title: Patient with Mastitis, Time 0 (initial), number MR06

description:
Sample name: Mastitis-MR06-I
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. control


title: Patient with Mastitis + probiotic, Time 21 days (final), number TP32

status: Public on Jan 21 2015

type: RNA

city: Espinardo

first: María-Teresa

last: García-Conesa

state: Murcia

address: Campus de Espinardo

department: Quality, Safety and Bioactivity of Plant Foods

country: Spain

institute: CEBAS-CSIC

description:
Sample name: Mastitis-TP32-F
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. Probiotic group. Time 21 days (final expression levels).

hyb_protocol: Following fragmentation, 12 μg RNA were hybridized for 16 hr at 45ºC 60 rpm on GeneChip PrimeView Human Gene Expression Array (Affymetrix 901837) ( Hybridization Oven 645). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (Affymetrix Protocol FS450_0002).

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

data_processing:
Data were analyzed with Robust MultiChip Average (RMA) using CEL files obtained from GeneChip Command Console (AGCC) and Affymetrix Expression Console Software (EC) (Affymetrix).
Stadistics and pathway analysis were generated with Partek Genomics Suite 6.6 and Partek Pathway.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Somatic cells isolated from breast-milk from patient with mastitis. Probiotic treatment. Time 21 days (final expression levels).

label_protocol: Biotinylated cRNA was prepared according to the One-Cycle target IVT labeling Affymetrix protocol from 0.1 μg total RNA GeneChip 3 ÍVT Express Kit (Affymetrix PN 702646 Rev 8, 2010)

growth_protocol: Female patients' breast milk was processed within 4 h after extraction and used to isolate somatic cells by centrifugation.

extract_protocol: Total RNA was isolated using the AllPrep® DNA/RNA/Protein Mini kit (Qiagen) according to the manufacturer's instructions. RNA was eluted in RNAse free water and the quality and quantity were measured in a ND-1000 spectrophotometer (NanoDrop®). Samples were aliquoted and stored at –80ºC until analysis. Purity was reevaluated measuring the RNA Integrity Number (RIN) algorithm and only those with a RIN value > 6 were further selected for microarray analyses.

treatment_protocol: RNA was prepared from breast-milk isolated somatic cells obtained at day 0 (initial) and day 21 (final) following the consumption of a strain of a probiotic from the following groups:i) Mastitis, n=14 arrays (7 patients with mastitis); ii) Healthy, n=6 arrays (3 healthy volunteers)

tag: individual

value: mastitis patient

tag: treatment

value: probiotic

tag: cell type

value: Somatic cells from breast milk


title: Human Colonic Mucin from the left colon of Healthy controls HC_33_LEFT

city: Dublin 4

first: Aine

middle: C

last: Balfe

address: Belfield

department: School of Medicine and Medical Science

country: Ireland

institute: University College Dublin

hyb_protocol: Affymetrix GeneChip WT terminal labelling and hybridisation kit- A hybridisation cocktail containing 1.7µl Control Oligonucleotide B2 (3nM), 5µl 20x Eukaroytic Hybridisation Controls, 7µl 2x Hybridisation Mix, 73µl Nuclease Free water was prepared according to manufactures instructions for 169 Format Array type. The hybridisation cocktail was incubated at 99°C for 5 minutes, cooled to 45°C for five minutes and added to 27µl of the fragmented single-strand cDNA.

scan_protocol: Affymetrix GeneChip® Scanner 3000

data_processing: Normalisation of global data was performed through RMA pre-processing, within the Bioconductor Oligo package

source_name: Human Colonic Mucin from Healthy controls

label_protocol: Affymetrix GeneChip WT terminal labelling and hybridisation kit- A master mix containing  5X TdTBuffer, TdT and DNA Labeling reagent was prepared and 15 μL was alliquoted into the 0.2 mL strip tubes containing the 45 μL of Fragmented Single-Stranded cDNA

extract_protocol: Qiagen Rneasy Fibrous Tissue Kit

tag: tissue source

value: Colon

tag: disease state

value: Healthy controls

tag: colonic location

value: Left


title: Human Colonic Mucin from the transverse colon of Healthy controls HC_33_TRANS

value: Transverse


title: neutrophils isolated from patient 6

type: genomic

city: OKC

first: Jonathan

middle: Daniel

last: Wren

state: OK

address: 825 NE 13th St

department: Arthritis & Clinical Immunology

country: USA

institute: Oklahoma Medical Research Foundation

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
Following multiple quality control measures, probe intensity values were normalized and used to determine the average methylation level on each methylation site in each sample (beta value or β). Probes that include a genetic variant within the first 10bp region of the 3’ end of the probe, and probes that had a detection P value (detection above background) of ≥0.05 were excluded from the analysis. Differentially methylated sites between groups were determined, and defined as methylation sites with an absolute difference in beta value (delta beta or Δβ) of at least 0.1 and that remained significant (P<0.01) after correction for multiple testing using a Benjamini and Hochberg false discovery rate of 0.05
Unmethylated and methylated signal intensities in Amr_raw_methylation_data_SLE_neutrophils.txt

label: Cy3 and Cy5

molecule: genomic DNA

source_name: neutrophils

label_protocol: DNA was extracted from each sample using the DNeasy Blood and Tissue Kit (Qiagen, Valencia, CA), then bisulfite-converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) for DNA methylation studies.

growth_protocol: N/A (patient-derived samples)

extract_protocol: Fresh peripheral blood samples (25 ml) were collected and density gradient centrifugation (Ficoll) was used to collect PBMCs. LDGs were then isolated from PBMCs using indirect labeling and magnetic bead separation with the following antibodies: anti-CD3, anti-CD7, anti-CD19, anti-CD79b, anti-CD56, anti-MHCII, anti-CD86 and anti-CD235a. LDG purity was confirmed by flow cytometry using forward and side scatter profiles and was over 95% in all samples. Neutrophils were extracted from the granulocyte layer after Ficoll density gradient centrifugation, following previously described protocols

treatment_protocol: Bisulfite DNA sequencing on selected differentially methylated CG sites was performed to validate the results obtained from the Infinium HumanMethylation450 BeadChip arrays. One differentially methylated CG site in MX1 was selected for validation. Primers were designed using Sequenom's EpiDesigner online tool to include this CG site and an additional 20 CG sites in its vicinity. Primer quality was verified using Premier Biosoft’s Netprimer online tool (Sequenom, San Diego, CA). The following primers were used: forward 5’-TTTAGTGGATGTTATGTTTGGGGT-3’, reverse 5’-CACTACTACCTACCAAAACCCCTAAA-3’. PCR was performed on a Bio-Rad T100 (Bio-Rad, Hercules, CA) using ZymoTaq one-step master mix (Zymo, Orange, CA). The cycling conditions were as follows: 95°C for 10 min followed by 40 cycles of 95°C for 30 seconds, then 58.3°C for 40 seconds, then 72°C for 1 min, followed by 72°C for 7 min. Each PCR product was confirmed with a small aliquot by 2% agarose gel electrophoresis. The remainder of the PCR product was then purified and sequenced using an Applied Biosystems 3730 XL sequencer. Sequencing trace files were then used to calculate the percentage of cytosine methylation on each CG site using ESME software package (Epigenomics AG, Berlin).

tag: age

tag: Sex

value: female

value: Lupus patient

value: lupus neutrophils


title: Patient with Mastitis + probiotic, Time 21 days (final), number MM35

description:
Sample name: Mastitis-MM35-F
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. Probiotic group. Time 21 days (final expression levels).


title: neutrophils isolated from control 4

value: control

value: normal neutrophils


title: Human Colonic Mucin from the rectum of Healthy controls HC_33_RECT

value: Rectum


title: neutrophils isolated from patient 8


title: neutrophils isolated from control 5


title: Human Colonic Mucus from the caecum of Healthy controls  HC_33_CAEC

value: Caecum


title: Patient with Mastitis, Time 0 (initial), number ML28

description:
Sample name: Mastitis-ML28-I
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. control

source_name: Somatic cells isolated from breast-milk from patient with mastitis. control


title: Patient with Mastitis + probiotic, Time 21 days (final), number BM01

description:
Sample name: Mastitis-BM01-F
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. Probiotic group. Time 21 days (final expression levels).


title: Patient with Mastitis + probiotic, Time 21 days (final), number EM36

description:
Sample name: Mastitis-EM36-F
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. Probiotic group. Time 21 days (final expression levels).


title: Patient with Mastitis + probiotic, Time 21 days (final), number EM18

description:
Sample name: Mastitis-EM18-F
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. Probiotic group. Time 21 days (final expression levels).


title: Patient with Mastitis, Time 0 (initial), number BM01

description:
Sample name: Mastitis-BM01-I
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. control


title: Patient with Mastitis, Time 0 (initial), number EM18

description:
Sample name: Mastitis-EM18-I
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. control


title: Patient with Mastitis + probiotic, Time 21 days (final), number ML28

description:
Sample name: Mastitis-ML28-F
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. Probiotic group. Time 21 days (final expression levels).


title: GSK126.2

status: Public on Jan 20 2015

city: Philadelphia

first: Louise

last: Showe

state: PA

address: 3601 Spruce St

institute: The Wistar Institute

description:
inhibition of EZH2 by GSK126
SAMPLE 8

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

source_name: OVISE cell line, GSK126 treated

label_protocol: Biotin Labeling of RNA at 400ng with Ambion Illumina® TotalPrep RNA Amplification Kit

growth_protocol: ARID1A mutated clear cell ovarian cancer OVISE cells restored for wild type ARID1A expression or treated with 5μM GSK126 were cultured in 3D using Matrigel.

extract_protocol: Extraction using trizol, Rneasy clean-up and Dnase I treated

treatment_protocol: Matrigel media was treated with either vehicle control DMSO, 1 ug/mL doxycycline to induce wild type ARID1A expression or 5μM GSK126 to inhibit EZH2

tag: cell line

tag: condition

value: EZH2 inhibited

tag: batch

value: batch 2


title: Patient with Mastitis, Time 0 (initial), number EM36

description:
Sample name: Mastitis-EM36-I
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. control


title: GSK126.3

description:
inhibition of EZH2 by GSK126
SAMPLE 9

value: ARID1A mutated clear cell ovarian cancer OVISE

value: batch 3


title: GSK126.1

description:
inhibition of EZH2 by GSK126
SAMPLE 7

value: batch 1


title: low-density granulocytes isolated from patient 4

source_name: low-density granulocytes

value: lupus low-density granulocytes


title: neutrophils isolated from patient 4


title: neutrophils isolated from control 2


title: ARID1A.2

description:
restored expression of ARID1A
SAMPLE 5

source_name: OVISE cell line, ARID1A restored

value: ARID1A induced


title: DMSO.1

description:
control
SAMPLE 1

source_name: OVISE cell line, DMSO treated

value: DMSO


title: DMSO.3

description:
control
SAMPLE 3


title: DMSO.2

description:
control
SAMPLE 2


title: C791

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

institute: IDIBAPS

description: patient reference in corresponding publication: P4

hyb_protocol: Labelled cRNAs were hybridised to the  Agilent Human SurePrintGE, 8x60K according to manufacturer´s instructions

scan_protocol: The arrays were washed, dried by centrifugation and scanned on an Agilent G2565BA microarray scanner at 100% PMT and 5 μm resolution

data_processing: Bioconductor limma package, using background correction (normexp) and quantiles normalization between arrays for final values

label_protocol: RNA (500 ng) was labeled using Agilent's Low Input RNA Labeling Kit, which involves reverse transcribing the mRNA in the presence of T7-oligo-dT primer to produce cDNA and then in vitro transcribing with T7 RNA polymerase in the presence of Cy3-CTP

extract_protocol: Total RNA was extracted from skeletal muscle biopsies with Qiagen (Qiagen, Hilden, Germany) RNeasy Fibrous Tissue mini kit following the manufacturer’s instructions

tag: tissue

value: skeletal muscle

tag: gender

value: male

value: 2 years

tag: sample type

value: mtDNA depletion


title: C774

description: patient reference in corresponding publication: P3


title: ARID1A.3

description:
restored expression of ARID1A
SAMPLE 6


title: ARID1A.1

description:
restored expression of ARID1A
SAMPLE 4


title: 04B-1864

description: patient reference in corresponding publication: P6

value: 7 years

value: mtDNA deletion


title: Tk2-02

description: patient reference in corresponding publication: P2

value: 3 years


title: B08-4721

description: patient reference in corresponding publication: *

value: 5 years

value: mitochondrial myopathy


title: B09-958

value: female


title: B05-9935

description: patient reference in corresponding publication: P8

value: 15 years


title: B08-2833

description: patient reference in corresponding publication: P10

value: 7 months


title: neutrophils isolated from control 1

value: control

value: normal neutrophils


title: N10-54

description: patient reference in corresponding publication: C4

source_name: Control

value: 1 year

value: normal muscle


title: neutrophils isolated from patient 2

value: lupus neutrophils


title: Tk2-01

description: patient reference in corresponding publication: P1

value: skeletal muscle


title: 00B-1337

description: patient reference in corresponding publication: P7

value: 30 years


title: neutrophils isolated from control 3


title: low-density granulocytes isolated from patient 3

value: Lupus patient

value: lupus low-density granulocytes


title: 00B-2526

description: patient reference in corresponding publication: P5

source_name: UCMD

value: 9 years

value: Ullrich Congenital Muscular Dystrophy


title: neutrophils isolated from patient 3


title: 06B-4168

value: male

value: 3 years


title: low-density granulocytes isolated from patient 2


title: Patient with Mastitis, Time 0 (initial), number MM35

description:
Sample name: Mastitis-MM35-I
Gene expression data from breast-milk somatic cells isolated from female patient with mastitis. control

value: mastitis patient

value: Somatic cells from breast milk


title: 96B-756

value: 5 years

value: mtDNA deletion


title: neutrophils isolated from patient 1

value: female


title: B07-2710


title: 98B-821

value: 5  years


title: B09-4528


title: 00B-2100

value: 7 years


title: 99B-928

description: patient reference in corresponding publication: CMD3

value: 14 years

value: Congenital Muscular Dystrophy


title: Control-2

description: patient reference in corresponding publication: C2

value: skeletal muscle

value: 13 years

value: normal muscle


title: low-density granulocytes isolated from patient 1

value: Lupus patient

value: lupus low-density granulocytes


title: DNA_methylation_BS_spermatozoa

type: SRA

city: Bethesda

first: Ian

last: Fingerman

state: MD

address: 45 Center Dr.

department: NCBI Epigenomics

institute: National Institutes of Health

description: DNA methylation, testis derived spermatozoa (average of 2 experiments)

library_source: genomic

data_processing:
For each tissue type, input tracks were selected based on the following criteria. Experiments from the Roadmap Epigenomics datasets were pooled, based on body site, tissue or cell type.  Donor age was weighed and sample data from adults was segregated from those of fetal or neonatal.  Donor sex was not taken into account, so some cases the track average is generated from pooled male and female tissues. Each input track was normalized by scaling all values to achieve a constant genome-wide summed signal. In the final track, the value in each 20 bp window is the arithmetic mean of the scaled input values.
Genome_build: GRCh37
Supplementary_files_format_and_content: WIG files generated by track averaging

source_name: spermatozoa

extract_protocol:
Refer to extraction protocols described in the individual sample inputs for each average track
Refer to library contruction protocols described in the individual sample inputs for each average track

tag: body site

value: testis

value: spermatzoa

tag: developmental stage

value: adult


title: DNA_methylation_BS_foreskin

description: DNA methylation, in various foreskin cells (average of 3 experiments)

source_name: foreskin

value: foreskin

value: male

value: neonate


title: 01B-4341

value: 20 years

value: Ullrich Congenital Muscular Dystrophy


title: 99B-4075

description: patient reference in corresponding publication: CMD1

value: female

value: 1  year


title: 92B-1025

description: patient reference in corresponding publication: DMD1

source_name: Pat 2

value: 4 years

value: Duchenne Muscular Dystrophy


title: 92B-627

description: patient reference in corresponding publication: DMD2

value: skeletal muscle

value: 2 years


title: Control-1

description: patient reference in corresponding publication: C1

value: 6 years

value: normal muscle


title: 91B-2585

description: patient reference in corresponding publication: DMD3


title: PatientID: 24806

city: Little Rock

first: Christoph

middle: J

last: Heuck

state: AR

address: 4301 W Markham

department: Myeloma Institute for Research and Therapy

institute: University of Arkansas for Medical Sciences

hyb_protocol: Samples were hybridized, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain kit (P/N 900720) according to the manufacturer's recommendations.

scan_protocol: Chips were scanned using the HG-U133 Plus 2.0 v2.2 on an Affymetrix Autoloader 3000DX scanner.

data_processing: Data are processed using the 'affy' Bioconductor library packages for R.

source_name: MM patient, previously treated, CD138+ selected cells

label_protocol: Samples were labels using the Affymetrix 3' IVT Express kit, according to the manufacturer's instructions.

extract_protocol: Following Ficoll-Hypaque gradient centrifugation, plasma cells obtained from the bone marrow were isolated from the mononuclear cell fraction by immunomagnetic bead selection using a monoclonal mouse anti-human CD138 antibody (Miltenyi-Biotec, Auburn, CA). More than 90 percent of the cells used for gene expression profiling were plasma cells, as shown by two-color flow cytometry using CD138+/CD45- and CD38+/CD45- markers, the presence of cytoplasmic immunoglobulin light chains by immunocytochemistry, and morphology by Wright-Giemsa staining. RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA).

value: CD138+ selected bone marrow plasma cells

tag: disease status

value: multiple myeloma

tag: treatment status

value: previously treated

tag: molecular subgroup

value: HY

tag: gep70 score

tag: OS time

tag: os censored


title: PatientID: 30175

tag: cell type

tag: treatment


title: PatientID: 29980


title: Control-3

description: patient reference in corresponding publication: C3

tag: age

value: 13 years


title: DNA_methylation_BS_brain

description: DNA methylation, brain hippocampus middle primary tissue (average of 2 experiments)

source_name: brain

value: brain

tag: tissue type

value: hippocampus middle

tag: Sex

value: male

value: adult


title: 02B-1353

description: patient reference in corresponding publication: CMD2

value: 1 year

value: Congenital Muscular Dystrophy


title: DNA_methylation_BS_breast

description: DNA methylation, in various breast cell types (average of 4 experiments)

source_name: breast

value: breast

value: female


title: PatientID: 29661


title: PatientID: 29819


title: PatientID: 30244

value: LB


title: PatientID: 29485


title: B07-2927

description: patient reference in corresponding publication: P3

value: skeletal muscle

value: 4 years

value: Ullrich Congenital Muscular Dystrophy


title: PatientID: 29265

value: CD138+ selected bone marrow plasma cells


title: PatientID: 28953

value: multiple myeloma


title: PatientID: 29436

value: previously treated


title: PatientID: 29268


title: PatientID: 29014

value: PR


title: PatientID: 29121


title: PatientID: 29643

value: HY


title: PatientID: 28535


title: PatientID: 28641


title: PatientID: 29447


title: PatientID: 28575


title: PatientID: 28924


title: PatientID: 29278


title: PatientID: 29233


title: PatientID: 28544


title: PatientID: 28494


title: PatientID: 28654


title: PatientID: 28408

value: MF


title: PatientID: 28411


title: PatientID: 28428

value: MS


title: PatientID: 28228


title: PatientID: 28385


title: TC036

city: Aarhus C

first: Jan

last: Alsner

address: Nørrebrogade 44, Bldg. 5

department: Experimental clinical Oncology

country: Denmark

institute: Aarhus University Hospital

hyb_protocol: Labeled cRNA was fragmented in fragmentation buffer (5x buffer:200 mM Tris-acetate (pH 8.1)/500nM KOAc/150 mM MgOAc) before hybridization on the array. Fragmented cRNA was hybridized to the nicroarrays in 90ul hybridization solution. GeneTitan Hybridization, Wash and Stain kit for 3`IVT arrays (Affymetrix) was used for preparing hybridization mixes and processing plate array in GeneTitan

scan_protocol: Human Genome U219 array plate was processed in GeneTitan according to manufacturer's instructions

data_processing: The data were analyzed with RMA method in R

source_name: Fresh frozen biopsy from primary papillary thyroid tumors

label_protocol: cRNA synthesis was made using 3`IVT Express kit (Affymetrix) following manufacterer's instructions and starting with 150ng of total RNA

extract_protocol: Total RNA from cell pellets was isolated with Rneasy Mini Kit (Qiagen), following the manufacterer's instructon. A fraction was quantitated by spectrophotometric measure using NanoDrop. RNA integrity was evaluated in agarose gel electrophoresis.

treatment_protocol: Fresh frozen tumor biopsy

tag: subject status

value: papillary thyroid carcinoma patient

tag: tumor stage


title: TC039

tag: gender


title: TC037


title: TC033

value: male


title: TC032


title: TC031


title: TC034


title: TC030


title: TC038


title: TC029


title: PatientID: 28158


title: PatientID: 28129


title: TC026


title: TC035


title: PatientID: 28146


title: TC027


title: TC025


title: TC022


title: TC028


title: PatientID: 27757


title: TC024


title: TC023


title: PatientID: 28028


title: PatientID: 28027


title: PatientID: 27729


title: PatientID: 27586


title: PatientID: 27179


title: PatientID: 27390


title: TC021


title: TC018


title: TC020


title: TC017


title: TC015


title: PatientID: 26613


title: PatientID: 26800


title: HTCC1062_thi limited_t2_rep3

city: Corvallis

first: Paul

last: Carini

address: 220 NASH hall

institute: Oregon State U

hyb_protocol: 10 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package.

organism: Candidatus Pelagibacter ubique HTCC1062

source_name: No vitamins added P. ubique time point 2 rep 3

label_protocol: RNA was labeled with biotin labeled nucleotides during the in-vitro transcription reaction.

growth_protocol: Artificial seawater media (AMS1 Carini et al., 2013) with no additional (Limted) or 1 µM (Control) Thiamine, 1.M oxaloacetate, 50 µM Methionine, 50 µM Glycine, 10 µM phosphate, and trace metals. Cells were grown at 20 °C in the dark with gentle agitation.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).

treatment_protocol: 15 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.

value: no thiamine added

tag: time


title: PatientID: 26875


title: TC014


title: HTCC1062_thi limited_t2_rep2

source_name: No vitamins added P. ubique time point 2 rep 2


title: HTCC1062_thi limited_t2_rep1

source_name: No vitamins added P. ubique time point 2 rep 1


title: HTCC1062_low thi_t1_rep3

source_name: No vitamins added P. ubique time point 1 rep 3


title: TC016


title: PatientID: 27585


title: HTCC1062_low thi_t1_rep2

source_name: No vitamins added P. ubique time point 1 rep 2


title: TC012

value: Unknown


title: PatientID: 26972


title: TC013


title: TC019


title: PatientID: 23067


title: DNA_methylation_BS_small_intestine

description:
DNA methylation, in small intestine primary tissue (average of 2 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: small intestine

tag: body site

value: small intestine

value: adult


title: DNA_methylation_BS_thymus

description:
DNA methylation, thymus primary tissue (average of 2 experiments)
Sequencing performed on multiple instruments: Illumina Genome Analyzer II, Illumina HiSeq 2000

source_name: thymus

value: thymus

tag: developmental stage


title: PatientID: 32456

tag: disease status

value: LB


title: HTCC1062_low thi_t1_rep1

source_name: No vitamins added P. ubique time point 1 rep 1


title: PatientID: 30826

tag: treatment status


title: TC011


title: HTCC1062_thi replete_t2_rep3

source_name: Thiamine replete P. ubique time point 2 rep 3

value: 1.0 uM thiamine added


title: DNA_methylation_BS_heart

description: DNA methylation, in adult heart primary tissue (average of 15 experiments)

source_name: heart

value: heart


title: TC010


title: DNA_methylation_BS_colon

description: DNA methylation, in sigmoid colon (average of 2 experiments)

source_name: colon

value: colon

value: sigmoid colon


title: PatientID: 31994

value: CD138+ selected bone marrow plasma cells

value: multiple myeloma

value: previously treated

tag: molecular subgroup


title: TC009


title: HTCC1062_thi replete_t2_rep1

source_name: Thiamine replete P. ubique time point 2 rep 1


title: HTCC1062_thi replete_t2_rep2

source_name: Thiamine replete P. ubique time point 2 rep 2


title: HTCC1062_thi replete t1_rep3

source_name: Thiamine replete P. ubique time point 1 rep 3


title: TC008


title: PatientID: 26147

source_name: MM patient, previously treated, CD138+ selected cells

value: PR

tag: gep70 score


title: TC007


title: PatientID: 31127

tag: OS time


title: HTCC1062_thi replete t1_rep2

source_name: Thiamine replete P. ubique time point 1 rep 2


title: PatientID: 31269

value: HY

tag: os censored


title: TC006

source_name: Fresh frozen biopsy from primary papillary thyroid tumors

value: papillary thyroid carcinoma patient


title: PatientID: 31582

tag: cell type


title: PatientID: 30952

tag: treatment


title: HTCC1062_thi replete t1_rep1

source_name: Thiamine replete P. ubique time point 1 rep 1


title: TC004

value: male

tag: age


title: TC005

value: female


title: TC003


title: TC002


title: PatientID: 30238


title: PatientID: 30796


title: ESF-1_Repl1

city: Nagpur

first: Dr. saravana

last: devi

state: Maharashtra

department: Environmental Health Division

country: India

institute: CSIR-National Environmental Engineering Research Institute

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HepG2 cells treated with 15µM of endosulfan in prescence of S9-mix for 24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) 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: HepG2 cells grown in DMEM media cointaning 10 % Fetal bovin serum

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HepG2 cells were treated with 15µM of endosulfan in prescence of S9-mix for 24 hours

tag: tissue

value: Liver

value: HepG2 (Hepatocellular carcinoma)


title: 5234_CD4_Memory_48 [Affymetrix]

city: La Jolla

first: Daniel

last: Salomon

state: CA

address: 10550 N Torrey Pines Rd, MEM-241

department: Molecular & Experimental Medicine

institute: The Scripps Research Institute

description: Gene expression data for anti-CD3/CD28 activated human memory CD4 T cells

hyb_protocol: Following labelling, 2.5 ug of cDNA were hybridized for 17 h at 48C on HuGene 1.1ST peg arraya (Affymetrix)

scan_protocol: Washing and staining and scanning  done per the Gene Titan MC protocol for HuGene 1.1ST peg arrays.

data_processing: The data were analyzed with Partek Genomics Suite (Partek Incorporated) and was Robust Multi-array Average (RMA) normalized

source_name: Human Memory CD4 T Cell

label_protocol: Biotinylated cDNA were prepared using the Ambion WT Expression Kit (Ambion Life Technologies) following manufacturer's instructions. cDNA was fragmented and labeled with GeneChip WT Terminial Labeling kit (Affymetrix).

growth_protocol: Naïve and memory CD4 cells were negatively selected using magnetic beads (Stem Cell Technologies).

extract_protocol: Total RNA was prepared from cell pellets using an All Prep kit (QIAGEN).

treatment_protocol: Purified naïve and memory CD4 T cells were cultured in RPMI supplemented with 10% FBS, 100 U/ml penicillin and 100mg/ml streptomycin at 37C and 5% CO2 with anti-CD3/CD28 activator beads (Invitrogen) for 0 or 48 hours.

tag: activation

value: anti-CD3/CD28 beads, 48 hours


title: Cer_treated_Infected_macrophage_3

city: Heidelberg

first: Jonathon

last: Blake

state: BW

address: Meyerhofstr 1

country: Germany

institute: EMBL

description: Cer (5mg/ml)  treated macrophages (ethanol 1ml/ml) infected with Mycobacterium smegmatis mc2155 for 1h.

hyb_protocol: Centrifuge samples for 5 sec at max speed. Heat hybridistion cocktail to 90C for 5 min. Cool tubes on ice for 5 min. Load arrays within 30 min of denatured cRNA. Hybridize at 37 C for 18-24 hours. Prepare 0.75x TNT buffer for 46C over night. Wash 3x in TNT covered from light. Put in Cy5-Strep solution, incubate 30 min at RT proteced from light. Repeat TNT washes 4x. Incubate in a large reservoir of 0.1xSSC/0.05%Tween20 for 30 seconds, centrifuge for 3 min at 200 rpm.

scan_protocol: Scanning was performed according to the CodeLink manual, paragraph 7, page 9 using an Axon 4200AL scanner wavelength 635 nm.  Scanned tif images were evaluated using CodeLink™ Expression Analysis software version 4.0.0.23520.

data_processing: Raw intensity values were median background subtracted.The background corrected intensity values for the discovery probes were median normalized using Bioconductor

organism: Mus musculus

source_name: macrophage cell line J774A.1

label_protocol: Synthesis of cRNA by IVT: Component 1x reaction,10x T7 reaction buffer 4ul  T7 ATP solution 4ul, T7 GTP solution 4ul,T7 CTP solution 4ul,T7 UTP solution 3ul, 10mM biotin-16-UTP 7,5ul,10x T7 enzyme mix 4ul,30.5 ul were was added to each sample and incubated at 37C for 14 hours.   Cleanup and Quantification of Biotin Labeled cRNA   Add 60ul Rnase free water and 350 ul buffer RLT to the IVT reaction, mix thoroughly. Add 250 ul ethanol (96-100%), mix well. Apply sample to an RNeasy spin column in a collection tube (2mL tube). Centrifuge for 15 seconds at 8000g (10000rpm). Add 500 ul buffer RPE Wash. Centrifuge for 15 seconds at 8000g (10000rpm). Repeat the last two steps. Replace the 2mL collection tube. Centrifuge for 2 minutes at 8000g (10000rpm). New 1,5mL collection tube: Add 50 ul nuclease-free water onto the filtermembrane. Incubate for 10 minutes at RT. Centrifuge for 1 minute at 8000g (10000rpm. Repeat the last three steps.    Synthesis of cRNA by IVT:   Component 1x reaction   10x T7 reaction buffer 4.0ul   T7 ATP solution 4ul   T7 GTP solution 4ul   T7 CTP solution 4ul   T7 UTP solution 3ul   10mM biotin-16-UTP 7,5ul   10x T7 enzyme mix 4ul   30,5 ul of mixture was added to each sample and incubated at 37C for 14 hours.   Cleanup and Quantification of Biotin Labeled cRNA   Add 60ul Rnase free water and 350 ul buffer RLT to the IVT reaction, mix thoroughly. Add 250 ul ethanol (96-100%), mix well. Apply sample to an RNeasy spin column in a collection tube (2mL tube). Centrifuge for 15 seconds at 8000g (10000rpm). Add 500 ul buffer RPE Wash. Centrifuge for 15 seconds at 8000g (10000rpm). Repeat the last two steps. Replace the 2mL collection tube. Centrifuge for 2 minutes at 8000g (10000rpm). New 1,5mL collection tube: Add 50 ul nuclease-free water onto the filtermembrane. Incubate for 10 minutes at RT. Centrifuge for 1 minute at 8000g (10000rpm. Repeat the last three steps.    Synthesis of cRNA by IVT:   Component 1x reaction   10x T7 reaction buffer 4.0ul   T7 ATP solution 4ul   T7 GTP solution 4ul   T7 CTP solution 4ul   T7 UTP solution 3ul   10mM biotin-16-UTP 7.5ul   10x T7 enzyme mix 4ul   30.5 ul of mixture was added to each sample and incubated at 37C for 14 hours.   Cleanup and Quantification of Biotin Labeled cRNA   Add 60ul Rnase free water and 350 ul buffer RLT to the IVT reaction, mix thoroughly. Add 250 ul ethanol (96-100%), mix well. Apply sample to an RNeasy spin column in a collection tube (2mL tube). Centrifuge for 15 seconds at 8000g (10000rpm). Add 500 ul buffer RPE Wash. Centrifuge for 15 seconds at 8000g (10000rpm). Repeat the last two steps. Replace the 2mL collection tube. Centrifuge for 2 minutes at 8000g (10000rpm). New 1,5mL collection tube: Add 50 ul nuclease-free water onto the filtermembrane. Incubate for 10 minutes at RT. Centrifuge for 1 minute at 8000g (10000rpm). Repeat the last three steps.

growth_protocol: A mouse macrophage cell line J774A.1 was grown in 6-well plates, at 90% confluence (1 million cells per well) in medium DMEM supplemented with 10% fetal bovine serum and 1% L-Glutamine.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer´s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Mouse macrophages were pre-treated with anti-inflammatory lipid Eicosapentaenoic acid (EPA) 15M or the pro-inflammatory lipid Ceramide (Cer) 5g/ml, dissolved in ethanol absolute. Ethanol absolute was used as mock control. Mouse macrophages were infected with a non-pathogenic bacteria, Mycobacterium smegmatis mc2155 EGFP, for 1h. Infected cells were then washed with PBS, and total RNA was extracted from cells.

tag: cell line

tag: infection

value: Mycobacterium smegmatis mc2155 for 1h


title: 5211_CD4_Memory_48 [Affymetrix]


title: EPA_treated_Infected_macrophage_2

description: EPA (15mM) treated macrophages (ethanol 1ml/ml) infected with Mycobacterium smegmatis mc2155 for 1h


title: Cer_treated_Infected_macrophage_2

value: Cer (5mg/ml)  treated macrophages (ethanol 1ml/ml)


title: EPA_treated_Infected_macrophage_3

value: EPA (15mM) treated macrophages (ethanol 1ml/ml)


title: 5157_CD4_Memory_48 [Affymetrix]


title: Cer_treated_Infected_macrophage_1


title: 5134_CD4_Memory_48 [Affymetrix]


title: ESF-2_Repl2

tag: gender


title: 5076_CD4_Memory_48 [Affymetrix]


title: control-1_Repl1

source_name: HepG2 cells (control)


title: EPA_treated_Iinfected_macrophage_1


title: leaves At5g57520/zfp2 mutant vs Col-0-WT REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

description:
Biological replicate 2 of 3: At5g57520/zfp2 mutant versus Wild Type
At5g57520/zfp2 mutant vs Col-0-WT REP2

hyb_protocol: Equal amounts of dye of each aRNA labeled with either Cy3 or Cy5, ranging from 200 to 300 pmol, were mixed with 20 ug of poly(A) and 20 µg of yeast tRNA (Sigma-Aldrich) in a volume of 9 µL. To this volume, 1 µL of RNA fragmentation buffer was added (RNA fragmentation reagents; Ambion) and after 15 min at 70°C, 1 µL of stop solution. Formamide, 20x SSC, 50x Denhardt's, and 20% SDS were added to a final concentration of 50% formamide, 6x SSC, 5x Denhardt's, and 0.5% SDS. This mix was boiled for 3 min at 95°C and then added to the prehybridized slide. Hybridization took place overnight at 37°C in a hybridization chamber. Arrays were then washed for 5 min at 37°C in 0.5x SSC and 0.1% SDS, twice for 5 min at room temperature (21°C) with 0.5x SSC and 0.1% SDS, three times with 0.5x SSC at room temperature, and 5 min with 0.1x SSC. The slides were then drained with a 2000-rpm spin for 2 min. The slides were stored in darkness until they were scanned.

scan_protocol: Images from Cy3 and Cy5 channels were equilibrated and captured with a GenePix 4000B (Molecular Devices) and spots quantified using GenePix 5.1 software (Molecular Devices).

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003).

organism: Arabidopsis thaliana

label_protocol: RNA was amplified with the MessageAmp aRNA amplification kit from Ambion following the instruction manual. To allow later labeling with Cy fluorophores, aminoallyl UTP (Ambion) was added to the mix of the T7 RNA polymerase-driven aRNA amplification reaction. The amount and quality of aRNA obtained was assessed as before. The aminoallyl-labeled aRNA (10 µg) was incubated in 1 M Na2CO3 with 8 nmol of dye monofunctional NHS ester (Cy3/Cy5) RPN 5661 (Amersham Biosciences) at room temperature in the dark for 1 h. Then, 35 µL of 0.1 M sodium acetate, pH 5.2, was added and incubated for a further 5 min in the dark. The Cy-labeled aRNA was purified with the Megaclear kit from Ambion and measured with the Nanodrop ND-100 spectrophotometer.

growth_protocol: 4-weeks old Arabidopsis thaliana plants were grown in a growth chamber (19-23C, 85% relative humidity, 100 mEm-2 sec-1 fluorescent illumination) on a 10-hr-light and 14-hr-dark cycle.  Plants were not treated prior to the RNA extraction.

extract_protocol: Leaves were excised from the plants and frozen immediately in liquid nitrogen. The frozen material was grinded using mortar and pestle and the RNA was isolated with Trizol (Invitrogen. www.invitrogen.com). RNA was quantified with a NanoDrop ND-100 spectrophotometer (NanoDrop Technologies. www.nanodrop.com). RNA quality was assessed with a 2100 Bioanalyzer from Agilent Technologies (www.agilent.com).

tag: ecotype

tag: genotype/variation

value: wild type

value: 4-weeks-old leaves

source_name: At5g57520/zfp2 mutant_leaves

value: At5g57520/zfp2 mutant


title: leaves At5g57520/zfp2 mutant vs Col-0-WT REP3

description:
Biological replicate 3 of 3: At5g57520/zfp2 mutant versus Wild Type
At5g57520/zfp2 mutant vs Col-0-WT REP3


title: leaves At5g65320/bhlh99 mutant vs Col-0-WT REP2

description:
Biological replicate 2 of 3: At5g65320/bhlh99 mutant versus Wild Type
At5g65320/bhlh99 mutant vs Col-0-WT REP2

source_name: At5g65320/bhlh99 mutant_leaves

value: At5g65320/bhlh99 mutant


title: leaves At5g65320/bhlh99 mutant vs Col-0-WT REP3

description:
Biological replicate 3 of 3: At5g65320/bhlh99 mutant versus Wild Type
At5g65320/bhlh99 mutant vs Col-0-WT REP3


title: Mocktreated_Infected_macrophage_3

description: Mock treated macrophages (ethanol 1ml/ml) infected with Mycobacterium smegmatis mc2155 for 1h


title: leaves At5g57520/zfp2 mutant vs Col-0-WT REP1

description:
Biological replicate 1 of 3: At5g57520/zfp2 mutant versus Wild Type
At5g57520/zfp2 mutant vs Col-0-WT REP1


title: GFP-ve4, Rho-eGFP, pn5 retina

city: Dublin

first: Fiona

middle: Catherine

last: Mansergh

address: Lincoln Place Gate

department: Smurfit Institute of Genetics

institute: Trinity College Dublin

description:
Gene expression data from other retinal neurons
Rho-eGFP mice express a human Rhodopsin-eGFP fusion protein that is visible in rod outer segments. Heterozygotes were used as homozygotes show retinal degeneration (Chan et al. 2004). Our Rho-eGFP are maintained on a largely 129Sv/J background

hyb_protocol: (Source Biosciences) aRNA was purified and hybridization cocktails were prepared according to the manufacturer's instructions and hybridised to Affymetrix mouse  A430_2 whole genome arrays, using the GeneChipHybridization, Wash and Stain Kit (Affymetrix), according to the manufacturer's protocol.

scan_protocol: (Source Biosciences) Arrays were scanned using a GeneChip Scanner 3000 (Affymetrix), according to the manufacturer's protocol.

data_processing:
Expression Analysis: Raw array data was loaded and normalized using the Affymetrix package for R (Gaultier et al. 2004, R Core Team, 2012). Expression across different conditions, along with associated significance tests, were perfomed using R and Limma (Smyth 2004, 2005).
Dimensionality reduction for visualization: Dimensionality reduction was performed using the Barnes-Hut-SNE implementation (van der Maaten, 2013) of the t-SNE algorithm (van der Maaten and Hinton, 2013). Each probe was represented as a 20-dimensional vector, with each vector component representing its normalized expression in a single sample and condition. The set of all probe vectors was passed as input to the Barnes-Hut-SNE algorithm.
Bioinformatic analysis: Following initial analysis, differentially regulated genes (adjusted P value < 0.001) from two way comparisons of the 5 datasets were added to an MS-Excel file and sorted. Genes differentially regulated in at least ¾ comparisons were retained for bioinformatic analysis. Initial bioinformatic analysis was carried out using the Gene, OMIM and PubMed databases (NCBI: www.ncbi.nlm.nih.gov ) and the RetNet database (RetNet; https://sph.uth.edu/retnet/ ).
Following conventional selection of differentially regulated genes, tSNE was used to identify the nearest expression neighbours of various key retinopathy genes across 20 samples (4 replicates per 5 sample types) (van der Maaten, 2013, van der Maaten and Hinton, 2008).

label: Biotin

source_name: GFP-ve cells from pn5 retinas, Rho-eGFP

label_protocol: (Source Biosciences) Samples were re-analysed for quality using a BioAnalyser 2100 (Agilent G2938A). FACS derived samples were amplified prior to labelling in order to increase the amount of input RNA, using the Ovation Pico WTA system (NuGen), then labelled using the Encore Biotin module (NuGen). Unamplified samples were labelled using the IVT Express kit (Affymetrix), according to the manufacturer's protocol.

growth_protocol:
retinas: Each retinal sample consists of pooled retinas (or FACS sorted retinal cells) dissected from litters of Rho-eGFP mice at the relevant stage (Pn1 or Pn5).
Tissue culture: Cells were dissociated from Pn5 retinas using Accutase and trituration via fire polished pipette. Cells (still in clumps) were plated at a concentration of 1 million cells per T25  and grown in DME/F12 supplemented with L-glutamine, penicillin-streptomycin, B27 without Vitamin A, bFGF, EGF and heparin as described previously (Mansergh et al. 2010). Dissociation prior to passage was carried out using Accutase according the the manufacturer's protocol (see also Mansergh et al. 2010).

extract_protocol:
Cell pellets were resuspended in 1ml TRI reagent (Sigma) and triturated using a P1000, while retinas were homogenized in 1ml TRI reagent using a 100ul mini Dounce homogenizer (Fisher)
RNA was prepared according to the manufacturer’s protocol. Samples for array were then re-purified using the RNeasy kit (Qiagen), incorporating the DNase step and according to the manufacturer’s instructions.
RNA samples were assayed for concentration and quality using a Nanodrop ND1000 (NanoDrop Technologies) spectrophotometer and a Qubit (Invitrogen). Samples were then exported to Source Bioscience for arraying.

treatment_protocol: FACS: Retinas were placed in 1ml HBSS (Lonza) and 100ul 10mg/ml trypsin (Sigma) was added. Retinas were incubated for 10 minutes at 37oC, after 5 minutes, 10μl 10 μg/ml DNase1 + 100μl 20mg/ml trypsin inhibitor were added and samples were triturated with a P1000 pipette (Gilson). Cells were spun for 5 minutes at 2000rpm (Thermo Microlite microcentrifuge) and cells were resuspended in 1 ml PBS with 10ul DNase1, then analysed by FACS. Cells were sorted based on GFP expression on an Aria Fusion cell sorter (Becton Dickinson, CA, USA) (Palfi et al. 2006). Following FACS analysis, cells were spun at 2000rpm for 5 minutes and resuspended in 100ul PBS. Cells were then subjected to RNA extraction.

tag: tissue or cells

value: FACS sorted retina

tag: developmental stage

value: postnatal day 5

tag: strain

value: 129Sv/J background


title: 5234_CD4_Naive_48 [Affymetrix]

description: Gene expression data for anti-CD3/CD28 activated human naive CD4 T cells

source_name: Human Naive CD4 T Cell


title: Untreated_Infected_macrophage_3

description: Untreated macrophages, infected with Mycobacterium smegmatis mc2155 for 1h

value: Untreated macrophages,


title: leaves At4g29080/pap mutant vs Col-0-WT REP3

description:
Biological replicate 3 of 3: At4g29080/pap mutant versus Wild Type
At4g29080/pap mutant vs Col-0-WT REP3

source_name: At4g29080/pap mutant_leaves

value: At4g29080/pap mutant


title: 5234_CD4_Memory_0 [Affymetrix]

description: Gene expression data for unactivated human naïve CD4 T cells


title: Untreated_Infected_macrophage_2


title: GFP-ve2, Rho-eGFP, pn5 retina


title: GFP-ve3, Rho-eGFP, pn5 retina


title: Mocktreated_Infected_macrophage_1

value: Mock treated macrophages (ethanol 1ml/ml)


title: 5211_CD4_Naive_48 [Affymetrix]


title: 5157_CD4_Naive_48 [Affymetrix]


title: 5134_CD4_Naive_48 [Affymetrix]


title: leaves At5g65320/bhlh99 mutant vs Col-0-WT REP1

description:
Biological replicate 1 of 3: At5g65320/bhlh99 mutant versus Wild Type
At5g65320/bhlh99 mutant vs Col-0-WT REP1


title: GFP+ve4, Rho-eGFP, pn5 retina

description:
Gene expression data from rod precursors
Rho-eGFP mice express a human Rhodopsin-eGFP fusion protein that is visible in rod outer segments. Heterozygotes were used as homozygotes show retinal degeneration (Chan et al. 2004). Our Rho-eGFP are maintained on a largely 129Sv/J background

source_name: GFP+ve cells from pn5 retinas, Rho-eGFP


title: leaves At1g66810 mutant vs Col-0-WT REP3

description:
Biological replicate 3 of 3: At1g66810 mutant versus Wild Type
At1g66810 mutant vs Col-0-WT REP3

source_name: At1g66810 mutant_leaves

value: At1g66810 mutant


title: control-2_Repl2

value: Liver

value: male


title: GFP-ve1, Rho-eGFP, pn5 retina


title: Untreated_Infected_macrophage_1


title: leaves At4g29080/pap mutant vs Col-0-WT REP1

description:
Biological replicate 1 of 3: At4g29080/pap mutant versus Wild Type
At4g29080/pap mutant vs Col-0-WT REP1


title: 5220_CD4_Memory_0 [Affymetrix]


title: GFP+ve3, Rho-eGFP, pn5 retina


title: Mocktreated_Infected_macrophage_2


title: leaves At4g29080/pap mutant vs Col-0-WT REP2

description:
Biological replicate 2 of 3: At4g29080/pap mutant versus Wild Type
At4g29080/pap mutant vs Col-0-WT REP2


title: Cer_treated_uninfected_macrophage_2

description: Cer (5mg/ml)  treated macrophages (ethanol 1ml/ml)


title: GFP+ve2, Rho-eGFP, pn5 retina


title: leaves At1g66810 mutant vs Col-0-WT REP2

description:
Biological replicate 2 of 3: At1g66810 mutant versus Wild Type
At1g66810 mutant vs Col-0-WT REP2


title: leaves At1g66810 mutant vs Col-0-WT REP1

description:
Biological replicate 1 of 3: At1g66810 mutant versus Wild Type
At1g66810 mutant vs Col-0-WT REP1


title: Ret3, Rho-eGFP, pn1

description:
Gene expression data from whole Pn1 retina
Rho-eGFP mice express a human Rhodopsin-eGFP fusion protein that is visible in rod outer segments. Heterozygotes were used as homozygotes show retinal degeneration (Chan et al. 2004). Our Rho-eGFP are maintained on a largely 129Sv/J background

source_name: Pooled Pn1 whole retinas, Rho-eGFP

value: Homogenized retina

value: postnatal day 1


title: 5211_CD4_Memory_0 [Affymetrix]


title: leaves RK32 vs Col-0-WT REP2

description:
Biological replicate 2 of 3: RK32 mutant versus Wild Type
RK32 vs Col-0-WT REP2

source_name: RK32 mutant_leaves

value: RK32 mutant


title: Cer_treated_uninfected_macrophage_1

value: Cer (5mg/ml)  treated macrophages (ethanol 1ml/ml)


title: EPA_treated_uninfected_macrophage_3

description: EPA (15mM) treated macrophages (ethanol 1ml/ml)


title: 5076_CD4_Memory_0 [Affymetrix]


title: leaves RK32 vs Col-0-WT REP3

description:
Biological replicate 3 of 3: RK32 mutant versus Wild Type
RK32 vs Col-0-WT REP3

value: wild type


title: EPA_treated_uninfected_macrophage_1

value: EPA (15mM) treated macrophages (ethanol 1ml/ml)


title: 5134_CD4_Memory_0 [Affymetrix]


title: Cer_treated_uninfected_macrophage_3


title: Ret4, Rho-eGFP, pn1


title: Mocktreated_uninfected_macrophage_3

description: Mock treated macrophages (ethanol 1ml/ml);


title: leaves RK28 vs Col-0-WT REP2

description:
Biological replicate 2 of 3: RK28 mutant versus Wild Type
RK28 vs Col-0-WT REP2

value: 4-weeks-old leaves

source_name: RK28 mutant_leaves

value: RK28 mutant


title: GFP+ve1, Rho-eGFP, pn5 retina

value: FACS sorted retina


title: leaves RK32 vs Col-0-WT REP1

description:
Biological replicate 1 of 3: RK32 mutant versus Wild Type
RK32 vs Col-0-WT REP1


title: 5157_CD4_Memory_0 [Affymetrix]


title: leaves RK28 vs Col-0-WT REP3

description:
Biological replicate 3 of 3: RK28 mutant versus Wild Type
RK28 vs Col-0-WT REP3


title: 4922_CD4_Memory_0 [Affymetrix]

description: Gene expression data for unactivated human naïve CD4 T cells


title: Ret2, Rho-eGFP, pn1


title: 5157_CD4_Naive_0 [Affymetrix]

description: Gene expression data for unactivated human memory CD4 T cells


title: Mocktreated_uninfected_macrophage_2

value: Mock treated macrophages (ethanol 1ml/ml);


title: EPA_treated_uninfected_macrophage_2


title: leaves RK28 vs Col-0-WT REP1

description:
Biological replicate 1 of 3: RK28 mutant versus Wild Type
RK28 vs Col-0-WT REP1


title: 5134_CD4_Naive_0 [Affymetrix]


title: Ret1, Rho-eGFP, pn1

value: 129Sv/J background


title: PDAC Late Ablation_anti-CTLA4 3

city: Houston

first: Valerie

last: LeBleu

state: TX

address: 1881 East Road

institute: MDACC

description:
Y817
GCV injected at PDAC  stage

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio

source_name: PDAC Late Ablation_anti-CTLA4

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

extract_protocol: RNA was extracted with Trizol reagent

tag: strain background

value: mixed C57BL/6 and Balb/c

value: Pancreatic ductal adenocarcinoma (PDAC)

tag: asma tk

value: Positive

tag: ctla4 treatment

value: Yes


title: Mocktreated_uninfected_macrophage_1


title: Ret3, Rho-eGFP, pn5

description:
Gene expression data from whole Pn5 retina
Rho-eGFP mice express a human Rhodopsin-eGFP fusion protein that is visible in rod outer segments. Heterozygotes were used as homozygotes show retinal degeneration (Chan et al. 2004). Our Rho-eGFP are maintained on a largely 129Sv/J background

source_name: Pooled Pn5 whole retinas, Rho-eGFP

value: postnatal day 5


title: Ret4, Rho-eGFP, pn5


title: Untreated_uninfected_macrophage_3

description: Untreated macrophages

value: Untreated macrophages


title: 5220_CD4_Naive_0 [Affymetrix]


title: 5234_CD4_Naive_0 [Affymetrix]


title: Untreated_uninfected_macrophage_2

description: Untreated macrophages


title: RPC3, Rho-eGFP, passage 2-5

description:
Gene expression data from cultured retinal progenitor cells
Rho-eGFP mice express a human Rhodopsin-eGFP fusion protein that is visible in rod outer segments. Heterozygotes were used as homozygotes show retinal degeneration (Chan et al. 2004). Our Rho-eGFP are maintained on a largely 129Sv/J background

source_name: Cultured RPCs derived from postnatal retina

value: cultured retinal progenitor cells


title: RPC4, Rho-eGFP, passage 2-5


title: 5211_CD4_Naive_0 [Affymetrix]


title: Ret2, Rho-eGFP, pn5

value: Homogenized retina


title: Untreated_uninfected_macrophage_1

description: Untreated macrophages


title: PDAC Late Ablation_anti-CTLA4 2

description:
Y810
GCV injected at PDAC  stage


title: PDAC Late Ablation_anti-CTLA4 1

description:
Y744
GCV injected at PDAC  stage


title: Hairy roots_35S::DASH_rep3

city: Shanghai

first: Jerome

last: Verdier

address: 3888 Chenhua road

country: China

institute: PSC, CAS

hyb_protocol: Affymetrix GeneChip®Expression Analysis

scan_protocol: GeneChip Operating Software version 1.4

data_processing: Each file from the hybridized Affymetrix array was exported from GeneChip Operating Software version 1.4 (Affymetrix) and imported into Robust Multiarray Average Express (Irizarry et al., 2003) for global normalization. Presence/absence call for each probe set to remove background noise was obtained using dCHIP (Li and Wong, 2001).

organism: Medicago truncatula

source_name: Hairy roots transformed with 35S::DASH

label_protocol: Affymetrix GeneChip 3’IVT express kit

growth_protocol: All plants were grown under greenhouse conditions in 1.5 litre pots filled with a mix of attapulgite: clay beads (60:40). Temperature was controlled to be 20°C during the day and above 18°C during the night. Artificial lighting was supplied to reach 16 hours light per day. The plants were not inoculated with Sinorhizobium sp. bacteria and were automatically supplied with 3.5N/3.1P/8.6K

extract_protocol: Cheng et al., 1996 CTAB RNA extraction

treatment_protocol: No treatment

tag: background cultivar

value: ectopic expression of 35S::DASH

value: hairy roots


title: 4922_CD4_Naive_0 [Affymetrix]


title: SEN_cDNA2_exp2

city: Toulouse

first: Estelle

last: Nicolas

address: 118 route de Narbonne

country: France

institute: INSERM

hyb_protocol: Differential cDNA populations were hybridized on the GeneChip Human Tiling 2.0R-A arrays (Affymetrix), which contain DNA probes from the forward DNA strand. Hybridization and scanning were performed according to the manufacturer protocol at the Plateforme Biopuces (INSA, Toulouse). Plus and minus strand expression were monitored by the cDNA2 and cDNA1 experiments, respectively.

scan_protocol: Tiling arrays were scanned with a 7000 3G Affymetrix scanner with autoloader and analyzed with Tiling Analysis Software (TAS)

data_processing:
Scanned array data normalization (quantile normalization, scale to 500) as well as calculation of the log2 (ratio) of the senescence signal over the control signal were performed using TAS (Affymetrix).
The result files are:CDNA1SENVSCONT-EXP1_signalSL.chp, CDNA2SENVSCONT-EXP1_signalSL.chp, CDNA1SENVSCONT_EXP2_signalSL.chp, CDNA2SENVSCONT_EXP2_signalSL.chp.
For images, data were calculated using a bandwidth of 300 (cDNA1SENvsCONT_EXP1_signal300.chp, cDNA2SENvsCONT_EXP1_signal300.chp, cDNA1SENvsCONT_EXP2_signal300.chp, cDNA2SENvsCONT_EXP2_signal300.chp) and visualized using the Integrated Genome Browser (IGB, Affymetrix) genome version H_sapiens_Mar_2006.

source_name: WI38 hTERT RAF1-ER cells treated with 4-HT for 4 days to induce senescence

label_protocol: Two different cDNAs populations were produced from the total RNA. cDNA1 was synthesized from 250 ng of total RNA (without rRNA reduction) according to the “GeneChip Whole Transcript Sense Target Labeling Assay” (Affymetrix) and is identical to RNA. cDNA2 was synthesized from 12 microgr of total RNA, as previously, but starting from the second cycle of cDNA synthesis thus skipping the first cycle cDNA synthesis and the “In Vitro Transcription” amplification step. Therefore, cDNA2 is complementary to RNA.

growth_protocol: WI38 hTERT RAF1-ER cells were maintained in MEM supplemented with glutamine, non-essential amino acids, sodium pyruvate, penicillin-streptomycin, and 10% FBS as per the ATCC in normoxic (5 % O2) culture conditions.

extract_protocol: Total RNA were prepared using the MasterPure RNA Purification Kit (Epicentre Biotechnologies) supplemented with Baseline-ZERO DNase (Epicentre)

treatment_protocol: For senescence induction, cells were treated with 20 nM 4-hydroxy-tamoxifen (4-HT) (Sigma) for 4 days.

tag: cell type

value: WI38 hTERT RAF1-ER


title: RPC2, Rho-eGFP, passage 2-5


title: CONT_cDNA2_exp2

data_processing:
Scanned array data normalization (quantile normalization, scale to 500) as well as calculation of the log2 (ratio) of the senescence signal over the control signal were performed using TAS (Affymetrix).
The result files are:CDNA1SENVSCONT-EXP1_signalSL.chp, CDNA2SENVSCONT-EXP1_signalSL.chp, CDNA1SENVSCONT_EXP2_signalSL.chp, CDNA2SENVSCONT_EXP2_signalSL.chp. For images, data were calculated using a bandwidth of 300 (cDNA1SENvsCONT_EXP1_signal300.chp, cDNA2SENvsCONT_EXP1_signal300.chp, cDNA1SENvsCONT_EXP2_signal300.chp, cDNA2SENvsCONT_EXP2_signal300.chp) and visualized using the Integrated Genome Browser (IGB, Affymetrix) genome version H_sapiens_Mar_2006.

source_name: WI38 hTERT RAF1-ER cells in proliferation


title: Ret1, Rho-eGFP, pn5


title: RPC1, Rho-eGFP, passage 2-5


title: Brain-Alzheimer's disease PSEN1 mutation carrier patient-7

first: Anna

last: Antonell

address: C/Casanova, 143

department: Unitat d'Alzheimer i altres transtorns cognitius

institute: Hospital Clínic Barcelona

description: Gene expression data of final stages of Alzheimer's disease

hyb_protocol: Following fragmentation, 5 ug of ssDNA were hybridized for 16 hr at 45C following Affymetrix standard procedures

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.1.0.1228, scanner PlateScanner M10)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package (version 1.30.0) from Bioconductor on R language (version 2.13.2).

source_name: Frozen brain tissue: posterior cingulate at thalamus level

label_protocol: Labeled ssDNA was prepared according to the standard Affymetrix Terminal labeling Kit protocol.

extract_protocol: Total RNA was extracted from frozen brain tissue (posterior cingulate area) using the RNeasy Lipid Tissue Mini Kit (Qiagen)

value: Male

tag: age at death

tag: post-mortem interval (hours)

tag: apoe genotype

tag: psen1 mutation

tag: neuropathological data (braak stage)

value: A3, B3, C3 + CAA severe


title: Hairy roots_35S::DASH_rep4

tag: tissue


title: SEN_cDNA1_exp2


title: PDAC Late Ablation 1

description:
GCV injected at PDAC stage
340

source_name: Pancreas

value: PDAC tumor

tag: treatment

value: Late Ablation

tag: genetic background


title: CONT_cDNA1_exp2

data_processing:
Scanned array data normalization (quantile normalization, scale to 500) as well as calculation of the log2 (ratio) of the senescence signal over the control signal were performed using TAS (Affymetrix).
The result files are:CDNA1SENVSCONT-EXP1_signalSL.chp, CDNA2SENVSCONT-EXP1_signalSL.chp, CDNA1SENVSCONT_EXP2_signalSL.chp, CDNA2SENVSCONT_EXP2_signalSL.chp.
 For images, data were calculated using a bandwidth of 300 (cDNA1SENvsCONT_EXP1_signal300.chp, cDNA2SENvsCONT_EXP1_signal300.chp, cDNA1SENvsCONT_EXP2_signal300.chp, cDNA2SENvsCONT_EXP2_signal300.chp) and visualized using the Integrated Genome Browser (IGB, Affymetrix) genome version H_sapiens_Mar_2006.


title: PDAC Late Ablation 3

description:
GCV injected at PDAC stage
1487


title: PDAC Late Ablation 2

description:
GCV injected at PDAC stage
986


title: Hairy roots_35S::DASH_rep2

tag: genotype/variation


title: CONT_cDNA2_exp1

treatment_protocol: For senescence induction, cells were treated with 20 nM 4-hydroxy-tamoxifen (4-HT) (Sigma) for 3 days.


title: PDAC Late Ablation Control 3

description:
No GCV
905

value: Late Ablation Control


title: PDAC Late Ablation Control 2

description:
No GCV
1484


title: SEN_cDNA1_exp1

source_name: WI38 hTERT RAF1-ER cells treated with 4-HT for 3 days to induce senescence


title: Hairy roots_35S::DASH_rep1


title: Brain-Alzheimer's disease PSEN1 mutation carrier patient-4

tag: gender

value: A3, B3, C3 + CAA moderate


title: Brain-Alzheimer's disease PSEN1 mutation carrier patient-6


title: PDAC Late Ablation Control 1

description:
No GCV
347

value: mixed C57BL/6 and Balb/c


title: Hairy roots_Empty_rep2

description: 2_Hairy root_Empty2_(Medicago)

source_name: Hairy roots transformed with empty vector

value: empty vector transformant (control)


title: Brain-Alzheimer's disease PSEN1 mutation carrier patient-2

value: A3, B3, C3 + LBD limbic predominant


title: Brain-Alzheimer's disease PSEN1 mutation carrier patient-5


title: PDAC Early Ablation 3

description:
GCV injected at PanIN stage
803

value: Positive

value: Early Ablation


title: SEN_cDNA2_exp1


title: Hairy roots_Empty_rep1

description: 1_Hairy root_Empty1_(Medicago)


title: Hairy roots_Empty_rep3

description: 11_Hairy root_Empty3_(Medicago)


title: CONT_cDNA1_exp1


title: PDAC Early Ablation 1

description:
GCV injected at PanIN stage
226


title: Brain-Early-onset Alzheimer disease- 6


title: dash_8DAP_rep3

source_name: dash mutant Medicago seeds 8 DAP

value: dash mutant

tag: time point

value: 8 days after pollination

value: seeds


title: PDAC Early Ablation Control 3

description:
No GCV
296

value: Early Ablation Control


title: dash_8DAP_rep2


title: PDAC Early Ablation Control 2

description:
No GCV
285


title: WT_8DAP_rep3

source_name: DASH WT Medicago seeds 8 DAP

value: wild type


title: Brain-Early-onset Alzheimer disease- 7

value: A3, B3, C3 + CAA moderate + isolated MVL


title: Brain-Early-onset Alzheimer disease- 4

value: Male


title: Brain-Early-onset Alzheimer disease- 3

value: A3, B3, C3 + CAA severe


title: Brain-Early-onset Alzheimer disease- 5

value: A3, B3, C3 + CAA mild


title: dash_8DAP_rep1


title: LTN013-2, aza-dc+TSA Rep1

city: Lanzhou

first: Yuan

last: Song

state: Gansu

address: the South of Tianshui Road

department: the school of life science

institute: Lanzhou University

description: Gene expression data from Arabidopsis seedlings were cold treated at 0 °C for 24 h following both aza and TSA treatment

hyb_protocol: Hybridization, washing, and staining were performed according to the Affymetrix manufacturer’s Instructions.

scan_protocol: Microarrays were scanned using a ScanArray 4000 Microarray Acquisition System.

data_processing: Microarray data were extracted from scanned GeneChip images and analyzed by use of Microarray Suite version 5.0.1 (Affymetrix) and BioConductor (http://www.bioconductor.org/).

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

growth_protocol: Seeds were sterilized with 70% ethanol, 0.05% Triton X-100 for 10 min and then washed with 95% ethanol, 0.05% Triton X-100 for 10 min, with 95% ethanol was for 10 min. A final washed with ddH2O for 3times, put into ddH2O in 4°C 48h. Seeds were sown on deep Petri plates with semisolid MS germination medium (Mock), added aza-dC and/or TSA. All seedlings kept in a growth chamber (16 h light and 8 h darkness, 70% relative humidity, 23 °C) for 16 days before being harvested.

extract_protocol: RNA were extracted using RNA purification kit (Norgen, Canada) following the manufacturer’s manual.

treatment_protocol: Arabidopsis seedlings were cold treated at 0 °C for 24 h in growth chamber (16-h day length at 70% relative humidity).

tag: ecotype

value: Columbia

tag: developmental stage

value: seedlings


title: PDAC Early Ablation Control 1

description:
No GCV
250

tag: asma tk

value: PDAC tumor


title: WT_8DAP_rep1


title: WT_8DAP_rep2


title: Brain-Alzheimer's disease PSEN1 mutation carrier patient-1

value: Female

value: A3, B3, C3 + CAA severe + LBD amygdala predominant


title: LTN014-2, aza-dc+TSA Rep2

source_name: Arabidopsis seedlings were cold treated at 0 °C for 24 h following both aza and TSA treatment


title: Brain-Alzheimer's disease PSEN1 mutation carrier patient-3

value: A3, B3, C3 + CAA moderate


title: Human Platelet-rep10

first: Leonard

middle: C.

last: Edelstein

address: 1015 Walnut St.

department: Medicine/Hematology

institute: Thomas Jefferson University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: data were analyzed in R using the GCRMA R package with defaults

source_name: Resting Human Platelet

label_protocol: standard Affymetrix protocol

extract_protocol: Trizol

value: Resting Human Platelet


title: Human Platelet-rep8


title: Human Platelet-rep9


title: Brain-Early-onset Alzheimer disease- 1


title: LTN012-2, Mock Rep2

description: Gene expression data from Arabidopsis seedlings were cold treated at 0 °C for 24 h.


title: Over expression day 1 (repeat 2)

city: london

first: mark

middle: christopher

last: howard

address: charterhouse Square

department: Endocrinology

country: United Kingdom

institute: QMUL

description:
Gene expression data from overexpression of Erg-010 driven by the Col2 promoter
Over_Ex_1_2_08

hyb_protocol: GeneChip Mouse Genome 430 2.0 arrays (Affymatrix)

data_processing: The raw fluorescence intensity values were normalized using a Robust Multi-array Average approach using dChip (V2005)

source_name: CH310T1/2 cells in micromass culture

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

growth_protocol: Standard CH310T1/2 micromass culture protocol

extract_protocol: RNA was extracted using an RNeasy plus mini kit (Qiagen)

treatment_protocol: Electroporated with na ECM 830 electroporator (Harvard apparatus) and pulsed once at 360 V, with a pulse length of 10 msec.


title: PDAC Early Ablation 2

description:
GCV injected at PanIN stage
589

value: Positive

value: Early Ablation

value: mixed C57BL/6 and Balb/c


title: Brain-Early-onset Alzheimer disease- 2


title: Over expression day 1 (repeat 1)

description:
Gene expression data from overexpression of Erg-010 driven by the Col2 promoter
Over_Ex_1_1_06

scan_protocol: GeneChip Mouse Genome 430 2.0 arrays (Affymatrix)


title: Control day 1 (repeat 2)

description:
Gene expression data from control plasmid
Cntl_1_2_07


title: LTN007-2, aza-dc Rep2

description: Gene expression data from Arabidopsis seedlings were cold treated at 0 °C for 24 h following aza treatment


title: LTN011-2, Mock Rep1

description: Gene expression data from Arabidopsis seedlings were cold treated at 0 °C for 24 h


title: Brain-control 7

value: No neuropathological findings


title: Control day 1 (repeat 1)

description:
Gene expression data from control plasmid
Cntl_1_1_05


title: LTN006-2, aza-dc Rep1

source_name: Arabidopsis seedlings were cold treated at 0 °C for 24 h following aza treatment


title: Control day 0 (repeat 2)

description:
Gene expression data from control plasmid
Cntl_0_2_04


title: LTN005-2, TSA Rep3

description: Gene expression data from Arabidopsis seedlings were cold treated at 0 °C for 24 h following TSA treatment


title: Brain-control 4


title: Human Platelet-rep5


title: Over expression day 0 (repeat 2)

description:
Gene expression data from overexpression of Erg-010 driven by CMV promoter
Over_Ex_0_2_03


title: Human Platelet-rep6


title: Brain-control 5


title: LTN008-2, aza-dc Rep3


title: Human Platelet-rep7


title: Wi38_cl1_nascentRNA_SNP6

status: Public on Jan 19 2015

city: Paris

first: Ronan

last: Chaligné

address: 26, Rue d'Ulm

institute: Institut Curie

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing:
Data was normalized by Genotyping console and raw single SNP intensities were taken as allelic expression of corresponding genes.
Each SNP was characterized by (i) global expression level score; (ii) allelic expression ratio score; and (iii) genomic status (loss or retention of heterozygosity score), which were summarized into a bi-allelic and mono- allelic expression status. Genome-wide bi-allelic and mono-allelic expression profiles were obtained by cumulating SNP status in a 50 SNPs window and at gene level.

source_name: Human Fibroblast

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: WI-38, ZR-75-1, SK-BR-3 and MDA-MB-436 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM; Invitrogen) containing 10% fetal bovine serum (FBS).

extract_protocol: Preparation of samples and analysis of nascent RNA were performed as described previously (Gimelbrant et al., 2007). Briefly, we purified nuclei of assessed cell lines (Nuclei Pure Isolation Kit, Sigma) and subsequently purified nuclear RNA (as described above for total RNA). Then, we hybridized cDNA obtained by reverse transcription of nuclear RNA of each sample onto Affymetrix SNP6.0 arrays.

tag: cell line

value: Normal_Non tumor


title: Wi38_cl28_gDNA_SNP6

data_processing:
Genomic profiling was performed at Institut Curie using Affymetrix SNPChip6.0 array; cell files were processed by Genotyping Console 3.0.2 (Affymetrix, reference model file HapMap270, version 29). SNP array data were mined using the previously described and validated GAP method (Popova et al., 2009). Segmental absolute copy numbers and allelic contents (major allele counts) were detected. R scripts and full details of the application are available at www.bioinfo-out.curie.fr/projects/snp_gap.
Each SNP was characterized by (i) global expression level score; (ii) allelic expression ratio score; and (iii) genomic status (loss or retention of heterozygosity score), which were summarized into a bi-allelic and mono- allelic expression status. Genome-wide bi-allelic and mono-allelic expression profiles were obtained by cumulating SNP status in a 50 SNPs window and at gene level.

extract_protocol: Phenol/chlorophrom extraction was used for gDNA isolation


title: Wi38_cl28_nascentRNA_SNP6


title: Human Platelet-rep4

city: Philadelphia


title: Brain-control 6

city: Barcelona


title: MDAMB436_gDNA_SNP6

source_name: Human Breast Cancer Cells

value: Basal-Like Carcinoma


title: ZR-75-1_gDNA_SNP6

value: Luminal


title: SKBR3_gDNA_SNP6


title: LTN004-2, TSA Rep2

source_name: Arabidopsis seedlings were cold treated at 0 °C for 24 h following TSA treatment


title: MDAMB436_nascentRNA_SNP6


title: SKBR3_nascentRNA_SNP6


title: Control day 0 (repeat 1)

description:
Gene expression data from control plasmid
Cntl_0_1_02


title: LTN003-2, TSA Rep1


title: Human Platelet-rep3


title: Over expression day 0 (repeat 1)

description:
Gene expression data from overexpression of Erg-010 driven by CMV promoter
Over_Ex_0_1_01


title: Brain-control 2


title: Human Platelet-rep2


title: Brain-control 1


title: Brain-control 3

value: Male


title: Wi38_cl1_gDNA_SNP6


title: Human Platelet-rep1


title: ZR-75-1_nascentRNA_SNP6


title: Cell lines_stablely transfected with vector [miRNA]

first: Hui

middle: zhen

last: Nie

address: 800 Dongchuan Road

institute: Shanghai Cancer Institute

description: Gene expression data from SMMC-7721 Cell line transfected with vector

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55℃，20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA，Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings.

data_processing: Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US)

source_name: SMMC-7721 Cell lines

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: Cell lines were grown under standard cell culture conditions in a 5% CO2-humidified chamber

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: shRNA-interference

tag: transfection

value: vector


title: mouse MABs, shPW1 transduced, proliferating, replicate 2

city: Milan

first: Giulio

last: Pavesi

address: Via Celoria 26

department: Biosciences

country: Italy

institute: Università di Milano

description:
polyclonal population
PW1-siRna_2

hyb_protocol: Hybridization was performed using the GeneChip® Hybridization, Wash and Stain Kit. It contains mix for target dilution, DMSO at a final concentration of 7% and pre-mixed biotin-labelled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat #900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM, respectively. Targets were diluted in hybridization buffer at a concentration of 25 ng/ul and denatured at 99 °C for 5 minutes incubated at 45 °C for 5 minutes  and centrifuged at maximum speed for 1 minute prior to introduction into the GeneChip® cartridge. A single GeneChip® MOUSE Gene 1.0 ST was then hybridized with each biotin-labeled sense target.   Hybridizations were performed for 16 h at 45 °C in a rotisserie oven. GeneChip®  cartridges were washed and stained with GeneChip®  Hybridization, Wash and Stain Kit in the Affymetrix Fluidics Station 450 following the FS450_0007 standard protocol, including the following steps: (1) (wash) 10 cycles of 2 mixes/cycle with Wash Buffer A at 30 °C; (2) (wash) 6 cycles of 15 mixes/cycle with Wash Buffer B at 50 °C; (3) stain of the probe array for 5 min in SAPE solution at 35 °C; (4) (wash) 10 cycles of 4 mixes/cycle with Wash Buffer A at 30 °C; (5) stain of the probe array for 5 min in antibody solution at 35 °C; (6) stain of the probe array for 5 min in SAPE solution at 35 °C; (7) (final wash) 15 cycles of 4 mixes/cycle with Wash Buffer A at 35 °C; (8) fill the probe array with Array Holding buffer.

scan_protocol: Standard Affymetrix protocol

data_processing: Partek Genomics Suite v 6.4 was used for analysis; RMA was used for summarization and normalization of probeset values

source_name: skeletal muscle,tibialis anterior

label_protocol: Double stranded cDNA synthesis and related cRNA was performed with GeneChip® WT cDNA Synthesis and Amplification Kit; labeling was performed using WT Teminal Labeling Kit (Affymetrix, Santa Clara, CA)

growth_protocol: Cells have cultured in DMEM medium plus 20% of Fetal Bovine Serum and mantained prolierating just before the total RNA extraction

extract_protocol: Total RNA was isolated using commercial homogenization (QIAshredder) and purification (RNeasy Mini Kit) reagents (QIAGEN).

treatment_protocol: Cells have been previuosly transduced with Lentiviral vectors expressing a shRNA targeting PW1. As control, we used a shScramble lentiviral vector which does not match with any mouse sequence.

tag: strain

value: male

value: adult

value: skeletal muscle

tag: cell type

value: mesoangioblasts (MAB)

tag: transduction


title: mouse MABs, shCtrl transduced, proliferating, replicate 1

description:
polyclonal population
Ctrl_1

value: Ctrl


title: mouse MABs, shCtrl transduced, proliferating, replicate2

description:
polyclonal population
Ctrl_2


title: mouse MABs, shPW1 transduced, proliferating, replicate 1

description:
polyclonal population
PW1-siRna_1


title: miRNA_MEF_ATF6bWT_Tun_24hr_rep2

status: Public on Jan 18 2015

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

country: Japan

institute: Institute for Genome Research

description:
miRNA expression of MEF (ATF6bWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_1_1_mi_ATF6bWT_Tun24hr_MEF_2.txt

hyb_protocol: Dried Cy3-labelled miRNA was resuspended in a reaction volume of 45 ul containing 45000000 fold-diluted Agilent Hyb Spike-In, 1x Agilent Gene Expression Blocking Agent and 1x Agilent Hi-RPM Hybridization Buffer following the manufacturers instructions. After denaturing the mixture by heating at 100 ºC for 5 minute and immediate cooling on ice for 5 minute, the mixture was hybridized to Agilent Mouse miRNA Microarrays (G4472B) for 21.5 hours at 55°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 5 minute at room temperature with GE Wash Buffer 1 (Agilent) and 5 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using miRNA scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol miRNA_107_Sep09 and Grid: 021828_D_20081121) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: miRNA_mouse embryonic fibroblast, ATF6bWT, Tun, 24hr, rep2

label_protocol: Directly Cyanine-3 (Cy3)-labeled miRNA was prepared from 100 ng total RNA using the miRNA Complete Labeling and Hyb kit (Agilent) according to the manufacturer's instructions, followed by MicroBioSpin 6 Columns purification (BioRad, Hercules, CA) and evaporation to dryness.

growth_protocol: MEFs were cultured in DMEM supplemented with 10% fetal bovine serum, 55uM 2-mercaptoethanol, 1x MEM non-essential amino acids, 100units/ml penicillin and 100ug/ml streptomycin at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored by agarose gel electrophoresis of RNA under denaturing conditions.

treatment_protocol: MEFs were treated with DMEM supplemented with 10% fetal bovine serum, 55uM 2-mercaptoethanol, 1x MEM non-essential amino acids, 100units/ml penicillin and 100ug/ml streptomycin containing 2ug/mL tunicamycin for 12 or 24 hours at 37 ºC in a humidified incubator with 5% CO2.

value: embryonic fibroblast

tag: background strain

tag: genotype

value: tunicamycin

tag: time


title: Cell lines_stablely transfected with shRNA-MR [miRNA]

description: Gene expression data from SMMC-7721 Cell line transfected with shRNA-MR

value: shRNA-MR


title: Ind3_L-iPSC_repB [Methylation]

city: Chicago

first: Nicholas

middle: E

last: Banovich

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description: Ind3 L-iPSC replicate B

hyb_protocol: The samples were bisulphite-converted and hybridized to the Infinium HumanMethylation450 BeadChip at the University of Chicago Functional Genomics facility.

scan_protocol: To ensure high data quality, probes were mapped to a bisulfite converted genome and only uniquely mapped probes were retained. Additionally, probes with low detection (P > 0.01) in more than 25% of samples were discarded. Samples were than normalized using the SWAN method to control for different probe types. Finally, red and green color channels were independently quantile normalized.

data_processing: We controlled for the difference in two probe types using a SWAN normalization. We then quantile normalized the red and green color channels independently.

source_name: iPSC

label_protocol: Standard illumina protocols

extract_protocol: DNA was extracted from samples using Zymo dual extraction kits (Zymo Research)

tag: age


title: Ind4_F-iPSC [Methylation]

description: Ind4 Fibroblast-derived iPSC

value: Female


title: Ind2_F-iPSC [Methylation]

description: Ind2 Fibroblast-derived iPSC


title: Ind1_L-iPSC_repC [Methylation]

description: Ind1 L-iPSC replicate C


title: Ind3_L-iPSC_repC [Methylation]

description: Ind3 L-iPSC replicate C


title: Ind3_Fibroblast [Methylation]

description: Ind3 source Fibroblast

source_name: Fibroblast


title: Ind4_L-iPSC_repB [Methylation]

description: Ind4 L-iPSC replicate B


title: miRNA_MEF_ATF6bWT_Tun_12hr_rep2

description:
miRNA expression of MEF (ATF6bWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_1_3_mi_ATF6bWT_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bWT, Tun, 12hr, rep2

tag: treatment


title: miRNA_MEF_ATF6bKO_UT_rep2

description:
miRNA expression of untreated MEF (ATF6bKO)
Raw data file: 100720_2_1_mi_ATF6bKO_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bKO, UT, rep2

value: untreated

value: control


title: miRNA_MEF_ATF6bWT_UT_rep2

description:
miRNA expression of untreated MEF (ATF6bWT)
Raw data file: 100720_1_1_mi_ATF6bWT_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bWT, UT, rep2


title: Ind2_L-iPSC_repC [Methylation]

description: Ind2 L-iPSC replicate C


title: Ind2_L-iPSC_repB [Methylation]

description: Ind2 L-iPSC replicate B


title: Ind3_LCL [Methylation]

description: Ind3 source LCL

source_name: LCL


title: miRNA_MEF_ATF6bKO_Tun_24hr_rep2

description:
miRNA expression of MEF (ATF6bKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_2_1_mi_ATF6bKO_Tun24hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bKO, Tun, 24hr, rep2


title: Ind4_LCL [Methylation]

description: Ind4 source LCL


title: Ind3_F-iPSC [Methylation]

description: Ind3 Fibroblast-derived iPSC


title: miRNA_MEF_ATF6bWT_Tun_12hr_rep1

description:
miRNA expression of MEF (ATF6bWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_1_2_mi_ATF6bWT_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bWT, Tun, 12hr, rep1


title: Ind1_Fibroblast [Methylation]

description: Ind1 source Fibroblast


title: miRNA_MEF_ATF6bWT_UT_rep1

description:
miRNA expression of untreated MEF (ATF6bWT)
Raw data file: 100715_1_4_mi_ATF6bWT_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bWT, UT, rep1


title: Ind4_Fibroblast [Methylation]

description: Ind4 source Fibroblast


title: Ind4_L-iPSC_repA [Methylation]

description: Ind4 L-iPSC replicate A


title: miRNA_MEF_ATF6aKO_Tun_24hr_rep2

description:
miRNA expression of MEF (ATF6aKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_2_2_mi_ATF6aKO_Tun24hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aKO, Tun, 24hr, rep2


title: Ind4_L-iPSC_repC [Methylation]

description: Ind4 L-iPSC replicate C


title: miRNA_MEF_ATF6aKO_Tun_12hr_rep2

description:
miRNA expression of MEF (ATF6aKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_2_4_mi_ATF6aKO_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aKO, Tun, 12hr, rep2


title: Ind1_L-iPSC_repB [Methylation]

description: Ind1 L-iPSC replicate B


title: Ind2_L-iPSC_repA [Methylation]

description: Ind2 L-iPSC replicate A


title: miRNA_MEF_ATF6bKO_Tun_12hr_rep1

description:
miRNA expression of MEF (ATF6bKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_2_2_mi_ATF6bKO_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bKO, Tun, 12hr, rep1


title: Ind1_L-iPSC_repA [Methylation]

description: Ind1 L-iPSC replicate A


title: Ind3_L-iPSC_repA [Methylation]

description: Ind3 L-iPSC replicate A


title: Ind1_F-iPSC [Methylation]

description: Ind1 Fibroblast-derived iPSC


title: Ind2_LCL [Methylation]

description: Ind2 source LCL


title: miRNA_MEF_ATF6aWT_Tun_24hr_rep2

description:
miRNA expression of MEF (ATF6aWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_1_2_mi_ATF6aWT_Tun24hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aWT, Tun, 24hr, rep2


title: Ind2_Fibroblast [Methylation]

description: Ind2 source Fibroblast


title: miRNA_MEF_ATF6aWT_Tun_12hr_rep2

description:
miRNA expression of MEF (ATF6aWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_1_4_mi_ATF6aWT_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aWT, Tun, 12hr, rep2


title: miRNA_MEF_ATF6aKO_Tun_24hr_rep1

description:
miRNA expression of MEF (ATF6aKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_2_3_mi_ATF6aKO_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aKO, Tun, 24hr, rep1


title: miRNA_MEF_ATF6aWT_UT_rep2

description:
miRNA expression of untreated MEF (ATF6aWT)
Raw data file: 100720_1_3_mi_ATF6aWT_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aWT, UT, rep2


title: miRNA_MEF_ATF6aKO_Tun_12hr_rep1

description:
miRNA expression of MEF (ATF6aKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_2_1_mi_ATF6aKO_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aKO, Tun, 12hr, rep1


title: miRNA_MEF_ATF6bKO_UT_rep1

description:
miRNA expression of untreated MEF (ATF6bKO)
Raw data file: 100715_2_4_mi_ATF6bKO_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bKO, UT, rep1


title: miRNA_MEF_ATF6bWT_Tun_24hr_rep1

description:
miRNA expression of MEF (ATF6bWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_1_4_mi_ATF6bWT_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bWT, Tun, 24hr, rep1


title: Ind1_LCL [Methylation]

description: Ind1 source LCL


title: miRNA_MEF_ATF6aKO_UT_rep2

description:
miRNA expression of untreated MEF (ATF6aKO)
Raw data file: 100720_2_3_mi_ATF6aKO_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aKO, UT, rep2


title: miRNA_MEF_ATF6aWT_Tun_24hr_rep1

description:
miRNA expression of MEF (ATF6aWT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_1_3_mi_ATF6aWT_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aWT, Tun, 24hr, rep1


title: miRNA_MEF_ATF6aWT_UT_rep1

description:
miRNA expression of untreated MEF (ATF6aWT)
Raw data file: 100715_1_2_mi_ATF6aWT_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aWT, UT, rep1


title: miRNA_MEF_ATF6aWT_Tun_12hr_rep1

description:
miRNA expression of MEF (ATF6aWT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_1_1_mi_ATF6aWT_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aWT, Tun, 12hr, rep1


title: miRNA_MEF_ATF6aKO_UT_rep1

description:
miRNA expression of untreated MEF (ATF6aKO)
Raw data file: 100715_2_2_mi_ATF6aKO_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6aKO, UT, rep1


title: miRNA_MEF_ATF4KO_Tun_12hr_rep2

description:
miRNA expression of MEF (ATF4KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_2_3_mi_ATF4KO_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4KO, Tun, 12hr, rep2


title: miRNA_MEF_ATF4KO_Tun_24hr_rep2

description:
miRNA expression of MEF (ATF4KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_2_1_mi_ATF4KO_Tun24hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4KO, Tun, 24hr, rep2


title: miRNA_MEF_ATF4WT_Tun_24hr_rep2

description:
miRNA expression of MEF (ATF4WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_1_1_mi_ATF4WT_Tun24hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4WT, Tun, 24hr, rep2


title: miRNA_MEF_ATF4KO_UT_rep2

description:
miRNA expression of untreated MEF (ATF4KO)
Raw data file: 100720_2_2_mi_ATF4KO_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4KO, UT, rep2


title: miRNA_MEF_ATF6bKO_Tun_24hr_rep1

description:
miRNA expression of MEF (ATF6bKO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101204_2_4_mi_ATF6bKO_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bKO, Tun, 24hr, rep1


title: miRNA_MEF_ATF4WT_Tun_12hr_rep2

description:
miRNA expression of MEF (ATF4WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_1_3_mi_ATF4WT_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4WT, Tun, 12hr, rep2


title: miRNA_MEF_ATF4WT_UT_rep2

description:
miRNA expression of untreated MEF (ATF4WT)
Raw data file: 100720_1_2_mi_ATF4WT_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4WT, UT, rep2


title: miRNA_MEF_XBP1KO_Tun_12hr_rep2

description:
miRNA expression of MEF (XBP1KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_2_4_mi_XBP1KO_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1KO, Tun, 12hr, rep2


title: miRNA_MEF_XBP1KO_Tun_24hr_rep2

description:
miRNA expression of MEF (XBP1KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_2_2_mi_XBP1KO_Tun24hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1KO, Tun, 24hr, rep2


title: miRNA_MEF_ATF4WT_UT_rep1

description:
miRNA expression of untreated MEF (ATF4WT)
Raw data file: 100715_1_3_mi_ATF4WT_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4WT, UT, rep1


title: miRNA_MEF_XBP1WT_Tun_24hr_rep2

description:
miRNA expression of MEF (XBP1WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_1_2_mi_XBP1WT_Tun24hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1WT, Tun, 24hr, rep2


title: miRNA_MEF_XBP1KO_UT_rep2

description:
miRNA expression of untreated MEF (XBP1KO)
Raw data file: 100720_2_4_mi_XBP1KO_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1KO, UT, rep2


title: miRNA_MEF_ATF4WT_Tun_12hr_rep1

description:
miRNA expression of MEF (ATF4WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_1_2_mi_ATF4WT_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4WT, Tun, 12hr, rep1


title: miRNA_MEF_ATF4KO_Tun_24hr_rep1

description:
miRNA expression of MEF (ATF4KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_2_4_mi_ATF4KO_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4KO, Tun, 24hr, rep1


title: miRNA_MEF_ATF4WT_Tun_24hr_rep1

description:
miRNA expression of MEF (ATF4WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_1_4_mi_ATF4WT_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4WT, Tun, 24hr, rep1


title: miRNA_MEF_ATF4KO_Tun_12hr_rep1

description:
miRNA expression of MEF (ATF4KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_2_2_mi_ATF4KO_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4KO, Tun, 12hr, rep1


title: miRNA_MEF_ATF4KO_UT_rep1

description:
miRNA expression of untreated MEF (ATF4KO)
Raw data file: 100715_2_3_mi_ATF4KO_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, ATF4KO, UT, rep1


title: miRNA_MEF_XBP1WT_Tun_12hr_rep2

description:
miRNA expression of MEF (XBP1WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101029_1_4_mi_XBP1WT_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1WT, Tun, 12hr, rep2


title: miRNA_MEF_XBP1WT_Tun_24hr_rep1

description:
miRNA expression of MEF (XBP1WT) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_1_3_mi_XBP1WT_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1WT, Tun, 24hr, rep1


title: miRNA_MEF_XBP1KO_Tun_12hr_rep1

description:
miRNA expression of MEF (XBP1KO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_2_1_mi_XBP1KO_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1KO, Tun, 12hr, rep1


title: miRNA_MEF_XBP1KO_UT_rep1

description:
miRNA expression of untreated MEF (XBP1KO)
Raw data file: 100715_2_1_mi_XBP1KO_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1KO, UT, rep1


title: miRNA_MEF_XBP1WT_UT_rep2

description:
miRNA expression of untreated MEF (XBP1WT)
Raw data file: 100720_1_4_mi_XBP1WT_UT_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1WT, UT, rep2


title: miRNA_MEF_XBP1WT_Tun_12hr_rep1

description:
miRNA expression of MEF (XBP1WT) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_1_1_mi_XBP1WT_Tun12hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1WT, Tun, 12hr, rep1


title: miRNA_MEF_XBP1KO_Tun_24hr_rep1

description:
miRNA expression of MEF (XBP1KO) after 24hr treatment of 2ug/mL tunicamycin
Raw data file: 101015_2_3_mi_XBP1KO_Tun24hr_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1KO, Tun, 24hr, rep1


title: miRNA_MEF_XBP1WT_UT_rep1

description:
miRNA expression of untreated MEF (XBP1WT)
Raw data file: 100715_1_1_mi_XBP1WT_UT_MEF_1.txt

source_name: miRNA_mouse embryonic fibroblast, XBP1WT, UT, rep1


title: miRNA_MEF_ATF6bKO_Tun_12hr_rep2

description:
miRNA expression of MEF (ATF6bKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101210_2_3_mi_ATF6bKO_Tun12hr_MEF_2.txt

source_name: miRNA_mouse embryonic fibroblast, ATF6bKO, Tun, 12hr, rep2


title: MEF_ATF6bKO_Tun_12hr_rep1

description:
Gene expression of MEF (ATF6bKO) after 12hr treatment of 2ug/mL tunicamycin
Raw data file: 101208_2_2_ATF6bKO_Tun12hr_MEF_1.txt

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent Fragmentation buffer and 2x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4852A) for 17.5 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028005_D_F_20100422) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse embryonic fibroblast, ATF6bKO, Tun, 12hr, rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 75 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.


title: MEF_ATF6bWT_UT_rep2

description:
Gene expression of untreated MEF (ATF6bWT)
Raw data file: 101215_1_1_ATF6bWT_UT_MEF_2.txt

source_name: mouse embryonic fibroblast, ATF6bWT, UT, rep2