID: 98419
ABC DLBCL

hyb_protocol: Agilent Hybridization Other: According to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505B US45102888

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. Data are shown as the Log2 ratio (Cy5/Cy3). Genes with log2 values of ± 0.3 change in at least 5/12 microarray KD samples for each cell line were considered significantly modulated.
FeatureExtractor_Version: 9.5.3.1
Protocol_Name: GE2-v5_95_Feb07 (Read Only)

source_name: HBL1 shControl with DOX - day 4

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
TRIzol and RNeasy Kit
Other: Total RNA was extracted using TRIzol reagent (Invitrogen) followed by clean-up using RNeasy kits (Qiagen).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 4 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 4 timepoint.

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

tag: shRNA

value: shControl

tag: timepoint

value: day 4

source_name: HBL1 shFOXP1 26 with DOX - day 4

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 4 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #26 GGCGGTCCAACGGAGAGACGC. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 4 timepoint.

value: shFOXP1 26


title: NF737_2 with array type Medgene -1.0stv1 from Affymetrix


title: HBL1 shFOXP1 36 - day 2 - mAdbID:98317

description:
mAdb experiment ID: 98317
ABC DLBCL

source_name: HBL1 shFOXP1 36 with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 2 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #36 GACCTCGCCCACGCCCAGCAG. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 2 timepoint.

tag: cell line

value: shFOXP1 36

value: day 2

source_name: HBL1 shControl with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 2 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 2 timepoint.


title: HBL1 shFOXP1 42 - day 3 - mAdbID:98414

description:
mAdb experiment ID: 98414
ABC DLBCL

source_name: HBL1 shControl with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 3 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 3 timepoint.

value: day 3

source_name: HBL1 shFOXP1 42 with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 3 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #42 GCAGCAACAGTGGCATCTCAT. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 3 timepoint.

value: shFOXP1 42


title: HBL1 shFOXP1 36 - day 3 - mAdbID:98318

description:
mAdb experiment ID: 98318
ABC DLBCL

source_name: HBL1 shFOXP1 36 with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 3 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #36 GACCTCGCCCACGCCCAGCAG. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 3 timepoint.


title: HBL1 shFOXP1 26 - day 3 - mAdbID:98418

description:
mAdb experiment ID: 98418
ABC DLBCL

source_name: HBL1 shFOXP1 26 with DOX - day 3

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 3 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #26 GGCGGTCCAACGGAGAGACGC. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 3 timepoint.


title: HBL1 shFOXP1 36 - day 4 - mAdbID:98319

description:
mAdb experiment ID: 98319
ABC DLBCL

source_name: HBL1 shFOXP1 36 with DOX - day 4

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 4 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #36 GACCTCGCCCACGCCCAGCAG. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 4 timepoint.


title: HBL1 shFOXP1 42 - day 2 - mAdbID:98413

description:
mAdb experiment ID: 98413
ABC DLBCL

source_name: HBL1 shFOXP1 42 with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 2 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #42 GCAGCAACAGTGGCATCTCAT. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 2 timepoint.


title: HBL1 shFOXP1 26 - day 1 - mAdbID:98416

description:
mAdb experiment ID: 98416
ABC DLBCL

source_name: HBL1 shControl with DOX - day 1

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 1 day
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 1 timepoint.

value: day 1

source_name: HBL1 shFOXP1 26 with DOX - day 1

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 1 day
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #26 GGCGGTCCAACGGAGAGACGC. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 1 timepoint.


title: HBL1 shFOXP1 42 - day 1 - mAdbID:98412

description:
mAdb experiment ID: 98412
ABC DLBCL

source_name: HBL1 shFOXP1 42 with DOX - day 1

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 1 day
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #42 GCAGCAACAGTGGCATCTCAT. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 1 timepoint.


title: HBL1 shFOXP1 26 - day 2 - mAdbID:98417

description:
mAdb experiment ID: 98417
ABC DLBCL

source_name: HBL1 shFOXP1 26 with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 2 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #26 GGCGGTCCAACGGAGAGACGC. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 2 timepoint.


title: HBL1 shFOXP1 42 - day 4 - mAdbID:98415

description:
mAdb experiment ID: 98415
ABC DLBCL

source_name: HBL1 shFOXP1 42 with DOX - day 4

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 4 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #42 GCAGCAACAGTGGCATCTCAT. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 4 timepoint.


title: TMD8 shFOXP1 36 - day 3 - mAdbID:104017

description:
mAdb experiment ID: 104017
ABC DLBCL

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization. Data are shown as the Log2 ratio (Cy5/Cy3). Genes with log2 values of ± 0.3 change in at least 5/12 microarray KD samples for each cell line were considered significantly modulated.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: TMD8 shControl with DOX - day 3

source_name: TMD8 shFOXP1 36 with DOX - day 3


title: TMD8 shFOXP1 36 - day 4 - mAdbID:104018

description:
mAdb experiment ID: 104018
ABC DLBCL

source_name: TMD8 shControl with DOX - day 4

source_name: TMD8 shFOXP1 36 with DOX - day 4


title: HBL1 shFOXP1 36 - day 1 - mAdbID:98316

description:
mAdb experiment ID: 98316
ABC DLBCL

source_name: HBL1 shFOXP1 36 with DOX - day 1

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 1 day
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #36 GACCTCGCCCACGCCCAGCAG. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 1 timepoint.


title: R108_2 with array type Medgene -1.0stv1 from Affymetrix

treatment_protocol: no treatment


title: R108_3 with array type Medgene -1.0stv1 from Affymetrix


title: induced neurons from MRC5

type: genomic

city: Buffalo

first: Jian

last: Feng

address: 955 Main Street, Room 3102

department: Department of Physiology and Biophysics

institute: State University of New York at Buffalo

description: comparison of genomic DNA from induced neurons and its parental MRC5 cells

hyb_protocol: Prior to hybridization, the test and reference probes were combined in a hybridization mixture with the following components: 50 ug human fluorimetric Cot-1 (Invitrogen) 52 ul of aCGH Blocking Agent (Agilent) and 260 ul of 2X HI-RPM Hybridization Buffer (Agilent).  The hybridization mixture was then heated to 95ºC for 3 minutes and incubated for 30 minutes at 37ºC to block repetitive elements on the probe. A 65ºC hybridization was then performed to Agilent CGH Human 244K array using a hybridization chamber and hybridization oven (Agilent) set at a rotational speed of 20 rpm for 40 hours. After hybridization, slides were washed using Oligo aCGH Wash Buffer 1 and 2 (Agilent), and dried with an Acetonitrile (Sigma) wash  and a Stabilization and Drying Solution (Agilent) wash.

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C. Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1), the final normalized/processed data are NOT included in the LogRatio column of the Agilent Feature Extraction files.

data_processing: Agilent CytoGenomics software (version 2.0.6.0) was used for background correction, normalization and final log2 ratios using CGH default - Image v2.

molecule: genomic DNA

source_name: Test sample iN

label_protocol: 1μg of genomic DNA was fluorescently labeled using the SureTag Complete DNA Labeling System (Agilent). Initially, the DNA was denatured in the presence of the random primer at 99ºC for 10 minutes in a thermalcycler, and then quickly cooled to 4ºC. The tubes were transferred to ice and labeling occurred with the addition of SureTag Labeling master mix. Samples were then incubated for 2 hours at 37ºC in a thermalcycler. The unincorporated nucleotides were removed using Suretag purification columns (Agilent) and the labeled probe was eluted with a single 80 ul wash

growth_protocol: MRC-5 cells grew in DMEM containg 10% FBS and 2mM L-Glutamine

extract_protocol: Genomic DNA were extracted with QIAamp DNA mini kit(QIAGEN).

treatment_protocol:
MRC-5 cells were infected with lentiviruse encoding human ASCL1, Nurr1, Lmx1a, miR-124, and shP53 overnight, wash out and starvated in DMEM/F12 without FBS for 24h, then cultured in DMEM/F12 containing 1X N2, 1X B27, 1X NEAA, 0.2 mM Vitmine C, 20 ng/ml NGF, GDNF, and BDNF,
1ng/ml TGF-beta3, 1 μM dorsomorphin, 10 μM SB431542, 3 μM CHIR 99021 2 μM Purmorphamine, and 1ug/ml DOX for 6 days. Then  iN cells were cultured in medium without dorsomorphin, SB431542, CHIR 99021 2, Purmorphamine, and DOX until DNA were extracted.

value: induced neurons

source_name: reference sample MRC-5

value: parental


title: TMD8 shFOXP1 42 - day 4 - mAdbID:104014

description:
mAdb experiment ID: 104014
ABC DLBCL

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 4 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 4 timepoint.

source_name: TMD8 shFOXP1 42 with DOX - day 4


title: TMD8 shFOXP1 36 - day 2 - mAdbID:104016

description:
mAdb experiment ID: 104016
ABC DLBCL

source_name: TMD8 shControl with DOX - day 2

source_name: TMD8 shFOXP1 36 with DOX - day 2

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 2 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #36 GACCTCGCCCACGCCCAGCAG. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 2 timepoint.


title: TMD8 shFOXP1 36 - day 1 - mAdbID:104015

description:
mAdb experiment ID: 104015
ABC DLBCL

source_name: TMD8 shControl with DOX - day 1

source_name: TMD8 shFOXP1 36 with DOX - day 1


title: Muskel Rind 241

source_name: M. longissimus dorsi

value: Holstein x Charolais F2

value: Musculus longissimus dorsi

value: low


title: TMD8 shFOXP1 42 - day 2 - mAdbID:104012

description:
mAdb experiment ID: 104012
ABC DLBCL

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 2 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 2 timepoint.

source_name: TMD8 shFOXP1 42 with DOX - day 2


title: TMD8 shFOXP1 26 - day 2 - mAdbID:104008

description:
mAdb experiment ID: 104008
ABC DLBCL

source_name: TMD8 shFOXP1 26 with DOX - day 2


title: TMD8 shFOXP1 42 - day 3 - mAdbID:104013

description:
mAdb experiment ID: 104013
ABC DLBCL

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 3 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 3 timepoint.

source_name: TMD8 shFOXP1 42 with DOX - day 3


title: TMD8 shFOXP1 26 - day 1 - mAdbID:104007

description:
mAdb experiment ID: 104007
ABC DLBCL

source_name: TMD8 shFOXP1 26 with DOX - day 1


title: T47D cells T6 hours Rep 3

city: Barcelona

first: Roni

last: Wright

address: C/ Doctor Aiguader, 88

country: Spain

institute: CRG-Centre de Regulació Genòmica

description: T6 Rep 3

hyb_protocol: Cyanine-3 (Cy3)  and Cyanine-5 (Cy5) labeled cRNA was prepared from 500ng of total RNA using the Quick Am Labeling kit Two colour (Agilent 5190-0424) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.  Cy3- used to label the HURR sample (reference sample)  Cy5 – used to label the test samples  After fragmentation, 825 ng of labelled- Cy5 cRNA was combined with 825ng of labelled-Cy3 cRNA from the reference sampleand was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 5um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing:
Raw data was also extracted by GenePix software (.gpr files), normalized log2 intensity values
Data analysis was done using the .gpr files (raw data extracted with GenePix)

source_name: T47D cells

label_protocol: Quick Am labelling Kit two colour (Agiglent 5190-0424 as per manufactuers instructions, 500ng starting material

growth_protocol: T47D were seeding in RPM1 minus phenol red, 10% CHS FCS, 24 hours prior to hormone addition cells were starved RPM1 minus phenol red minus FCS.

extract_protocol: Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions

value: Breast

tag: time hormone (r5020) hours

value: no inhibitor

source_name: HURR reference sample

tag: sample type

value: Universal reference RNA


title: TMD8 shFOXP1 26 - day 3 - mAdbID:104009

description:
mAdb experiment ID: 104009
ABC DLBCL

source_name: TMD8 shControl with DOX - day 3

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: TMD8 shFOXP1 26 with DOX - day 3


title: T47D cells T6 hours Rep 3 treated 3AB

description: T6 Rep 3 3AB

value: inhibitor 3AB


title: T47D cells T0 hours  Rep 3 treated 3AB

description: T0 Rep 3 3AB


title: T47D cells T1 hours Rep 1

description: T1 Rep 1


title: T47D cells T1 hours Rep 1 treated 3AB

description: T1 Rep 1 3AB


title: T47D cells T0 hours  Rep 1 treated 3AB

description: T0 Rep 1 3AB


title: T47D cells T1 hours Rep 3 treated 3AB

description: T1 Rep 3 3AB


title: T47D cells T1 hours Rep 2 treated 3AB

description: T1 Rep 2 3AB


title: T47D cells T6 hours Rep 1

description: T6 Rep 1


title: T47D cells T6 hours Rep 2

description: T6 Rep 2


title: T47D cells T6 hours Rep 1 treated 3AB

description: T6 Rep 1 3AB


title: T47D cells T1 hours Rep 2

description: T1 Rep 2


title: T47D cells T6 hours Rep 2 treated 3AB

description: T6 Rep 2 3AB


title: T47D cells T0 hours  Rep 2 treated 3AB

description: T0 Rep 2 3AB


title: T47D cells T0 hours  Rep 3

description: T0 Rep 3


title: T47D cells T1 hours Rep 3

description: T1 Rep 3


title: T47D cells T0 hours  Rep 1

description: T0 Rep 1


title: TMD8 shFOXP1 26 - day 4 - mAdbID:104010

description:
mAdb experiment ID: 104010
ABC DLBCL

source_name: TMD8 shControl with DOX - day 4

value: shControl

value: day 4

source_name: TMD8 shFOXP1 26 with DOX - day 4

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 4 days
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing shRNA targeted to FOXP1. The sequence of the 21bp DNA stem of the shRNA used in the study was #26 GGCGGTCCAACGGAGAGACGC. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 4 timepoint.


title: RKO

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 °C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version 8.5.1). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA.

source_name: Colon cancer cell line

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

growth_protocol: total RNA

extract_protocol: Total RNA was isolated with Trizol (Invitrogen, breda, The Netherlands), according to the manufacturer's instructions. Total RNA was further analyzed on the bioanalyzer (Agilent) and only RIN values of 8 or above were included.

value: RKO

value: colon cancer

source_name: Reference

value: Blood

tag: reference

value: Pooled RNA


title: Caco2

tag: tissue


title: LIM1863


title: LS174T


title: SW1398


title: HT29


title: T47D cells T0 hours  Rep 2

description: T0 Rep 2


title: SW480


title: Colo320


title: PTHrP treatment, biological rep 1

city: Boston

first: Serkan

last: KIR

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Inst.

description: Gene expression data from primary white adipocytes

hyb_protocol: Following fragmentation, cRNA were hybridized at 45C to Affymetrix mouse genome 430A v2.0 arrays, according to established methods.

scan_protocol: Labeling, hybridization, and scanning were performed by the Dana-Farber Cancer Institute Microarray Core Facility using established methods.

data_processing: The data were normalized and analyzed using the dChip software.

source_name: primary white adipocytes treated with PTHrP

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

growth_protocol: Inguinal stromal-vascular (SV) fractions were obtained from 30-35 days-old male C57BL6 mice by the following procedure. Inguinal fat tissue was dissected, washed with PBS, minced and digested for 45 min at 37°C in PBS containing 10 mM CaCl, 2.4 U/mL dispase II (Roche), and 1.5 U/mL collagenase D (Roche). Digested tissue was filtered through a 100-μm cell strainer and centrifuged at 600g for 5 min to pellet the SV cells. These were then resuspended in adipocyte culture medium (DMEM/F12 plus glutamax (1:1; Invitrogen), pen/strep, and 10% FBS), filtered through a 40-μm cell strainer, centrifuged as above, resuspended in adipocyte culture medium and plated. The SV cells were grown to confluency for differentiation, which was induced by the adipogenic cocktail containing 1 μM dexamethasone, 5 μg/mL insulin, 0.5 μM isobutylmethylxanthine (DMI), and 1 μM rosiglitazone in adipocyte culture medium. 2 days after induction, cells were maintained in adipocyte culture medium containing 5 μg/mL insulin and 1 μM rosiglitazone. Starting at day 6, cells were maintained in adipocyte culture medium only.

extract_protocol: Total RNA was isolated with Trizol and purified using Qiagen RNEasy mini columns according to the manufacturer's instructions.

treatment_protocol: Cells were treated 8 days post differentiation with 100 ng/ml of PTH(1-34) or PTHrP(1-34) for 4 hours.

value: primary adipocytes

value: male

tag: strain


title: SW48


title: HCT15


title: Colo205


title: GGTase-Iβ deficient, biological rep2

city: Erlangen

first: Rocío

last: López Posadas

address: TRC, Schwabachanlage 12

department: Medicine Clinic 1

institute: University of Erlangen-Nuremberg

description: Pggt-Iβ floxed; VillincreERT2 positive

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneScan 3000 7G.

data_processing: Data were summarized, scaled and normalized while importing to Partek Genomics Suite 6.5; Background correction: GC-RMA Backgorung Correction; Normalization: Quantile Normalization; Summarization: Median Polish

source_name: Intestinal Epithelial Cells  (IECs) from KO mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: not applicable

extract_protocol: Extraction of total RNA was performed using the Qiagen RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: Mice were injected with 1 mg of tamoxifen during three consecutive days; IECs were isoalted on Day 6 after tamoyifen treatment starts

tag: background strain

value: (mixed, 129/SV and C57BL/6)

value: Intestinal Epitehlial Cells

value: Pggt-Ibeta floxed; VillincreERT2 positive


title: PTH treatment, biological rep 1

source_name: primary white adipocytes treated with PTH

tag: cell type

tag: gender


title: PTH treatment, biological rep 2


title: GGTase-Iβ deficient, biological rep3

description: Pggt-Iβ floxed; VillincreERT2 positive


title: Control group, biological rep 1

source_name: primary white adipocytes


title: HCT116


title: Control group, biological rep 3


title: PTHrP treatment, biological rep 2


title: PTH treatment, biological rep 3


title: PTHrP treatment, biological rep 3


title: Control group, biological rep 2


title: DMSO 6d biological rep1

city: Shanghai

first: Ming

last: Sun

address: 320 Yueyang Road

country: China

institute: Institute for Biological Sciences, Chinese Acadamy of Sciences

description: Gene expression data from DMSO 6d

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)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 (Cat#00-00212, Affymetrix, 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 MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: DMSO 6d

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Reprogramming cells were cultured in the mouse ESC medium consisting of DMEM supplemented with 15% FBS, L-glutamine, NEAA, sodium pyruvate, penicillin/streptomycin, β-ME, and 100 units/ml leukemia inhibitory factor.

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: Mouse ESC medium supplemented with 2 mg/ml dox was added to cultures to initiate the reprogramming.

value: Reprogramming cells

tag: reprogramming day

value: day 6

tag: genetic background


title: GGTase-Iβ deficient, biological rep1

description: Pggt-Iβ floxed; VillincreERT2 positive


title: CSA (10 mM) 6d  biological rep1

description: Gene expression data from CSA (10 mM) 6d

source_name: CSA (10 mM) 6d


title: DMSO 6d biological rep2

description: Gene expression data from DMSO 6d


title: CSA (10 mM) 3d  biological rep2

description: Gene expression data from CSA (10 mM) 3d

source_name: CSA (10 mM) 3d

value: day 3


title: floxed control, biological rep3

description: Pggt-Iβ floxed; VillincreERT2 negative

source_name: Intestinal Epithelial Cells  (IECs) from control mice

value: Pggt-Ibeta floxed; VillincreERT2 negative


title: Participant_13_baseline_outlier

city: La Jolla

first: Brinda

last: Rana

state: CA

address: 9500 Gilman

department: Psychiatry

institute: UCSD

description:
5626686021_K_Grn.idat
5626686021.sdf

hyb_protocol: Hybridization of labeled cRNA to the BeadChip, and washing and scanning were performed according to the manufacturer's instructions.

scan_protocol: BeadArrays were scanned using an Illumina BeadArray Reader. Scanner settings were set at a default for DirectHyb.

data_processing: Raw data were extracted using Illumina GenomeStudio Gene Expression Module v1.1. The data were transformed using variance-stabilizing transformation and normalized using robust spline normalization with Bioconductor package lumi in R. All the genes not detected in any of the samples were removed from the analyses.

source_name: leukocytes, baseline

label_protocol: Total RNA (100 ng per sample) was used for preparation of biotin-labeled targets (cRNA) using Illumina® TotalPrep™ RNA Amplification Kit (Life Technologies, Inc., Austin, TX) and one round of amplification. The cRNA yields were quantified by UV spectrophotometry and the distribution of transcript sizes was assessed using the Agilent Bioanalyzer 2100 capillary electrophoresis system.

extract_protocol: RNA was extracted using LeukoLOCK Total RNA isolation kit following manufacturer’s instructions (Ambion, Inc. Austin, TX). RNA was subsequently DNased using the on-column DNase digestion protocol from Qiagen, Inc. (QIAGEN, Germantown, MD). RNA quality was assessed by 260/280 ratio using Nanodrop 1000 (Thermo Scientific, Wilmington, DE) and by determining an RNA integrity number (RIN) using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: leukocytes

tag: time point

value: baseline

tag: Sex

tag: disease status

value: healthy


title: DMSO 3d biological rep2

description: Gene expression data from DMSO 3d

source_name: DMSO 3d


title: Participant_9_baseline_outlier

description:
5626686021_H_Grn.idat
5626686021.sdf


title: floxed control, biological rep2

description: Pggt-Iβ floxed; VillincreERT2 negative

tag: genotype


title: Participant_5_post_outlier

description:
5626686002_B_Grn.idat
5626686002.sdf

source_name: leukocytes, post-landing

value: post-landing


title: CSA (10 mM) 6d  biological rep2


title: CSA (10 mM) 3d  biological rep1


title: floxed control, biological rep1

description: Pggt-Iβ floxed; VillincreERT2 negative


title: Participant_1_onehr_post_outlier

description:
5626686021_G_Grn.idat
5626686021.sdf

source_name: leukocytes, one-hour post-landing

value: one-hour post-landing


title: Participant_10_onehr_post

description:
5626686001_D_Grn.idat
5626686001.sdf

value: female


title: Participant_15_onehr_post

description:
5626686059_K_Grn.idat
5626686059.sdf


title: Participant_20_onehr_post

description:
5626686059_F_Grn.idat
5626686059.sdf


title: Participant_12_onehr_post

description:
5626686021_A_Grn.idat
5626686021.sdf


title: Participant_13_onehr_post

description:
5626686002_H_Grn.idat
5626686002.sdf


title: Participant_6_onehr_post

description:
5626686008_B_Grn.idat
5626686008.sdf


title: Participant_14_onehr_post

description:
5626686059_D_Grn.idat
5626686059.sdf


title: Participant_7_onehr_post

description:
5626686002_E_Grn.idat
5626686002.sdf


title: Participant_9_onehr_post

description:
5626686002_J_Grn.idat
5626686002.sdf


title: DMSO 3d biological rep1

description: Gene expression data from DMSO 3d


title: Participant_8_onehr_post

description:
5626686008_I_Grn.idat
5626686008.sdf


title: Participant_14_baseline_outlier

description:
5626686002_A_Grn.idat
5626686002.sdf


title: Participant_4_onehr_post

description:
5626686001_J_Grn.idat
5626686001.sdf


title: Participant_10_post

description:
5626686008_J_Grn.idat
5626686008.sdf


title: Participant_14_post

description:
5626686001_K_Grn.idat
5626686001.sdf


title: Participant_18_post

description:
5626686059_L_Grn.idat
5626686059.sdf


title: Participant_13_post

description:
5626686059_E_Grn.idat
5626686059.sdf


title: Participant_7_post

description:
5626686021_I_Grn.idat
5626686021.sdf


title: Participant_16_post

description:
5626686021_F_Grn.idat
5626686021.sdf


title: Participant_20_post

description:
5626686001_E_Grn.idat
5626686001.sdf


title: RNA-30 days-neuron-PD patient LRRK2 G2019S mutation carrier 4

first: Mario

last: Ezquerra

state: Catalonia

address: Villarroel 170

department: Neurology

institute: Fundacio Clinic/IDIBAPS

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Chips were processed on an Affymetrix GeneChip Fluidics Station 450. Background adjustment by Robust Multi-Array (RMA) algorithm and quantile normalization was applied to probes intensities. Gene level expression were summarized from the corrected intensities using the 'core' exon annotations.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: 30-days RNA from IPSC-derived DAn LRRK5

label_protocol: Samples were enzymatically fragmented and biotinylated using the Affymetrix GeneChip WT sense target labelling and control reagents kit (Affymetrix)

growth_protocol: Keratinocytes or dermal fibroblasts were cultured using standard protocols from skin biopsy obtained from participating subjects [Sanchez-Danes et al., 2012]. Briefly, keratinocytes and/ or fibroblasts were transformed to induced pluripotent stem cells (iPSC) by retroviral transduction of three transcription factors (OTC4, SOX2 and KLF4). Subsequently, iPSC were differentiated into DAn specific growth factor medium supplementation (bFGF, FGF-8 and SHH) and lentiviral LMX1A delivery.Described in Sanchez-Danes et al., EMBO Mol Med. 2012 ;4(5):380-95. doi: 10.1002/emmm.201200215.

extract_protocol: RNA isolation from cell pellets was performed using the Allprep DNA RNA Protein Minikit from Quiagen following manufacter instructions. The RNA concentration was measured by analysing the absorbance at 260 nanometers and RNA with the Nanodrop 1000 Spectrophotometer (Thermo Fisher Scientific). RNA quality was evaluated by using the 2100 Bioanalyzer (Agilent). Isolated samples were stored at -80ºC..

treatment_protocol: no specific treatment of cells

tag: patient id2

tag: number of ipsc obtained to generate neurons

tag: family history of pd

value: yes

tag: age at onset (years)

tag: age at tissue collection (years)

tag: l-dopa response

value: good

tag: initial symptoms

value: tremor

value: iPSC-derived dopaminergic neuron

tag: disease state

value: Parkinson's disease


title: RNA-30 days-neuron-PD patient LRRK2 G2019S mutation carrier 3

source_name: 30-days RNA from IPSC-derived DAn LRRK4


title: RNA-30 days-neuron-idiopathic PD patient6

source_name: 30-days RNA from IPSC-derived DAn IPD

value: no

value: Bradykinesia


title: Participant_15_post

description:
5626686021_D_Grn.idat
5626686021.sdf

value: male


title: RNA-30 days-neuron-PD patient LRRK2 G2019S mutation carrier 1

source_name: 30-days RNA from IPSC-derived DAn LRRK2


title: TMD8 shFOXP1 42 - day 1 - mAdbID:104011

description:
mAdb experiment ID: 104011
ABC DLBCL

source_name: TMD8 shControl with DOX - day 1

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 5-10 ug/mL
Treatment time: 1 day
In-vitro treatment: All cells were stably transduced with a retrovirus expressing the bacterial tetracycline repressor (TETR) and the blasticidin resistance gene, followed by retroviral transduction with a Phoenix-E packaged pRSMX-PG TETR-inducible vector containing a scrambled control shRNA. Doxycycline (5-10 ug/mL) was applied for induction of shRNA expression. Cells were harvested for total RNA isolation at the day 1 timepoint.

tag: cell line

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

tag: shRNA

value: shControl

tag: timepoint

value: day 1

source_name: TMD8 shFOXP1 42 with DOX - day 1

value: shFOXP1 42


title: Participant_6_post

description:
5626686001_I_Grn.idat
5626686001.sdf

tag: cell type

value: leukocytes


title: Participant_4_post

description:
5626686008_A_Grn.idat
5626686008.sdf

value: healthy


title: RNA-30 days-neuron-PD patient LRRK2 G2019S mutation carrier 2

source_name: 30-days RNA from IPSC-derived DAn LRRK3

tag: gender


title: Participant_9_post

description:
5626686008_G_Grn.idat
5626686008.sdf

tag: time point

value: post-landing


title: Participant_15_pre

description:
5626686008_E_Grn.idat
5626686008.sdf

source_name: leukocytes, pre-boarding

value: pre-boarding

tag: Sex


title: RNA-30 days-neuron-idiopathic PD patient5

value: foot distonia


title: RNA-30 days-neuron-idiopathic PD patient4

value: female


title: Participant_2_post

description:
5626686002_F_Grn.idat
5626686002.sdf

tag: disease status


title: Participant_1_post

description:
5626686059_H_Grn.idat
5626686059.sdf


title: RNA-30 days-neuron-control4

source_name: 30 days-RNA from IPSC-derived DAn control

value: control


title: RNA-30 days-neuron-control3


title: RNA-30 days-neuron-idiopathic PD patient1

value: Tremor-Badykinesia


title: Participant_14_pre

description:
5626686008_H_Grn.idat
5626686008.sdf


title: Participant_20_pre

description:
5626686002_K_Grn.idat
5626686002.sdf


title: Participant_11_pre

description:
5626686002_D_Grn.idat
5626686002.sdf


title: RNA-30 days-neuron-control2

value: iPSC-derived dopaminergic neuron


title: RNA-30 days-neuron-control1


title: RNA-30 days-neuron-idiopathic PD patient3

value: good

value: Parkinson's disease


title: Participant_5_pre

description:
5626686001_H_Grn.idat
5626686001.sdf


title: Participant_9_pre

description:
5626686059_B_Grn.idat
5626686059.sdf


title: Participant_6_pre

description:
5626686002_G_Grn.idat
5626686002.sdf


title: Participant_10_pre

description:
5626686021_B_Grn.idat
5626686021.sdf


title: Participant_2_pre

description:
5626686001_A_Grn.idat
5626686001.sdf


title: Ama-KTT/M/2 non-toxic food replicate 5

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

description: Ama-KTT/M/2 is an isochromosome stock for chromosomes 2 and 3 derived from the Ama-KTT stock available from the Drosophila Species Stock Center at the University of California, San Diego as stock #14021 0231.07

hyb_protocol: Biotinylated cDNA was fragmented, then hybridized, washed, and stained using a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA, USA) according to the manufacturer's specifications.

scan_protocol: Arrays were post-processed on the AFX 450 Fluidics Station before they were scanned on an AFX GC3000 G7 Scanner (Affymetrix, Austin, TX, USA).

data_processing: Data were extracted from the raw images using the Affymetrix Expression Console v. 1.2 software.

organism: Drosophila melanogaster

source_name: ten late third instar larvae

label_protocol: Prior to labeling, total RNA samples were checked for purity and concentration, using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher, Waltham, MA, USA) and for integrity, using RNA 6000 Nano Chips in a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). cDNA for hybridization was synthesized and biotin labeled from 400 ng of total RNA using a MessageAmp Premier IVT kit (Ambion, Austin, TX, USA) according to the manufacturer's specifications.

growth_protocol: Freshly-hatched first-instar larvae of the sensitive Canton-S stock and the resistant Ama-KTT/M/2 stock were placed in groups of ten into 2 mL plastic test tubes (USA Scientific, Orlando, FL), containing 500 mg of food.  All larvae were raised until they reached the late third instar at 25° C, 70% humidity, and a 12:12 hour light:dark cycle.

extract_protocol: Groups of ten late, but still feeding third-instar larvae were randomly picked from across all tubes and flash-frozen in batches of ten in liquid nitrogen, each batch providing the RNA for one microarray chip. All samples were collected on the same morning. RNA extraction was performed without delay, using the RNeasy microarray tissue kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: To identify the genes that are inducible by α-amanitin, one group of Ama-KTT/M/2 larvae were raised on 1.5 mg of α-amanitin per g of food, which is the approximate LC50 concentration of this stock.  All other larvae were raised on non-toxic food.

tag: stock

tag: tissue

value: ten larvae

tag: food

value: non-toxic

tag: developmental stage

value: late third instar


title: Participant_12_pre

description:
5626686059_I_Grn.idat
5626686059.sdf

value: male


title: Ama-KTT/M/2 non-toxic food replicate 2


title: Ama-KTT/M/2 food containing the LC-50 of α-amanitin for Ama-KTT/M/2 replicate 6


title: Ama-KTT/M/2 food containing the LC-50 of α-amanitin for Ama-KTT/M/2 replicate 4


title: Participant_6_baseline

description:
5626686021_E_Grn.idat
5626686021.sdf

value: baseline


title: Participant_7_pre

description:
5626686001_F_Grn.idat
5626686001.sdf


title: Participant_15_baseline

description:
5626686002_I_Grn.idat
5626686002.sdf


title: Ama-KTT/M/2 food containing the LC-50 of α-amanitin for Ama-KTT/M/2 replicate 5


title: Ama-KTT/M/2 food containing the LC-50 of α-amanitin for Ama-KTT/M/2 replicate 2


title: Ama-KTT/M/2 food containing the LC-50 of α-amanitin for Ama-KTT/M/2 replicate 1


title: Ama-KTT/M/2 non-toxic food replicate 1


title: Canton-S non-toxic food replicate 4

description: Canton-S is available as stock #1 from the Bloomington Stock Center, Bloomington, Indiana

value: Canton-S


title: Participant_20_baseline

description:
5626686008_D_Grn.idat
5626686008.sdf

value: leukocytes


title: Participant_19_baseline

description:
5626686059_J_Grn.idat
5626686059.sdf

value: healthy


title: Ama-KTT/M/2 non-toxic food replicate 4


title: Participant_3_baseline

description:
5626686059_G_Grn.idat
5626686059.sdf


title: Canton-S non-toxic food replicate 5


title: Canton-S non-toxic food replicate 2


title: Participant_17_baseline

description:
5626686008_F_Grn.idat
5626686008.sdf


title: Ama-KTT/M/2 food containing the LC-50 of α-amanitin for Ama-KTT/M/2 replicate 3


title: Participant_8_baseline

description:
5626686001_B_Grn.idat
5626686001.sdf


title: RNA-30 days-neuron-idiopathic PD patient2

tag: patient id2

tag: number of ipsc obtained to generate neurons

tag: family history of pd

value: no

tag: age at onset (years)

value: tremor


title: Participant_2_baseline

description:
5626686008_K_Grn.idat
5626686008.sdf


title: Ama-KTT/M/2 non-toxic food replicate 3


title: Canton-S non-toxic food replicate 1


title: Participant_11_baseline

description:
5626686001_G_Grn.idat
5626686001.sdf


title: Participant_7_baseline

description:
5626686059_A_Grn.idat
5626686059.sdf


title: Canton-S non-toxic food replicate 3


title: TKO3

city: Kyoto

first: Peter

last: Carlton

state: Kyoto

address: Sakyo-ku, Yoshida Honmachi, iCeMS Complex 2

department: Institute for Integrated Cell-Material Sciences

country: Japan

institute: Kyoto University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tet1, Tet2, Tet3 knockout mouse (derived from BJ FF2 ES) sample#3

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Embryonic stem cells were maintained in standard 2i conditions at at 37 ºC in a humidified incubator with 5% CO2 on inactivated mouse embryonic feeder (MEF) cells. Media was exchanged daily and cells were split every 3-4 days at a ratio of 1:6. Prior to collection, embryonic stem cells were switched to feeder-free conditions (following standard MEF removal protocols) and grown on ES-quality matrigel (BD Biosciences).

extract_protocol: For each sample, one 35 mm dish of cells was trypsinized and pelleted. Cell pellets were washed twice with PBS before RNA was extracted using a RNeasy RNA extraction kit (Qiagen) with DNAse treatment as per the manufacturer's specifications. The quality and quantity of RNA was measured using a NanoDrop 2000 spectrophotometer.

value: ES cell

tag: genotype

value: Tet1,2,3 Knockout


title: TKO2

source_name: Tet1, Tet2, Tet3 knockout mouse (derived from BJ FF2 ES) sample#2


title: WT3

source_name: Wild-type mouse (BJ FF2 ES) sample#3

value: wild-type


title: WT2

source_name: Wild-type mouse (BJ FF2 ES) sample#2


title: WT1

source_name: Wild-type mouse (BJ FF2 ES) sample#1


title: ctrl1

city: Tokyo

first: Hiroyuki

last: Matsumura

state: Bunkyo-ku

address: Room 213, Chemistry East Building, Department of Chemistry, 7-3-1 Hongo

department: Graduate School of Science

institute: The University of Tokyo

description: Gene expressions in TAM injected WT HFSCs

hyb_protocol: 1.3 μg Cy3 labeled cDNA were fragmented, and hybridized at 65°C for 17 hr to an Agilent SurePrint G3 Mouse GE v2 8x60K Microarray (Design ID: 028005).

scan_protocol: After washing, microarrays were scanned using an Agilent DNA microarray scanner.

data_processing: For normalization of microarray data, intensity values of each scanned feature were quantified using Agilent feature extraction software version 10.7.3.1, which performs background subtractions. We only used features that were flagged as no errors (Detected flags) and excluded features that were not positive, not significant, not uniform, not above background, saturated or population outliers (Compromised and Not Detected flags).

source_name: TAM(tamoxifen 2mg for 5days, i.p.)injected WT HFSCs

label_protocol: Total RNA was isolated using a RNA easy micro Kit (Qiagen) according to the manufacturer’s instructions. cDNA samples were prepared from 1-10 ng RNA using the Ovation Pico WTA System V2 (NuGen, San Carlos, CA, USA) according to the manufacturer’s instructions. Amplified cDNAs were labeled with Cyanine 3 (Cy3) using a SureTag DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) following the manufacturer's instructions.

extract_protocol: HFSCs (CD34(Hi)/ITGA6(Hi)/ScaI(-)), IFE (ITGA6(Hi)/ScaI(Hi)) and total epidermal cells were harvested from young and from aged mice. Dissociated cells were FACS-sorted by FACC ariaII and reserved into Buffer RLT (Qiagen) by FACS aria II.

treatment_protocol: Tamoxifen i.p. injection (2mg/mice for 5days) or hair depilation by hand

tag: age

value: young (12w)

value: Wild Type

tag: strain


title: cKO1

description: Gene expressions in TAM injected Col17a1cKO(k14 promoter) HFSCs

value: Col17a1 cKO


title: TKO1

source_name: Tet1, Tet2, Tet3 knockout mouse (derived from BJ FF2 ES) sample#1


title: ctrl-pk1

description: Gene expressions in TAM injected WT HFSCs, plucking 3days

source_name: TAM injected WT HFSCs, plucking 3days


title: oHFSCs1

description: Gene expressions in aged HFSCs

source_name: Aged HFSCs

value: aged (22M>)


title: oIFE1

description: Gene expressions in aged IFEs

source_name: Aged IFEs


title: oHFSCs-pk1

description: Gene expressions in aged HFSCs, plucking 3days

source_name: Aged HFSCs, plucking 3days


title: ∆ryhB Aerobic

city: Madison

first: Patricia

middle: J

last: Kiley

state: WI

address: 420 Henry Mall, Room 1135 Biochemistry Building

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

hyb_protocol: ~0.6-1.5 ug of Cy3-labelled cDNA was hybridized to a custom-made E. coli K-12 MG1655 tiled genome microarray. Hybridization was performed overnight for ~17 hours at 42°C in a NimbleGen Hybridization System 4, according to the NimbleGen hybridization protocol.

scan_protocol: Hybridized tiling arrays were scanned using a GenePix 4000B microarray scannner (Axon Instruments). The PMT for 532 nm was adjusted so that the median fluorescence was just below 100.

data_processing:
Raw probe intensities were normalized across all samples using the Robust Multichip Average (RMA) algorithm in the NimbleScan software package (version 2.5).
RMA normalized probe data was uploaded into the Mochiview visualization software where data cooresponding to the plus and minus strands were subtracted to get a strand-specific probe intesenity per base as reported in the processed data files.

label: Cy3  monoreactive dye

organism: Escherichia coli str. K-12 substr. MG1655

label_protocol: 10 µg of RNA was reverse transcribed with amino-allyl dUTP and actinomycin D (Cho et. al, Nature Biotechnology 2009). Purified 1st-strand, amino-allyl labeled cDNA was coupled to Amersham Cy3 monoreactive dye (GE Healthcare) in 0.1 M sodium carbonate buffer for 1 hour, at room temperature, in the dark. The reaction was stopped with NH2OH.  The purified, labeled cDNAs were fragmented with DNase I (0.1 U per ug of cDNA) for 10 min at 37°C. DNase I was then inactivated at 95°C for 10 min; samples from RyhB- and Fur-RyhB- strains also included 0.85 mM EDTA in this reaction. Cy3-labelled cDNAs were precipitated and fragmentation was verified by running a 2% agarose gel.

growth_protocol: Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of ~0.3-0.35) in MOPS minimal glucose media containing 10 µM FeSO4.

extract_protocol: Total RNA was extracted using a hot phenol method (Khodursky et al, Methods in Molecular Biology 2003).

treatment_protocol: Cells were treated with a stop solution of phenol and ethanol (Khodursky et al, Methods in Molecular Biology 2003), spun down, and flash frozen and stored at -80°C.

tag: genotype/variation

value: lacking the small RNA RyhB

tag: culture condition

value: Aerobic cultures


title: yIFE1

description: Gene expressions in young Interfollicular epidermis (IFEs)

source_name: Young Interfollicular epidermis (IFEs)

value: young (8w)


title: ∆fur Aerobic A

value: lacking the transcription factor Fur


title: ∆fur ∆ryhB Anaerobic B

value: lacking the transcription factor Fur and the small RNA RyhB

value: Anaerobic cultures


title: oTotal-Epi1

description: Gene expressions in aged Total epidermis

source_name: Aged Total epidermis


title: cKO-pk1

description: Gene expressions in TAM injected Col17a1cKO(k14 promoter) HFSCs, plucking 3days


title: ∆fur ∆ryhB Aerobic B


title: ∆fur ∆ryhB Aerobic A


title: Wild-type Anaerobic B

value: wild type


title: ∆fur Anaerobic [IP vs nput]

hyb_protocol: Hybridization was performed overnight for ~17 hours at 42°C in a NimbleGen Hybridization System 4, according to the NimbleGen hybridization protocol.

scan_protocol: Arrays were scanned using the GenePix 4000B (Axon Instruments) microarray scanner at 532 nm (Cy3) and 635 nm (Cy5) with a pixel size of 5 µm. The PMT was adjusted until ~1% of the total probes were saturated for the fluorescence intensity of each dye used.

data_processing: NimbleScan software package, version 2.5 (Roche NimbleGen) was used to extract the scanned data, which was subsequently qunatile normalized using the statistical program R. The sample data table contains the log2 ratio of the IP/Input after data was quantile normalized.

source_name: IP ∆fur Anaerobic

label_protocol: DNA was amplified by linker-mediated PCR and labelled with Cy5 (IP) or Cy3 (input) dye.

growth_protocol: Cultures grown in MOPS minimal glucose media containing 10 µM FeSO4

extract_protocol:
Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C. Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.

tag: ip antibody

value: affinity purified anti-Fur antibody

source_name: Input ∆fur Anaerobic

tag: sample type

value: input control


title: ∆ryhB Anaerobic


title: ∆fur Anaerobic B


title: ∆fur Anaerobic A


title: ∆fur Aerobic B


title: Wild-type Anaerobic A


title: Peg(-0.5)_3

city: Lausanne

first: Silvia

middle: K.

last: Moreno-Forero

state: Vaud

address: Batiment Biophore, Unil Sorge

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description: Hot-phenol extraccion

hyb_protocol: The volume of the different samples was adjusted for the hybridization in order to add 60 ng of labelled Cy3-cDNA per array on the slide. Hybridization was performed at 65°C for 17 hours, after which slides were washed according to Agilent procedures and scanned. The fragmentation step (heating to 60°C for 30 minutes) was omitted.

scan_protocol: Microarray slides were scanned using an Agilent High-Resolution Microarray Scanner (G2505), immediately after hybridization using the One-Color microarray -based gene expression analysis protocol provided by Agilent (scan area 61x21.6mm XDRHi:100% XDRLo:10%). The AGILENT FEATURE EXTRACTION SOFTWARE was used to extract the signal intensities of the probes from the scanned images.

data_processing: The text data file was used as input in GeneSpring GX v12. Expression data were quantile normalized by GeneSpring and baseline transformed. All genes were filtered by expression and were retained when the signal intensity was above the 20th percentile in at least one of the samples.

label: Cyanine 3-dCTP

organism: Pseudomonas veronii 1YdBTEX2

source_name: Matric stress -0.5Mpa

label_protocol: Labelled cDNAs were produced in a reverse transcription reaction using cyanine-3-labeled dCTP. The labelled cDNA was purified with a MinElute PCR purification kit (Qiagen 28004). The percentage of incorporation of Cy-3-dCTP was calculated by the MICROARRAY function of the Nanodrop spectrophotometer.

growth_protocol: Pseudomonas veronii (1YdBTEX2) was cultured in 21C medium with succinate 5mM as carbon source at 30°C and 180 rpm until exponential phase (OD600= 0.3)

extract_protocol: After 30 min incubation samples were immediately filtered over a 0.2 µm membrane filter by vacuum suction. The filter with the cells was removed and frozen in liquid nitrogen. The filters were stored at -80°C until RNA isolation. RNA was extracted from frozen cells on filters with an acid-phenol method.

treatment_protocol: 10 ml of culture sample was added to 10 ml of 21CS medium  containing PEG8000 so as to obtain a final matric potential of -0.5 Mpa  or 10ml  of 21CS medium containing NaCl to obtain a final solute potential of -0.5Mpa and incubated for 30 min. Each treatment or control was run in independent replicates.

tag: media

value: 21C minimal medium with 5mM succinate and PEG8000 at -0.5Mpa


title: Peg(-0.5)_2

description: Hot-phenol extraccion


title: Inflamed, biological rep5

source_name: Intestinal Epithelial Cells  (IECs) from Crohn´s Disease (CD) patient

treatment_protocol: not applicable

value: Intestinal Epitehlial Cells (terminal ileum)


title: Wild-type Aerobic A


title: NaCl(-0.5)_4

description: Hot-phenol extraccion

source_name: Solute stress -0.5Mpa

value: 21C minimal medium with 5mM succinate and Nacl at -0.5Mpa


title: Peg(-0.5)_1

description: Hot-phenol extraccion


title: Inflamed, biological rep2


title: NaCl(-0.5)_3

description: Hot-phenol extraccion


title: ∆fur ∆ryhB Anaerobic A


title: yHFSCs-pk1

description: Gene expressions in young HFSCs, plucking 3days

source_name: Young HFSCs, plucking 3days


title: yTotal-Epi1

description: Gene expressions in young Total epidermis

source_name: Young Total epidermis


title: Inflamed, biological rep4


title: Wild-type Aerobic B


title: NaCl(-0.5)_1

description: Hot-phenol extraccion


title: NaCl(-0.5)_2

description: Hot-phenol extraccion


title: Control 5

description: Hot-phenol extraccion

source_name: Control culture for solute stress

value: 21C minimal medium with 5mM succinate (21CS)


title: Inflamed, biological rep3


title: yHFSCs1

description: Gene expressions in young HFSCs (hair follicle stem cells)

source_name: Young HFSCs (hair follicle stem cells)


title: Inflamed, biological rep1


title: Control 3

description: Hot-phenol extraccion


title: lymphoma_hoz_M

city: Turku

first: Jukka

last: Westermarck

state: Southwest Finland

address: Tykistökatu 6 B

country: Finland

institute: University of Turku/BTK

description:
Lymphoma cells isolated from spleen
KO_TKEM_206

hyb_protocol: Standard Agilent GE hybridization kit used in accordance with the prescribed protocol provided with the kit.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2565CA.  Scan profile: AgilentG3_GX_1Color

data_processing: The data were normalized using quantile normalization

source_name: spleen

label_protocol: Standard Agilent Low Input Quick Amp Labeling kit, one-color protocol (Product number 5190-2331) used in accordance with the prescribed protocol provided with the kit.

growth_protocol: TK13: Naïve B cell's enrichment from isolated spleens using the MACS B cell isolation kit (Miltenyi).  B-cells were subsequently activated (refer treatment protocol) ex vivo for 7 days.  TKEM:  Enriched Lymphoma cells isolated from mouse spleen were not cultured ex vivo.

extract_protocol: TK13: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit.  TKEM: RNA was extracted with Macherey-Nagel NucleoSpin® RNA isolation kit in accordance with the prescribed protocol provided with the kit.   Quality of all samples was controlled by Agilent 2100 bioanalyzer RNA 6000 Nano kit (Product number 5067-1511)

treatment_protocol: TK13: B-cells were activated with 1.25µg/ml antiCD40, 25ng/ml IL-4.   TKEM: No treatment was used.

value: C57BL/6Jx 129Ola x Emu-myc

value: homozygous

tag: mouse id

tag: gender

value: male


title: Control 2

description: Hot-phenol extraccion


title: Uninflamed, biological rep3

source_name: Intestinal Epithelial Cells  (IECs) from Healthy patient

tag: tissue


title: lymphoma_wt_F

description:
Lymphoma cells isolated from spleen
WT_TKEM_306

value: female


title: Uninflamed, biological rep2


title: Control 1

description: Hot-phenol extraccion


title: Uninflamed, biological rep4


title: OECM1-mCherry

city: Taipei

first: Tsai-Tsen

last: Liao

state: State...

address: No.201, Sec.2, Shih-Pai Rd. Peitou, Taipei, Taiwan, 11221, R.O.C

country: Taiwan

institute: Institute of Clinical Medicine

description: transfection: pmR-mCherry empty vector

hyb_protocol: Hybridization was performed according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

scan_protocol: Arrays were scanned with the Affymetrix GeneChip® Scanner 3000 7G and the data was extracted using Microarray Analysis Suite 5.0 (Affymetrix).

data_processing: We used the Affymetrix GeneChip Suite 5.0 software (MAS 5.0) to calculate raw expression values for each probe sets on the U133 2.0 oligonucleotide arrays.

source_name: Head and neck cancer cell line OECM1 transfected with pmR-mCherry empty vector

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (see complete protocol descriptions: http://www.affymetrix.com/support/technical/manual/expression_manual.affx)

growth_protocol: cultivated in RPMI + 10% fetal bovine serum

extract_protocol: Cells were lysed by adding 2 ml of trizol reagent (Invitrogen) and homogenized by passing through a syringe with a needle (26G). RNA was picked up in the aqueous phase following phase separation by chloroform. The RNA was then precipitate with isopropanol, washed with ethanol (75%), dissolved in DEPC-treated RNAse/DNAse free water and quantified by spectrophotometry.

treatment_protocol: OECM1 transfected with pmCherry-let7i or empty vector control.

tag: cell line


title: lymphoma_wt_M

description:
Lymphoma cells isolated from spleen
WT_TKEM_160


title: Uninflamed, biological rep1


title: hoz_rep2

description:
Naïve B cell's enrichment from isolated spleens using the MACS B cell isolation kit (Miltenyi).
KO_TK13_7B

value: C57BL/6Jx 129Ola


title: RetinoicAcid_vs_Saline_Rep8

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

country: United Kingdom

institute: Biomathematics & Statistics Scotland

description: Sample 8

hyb_protocol: For hybridisation, the Gene Expression Hybridisation Kit (Agilent Technologies) was used. Labelled cRNA was hybridised to SurePrint G3 Rat GE 8x60K microarray slides (Agilent Technologies) rotating at 65C for 17 hours.

scan_protocol: The arrays were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies) and then scanned on a SureScan High Resolution Scanner (Agilent Technologies).

data_processing:
The Bioncductor library limma was used for loess normalisation of the data; intensities were averaged across replicated spots (same Agilent ID) and then probes were tested for differential expression with the moderated t=test provided by limma
Values are normalised log2(treatment/control) values; for samples 1,3,6, 8 this identical to log2(Cy5/Cy3) values, the other arrays were dye swapped so for samples 2,4,5,7 we give log2(Cy3/Cy5 values)

organism: Rattus norvegicus

source_name: Saline (vehicle)_hypothalamus

label_protocol: 100ng of total RNA was used with the Low Input Quick Amp Labelling kit, two-colour (Agilent Technologies) following the manufacturer’s instructions. RNA was amplified in two steps to cRNA, incorporating Cy-3 and Cy-5 dyes, and was purified with RNeasy mini spin columns.

extract_protocol: Total RNA was extracted from 60 to 80mg of frozen hypothalamic tissue blocks including the arcuate nuclei using an RNeasy Mini Kit with on-column DNase treatment (Qiagen) following the manufacturer’s instructions. Quantity and quality of the resulting RNA was measured using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington, DE, USA) and a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), respectively.

tag: strain background

tag: injected with

value: Saline (vehicle)

value: hypothalamus

source_name: Retinoic Acid_hypothalamus

value: 10^-5 M all-trans Retinoic Acid


title: wt_rep1

description:
Naïve B cell's enrichment from isolated spleens using the MACS B cell isolation kit (Miltenyi).
WT_TK13_1B


title: RetinoicAcid_vs_Saline_Rep5

description: Sample 5


title: RetinoicAcid_vs_Saline_Rep6

description: Sample 6


title: wt_rep2

description:
Naïve B cell's enrichment from isolated spleens using the MACS B cell isolation kit (Miltenyi).
WT_TK13_15B


title: siSAFB1 repeat 5

city: Bristol

first: James

last: Uney

address: Medical School, University Walk

department: School of Clinical Sciences

institute: University of Bristol

scan_protocol: Affymetrix GeneChip® Scanner

data_processing:
AltAnalyze processes raw Affymetrix image files (CEL files) using the RMA algorithm.
Ensembl build: Assembly build-34    genome build: hg16    AltAnalyze version number information: AltAnalyze version 2.0.7
HuEx-1_0-st-v2

source_name: SHSY-5Y cells

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

growth_protocol: Standard cell culture in DMEM:F12 media

extract_protocol: RNA was extracted with Ambion mirVana™ miRNA Isolation Kit using total RNA protocol.

treatment_protocol: Transfection with siRNA, harvest after 24 hrs.

tag: disease

value: Neuroblastoma


title: RetinoicAcid_vs_Saline_Rep3

description: Sample 3


title: hoz_rep1

description:
Naïve B cell's enrichment from isolated spleens using the MACS B cell isolation kit (Miltenyi).
KO_TK13_6B


title: RetinoicAcid_vs_Saline_Rep2

description: Sample 2


title: RetinoicAcid_vs_Saline_Rep4

description: Sample 4


title: OECM1-let7i

description: transfection: pmR-mCherry-let7i

source_name: Head and neck cancer cell line OECM1 transfected with pmCherry-let7i


title: siSAFB1 repeat 4


title: siControl repeat 3

description: siControl


title: T47D cells T6 hours Rep 2 treated TA

description: Gene expression after 24 hours starvation and 6 hours R5020, presence TA

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing:
The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: T47D cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions

treatment_protocol: Cells were treated with R5020 for 6 hours.

value: breast

tag: treatment

value: TA

tag: time hormone (r5020) hours


title: RetinoicAcid_vs_Saline_Rep1

description: Sample 1


title: siSAFB1 repeat 6


title: RetinoicAcid_vs_Saline_Rep7

description: Sample 7


title: T47D cells T6 hours Rep 3 treated TA


title: T47D cells T6 hours Rep 1 treated TA


title: lymphoma_hoz_F

description:
Lymphoma cells isolated from spleen
KO_TKEM_396

tag: genotype


title: Control 4

description: Hot-phenol extraccion


title: T47D cells T0 hours Rep 2 treated TA

description: Gene expression after 24 hours starvation presence TA


title: T47D cells T0 hours Rep 1 treated TA


title: T47D cells T0 hours Rep 3 treated TA


title: T47D cells T6 hours Rep 3 treated NUDIXsi

description: Gene expression after 24 hours starvation and 6 hours R5020, presence NUDIX inhibition

value: NUDIX5 specific siRNA


title: T47D cells T0 hours Rep 2 treated NUDIXsi

description: Gene expression after 24 hours starvation NUDIX5 inhibition


title: T47D cells T6 hours Rep 2 treated NUDIXsi