title: 14178547 - 1093 -2 vs 1065 -2

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1065 -2 Cy5 / 1093 -2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: HL-60-L359V_rep1

status: Public on Aug 20 2011

type: RNA

city: Adelaide

first: Chung

middle: H

last: Kok

state: South Australia

address: North Terrace

country: Australia

institute: South Australia Health and Medical Research Institute

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner.

data_processing: Raw CEL files were normalised with RMA method using aroma.affymetrix and the batch effect was removed using ComBat analysis.

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: HL-60 cells constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 L359V

label_protocol: Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

growth_protocol: HL-60 cell lines were grown in RPMI containing 10%FBS (Sigma-Aldrich), 500 µg/ml hygromycin, 3 µg/ml puromycin, 10 µg/ml gentamicin at density of 1-5x106/ml. 24 hours prior to 4HT addition, the cells were changed into fresh RPMI medium containing 5% FBS with 10 µg/ml gentamicin and without hygromycin and puromycin.

extract_protocol: Total RNA was purified using the RNeasy protocol (Qiagen)

treatment_protocol: 24 hours prior to 4HT addition, the cells were changed into fresh RPMI medium containing 5% FBS with 10 µg/ml gentamicin and without hygromycin and puromycin. HL-60 cell lines were then treated with 100nM 4HT for 24 hours and, after this time, cells were harvested and RNA purified.

tag: cell line

tag: cell type

value: Promyelocytic Leukaemia

tag: genotype/variation


title: P0*54_GPL97

city: Little Rock

first: Yiming

last: Zhou

state: AR

address: 4301 West Markham St., Slot 776

country: USA

institute: Myeloma Institute for Research and Therapy

description: Gene expression data from myeloma patient before DEXA treatment

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

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: human myeloma cell  P0*54_GPL97

label_protocol: Biotinylated cRNA were prepared according to the standard affymetrix protocol

extract_protocol: RNeasy Mini Kit(50)

tag: human myeloma cell  P0*54_GPL97


title: 14178540 - 1065 -1 vs 1093 -1

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

country: France

institute: INRA

description: Genes regulated by MPK4 pathway.

hyb_protocol: 1093 -1 Cy5 / 1065 -1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: whole plant - Media: MS-Agar 0.5X with MES - 1% sucrose  Hygrometry: 75% Temperature: 26°C 16h light/8h dark

extract_protocol: 1093 -1:14.2ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: mpk4/MPK4 GOF

tag: age

value: 13 days

tag: developmental stage

value: boyes 1.02 (Boyes et al. Plant Cell 2001, PMID:11449047)

extract_protocol: 1065 -1:15.3ug. (Qiagen_RNeasy.pdf)


title: P0*52_GPL97

source_name: human myeloma cell  P0*52_GPL97

tag: human myeloma cell  P0*52_GPL97


title: Shewanella Onidensis MR-1 -MEC- Fe Nano-Decorared-Carbon-rep1

city: corvallis

first: Shoutao

last: Xu

state: OR

address: 116 gilmore hall, OSU

department: Department of biological and ecological engineering

institute: oregon State University

description:
ATCC 700550
This sample is of shewanella oneidensis MR-1 growing on Fe nano decraded anode. It is the first of three  biological replicates used in this experiment, each from separate cultures at the same batch.

hyb_protocol: Hybridization was performed by NimbleGen platform in CGRB Core Laboratories at Oregon State University following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen platform in CGRB Core Laboratories at Oregon State University, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Shewanella oneidensis MR-1

source_name: S. onidensis MR-1 -MEC-Fe Nano-Decorared-Carbon

label_protocol: Labeling was performed by NimbleGen platform in CGRB Core Laboratories at Oregon State University following their standard operating protocol. See www.nimblegen.com.

growth_protocol: S. oneidensis MR-1 was grown aerobically using a medium containing 30 g/L Trypticase Soy Broth at 30°C. Cells in early stationary growth phase (optical density of 1.5-1.6 at 600nm) were washed two times then injected into the chamber of the MEC for current production. Trypticase Soy Broth medium with 30 mM sodium lactate as electron donor was used in MECS. Phosphate buffer (100mM) was used to maintain the solution pH 7 and solution conductivity at 15 mS/cm

extract_protocol: Total RNA was extracted using Trizol (Ambion inc., Austin,TX) following the manufacturer’s instructions.DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.MessageAmpTM II-Bacteria Prokaryotic RNA Amplification kit was used to amplify RNA.

tag: growth condition

value: biofilm on Fe nano decreted graphite disk anode


title: P0*48_GPL97

source_name: human myeloma cell  P0*48_GPL97

tag: human myeloma cell  P0*48_GPL97


title: HL-60-355delT_rep1

source_name: HL-60 cells constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 355delT


title: P0*29_GPL97

source_name: human myeloma cell  P0*29_GPL97

tag: human myeloma cell  P0*29_GPL97


title: P0*36_GPL97

source_name: human myeloma cell  P0*36_GPL97

tag: human myeloma cell  P0*36_GPL97


title: BM_wt_rep3

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

institute: Univ of Alabama at Birmingham

hyb_protocol: Hybridization of the GeneChips was carried out in the following the manufacturer’s protocol. Briefly, the fragmented biotin labeled cRNA was mixed with 0.05nM control oligonucleotide B2, 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 0.1 mg/mL herring sperm DNA, 0.5 mg/mL BSA, 2X hybridization buffer (1X 100mM MES/1M NaCl/20mM EDTA/0.01% Tween-20) and 10% DMSO.  The hybridization cocktail was incubated at 99oC for 5 minutes to denature the herring sperm DNA and any secondary structure on the cRNA.  The cocktail was then equilibrated to 45oC for 5 minutes prior to addition to the GeneChip.  Hybridiztion was carried out in the Affymetrix Hybridization Oven 640 at 45oC with rotation at 60rpm for 16 hours.  Following the hybridization step the GeneChips were washed and stained in the Affymetrix Fluidics Station 450 following Fluidics Protocol Mini_euk2v3 as recommended by the manufacturer for this Chip type.  The GeneChips were first washed in a non-stringent wash buffer of 6X SSPE/0.01% Tween-20 followed by stringent wash with 100mM MES/0.1M NaCl/0.01% Tween-20.  The first staining of the GeneChips was done in 2X stain buffer (1X 100mM MES/1M NaCl/0.05% Tween-20), 2mg/mL BSA, and 0.01 mg/mL Streptavidin Phycoerythrin (SAPE).  The GeneChips were washed in non-stringent wash buffer.  A second stain comprised of 2X staining buffer, 2mg/mL BSA, 0.1mg/mL Goat IgG, and 0.003mg/mL of biotinylated antibody was conducted immediately followed by a third stain comprised of the SAPE solution (see above).  Finally, the GeneChips were washed in non-stringent wash buffer prior to scanning.

scan_protocol: Scanning of the GeneChips was done using the Affymetrix 3000 7G scanner as described by the manufacturer. The Fluidics station and Scanner were controlled using Affymetrix GeneChip Command Console (AGCC).

data_processing: The raw data were obtained through GCOS, background subtracted, and normalized through GC-RMA methods.

organism: Mus musculus

source_name: bone marrow macrophages

label_protocol: The labeling of the RNA was done as per the manufacturers instructions (Affymetrix, Santa Clara, CA).  Briefly, One microgram of total RNA was reverse transcribed using an oligo dT-T7 primer under standard conditions.  The resulting first strand cDNA was incubated with RNAse H, E. coli DNA ligase, and E. coli DNA polymerase, dNTPs and buffer to produce second-stranded cDNA.  The cDNA was purified using spin columns following the manufacturer’s instructions (Qiagen).  The purified cDNA was then used in an in vitro transcription assay to produce the target biotin labeled cRNA for hybridization using the 3’ IVT kit from Affymetrix following the manufacturer’s instructions.  The cRNA was purified using a spin column following the kit’s instructions (Qiagen), and fragmented prior to hybridization onto the GeneChips.

growth_protocol: TNFR1-/-R2-/- BMMs were isolated from TNFR1-/-R2-/- double KO mice from The Jackson Laboratory (Bar Harbor, ME). TNFR1-/-R2-/- BMMs expressing WT chimeric receptor or Mu chimeric receptor were prepared by infecting TNFR1-/-R2-/- BMMs with retrovirus encoding WT chimeric receptor or Mu chimeric receptor. Positive cells were selected with puromycin (2ug/ml) for 3 days.

extract_protocol: Standard Affymetrix protocol

treatment_protocol: TNFR1-/-R2-/- BMMs expressing a chimeric receptor consisting of the external domain of mouse TNFR1 linked to the transmembrane and intracellular domain of mouse RANK (WT) or TNFR1-/-R2-/- BMMs expressing a chimeric receptor consisting of the external domain of mouse TNFR1 linked to the transmembrane and intracellular domain of mouse RANK bearing inactivating mutations in the IVVY motif (Mu) were cultured in six 60-mm tissue culture dishes with α-MEM containing 10% heat-inactivated FBS and treated with M-CSF (44ng/ml) and TNFα (10ng/ml) for 24 hours. Total RNA was isolated from the six dishes and pooled. The RNA sample preparation was repeated independently two more times. Three sets of total RNA samples prepared from three independent assays were subject to microarray analysis using Mouse Genome 430 2.0 Array at the UAB Microarray Shared Facility.

tag: strain


title: BM_wt_rep2

value: TNFR1-/-R2-/- BMMs expressing a chimeric receptor consisting of the external domain of mouse TNFR1 linked to the transmembrane and intracellular domain of mouse RANK


title: BM_mutant_rep3

value: TNFR1-/-R2-/- BMMs expressing a chimeric receptor consisting of the external domain of mouse TNFR1 linked to the transmembrane and intracellular domain of mouse RANK bearing inactivating mutations in the IVVY motif


title: P0*43_GPL97

source_name: human myeloma cell  P0*43_GPL97

tag: human myeloma cell  P0*43_GPL97


title: HL-60-WT_rep2

source_name: HL-60 cells constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 WT


title: BM_mutant_rep2


title: HL-60-EV_rep2

source_name: HL-60 cells constitutively expressing GAL4-ER-VP16 tripartitie fusion protein only


title: Scramble control in MCF-7 cell line at 24 hours, rep3

city: Copenhagen

first: Jiayu

last: Wen

address: Ole Maaloes Vej 5

country: Denmark

institute: University of Copenhagen

description: Scramble control transfection.

hyb_protocol: The labeled samples were hybridized to the GeneChip Genome U133 plus 2 arrays (Affymetrix, Santa Clara, CA, USA) using standard Affymetrix procedures.

scan_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450, and the arrays were scanned in the Affymetrix GeneArray® 2500 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol.

data_processing: Affymetrix probeset intensity of miR-101 and scramble transfection experiments were preprocessed using the affy package in BioConductor, including steps of background correction, between-array normalization and transformation by VSN (Variance stabilization and calibration) method, and a summarization step by RMA (Robust Multichip Average) method.

label: biotin

source_name: MCF-7 cell line

label_protocol: RNA was amplified and labeled using the 3’ IVT Express kit (Affymetrix, Santa Clara, CA, USA) according to manufactures instructions. 250 ng total RNA was used as input.

extract_protocol: MCF-7 cells were seeded in 6-cm plates and independent triplicate transfections were performed the following day with 50 nM miR-101 or scramble control using Lipofectamine 2000. Total RNA was harvested 24 h after transfection using Trizol reagent.

value: MCF-7 cells

tag: conditions

value: transfection with 50 nM scramble control


title: Scramble control in MCF-7 cell line at 24 hours, rep1

description: Scramble control transfection

scan_protocol: The arrays were washed and stained with phycoerytrin conjugated streptavidin (SAPE) using the Affymetrix Fluidics Station® 450, and the arrays were scanned in the Affymetrix GeneArray® 2500 scanner to generate fluorescent images, as described in the Affymetrix GeneChip® protocol


title: BM_wt_rep1


title: HL-60-T354M_rep1

source_name: HL-60 cells constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 T354M


title: HL-60-T354M_rep2

value: constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 T354M


title: miR-101 transfection in MCF-7 cell line at 24 hours, rep2

description: miR-101 transfection

value: MCF-7 cells conditions:transfection with 50 nM miR-101


title: miR-101 transfection in MCF-7 cell line at 24 hours, rep3

description: miR-101 transfection.

value: transfection with 50 nM miR-101


title: P0*890_GPL97

source_name: human myeloma cell  P0*890_GPL97

tag: human myeloma cell  P0*890_GPL97


title: HL-60-WT_rep1

value: constitutively expressing GAL4-ER-VP16 tripartitie fusion protein and induced expression of GATA2 WT


title: Scramble control in MCF-7 cell line at 24 hours, rep2

description: Scramble control transfection


title: BM_mutant_rep1


title: miR-101 transfection in MCF-7 cell line at 24 hours, rep1

description: miR-101 transfection.


title: Tc_MvB_r5

status: Public on Aug 19 2011

type: genomic

city: Reading

first: Nicholas

last: Cryer

state: Berkshire

address: Whiteknights Campus

department: School of Biological Sciences

country: United Kingdom

institute: University of Reading

hyb_protocol: Microarrays were first pre-hybridised in 3.4xSSC, 0.3%SDS, 1%BSA at 42°C for 45 min., then briefly washed one with distilled water, once with isopropanol and spin-dried. Labelled targets were dissolved in 3.4xSSC, 0.3%SDS buffer and hybridized to microarrays under plastic coverslips in 3.4XSSC moist hybridization chamber in the oven at 55°C for 16-18 hrs. After hybridisation, microarrays were washed at room temperature for 3 min each, once in 1xSSC, once in 0.03%SDS, once in 0.2xSSC and once in 0.05xSSC, and spin-dried.

scan_protocol: Microarrays were scanned on GenePix Professional 4200A scanner (Molecular Devices, USA) using AutoPMT function (saturation of 0.005%). Images were analysed with GenePixPro v.6 software (Molecular Devices, USA).

data_processing: Per array, spots with the poor morphology or weak intensities according to signal-to-noise ratio <3 criterion were removed from further analysis. For the rest of the spots, spot signal median intensities were adjusted for local background, log2-ratios were calculated and normalized to median. Differential methylation were accessed by one-sample t-test, as implemented in TM4 software.

label: Alexa Fluor® 3 (555/565 nm)

molecule: genomic DNA

organism: Theobroma cacao

source_name: Plant 52

label_protocol: 2.0 μg WGA product was input to a BioPrime Total Genomic Labelling System (Invitrogen) for labelling with Alexa Fluor 3 or Alexa Fluor 5 dye following manufactures recommended procedure before being dryed under vacuum.

extract_protocol:
DNA was extracted from cocoa leaf material taken from between the 3rd and 5th inter venial rib adjacent to the petiole.  100 mg of frozen tissue was ground under N2(l) and DNA extracted using a DNeasy mini kit (Qiagen) following the manufacturers recommendations.
Immuno_precipitation_protocol: One milligram of genomic DNA was disrupted by sonication to give a fragment size of between 300 and 1000 bp in 100 μL of TE buffer. DNA containing methylcytosine was recovered utilising a Methylamp Methylated DNA Capture kit (Epigentek) using the suppliers’ standard protocol. The methyl fraction was eluted in 20 μL of buffer. The quantity of DNA in the elutant was assessed using a nanodrop spectrophotometer. Typically 1.0 μg of sonicated genomic DNA yielded 50 ng of DNA in the methyl fraction.
Whole_Genome_Amplification_Protocol:20 ng of methyl captured DNA was input to the Whole Genome Amplification procedure (Sigma) following manufacturers recommendations.

treatment_protocol: Temperature range 24 to 32 degree C

tag: fraction

value: Methyl captured fraction WGA from Plant 52

tag: condition

value: Malaysian temperature

tag: clone

value: SIC 5

label: Alexa Fluor® 5 (650/670 nm)

source_name: Plant 77

treatment_protocol: Temperature range 20 to 32 degree C

value: Methyl captured fraction WGA from Plant 77

value: Brazilian temperature


title: Tc_MvB_r4

source_name: Plant 65

value: Methyl captured fraction WGA from Plant 65

source_name: Plant 78

value: Methyl captured fraction WGA from Plant 78


title: Tc_MvB_r6

source_name: Plant 49

value: Methyl captured fraction WGA from Plant 49

source_name: Plant 79

value: Methyl captured fraction WGA from Plant 79


title: Tc_MvB_r7

source_name: Plant 53

value: Methyl captured fraction WGA from Plant 53

source_name: Plant 80

value: Methyl captured fraction WGA from Plant 80


title: HL-60-EV_rep1

tag: cell line

tag: cell type

value: Promyelocytic Leukaemia

tag: genotype/variation

value: constitutively expressing GAL4-ER-VP16 tripartitie fusion protein only


title: Tc_MvB_r3

source_name: Plant 38

value: Methyl captured fraction WGA from Plant 38


title: P0*19_GPL97

source_name: human myeloma cell  P0*19_GPL97

tag: human myeloma cell  P0*19_GPL97


title: Tc_MvB_r1

source_name: Plant 13

value: Methyl captured fraction WGA from Plant 13

source_name: Plant 7

value: Methyl captured fraction WGA from Plant 7


title: Tc_MvB_r2

source_name: Plant 9

value: Methyl captured fraction WGA from Plant 9

source_name: Plant 3

value: Methyl captured fraction WGA from Plant 3


title: Roots_sclareol_2h_rep.3

city: Tsukuba

first: Shigemi

last: Seo

state: Ibaraki

address: 2-1-2 Kannondai

department: Plant and Microbial Research Unit, Division of Plant and Microbial Sciences

country: Japan

institute: National Institute of Agrobiological Sciences

description: Gene expression after treatment with sclareol for 2 h

hyb_protocol: 1.65 ug of Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Oligo DNA microarray ver. 4.0 (catalog number G4136A) for 17 hours at 65C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 2 minute with 37C GE Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Each slide was 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 5 um, 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: Roots, sclareol, 2h, replicate 3

label_protocol: 500 ng RNA was labeled with cyanine-3 using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) and the labeled cRNA was purified using RNeasy mini spin columns (Qiagen) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Sterilized seeds of Arabidopsis Columbia (Col-0) plants were placed on on half-strength Murashige and Skoog (MS) medium (Wako Pure Chemical, Osaka, Japan) supplemented with 0.7% agar and incubated for 7 days. The seedlings were transferred to peat moss pellets (Jiffy-7C, Jiffy Products of America Inc., OH) and grown under a cycle of 10 h of light and 14 h of dark at 20C for 3 to 4 weeks.

extract_protocol: Roots samples in each treatment were harvested in triplicate and used for total RNA extraction. Total RNA was extracted using TRIzol reagent (Invitrogen) and purified using RNA purification columns (RNeasy, Qiagen) according to the manufacturer's instructions.

treatment_protocol: Sclareol was purchased from (Sigma-Aldrish). Sclareol was dissolved in methanol and diluted to a final concentration of 100 uM with water. Roos of Arabidopsis plants grown on peat moss pellets were treated with 100 uM sclareol or with 0.1% methanol by immersing the roots into a solution containing the chemical and incubating for 2 h at 20C under continuous light.

tag: tissue

value: root


title: Roots_sclareol_2h_rep.1

source_name: Roots, sclareol, 2h, replicate 1


title: HCT116 non-recombinant clone 27 (STAG2 wild-type)

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

description: STAG2 wild-type cells

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Human GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using  standard Affymetrix protocols.

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: HCT116 cells

label_protocol: 300 ng of total RNA was used for labeling.  The probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: Cells were grown in vitro in DMEM + 10% FBS + Pen/Strep.

extract_protocol: RNA was prepared from subconfluent asynchronously proliferating cells using TRIZOL and purified by RNeasy MinElute Cleanup kit (Qiagen).

treatment_protocol: No treatments were performed.

value: colorectal cancer cells

value: HCT116 cells

tag: genotype


title: Roots_sclareol_2h_rep.2

source_name: Roots, sclareol, 2h, replicate 2


title: 42MGBA STAG2 knock-in post-Cre clone 53-7 (STAG2 corrected)

description: STAG2 corrected cells

source_name: 42MGBA cells

value: glioblastoma cells

value: 42MGBA cells


title: H4 non-recombinant clone 12 (STAG2 mutant)

description: STAG2 mutant cells

source_name: H4 cells

value: H4 cells

value: non-recombinant clone 12 (STAG2 mutant)


title: HCT116 non-recombinant clone 24 (STAG2 wild-type)

description: STAG2 wild-type cells


title: 42MGBA STAG2 knock-in post-Cre clone 92-6 (STAG2 corrected)

description: STAG2 corrected cells


title: Roots_methanol_2h_rep.3

description: Gene expression after treatment with methanol for 2 h

source_name: Roots, methanol, 2h, replicate 3


title: HCT116 STAG2 knockout clone 7 (STAG2 deficient)

description: STAG2 deficient cells


title: Roots_methanol_2h_rep.2

source_name: Roots, methanol, 2h, replicate 2


title: H4 STAG2 knock-in post-Cre clone 8-3 (STAG2 corrected)

description: STAG2 corrected cells


title: Roots_methanol_2h_rep.1

source_name: Roots, methanol, 2h, replicate 1


title: H4 STAG2 knock-in post-Cre clone 88-1 (STAG2 corrected)

description: STAG2 corrected cells


title: H4 STAG2 knock-in post-Cre clone 8-1 (STAG2 corrected)

description: STAG2 corrected cells


title: H4 parental cells (STAG2 mutant)

description: STAG2 mutant cells

value: parental cells (STAG2 mutant)


title: 42MGBA STAG2 knock-in pre-Cre clone 92 (STAG2 deficient)

description: STAG2 deficient cells


title: 42MGBA STAG2 knock-in post-Cre clone 53-1 (STAG2 corrected)

description: STAG2 corrected cells


title: 42MGBA parental cells (STAG2 mutant)

description: STAG2 mutant cells


title: H4 non-recombinant clone 10 (STAG2 mutant)

description: STAG2 mutant cells

value: non-recombinant clone 10 (STAG2 mutant)


title: 42MGBA STAG2 knock-in pre-Cre clone 53 (STAG2 deficient)

description: STAG2 deficient cells


title: HCT116 STAG2 knockout clone 21 (STAG2 deficient)

description: STAG2 deficient cells


title: Intact + estradiol rep2 [Estradiol expt]

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

description:
replicate 2
6042501090_D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BeadStudio Program from Illumina.

source_name: mouse prostate from estradiol experiment

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

growth_protocol: Androgen reporter mice have the luciferase reporter gene driven by thymidine kinase promoter and specific androgen response elements (Slp-HRE2) integrated into their genome. The genomic background of androgen reporter mice is FVB/N. The mice were housed in the environment with a 12-hour dark-light cycle and they had food and water ad libitum. All the experiments were carried out with 8–12-week-old heterozygous male mice.

extract_protocol: Tissues were stored in RNALater (Qiagen). RNA was extracted with QIAGEN RNeasy midi kit for lipid tissues with DNaseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Genistein or vehicle was administered sc to intact or castrated males four days after surgical castration for five days at a dose of 300 μg/mouse/day in 0.1 ml of mineral oil containing 2% dimethylsulfoxide, corresponding to a dose of 10 μg/g body weight. 17β-Estradiol was administered sc to intact males for four days at a dose of 0.25 μg/mouse/day in 0.1 ml of mineral oil containing 0.5% ethanol, corresponding to a dose of 10 μg/kg body weight. The prostates were harvested 24 hours after final injection.

tag: gender

value: male

value: FVB/N

tag: age

value: 8-12 weeks

value: prostate


title: Intact + estradiol rep3 [Estradiol expt]

description:
replicate 3
6042501090_E


title: Intact + vehicle rep1 [Estradiol expt]

description:
replicate 1
6042501090_A


title: Intact + vehicle rep2 [Estradiol expt]

description:
replicate 2
6042501090_B


title: Intact + vehicle rep3 [Estradiol expt]

description:
replicate 3
6042501093_E


title: Intact + estradiol rep1 [Estradiol expt]

description:
replicate 1
6042501090_C


title: Intact + estradiol rep4 [Estradiol expt]

description:
replicate 4
6042501090_F


title: Intact + vehicle rep5 [Estradiol expt]

description:
replicate 5
6042501105_A


title: Intact + vehicle rep4 [Estradiol expt]

description:
replicate 4
6042501093_F


title: Intact + genistein rep1 [Genistein expt]

description:
replicate 1
5398599013_D

source_name: mouse prostate from genistein experiment


title: Intact + genistein rep2 [Genistein expt]

description:
replicate 2
5398599013_E


title: 808-CE-20

city: Los Angeles

first: Jessica

middle: Aaron

last: Fowler

state: CA

address: 675 Charles E. Young Drive south

department: Pathology

institute: University of California, Los Angeles

description: Flushed whole bone marrow from C57Bl/KaLwRij

hyb_protocol: 2 human gene 1.0 arrays were hybed for samples 808-CE-19 and 808-CE-20 on 3/4/08.

scan_protocol: Two Mouse Gene arrays were scanned and analyzed.

data_processing:
Data was imported into Expression Console and normalized with the default settings (RMA).
Pivot data (a spreadsheet of calculated log base 2 signal values) was exported along with annotation. This file was used to create log2 ratio values for the 19 (baseline) versus 20 (experimental) comparison. Probes with a log2 ratio of greater than 1 (so 2 fold or more upregulated) as well as less than -1 (2 fold or more down-regulated) are contained in file 808CE19-20_DataSummary.xls. Red indicates up-regulated probes and blue, down-regulated.
It should also be pointed out that newly posted two-fold comparison contain both a 'two fold change--all and two fold change--trim. The 'trim' worksheets have all the negative and positive controls stripped from the data.

source_name: Pooled C57Bl/KaLwRij samples (808-CE-16, -17, -18)

label_protocol:
Reactions for FFPE target production were set up in 96 well format 022108 with a total of 31 samples. A total of 10ng of Total RNA was used in project 808 reactions (808CE19, 20). Each sample was diluted 80X in order to sample with a minimum volume of ~1ul into the reactions. Additionally, Affymetrix polyA spike in controls were added to the reactions at the appropriate concentration, relative to sample input amount. Nugen Kit #3400-60, lot# 801142-A was used to generate the target. The samples were run through First Strand and Second Strand synthesis 02-22-08, followed by 2 rounds of SPIA amplification to generate cDNA. The cDNA was cleaned up 02-22-08 using Agencourt's RNA Clean and quantitated by Nanodrop spectrophotometry. Smear analysis of the targets was also performed. All targets met criteria for proceeding with the Exon Module. A total of ~ 16 - 19UG of target was generated and smear assessment showed ~83 - 84% of target greater than 200nt. A total of 3UG is required for the Exon Module with the majority of product greater than 200nt.
The Exon Module, Nugen Kit #2000, lot #711127-D, reactions were set up 02-26-08 and yields were good, with enough target generated to Fragment and Biotinylate with Nugen Kit 4200, (lots 708126E and 709151F used to make a Master Mix). The fragmentation and Biotinylation was completed 022808 and the targets were added to Hyb Cocktail and stored at -80C until hybridizations could be scheduled.

extract_protocol: Total RNA isolated using Trizol/Rneasy.


title: Castrated + genistein rep2 [Genistein expt]

description:
replicate 2
5398599036_E


title: Intact + vehicle rep2 [Genistein expt]

description:
replicate 2
5398599013_B


title: Castrated + vehicle rep2 [Genistein expt]

description:
replicate 2
5398599036_B


title: Intact + genistein rep3 [Genistein expt]

description:
replicate 3
5398599013_F


title: Castrated + vehicle rep3 [Genistein expt]

description:
replicate 3
5398599036_C


title: Intact + vehicle rep1 [Genistein expt]

description:
replicate 1
5398599013_A


title: Castrated + genistein rep3 [Genistein expt]

description:
replicate 3
5398599036_F


title: Castrated + genistein rep1 [Genistein expt]

description:
replicate 1
5398599036_D


title: 808-CE-19

description: Flushed whole bone marrow from C57Bl6


title: EpiSC_CHIR/XAV_rep3

city: los angeles

first: Qilong

last: Ying

address: 1425 san pablo st BCC509b

institute: USC

hyb_protocol: Performed by UCLA DNA Microarray core facility

data_processing: The data analysis was performed using Partek Microarray Software with RMA background correction and quantile normalization.

source_name: Epiblast stem cells maintained in CHIR/XAV condition

growth_protocol: GMEM medium (Sigma) supplemented with 10% fetal bovine serum (FBS) (Hyclone), 2 mM L-glutamine (Gibco), 1 mM sodium pyruvate (Gibco), 1% nonessential amino acids (Gibco), 0.1 mM β-mercaptoethanol (Sigma)

extract_protocol: Total RNA was extracted with the RNeasy Mini Kit (Qiagen).

value: Mouse embryonic stem cell


title: EpiSC_FGF2/activin_rep1

scan_protocol: Performed by UCLA DNA Microarray core facility

source_name: Epiblast stem cells maintained in FGF2/activin condition


title: EpiSC_FGF2/activin_rep2

label_protocol: Performed by UCLA DNA Microarray core facility


title: EpiSC_CHIR/XAV_rep2


title: Castrated + vehicle rep1 [Genistein expt]

description:
replicate 1
5398599036_A


title: EpiSC_FGF2/activin_rep3


title: ESC_2i_rep3

source_name: Embryonic stem cells maintained in 2i condition


title: EpiSC_CHIR/XAV_rep1


title: ESC_2i_rep1


title: ESC_2i_rep2


title: Intact + vehicle rep3 [Genistein expt]

description:
replicate 3
5398599013_C


title: Nickel 400 µM, biologcial rep4, repeated microarray

city: Ft. Detrick

first: John

last: Lewis

state: MD

address: 568 Doughten Drive

department: Biomarkers Program

institute: U.S. Army Center for Environmental Health Research

hyb_protocol: Samples were hybridized on the GeneChip Rat Genome 230 2.0 Array using Affymetrix instrumentation according to the manufacturer’s instructions

scan_protocol: Affymetrix protocol

data_processing: Microarray data was processed for background adjustment, normalization, and summarization using the Robust Multi-Array Averaging method (RMA) using Partek Genomic Suite (GS) software (Version 6.4 Copyright 2009, St. Louis, MO)

organism: Rattus norvegicus

source_name: H4-II-E-C3 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: H4-II-E-C3 cells (ATCC, Manassas, VA) were grown in Dulbecco's Modified Eagle's Medium (DMEM; Lonza,Walkersville, MD) containing 10% fetal bovine serum (Invitrogen, Carlsbad, CA) and 10 mL Glutamax (Invitrogen) in T75 flasks incubated at 37 °C with 5% carbon dioxide.

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

treatment_protocol: Exposures of 24 hours in duration were initiated once flasks were 90 ± 10% confluent using the test chemicals NiCl2, CdCl2, and Na2Cr2O7.

tag: agent

value: Nickel 400 µM


title: Cadmium 0.2 µM, biological rep4

value: Cadmium 0.2 µM


title: Nickel 140 µM, biological rep4, repeated microarray

value: Nickel 140 µM


title: Cadmium 0.55 µM, biological rep4

value: Cadmium 0.55 µM


title: Chromium 0.275 µM, biological rep4, repeated microarray

value: Chromium 0.275 µM


title: Chromium 1 µM, biological rep4

value: Chromium 1 µM


title: Chromium 10 µM, biological rep4

value: Chromium 10 µM


title: Control 1, biological rep4

value: Control


title: Nickel 40 µM, biological rep4

value: Nickel 40 µM


title: Cadmium 0.55 µM, biological rep3


title: Chromium 1 µM, biological rep3


title: Nickel 140 µM, biological rep3


title: Control 2, biological rep4


title: Nickel 400 µM, biologcial rep3


title: Cadmium 0.2 µM, biological rep3


title: Chromium 10 µM, biological rep3


title: Cadmium 1.2 µM, biological rep3

value: Cadmium 1.2 µM


title: Cadmium 1.2 µM, biological rep2


title: Control 2, biological rep3


title: Chromium 10 µM, biological rep2


title: Cadmium 0.55 µM, biological rep2, repeated microarray


title: Control 1, biological rep3


title: Nickel 40 µM, biological rep3


title: Chromium 0.275 µM, biological rep3


title: Nickel 400 µM, biologcial rep2


title: Cadmium 0.2 µM, biological rep2


title: Nickel 140 µM, biological rep2


title: Chromium 0.275 µM, biological rep2


title: Nickel 400 µM, biologcial rep1


title: Mock ribonucleoprotein complex immunoprecipitation, biological replicate 3

type: other

city: Durham

first: Neelanjan

last: Mukherjee

state: NC

address: 101 Science Drive

department: Institute for Genome Sciences & Policy

institute: Duke University

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200μl of hyb solution to each array, then tape holes and parafilm. Hybridize 16 hours at 45° at 60rpm. Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Affymetrix power tools. PLIER was used to normalize the data and  and probe expression was filtered based on detection p-value. For creating gene expression estimates, the median value for probesets matching the same gene was calculated.
probe group file: HuEx-1_0-st-v2.r2.pgf

molecule: other

source_name: HEK 293 cell FLAGHA-HuR

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

growth_protocol: HEK 293 Flip-In T-REx cells containing a FLAG-HA-tagged HuR were cultured in DMEM supplemented with 10% tet-reduced FBS and appropriate selection antibiotics.

extract_protocol: For knockdown experiments, cells were washed with PBS and then lysed using TRIzol followed by RNA extraction. For RIP experiments, cells were wased and collected in ice-cold PBS and then resuspended and frozen (-80C) in polysome lysis buffer (see Keene 2006 for details)

treatment_protocol: For knockdown experiments, siRNA ransfections were performed using RNAiMAX (Invitrogen). Independent biological triplicates of RNA from samples treated with 50 nM scramble siRNA or HuR siRNA for 72 hrs.

value: HEK 293 cell FLAGHA-HuR

tag: ip ab

value: Mouse IgG conjugated beads


title: Control 2, biological rep2


title: Chromium 1 µM, biological rep2


title: Cadmium 1.2 µM, biological rep4


title: Control 1, biological rep2


title: Bac

status: Public on Aug 18 2011

city: Chiyoda-ku

first: Hiromasa

last: Tsuda

state: Tokyo

address: 1-8-13 Kanda-surugadai

department: Biochemistry

institute: Nihon University School of Dentistry

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

organism: Streptococcus mutans UA159

source_name: Streptcoccus mutans, wild-type, bacitracin-treated.

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Two milliliters of overnight culture of S. mutans wild-type strain UA159 were inoculated into 18 ml of BHI broth and incubated at 37°C.

extract_protocol: Total RNA was extracted using the ISOGEN-LS (Nippon Gene, Tokyo, Japna) and purified using RNeasy Mini Kit (QIAGEN, Valencia, CA).

treatment_protocol: When S. mutans wild-type strain UA159 were grown to the optical density at 550 nm (OD550), the culture was exposed to 0 or 4 units (U)/ml bacitracin for 30 min at 37°C.

tag: type

value: wild-type

tag: strain

value: bacitracin


title: Cont

source_name: Streptcoccus mutans, wild-type, non-treated.

value: non-treated


title: Cadmium 0.55 µM, biological rep1


title: Nickel 40 µM, biological rep2


title: Mock ribonucleoprotein complex immunoprecipitation, biological replicate 2


title: HuR siRNA knockdown, biological replicate 3

description: HuR siRNA knockdown

tag: sirna

value: HuR siRNA knockdown


title: Nickel 40 µM, biological rep1


title: Cadmium 0.2 µM, biological rep1


title: Nickel 140 µM, biological rep1


title: Mock siRNA knockdown, biological replicate 3

description: Mock siRNA knockdown

value: Mock siRNA knockdown


title: HuR ribonucleoprotein complex immunoprecipitation, biological replicate 2

value: Flag M2 conjugated beads


title: Mock siRNA knockdown, biological replicate 1

description: Mock siRNA knockdown


title: Mock siRNA knockdown, biological replicate 2

description: Mock siRNA knockdown


title: Chromium 10 µM, biological rep1


title: Chromium 1 µM, biological rep1


title: HuR siRNA knockdown, biological replicate 1

description: HuR siRNA knockdown


title: HuR siRNA knockdown, biological replicate 2

description: HuR siRNA knockdown


title: NA18489_E_trep2_brep2

city: Chicago

first: Joseph

middle: C

last: Maranville

state: IL

address: 920 E. 58th Street

institute: 920 E. 58th Street

description: technical replicate 2, biological replicate 2

data_processing: The data were normalised using quantile normalisation with lumi in R

source_name: lymphoblastoid cell line

extract_protocol: RNA was extracted with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: EBV-transformed B lymphocytes

tag: population

value: Yoruba in Ibadan, Nigeria

tag: treatment

value: vehicle(EtOH)


title: NA19099_E_trep2

description: technical replicate 2


title: NA20828_E_trep2

description: technical replicate 2

value: Toscani in Italia


title: NA18489_D_trep2_brep2

value: dexamethasone


title: NA20772_D_trep2

description: technical replicate 2


title: Mock ribonucleoprotein complex immunoprecipitation, biological replicate 1


title: Chromium 0.275 µM, biological rep1

value: Chromium 0.275 µM


title: NA20528_E_trep2_brep2


title: NA20828_D_trep2

description: technical replicate 2


title: Cadmium 1.2 µM, biological rep1


title: NA20796_D_trep2

description: technical replicate 2


title: NA20818_D_trep2_brep2


title: Control 1, biological rep1

value: Control


title: NA18523_D_trep2

description: technical replicate 2


title: Control 2, biological rep1


title: HuR ribonucleoprotein complex immunoprecipitation, biological replicate 3


title: NA18909_D_trep2

description: technical replicate 2


title: NA20528_D_trep2_brep2


title: NA20772_E_trep2

description: technical replicate 2


title: NA18859_E_trep2

description: technical replicate 2


title: NA20796_E_trep2

description: technical replicate 2


title: NA20520_E_trep2

description: technical replicate 2


title: NA19239_D_trep2_brep2


title: NA20520_D_trep2

description: technical replicate 2


title: NA18859_D_trep2

description: technical replicate 2


title: NA19203_E_trep2

description: technical replicate 2


title: NA20818_E_trep2_brep2


title: NA19203_D_trep2

description: technical replicate 2


title: NA18909_E_trep2

description: technical replicate 2


title: NA19239_E_trep2_brep2


title: NA20801_D_trep2

description: technical replicate 2


title: NA18523_E_trep2

description: technical replicate 2


title: NA19099_D_trep2

description: technical replicate 2


title: NA20801_E_trep2

description: technical replicate 2


title: NA18486_D_trep2

description: technical replicate 2


title: NA18486_E_trep2

description: technical replicate 2


title: HuR ribonucleoprotein complex immunoprecipitation, biological replicate 1

source_name: HEK 293 cell FLAG-HA-HuR

value: HEK 293 cell FLAG-HA-HuR


title: NA19190_E_trep2

description: technical replicate 2


title: NA20544_D_trep2

description: technical replicate 2


title: NA20804_E_trep2

description: technical replicate 2


title: NA19141_E_trep2

description: technical replicate 2


title: NA19190_D_trep2

description: technical replicate 2


title: NA20756_E_trep2

description: technical replicate 2


title: NA20756_D_trep2

description: technical replicate 2


title: NA19141_D_trep2

description: technical replicate 2


title: NA20804_D_trep2

description: technical replicate 2


title: NA20544_E_trep2

description: technical replicate 2


title: NA20522_E_trep2

description: technical replicate 2


title: NA20519_D_trep2

description: technical replicate 2


title: NA20522_D_trep2

description: technical replicate 2


title: NA19207_E_trep2

description: technical replicate 2


title: NA19108_E_trep2

description: technical replicate 2


title: NA20519_E_trep2

description: technical replicate 2


title: NA19108_D_trep2

description: technical replicate 2


title: NA18502_D_trep2

description: technical replicate 2


title: NA18502_E_trep2

description: technical replicate 2


title: NA18501_D_trep2

description: technical replicate 2


title: NA20805_D_trep2

description: technical replicate 2


title: NA19207_D_trep2

description: technical replicate 2


title: NA20581_D_trep2

description: technical replicate 2


title: NA19222_E_trep2

description: technical replicate 2


title: NA19222_D_trep2

description: technical replicate 2


title: NA20766_E_trep2

description: technical replicate 2


title: NA20766_D_trep2

description: technical replicate 2


title: NA19239_D_trep2_brep1

description: technical replicate 2, biological replicate 1


title: NA20528_E_trep2_brep1


title: NA20589_D_trep2

description: technical replicate 2


title: NA19092_D_trep2

description: technical replicate 2


title: NA20589_E_trep2

description: technical replicate 2


title: NA19239_E_trep2_brep1


title: NA18489_E_trep2_brep1


title: NA18489_D_trep2_brep1


title: NA20818_E_trep2_brep1


title: NA20773_D_trep2

description: technical replicate 2


title: NA20818_D_trep2_brep1


title: NA20815_D_trep2

description: technical replicate 2


title: NA18505_E_trep2

description: technical replicate 2


title: NA20815_E_trep2

description: technical replicate 2


title: NA18516_E_trep2

description: technical replicate 2


title: NA20581_E_trep2

description: technical replicate 2


title: NA18505_D_trep2

description: technical replicate 2


title: NA18516_D_trep2

description: technical replicate 2


title: NA19092_E_trep2

description: technical replicate 2


title: NA20528_D_trep2_brep1


title: NA20773_E_trep2

description: technical replicate 2


title: NA20512_D_trep2

description: technical replicate 2


title: NA18511_E_trep2

description: technical replicate 2


title: NA18511_D_trep2

description: technical replicate 2


title: NA20505_E_trep2

description: technical replicate 2


title: NA20505_D_trep2

description: technical replicate 2


title: NA20769_E_trep2

description: technical replicate 2


title: NA18507_D_trep2

description: technical replicate 2


title: NA20769_D_trep2

description: technical replicate 2


title: NA20512_E_trep2

description: technical replicate 2


title: NA18504_D_trep2

description: technical replicate 2


title: NA18507_E_trep2

description: technical replicate 2


title: NA18522_E_trep2

description: technical replicate 2


title: NA19102_E_trep2

description: technical replicate 2


title: NA18508_D_trep2

description: technical replicate 2


title: NA19102_D_trep2

description: technical replicate 2


title: NA18522_D_trep2

description: technical replicate 2


title: NA20812_D_trep2

description: technical replicate 2


title: NA20805_E_trep2

description: technical replicate 2


title: NA19116_E_trep2

description: technical replicate 2


title: NA20582_E_trep2

description: technical replicate 2


title: NA20539_D_trep2

description: technical replicate 2


title: NA20539_E_trep2

description: technical replicate 2


title: NA20787_D_trep2

description: technical replicate 2


title: NA18504_E_trep2

description: technical replicate 2


title: NA20582_D_trep2

description: technical replicate 2


title: NA20787_E_trep2

description: technical replicate 2


title: NA20765_D_trep2

description: technical replicate 2


title: NA18501_E_trep2

description: technical replicate 2


title: NA19160_D_trep2

description: technical replicate 2


title: NA19138_E_trep2

description: technical replicate 2


title: NA18499_E_trep2

description: technical replicate 2


title: NA19128_E_trep2

description: technical replicate 2


title: NA19160_E_trep2

description: technical replicate 2


title: NA20768_E_trep2

description: technical replicate 2


title: NA18499_D_trep2

description: technical replicate 2


title: NA20535_D_trep2

description: technical replicate 2


title: NA20529_D_trep2

description: technical replicate 2


title: NA20812_E_trep2

description: technical replicate 2


title: NA18508_E_trep2

description: technical replicate 2


title: NA19159_D_trep2

description: technical replicate 2


title: NA19137_D_trep2

description: technical replicate 2


title: NA20529_E_trep2

description: technical replicate 2


title: NA20586_E_trep2

description: technical replicate 2


title: NA20586_D_trep2

description: technical replicate 2


title: NA20768_D_trep2

description: technical replicate 2


title: NA20535_E_trep2

description: technical replicate 2


title: NA20809_E_trep2

description: technical replicate 2


title: NA19116_D_trep2

description: technical replicate 2


title: NA20765_E_trep2

description: technical replicate 2


title: NA19137_E_trep2

description: technical replicate 2


title: NA20802_E_trep2

description: technical replicate 2


title: NA20809_D_trep2

description: technical replicate 2


title: NA19128_D_trep2

description: technical replicate 2


title: NA20802_D_trep2

description: technical replicate 2


title: NA19159_E_trep2

description: technical replicate 2


title: NA19138_D_trep2

description: technical replicate 2


title: NA18871_E_trep2

description: technical replicate 2


title: NA20585_D_trep2

description: technical replicate 2


title: NA18871_D_trep2

description: technical replicate 2


title: NA19144_E_trep2

description: technical replicate 2


title: NA20792_E_trep2

description: technical replicate 2


title: NA20585_E_trep2

description: technical replicate 2


title: NA20792_D_trep2

description: technical replicate 2


title: NA18870_E_trep2

description: technical replicate 2


title: NA18870_D_trep2

description: technical replicate 2


title: NA19238_D_trep2

description: technical replicate 2


title: NA19144_D_trep2

description: technical replicate 2


title: NA20525_D_trep2

description: technical replicate 2


title: NA20525_E_trep2

description: technical replicate 2


title: NA19238_E_trep2

description: technical replicate 2


title: NA18856_D_trep2

description: technical replicate 2


title: NA19200_D_trep2

description: technical replicate 2


title: NA19223_E_trep2

description: technical replicate 2


title: NA20819_D_trep2

description: technical replicate 2


title: NA18858_D_trep2

description: technical replicate 2


title: NA18858_E_trep2

description: technical replicate 2


title: NA19223_D_trep2

description: technical replicate 2


title: NA20799_E_trep2

description: technical replicate 2


title: NA20810_E_trep2

description: technical replicate 2


title: NA19200_E_trep2

description: technical replicate 2


title: NA20810_D_trep2

description: technical replicate 2


title: NA20778_E_trep2

description: technical replicate 2


title: NA19225_D_trep2

description: technical replicate 2


title: NA20508_E_trep2

description: technical replicate 2


title: NA20508_D_trep2

description: technical replicate 2


title: NA19225_E_trep2

description: technical replicate 2


title: NA20799_D_trep2

description: technical replicate 2


title: NA20819_E_trep2

description: technical replicate 2


title: NA18856_E_trep2

description: technical replicate 2


title: NA20534_E_trep2

description: technical replicate 2


title: NA20534_D_trep2

description: technical replicate 2


title: NA20778_D_trep2

description: technical replicate 2


title: NA19130_D_trep2

description: technical replicate 2


title: NA18517_D_trep2

description: technical replicate 2


title: NA18517_E_trep2

description: technical replicate 2


title: NA20540_D_trep2

description: technical replicate 2


title: NA18916_D_trep2

description: technical replicate 2


title: NA19130_E_trep2

description: technical replicate 2


title: NA19153_E_trep2

description: technical replicate 2


title: NA20509_E_trep2

description: technical replicate 2


title: NA20540_E_trep2

description: technical replicate 2


title: NA20813_E_trep2

description: technical replicate 2


title: NA19153_D_trep2

description: technical replicate 2


title: NA18916_E_trep2

description: technical replicate 2


title: NA19171_E_trep2

description: technical replicate 2


title: NA18907_E_trep2

description: technical replicate 2


title: NA18907_D_trep2

description: technical replicate 2


title: NA20803_D_trep2

description: technical replicate 2


title: NA20542_E_trep2

description: technical replicate 2


title: NA18510_D_trep2

description: technical replicate 2


title: NA20510_D_trep2

description: technical replicate 2


title: NA20757_E_trep2

description: technical replicate 2


title: NA19171_D_trep2

description: technical replicate 2


title: NA20509_D_trep2

description: technical replicate 2


title: NA19114_E_trep2

description: technical replicate 2


title: NA19147_D_trep2

description: technical replicate 2


title: NA20510_E_trep2

description: technical replicate 2


title: NA20752_D_trep2

description: technical replicate 2


title: NA20803_E_trep2

description: technical replicate 2


title: NA20757_D_trep2

description: technical replicate 2


title: NA18510_E_trep2

description: technical replicate 2


title: NA20752_E_trep2

description: technical replicate 2


title: NA19114_D_trep2

description: technical replicate 2


title: NA20813_D_trep2

description: technical replicate 2


title: NA20807_D_trep2

description: technical replicate 2


title: NA19147_E_trep2

description: technical replicate 2


title: NA20797_E_trep2

description: technical replicate 2


title: NA20524_E_trep2

description: technical replicate 2


title: NA18861_D_trep2

description: technical replicate 2


title: NA19119_D_trep2

description: technical replicate 2


title: NA20795_D_trep2

description: technical replicate 2


title: NA20785_E_trep2

description: technical replicate 2


title: NA18853_D_trep2

description: technical replicate 2


title: NA20797_D_trep2

description: technical replicate 2


title: NA20807_E_trep2

description: technical replicate 2


title: NA19127_D_trep2

description: technical replicate 2


title: NA20785_D_trep2

description: technical replicate 2


title: NA18861_E_trep2

description: technical replicate 2


title: NA18519_D_trep2

description: technical replicate 2


title: NA19127_E_trep2

description: technical replicate 2


title: NA18519_E_trep2

description: technical replicate 2


title: NA19119_E_trep2

description: technical replicate 2


title: NA20808_E_trep2

description: technical replicate 2


title: NA19257_E_trep2

description: technical replicate 2


title: NA20524_D_trep2

description: technical replicate 2


title: NA18853_E_trep2

description: technical replicate 2


title: NA20754_E_trep2

description: technical replicate 2


title: NA19257_D_trep2

description: technical replicate 2


title: NA20808_D_trep2

description: technical replicate 2


title: NA20754_D_trep2

description: technical replicate 2


title: NA18498_E_trep2

description: technical replicate 2


title: NA18498_D_trep2

description: technical replicate 2


title: NA20795_E_trep2

description: technical replicate 2


title: NA20517_E_trep2

description: technical replicate 2


title: NA20783_D_trep2

description: technical replicate 2


title: NA19210_D_trep2

description: technical replicate 2


title: NA19210_E_trep2

description: technical replicate 2


title: NA20783_E_trep2

description: technical replicate 2


title: NA20517_D_trep2

description: technical replicate 2


title: NA20818_D_trep1_brep2

description: technical replicate 1, biological replicate 2


title: NA18520_E_trep2

description: technical replicate 2


title: NA18489_D_trep1_brep2


title: NA20796_D_trep1

description: technical replicate 1


title: NA18520_D_trep2

description: technical replicate 2


title: NA20772_E_trep1

description: technical replicate 1


title: NA20528_E_trep1_brep2


title: NA19239_D_trep1_brep2


title: NA18489_E_trep1_brep2


title: NA20796_E_trep1

description: technical replicate 1


title: NA19239_E_trep1_brep2


title: NA20528_D_trep1_brep2


title: NA19099_D_trep1

description: technical replicate 1


title: NA19099_E_trep1

description: technical replicate 1


title: NA20772_D_trep1

description: technical replicate 1


title: NA20818_E_trep1_brep2


title: NA18859_D_trep1

description: technical replicate 1


title: NA20828_E_trep1

description: technical replicate 1


title: NA20542_D_trep2

description: technical replicate 2


title: NA19203_D_trep1

description: technical replicate 1


title: NA19203_E_trep1

description: technical replicate 1


title: NA18909_E_trep1

description: technical replicate 1


title: NA20520_D_trep1

description: technical replicate 1


title: NA18523_D_trep1

description: technical replicate 1


title: NA18859_E_trep1

description: technical replicate 1


title: NA18909_D_trep1

description: technical replicate 1


title: NA18523_E_trep1

description: technical replicate 1


title: NA20522_D_trep1

description: technical replicate 1


title: NA20801_E_trep1

description: technical replicate 1


title: NA18486_D_trep1

description: technical replicate 1


title: NA20828_D_trep1

description: technical replicate 1


title: NA19190_D_trep1

description: technical replicate 1


title: NA20544_D_trep1

description: technical replicate 1


title: NA19190_E_trep1

description: technical replicate 1


title: NA20801_D_trep1

description: technical replicate 1


title: NA19141_E_trep1

description: technical replicate 1


title: NA20804_D_trep1

description: technical replicate 1


title: NA20522_E_trep1

description: technical replicate 1


title: NA20756_E_trep1

description: technical replicate 1


title: NA20804_E_trep1

description: technical replicate 1


title: NA20756_D_trep1

description: technical replicate 1


title: NA18486_E_trep1

description: technical replicate 1


title: NA19207_D_trep1

description: technical replicate 1


title: NA20544_E_trep1

description: technical replicate 1


title: NA19141_D_trep1

description: technical replicate 1


title: NA19108_D_trep1

description: technical replicate 1


title: NA19207_E_trep1

description: technical replicate 1


title: NA20519_E_trep1

description: technical replicate 1


title: NA18502_E_trep1

description: technical replicate 1


title: NA20805_D_trep1

description: technical replicate 1


title: NA18502_D_trep1

description: technical replicate 1


title: NA20805_E_trep1

description: technical replicate 1


title: NA20766_D_trep1

description: technical replicate 1


title: NA19108_E_trep1

description: technical replicate 1


title: NA18501_E_trep1

description: technical replicate 1


title: NA18501_D_trep1

description: technical replicate 1


title: NA19222_D_trep1

description: technical replicate 1


title: NA20581_D_trep1

description: technical replicate 1


title: NA20766_E_trep1

description: technical replicate 1


title: NA19092_E_trep1

description: technical replicate 1


title: NA19239_E_trep1_brep1

description: technical replicate 1, biological replicate 1


title: NA20818_D_trep1_brep1


title: NA20528_D_trep1_brep1


title: NA20589_E_trep1

description: technical replicate 1


title: NA20818_E_trep1_brep1


title: NA18489_E_trep1_brep1


title: NA20581_E_trep1

description: technical replicate 1


title: NA18505_D_trep1

description: technical replicate 1


title: NA19092_D_trep1

description: technical replicate 1


title: NA20589_D_trep1

description: technical replicate 1


title: NA18489_D_trep1_brep1


title: NA19222_E_trep1

description: technical replicate 1


title: NA20528_E_trep1_brep1


title: NA20815_E_trep1

description: technical replicate 1


title: NA18505_E_trep1

description: technical replicate 1


title: NA20815_D_trep1

description: technical replicate 1


title: NA20773_D_trep1

description: technical replicate 1


title: NA19239_D_trep1_brep1


title: NA18516_D_trep1

description: technical replicate 1


title: NA18516_E_trep1

description: technical replicate 1


title: NA18511_D_trep1

description: technical replicate 1


title: NA20773_E_trep1

description: technical replicate 1


title: NA20512_D_trep1

description: technical replicate 1


title: NA20505_E_trep1

description: technical replicate 1


title: NA20512_E_trep1

description: technical replicate 1


title: NA18507_E_trep1

description: technical replicate 1


title: NA20505_D_trep1

description: technical replicate 1


title: NA18507_D_trep1

description: technical replicate 1


title: NA18511_E_trep1

description: technical replicate 1


title: NA18522_E_trep1

description: technical replicate 1


title: NA20769_D_trep1

description: technical replicate 1


title: NA19102_D_trep1

description: technical replicate 1


title: NA19116_E_trep1

description: technical replicate 1


title: NA20769_E_trep1

description: technical replicate 1


title: NA20539_D_trep1

description: technical replicate 1


title: NA18504_D_trep1

description: technical replicate 1


title: NA20520_E_trep1

description: technical replicate 1


title: NA18522_D_trep1

description: technical replicate 1


title: NA19102_E_trep1

description: technical replicate 1


title: NA18504_E_trep1

description: technical replicate 1


title: NA20539_E_trep1

description: technical replicate 1


title: NA18508_E_trep1

description: technical replicate 1


title: NA20535_E_trep1

description: technical replicate 1


title: NA20787_E_trep1

description: technical replicate 1


title: NA19138_D_trep1

description: technical replicate 1


title: NA18508_D_trep1

description: technical replicate 1


title: NA19116_D_trep1

description: technical replicate 1


title: NA20519_D_trep1

description: technical replicate 1


title: NA20812_D_trep1

description: technical replicate 1


title: NA20582_E_trep1

description: technical replicate 1


title: NA20529_E_trep1

description: technical replicate 1


title: NA20812_E_trep1

description: technical replicate 1


title: NA19128_E_trep1

description: technical replicate 1


title: NA20787_D_trep1

description: technical replicate 1


title: NA19128_D_trep1

description: technical replicate 1


title: NA20529_D_trep1

description: technical replicate 1


title: NA20765_E_trep1

description: technical replicate 1


title: NA20535_D_trep1

description: technical replicate 1


title: NA20765_D_trep1

description: technical replicate 1


title: NA19138_E_trep1

description: technical replicate 1


title: NA20768_D_trep1

description: technical replicate 1


title: NA19160_D_trep1

description: technical replicate 1


title: NA20809_D_trep1

description: technical replicate 1


title: NA19160_E_trep1

description: technical replicate 1


title: NA18499_E_trep1

description: technical replicate 1


title: NA19159_E_trep1

description: technical replicate 1


title: NA19159_D_trep1

description: technical replicate 1


title: NA18499_D_trep1

description: technical replicate 1


title: NA19137_D_trep1

description: technical replicate 1


title: NA20768_E_trep1

description: technical replicate 1


title: NA20809_E_trep1

description: technical replicate 1


title: NA19137_E_trep1

description: technical replicate 1


title: NA20802_E_trep1

description: technical replicate 1


title: NA20585_E_trep1

description: technical replicate 1


title: NA20586_D_trep1

description: technical replicate 1


title: NA20586_E_trep1

description: technical replicate 1


title: NA20792_E_trep1

description: technical replicate 1


title: NA18871_D_trep1

description: technical replicate 1


title: NA20792_D_trep1

description: technical replicate 1


title: NA19144_E_trep1

description: technical replicate 1


title: NA19223_D_trep1

description: technical replicate 1


title: NA20802_D_trep1

description: technical replicate 1


title: NA18870_D_trep1

description: technical replicate 1


title: NA18871_E_trep1

description: technical replicate 1


title: NA20525_D_trep1

description: technical replicate 1


title: NA19144_D_trep1

description: technical replicate 1


title: NA19238_E_trep1

description: technical replicate 1


title: NA20585_D_trep1

description: technical replicate 1


title: NA20819_E_trep1

description: technical replicate 1


title: NA19238_D_trep1

description: technical replicate 1


title: NA20819_D_trep1

description: technical replicate 1


title: NA18870_E_trep1

description: technical replicate 1


title: NA18858_D_trep1

description: technical replicate 1


title: NA18858_E_trep1

description: technical replicate 1


title: NA20799_E_trep1

description: technical replicate 1


title: NA20810_D_trep1

description: technical replicate 1


title: NA19200_E_trep1

description: technical replicate 1


title: NA20525_E_trep1

description: technical replicate 1


title: NA20810_E_trep1

description: technical replicate 1


title: NA20799_D_trep1

description: technical replicate 1


title: NA20508_D_trep1

description: technical replicate 1


title: NA20508_E_trep1

description: technical replicate 1


title: NA20778_E_trep1

description: technical replicate 1


title: NA18856_E_trep1

description: technical replicate 1


title: NA19200_D_trep1

description: technical replicate 1


title: NA19225_D_trep1

description: technical replicate 1


title: NA18517_D_trep1

description: technical replicate 1


title: NA18856_D_trep1

description: technical replicate 1


title: NA20778_D_trep1

description: technical replicate 1


title: NA20582_D_trep1

description: technical replicate 1


title: NA19223_E_trep1

description: technical replicate 1


title: NA19130_E_trep1

description: technical replicate 1


title: NA19225_E_trep1

description: technical replicate 1


title: NA20534_E_trep1

description: technical replicate 1


title: NA18916_D_trep1

description: technical replicate 1


title: NA20534_D_trep1

description: technical replicate 1


title: NA18517_E_trep1

description: technical replicate 1


title: NA20509_D_trep1

description: technical replicate 1


title: NA20540_E_trep1

description: technical replicate 1


title: NA19130_D_trep1

description: technical replicate 1


title: NA18916_E_trep1

description: technical replicate 1


title: NA20509_E_trep1

description: technical replicate 1


title: NA20813_D_trep1

description: technical replicate 1


title: NA20540_D_trep1

description: technical replicate 1


title: NA19153_D_trep1

description: technical replicate 1


title: NA20813_E_trep1

description: technical replicate 1


title: NA19114_E_trep1

description: technical replicate 1


title: NA20803_E_trep1

description: technical replicate 1


title: NA19171_E_trep1

description: technical replicate 1


title: NA20542_D_trep1

description: technical replicate 1


title: NA20803_D_trep1

description: technical replicate 1


title: NA20757_D_trep1

description: technical replicate 1


title: NA20542_E_trep1

description: technical replicate 1


title: NA19171_D_trep1

description: technical replicate 1


title: NA20510_E_trep1

description: technical replicate 1


title: NA19114_D_trep1

description: technical replicate 1


title: NA19147_E_trep1

description: technical replicate 1


title: NA20757_E_trep1

description: technical replicate 1


title: NA18510_D_trep1

description: technical replicate 1


title: NA20807_E_trep1

description: technical replicate 1


title: NA18907_E_trep1

description: technical replicate 1


title: NA20510_D_trep1

description: technical replicate 1


title: NA18907_D_trep1

description: technical replicate 1


title: NA18510_E_trep1

description: technical replicate 1


title: NA20752_D_trep1

description: technical replicate 1


title: NA19147_D_trep1

description: technical replicate 1


title: NA20807_D_trep1

description: technical replicate 1


title: CPG-stimulated B-CLL_mutated repl 8

city: Aviano

first: daniela

last: marconi

address: Via franco Gallini 2

country: Italy

institute: CRO AVIANO

description:
Biological replicate 8 of 8
251485057173_1_1_G48_CpG

hyb_protocol: The Hybridization was performed acording to Ambion protocol

scan_protocol: Slides were analysed by Agilent Microarray Scanner G2565AA

data_processing: Background subtraction method: Marginal log-likelihood of foreground values for normal + exponential model and its derivatives.Whithin Normalization method: loess. Between Normalization method: quantile

source_name: CPG stimulated purified cell of  CLL mutated

label_protocol: Total RNA was labelled according to Ambion protocol. 825 ng of Cy3-labeled reference aRNA (according to Agilent protocol)

extract_protocol: CLL cells were purified by negative selection using anti-CD3, anti-CD14 and anti-CD16 mouse monoclonal antibodies and Dynabeads coated with a pan anti-mouse IgG antibody. The purity of the CLL cells after negative selection was monitored by flow-cytometry and the percentage of CD5+/CD19+ cells exceeded 98% for each sample. CLL cells were resuspended in RPMI complete medium at a density of 2 × 105 and stimulated with 7.5 μg/ml complete phosphorothioate CpG ODN oligonucleotide 2006 (5′-TCGTCGTTTTGTCGTTTTGTCGTT-3′) or left unstimulated for 18 h.Total RNA was extracted according to TRIZOL reagent protocol

value: purified CLL cells

source_name: reference

tag: sample origin

value: pooled normal PB B cells of healthy donors


title: CPG-stimulated B-CLL_mutated repl 7

description:
Biological replicate 7 of 8
251485057174_1_1_G202_CpG


title: CPG-stimulated B-CLL_mutated repl 5

description:
Biological replicate 5 of 8
251485057174_1_1_G158_CpG


title: NA20752_E_trep1

description: technical replicate 1


title: NA18853_E_trep1

description: technical replicate 1


title: NA18853_D_trep1

description: technical replicate 1


title: CPG-stimulated B-CLL_mutated repl 6

description:
Biological replicate 6 of 8
251485057174_1_1_G194_CpG


title: flat PS (fPS) cells sample3

city: beijing

first: Yan

last: Shen

address: yiheyuan lu No.5

country: China

institute: Laboratory of Stem Cell and Regenerative Biology

description: Gene expression data from Sprague-Dawley rats embryonic stem cells

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

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

data_processing: An invariant set normalization procedure was performed to normalize the different arrays using DNA-chip analyzer [dChip]

source_name: rat pluripotent stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Rat pluripotent stem (PS) cell were cultured in 50% DMEM/F12 (Gibco), 50% Neurobasal medium (Gibco), 0.5×N2 (Gibco), 0.5×B27 (Gibco), 2 mM L-Glutamax1 (Gibco), 10 ng/ml recombinant hLIF (Chemicon), 3 μM CHIR99021(StemGent), and 0.5 μM PD0325901(Axon) (PS medium). Rat pluripotent stem (PS) cell were maintained on mitomycin C-treated MEFs in DMEM (Invitrogen) with 15% FBS (Hyclone).

treatment_protocol: Rat pluripotent stem (PS) cell were manually removed from culture, rinsed with PBS and placed on ice in the Trizol solution (GibcoBRL) for total RNA purification.

value: Sprague-Dawley

value: flat pluripotent stem (fPS) cells


title: rat embryonic stem cells sample1

source_name: rat embryonic stem cells

value: embryonic stem (ES) cells


title: CPG-stimulated B-CLL_mutated repl 1

description:
Biological replicate 1 of 8
251485057173_1_1_G57_CpG


title: CPG-stimulated B-CLL_mutated repl 2

description:
Biological replicate 2 of 8
251485057173_1_1_G148_CpG


title: MEFs SKO+MEF2C,D10-2

city: Guangzhou

first: Duanqing

last: Pei

state: Guangdong

address: Room 301, International Business Incubator, Guangzhou science park

department: Center for Molecular Medicine

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences(GIBH.CAS)

description: Gene expression data from MaF pre-iPSC9P2, Vc-, D3

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using  Partek GS Version 6.5 according to use's manual. In brief, we normalized data using RMA algorithm, summarized exons to genes, and then detected differentially expression genes.

source_name: MEFs SKO+MEF2C,lysed on D10,experiment 2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: MEFs were cultured in mESC medium. Media were changed everyday.

extract_protocol: Cells were trypsinized and feeder cells were eliminated. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

value: mouse embryonic fibroblast cells

value: ICR

tag: time

value: lysed on D10


title: NA19119_E_trep1

description: technical replicate 1


title: Unstimulated B-CLL_mutated repl 8

description:
Biological replicate 8 of 8
251485054699_1_4_G48_U

source_name: unstimulated purified cell of  CLL mutated


title: CPG-stimulated B-CLL_mutated repl 4

description:
Biological replicate 4 of 8
251485057174_1_1_G220_CpG


title: MEFs SKO+MEF2C,D6-2

source_name: MEFs SKO+MEF2C,lysed on D6,experiment 2

value: lysed on D6


title: flat PS (fPS) cells sample2


title: rat embryonic stem cells sample2


title: MEFs SKO+HDAC7,D10-1

source_name: MEFs SKO+HDAC7,lysed on D10,experiment 1


title: NA20797_E_trep1

description: technical replicate 1

value: EBV-transformed B lymphocytes


title: NA19119_D_trep1

description: technical replicate 1

value: Yoruba in Ibadan, Nigeria


title: Unstimulated B-CLL_mutated repl 7

description:
Biological replicate 7 of 8
251485054699_1_2_G158_U


title: rat embryonic stem cells sample3


title: flat PS (fPS) cells sample1


title: MEFs SKO+MEF2C,D10-1

source_name: MEFs SKO+MEF2C,lysed on D10,experiment 1


title: CPG-stimulated B-CLL_mutated repl 3

description:
Biological replicate 3 of 8
251485057173_1_1_G42_CpG


title: NA20797_D_trep1

description: technical replicate 1


title: MEFs SKO+MEF2C,D6-1

source_name: MEFs SKO+MEF2C,lysed on D6,experiment 1


title: Unstimulated B-CLL_mutated repl 6

description:
Biological replicate 6 of 8
251485059531_1_4_G194_U


title: MEFs SKO+HDAC7,D6-1

source_name: MEFs SKO+HDAC7,lysed on D6,experiment 1


title: NA20524_D_trep1

description: technical replicate 1


title: NA20524_E_trep1

description: technical replicate 1

value: vehicle(EtOH)


title: NA18861_E_trep1

description: technical replicate 1


title: NA18861_D_trep1

description: technical replicate 1


title: MEFs GFP,D10

source_name: MEFs GFP,lysed on D10

value: GFP


title: MEFs SKO+HDAC7,D6-2

source_name: MEFs SKO+HDAC7,lysed on D6,experiment 2


title: Unstimulated B-CLL_mutated repl 5

description:
Biological replicate 5 of 8
251485059111_1_1_G220_U


title: gDNA_Culture ANAS_rep3

city: Berkeley

first: Patrick

last: Lee

address: 209 O'Brien Hall

department: Civil and Environmental Engineering

institute: University of California, Berkeley

hyb_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

data_processing: Data analysis was performed using Affymetrix GeneChip software and the MAS5 algorithm. Each microarray was normalized by scaling the signal intensities of the positive control spike-mix to a target signal intensity of 2500 to allow comparison between microarrays.

organism: Dehalococcoides

source_name: 1 µg of gDNA

label_protocol: One µg of gDNA was prepared for each microarray according to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).

growth_protocol: For isolates, multiple 100 mL cultures were grown in parallel in order to obtain enough biomass. Pure cultures were provided with the appropriate chlorinated ethene, hydrogen and acetate. The enrichment culture was maintained in a semi-batch reactor with lactate and trichloroethene.

extract_protocol: gDNA was extracted using either the Qiagen (Valencia, CA) DNeasy Blood & Tissue kit or the AllPrep DNA/RNA Mini Kit according to the manufacturers’ recommendations.

tag: bacterial culture

value: Enrichment culture


title: Unstimulated B-CLL_mutated repl 4

description:
Biological replicate 4 of 8
251485054701_1_2_G148_U

tag: cell type


title: MEFs SKO+Flag,D10-2

source_name: MEFs SKO+Flag,lysed on D10,experiment 2

tag: genotype/variation

value: SKO+Flag


title: gDNA_Culture ANAS_rep2

scan_protocol: According to the protocols outlined in section 3, chapter 3 of the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA).


title: MEFs SKO+Flag,D6-1

source_name: MEFs SKO+Flag,lysed on D6,experiment 1


title: Unstimulated B-CLL_mutated repl 3

description:
Biological replicate 3 of 8
251485054701_1_1_G57_U


title: MEFs SKO+Flag,D6-2

source_name: MEFs SKO+Flag,lysed on D6,experiment 2


title: NA19127_D_trep1

description: technical replicate 1

source_name: lymphoblastoid cell line

value: dexamethasone


title: Unstimulated B-CLL_mutated repl 2

description:
Biological replicate 2 of 8
251485054700_1_2_G42_U

source_name: reference


title: MEFs GFP,D6

source_name: MEFs GFP,lysed on D6


title: NA20785_D_trep1

description: technical replicate 1

value: Toscani in Italia


title: NA20785_E_trep1

description: technical replicate 1


title: MEFs SKO+Flag,D10-1

source_name: MEFs SKO+Flag,lysed on D10,experiment 1


title: Mouse ES-derived motor neuron_GFP hi_rep2

city: Cambridge

first: Esther

middle: Yesde

last: Son

state: MA

address: 7 Divinity Avenue

department: Stem Cells and Regenerative Biology

institute: Harvard University

description: FACS-purified and double-amplified

data_processing: The data were normalized using cubic spline normalization in BeadStudio.

source_name: Mouse embryonic stem cell-derived motor neurons

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

extract_protocol: RNA was extracted with Trizol reagent

tag: gfp fluorescence

value: GFP-high

tag: cell line


title: gDNA_Culture ANAS_rep1


title: Mouse ES-derived motor neuron_GFP med_rep1

description: FACS-purified and double-amplified

tag: genotype

value: GFP-medium


title: gDNA_Strain ANAS2_rep3

organism: Dehalococcoides sp. ANAS2

value: Dehalococcoides sp. ANAS2

value: Pure culture


title: Mouse ES-derived motor neuron_GFP med_rep2

description: FACS-purified and double-amplified


title: Unstimulated B-CLL_mutated repl 1

description:
Biological replicate 1 of 8
251485054700_1_1_G202_U

source_name: unstimulated purified cell of  CLL mutated

value: purified CLL cells

value: pooled normal PB B cells of healthy donors


title: Mouse induced motor neuron_GFP med

description: FACS-purified and double-amplified

source_name: Mouse induced (reprogrammed) motor neurons

tag: background mouse strain


title: NA18519_D_trep1

description: technical replicate 1


title: NA19127_E_trep1

description: technical replicate 1


title: NA18519_E_trep1

description: technical replicate 1


title: NA19257_D_trep1

description: technical replicate 1


title: gDNA_Strain ANAS1_rep3

organism: Dehalococcoides sp. ANAS1

value: Dehalococcoides sp. ANAS1


title: gDNA_Strain ANAS2_rep1


title: Mouse induced motor neuron_GFP hi

description: FACS-purified and double-amplified


title: Mouse embryonic motor neuron_GFP hi_rep2

description: FACS-purified and double-amplified

source_name: Mouse embryonic motor neurons (E13.5)


title: gDNA_Strain ANAS2_rep2


title: Mouse ES-derived motor neuron_GFP hi_rep1

description: FACS-purified and double-amplified


title: gDNA_Strain ANAS1_rep2


title: NA19257_E_trep1

description: technical replicate 1


title: NA19153_E_trep1

description: technical replicate 1


title: gDNA_Negative_rep3

description: gDNA purchased from the American Type Culture Collection (Manassas, VA)

organism: Anaeromyxobacter dehalogenans 2CP-C

value: Anaeromyxobacter dehalogenans strain 2CP-C


title: gDNA_Strain ANAS1_rep1


title: Mouse embryonic motor neuron_GFP med_rep2

description: FACS-purified and double-amplified


title: NA20795_E_trep1

description: technical replicate 1


title: Mouse embryonic motor neuron_GFP med_rep1

description: FACS-purified and double-amplified


title: gDNA_Negative_rep2


title: NA20808_E_trep1

description: technical replicate 1


title: NA20795_D_trep1

description: technical replicate 1


title: NA20754_D_trep1

description: technical replicate 1


title: gDNA_Negative_rep1


title: Mouse embryonic motor neuron_GFP hi_rep1

description: FACS-purified and double-amplified


title: NA20754_E_trep1

description: technical replicate 1


title: gDNA_195_BAV1_3 to 1_rep3

description: 0.75 µg of strain 195 gDNA and 0.25 µg of strain BAV1 was used

organism:
Dehalococcoides mccartyi BAV1
Dehalococcoides mccartyi 195

value: Dehalococcoides strains 195 & BAV1

value: Mixture of two cultures


title: MEFs SKO+HDAC7,D10-2

source_name: MEFs SKO+HDAC7,lysed on D10,experiment 2

value: mouse embryonic fibroblast cells

value: ICR

value: lysed on D10


title: gDNA_195_BAV1_3 to 1_rep1


title: NA20808_D_trep1

description: technical replicate 1

value: EBV-transformed B lymphocytes


title: NA20517_E_trep1

description: technical replicate 1

value: vehicle(EtOH)


title: gDNA_195_BAV1_3 to 1_rep2


title: NA18498_E_trep1

description: technical replicate 1

value: Yoruba in Ibadan, Nigeria


title: gDNA_195_BAV1_1 to 1_rep2

description: 0.5 µg of gDNA from each culture was used


title: gDNA_195_BAV1_1 to 1_rep1


title: NA18498_D_trep1

description: technical replicate 1

value: dexamethasone


title: gDNA_195_BAV1_1 to 1_rep3


title: BY4741_NaCl_t090_rep3

type: mixed

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

description: This sample was taken 90 minutes after the addition of 0.7M NaCl. Biological replicate #3

hyb_protocol: Hybridized for 16 hours on a Maui hybridization machine as per Nimblegen protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner

data_processing:
Data were extracted using Nimblescan version 2.6.0.0. Probe data for all 18 arrays were quantile normalized using the bioconductor package limma, and log2 ratio of cyanine550/cyanine650 for each time point compared to the t0 sample was calculated for each probe. Gene expression change was calculated as the median log2 ratio for all probes completely encompassed by the open reading frame of interest.
Quantile normalized signal intensity for each probe on each array

label: Oyster cyanine 550 dye

organism: Saccharomyces cerevisiae

label_protocol: Indirect labeling using amino-allyl-dUTP and cyanine dyes from Flownamics (Madison, Wi) as described in Gasch AP Methods in Enzymology (2002) 350: 393-414

growth_protocol: Cells were grown at least 7 doublings in log phase in YPD medium at 30C before addition of NaCl to a final concentration of 0.7M

extract_protocol: Hot-phenol RNA extraction as described in Gasch AP Methods in Enzymology (2002) 350: 393-414

treatment_protocol: Osmotic shock: an aliquot of pre-warmed YPD+4M NaCl was added, to a final concentration of 0.7M NaCl

tag: treatment group

value: genome DNA reference

label: Oyster cyanine 650 dye

value: 90 min post NaCl


title: gDNA_Strain BAV1_rep3

organism: Dehalococcoides mccartyi BAV1

value: Dehalococcoides sp. BAV1


title: BY4741_NaCl_t240_rep3

description: This sample was taken 240 minutes after the addition of 0.7M NaCl. Biological replicate #3

value: 240 min post NaCl


title: NA20517_D_trep1

description: technical replicate 1

value: Toscani in Italia


title: NA19210_D_trep1

description: technical replicate 1


title: BY4741_NaCl_t120_rep3

description: This sample was taken 120 minutes after the addition of 0.7M NaCl. Biological replicate #3

value: 120 min post NaCl


title: NA19210_E_trep1

description: technical replicate 1


title: NA20783_D_trep1

description: technical replicate 1


title: NA20783_E_trep1

description: technical replicate 1


title: BY4741_NaCl_t060_rep3

description: This sample was taken 60 minutes after the addition of 0.7M NaCl. Biological replicate #3

value: 60 min post NaCl


title: BY4741_NaCl_t030_rep3

description: This sample was taken 30 minutes after the addition of 0.7M NaCl. Biological replicate #3

value: 30 min post NaCl


title: gDNA_Strain 195_rep3

organism: Dehalococcoides mccartyi 195

value: Dehalococcoides ethenogenes 195

value: Pure culture


title: gDNA_Strain BAV1_rep2


title: gDNA_Strain 195_rep2


title: BY4741_NaCl_t240_rep2

description: This sample was taken 240 minutes after the addition of 0.7M NaCl. Biological replicate #2


title: NA18520_E_trep1

description: technical replicate 1


title: NA18520_D_trep1

description: technical replicate 1


title: BY4741_NaCl_t000_rep3

description: This sample was taken pre-stress. Biological replicate #3.

value: 0 min (before NaCl addition)


title: gDNA_Strain BAV1_rep1


title: BY4741_NaCl_t120_rep2

description: This sample was taken 120 minutes after the addition of 0.7M NaCl. Biological replicate #2


title: gDNA_Strain 195_rep1


title: MCF7 cells after 72hr treatment with 5uM 5-Aza-2'-deoxycytidine(Aza)

city: seoul

first: Ju Hee

last: Kim

address: pil-dong 3-ga

department: Life Science

country: South Korea

institute: Dongguk University

description: Analysis used aerobic steady state RNA as control samples for comparison to the experimental samples taken at 5, 10, 15 and 60 min.

hyb_protocol: standard Phalanx protocol (See http://www.phalanxbiotech.com/)

growth_protocol: A human breast cancer cell line, MCF-7, was grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA from the MCF-7 cell was isolated using the Trizol (Qiagen, Valencia, CA) according to the supplier's protocols.

treatment_protocol: A human breast cancer cell line, MCF-7, was treated with 5-Aza-2'-deoxycytidine(Aza), at 5μM and 10μM for 72hr. Culture medium with or without treatment was changed every 24 hr.

value: 5uM 5-Aza-2'-deoxycytidine for 72 h

source_name: untreated

value: untreated


title: BY4741_NaCl_t060_rep2

description: This sample was taken 60 minutes after the addition of 0.7M NaCl. Biological replicate #2


title: MCF7 cells after 72hr treatment with 10uM 5-Aza-2'-deoxycytidine(Aza)

scan_protocol: standard Phalanx protocol (See http://www.phalanxbiotech.com/)

value: 10uM 5-Aza-2'-deoxycytidine for 72 h


title: SK-N-SH PARP3 versus IgG GPL4124 replicate 1

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

data_processing: Raw data were first background subtracted and normalized using median normalization. Regions significantly enriched for PARP3 relative to IgG were identified as described (Lee et al. 2006). Briefly, the genome was scanned three probes at a time. When three probes were in a window of 1000 bp or less, they were further refered to as triplets. Triplets were considered significant when the PARP3 signal in 2 out of 3 probes had a p-value lower than 0.05 or when the center probe signal had a p-value lower than 0.01 and the first and last probes had a p-value lower than 0.1. The false discovery rate is estimated at 0.005%. All the data were process within R using the limma package.

source_name: Unsynchronized SK-N-SH

growth_protocol: The human neuroblastoma cell line SK-N-SH (ATCC: HTB-11) was grown at 37°C in a 5% CO2 environment in DMEM (Invitrogen Corp.) supplemented with 1% Glutamax (Invitrogen), 10% foetal bovine serum (Wisent), 100 IU/ml penicillin and 100 μg/ml streptomycin (Invitrogen).

extract_protocol: Cells were treated with 1% formaldehyde for 8 min to crosslink proteins to DNA. Glycine (0.125 M) was added to quench the reaction. Cells were collected using a cell scraper, washed twice in cold PBS1X, washed for 10 min in solution I (10 mM HEPES, pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100) and 10 min in solution II (10 mM HEPES, pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). Cells were resuspended in lysis buffer (25 mM Tris–HCl, pH 7.5, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) and sonicated for 6 times 10 s (30% output) to shear chromatin to an average size of 0.5 kb using a Fisher Sonic Dismembrator sonicator.

value: SK-N-SH (ATCC:HTB-11)

tag: antibody

value: Rabbit IgG


title: BY4741_NaCl_t240_rep1

description: This sample was taken 240 minutes after the addition of 0.7M NaCl. Biological replicate #1


title: THP-1 1,25D 4h rep3

status: Public on Aug 17 2011

city: Kuopio

first: Sami

last: Heikkinen

address: Yliopistonranta 1E

department: Institute of Biomedicine

institute: University of Eastern Finland

description: replicate 3

data_processing: The data were normalized using VST transformation and RSN normalization used as standard approach for Illumina arrays with the R/lumi package

source_name: THP-1 cells 1,25D 4h rep3

growth_protocol: Cells were grown in RPMI 1640 medium supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin, and kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.

extract_protocol: Total RNA was extracted with Mini RNA Isolation II kit (Zymo Research). Quality control, including verification of the absence of genomic DNA, was performed with Biorad Experion.

treatment_protocol: Prior to mRNA extraction, cells were grown overnight in phenol red-free medium supplemented with charcoal-stripped fetal bovine serum. Then, cells were treated for indicated time(s) with vehicle (ethanol, finally 0.1%) or 100 nM 1α,25(OH)2D3 (Sigma-Aldrich)

value: monocytic leucemia

value: 4 h


title: THP-1 vehicle 4h rep3

description: replicate 3

source_name: THP-1 cells vehicle 4h rep3

value: vehicle


title: SK-N-SH PARP3 versus IgG GPL4124 replicate 2


title: BY4741_NaCl_t120_rep1

description: This sample was taken 120 minutes after the addition of 0.7M NaCl. Biological replicate #1

value: genome DNA reference


title: THP-1 1,25D 4h rep2

description: replicate 2

source_name: THP-1 cells 1,25D 4h rep2


title: BY4741_NaCl_t090_rep2

description: This sample was taken 90 minutes after the addition of 0.7M NaCl. Biological replicate #2

value: 90 min post NaCl


title: THP-1 vehicle 4h rep1

description: replicate 1

source_name: THP-1 cells vehicle 4h rep1


title: THP-1 vehicle 4h rep2

description: replicate 2

source_name: THP-1 cells vehicle 4h rep2


title: SK-N-SH PARP3 versus IgG GPL4125 replicate 2


title: BY4741_NaCl_t030_rep2

description: This sample was taken 30 minutes after the addition of 0.7M NaCl. Biological replicate #2


title: SK-N-SH PARP3 versus IgG GPL4125 replicate 1


title: BY4741_NaCl_t030_rep1

description: This sample was taken 30 minutes after the addition of 0.7M NaCl. Biological replicate #1


title: PB-Tumor86-L1

city: CHAPEL HILL

first: PILAR

last: BLANCAFORT

state: NORTH CAROLINA

address: 4009 MASON FARM RD

department: PHARMACOLOGY

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

description: C_RMF:Tumor generated from OTBCs-L1

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 5.1 analysis software.

data_processing: Data for both channels were Lowess-normalized and then log(2) ratio was taken

source_name: Stratagene Human Universal Reference that contained 1/10 added MCF7 and ME16C RNAs

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-125

extract_protocol: Total RNA isolated by Stratagene

tag: reference

value: Human Reference B

extract_protocol: Qiagen Rneasy Kit

tag: tumor

value: from OTBCs86-L1


title: THP-1 1,25D 4h rep1

description: replicate 1

source_name: THP-1 cells 1,25D 4h rep1


title: BY4741_NaCl_t000_rep2

description: This sample was taken pre-stress. Biological replicate #2.

tag: strain


title: BY4741_NaCl_t090_rep1

description: This sample was taken 90 minutes after the addition of 0.7M NaCl. Biological replicate #1


title: BY4741_NaCl_t060_rep1

description: This sample was taken 60 minutes after the addition of 0.7M NaCl. Biological replicate #1

value: 60 min post NaCl


title: BY4741_NaCl_t000_rep1

description: This sample was taken pre-stress. Biological replicate #1.


title: PB-OTBCs86-L1-OCT4siRNA Repl1

description: C_RMF:OTBCs-86-L1; OCT4 transduced breast colonies derived from p86 and transfected with an OCT4 siRNA replicate

source_name: PB-OTBCs86-L1-OCT4siRNA Repl1

value: OTBCs81-L1 OCT4 transduced breast cells transfected with an OCT4 siRNA replicate


title: PB-OTBCs86-L6

description: C_RMF:OTBCs-86; OCT4 transduced breast colonies derived from p86

value: OTBCs86-L6 OCT4 transduced breast cells


title: PB-OTBCs48-L2

description: C_RMF:OTBCs-48; OCT4 transduced breast colonies derived from p48

value: OTBCs48-L1 OCT4 transduced breast cells


title: PB-OTBCs86-L1

value: OTBCs86-L1 OCT4 transduced breast cells


title: PB-OTBCs86-L4

value: OTBCs86-L4 OCT4 transduced breast cells


title: PB-OTBCs78-L1

description: C_RMF:OTBCs-78; OCT4 transduced breast colonies derived from p78

value: OTBCs78-L1 OCT4 transduced breast cells


title: PB-p78

description: C_RMF:p52 Normal breast epithelial cell preparation derived from a reduction mammoplasty

value: p78 human mammary epithelial cell preparation


title: PB-OTBCs52-L1

description: C_RMF:OTBCs-52; OCT4 transduced breast colonies derived from p52

value: OTBCs52-L1 OCT4 transduced breast cells


title: PB-p52

description: C_RFM: p48 Normal breast epithelial cell preparation derived from a reduction mammoplasty

value: p52 human mammary epithelial cell preparation


title: PB-p86

description: C_RMF:p78 Normal breast epithelial cell preparation derived from a reduction mammoplasty

value: p86 human mammary epithelial cell preparation


title: PB-p48

description: C_RMF:p86 Normal breast epithelial cell preparation obtained from Lonza

value: p48 human mammary epithelial cell preparation