title: SL29-mock-2

description: Gene expression data from mock-infected SL-29s,24 hpi

data_processing: The data were normalized using Robust Multichip Average normalization and analyzed using MeV v. 4.6.1 from the TM4 software suite

source_name: SL-29 chicken embryonic fibroblasts, mock-infected

treatment_protocol: SL-29 cells were infected with Toxoplasma gondii tachyzoites (prepared by syringe-lysis from infected HFFs and extensive washing in PBS) of the indicated strain at multiplicity of infection ~3; mock-infection was carried out by syringe-lysing HFFs instead of HFFs and adding equivalent volume of resuspension to SL-29 cells; 24 hours post-infection, the supernatant was removed and cells were lysed in Trizol for RNA extraction.

value: none (mock-infected)


title: SL29-ME49-2

status: Public on May 27 2011

type: RNA

city: Stanford

first: Yi-Ching

last: Ong

state: CA

address: 299 W. Campus Dr.

department: Microbiology & Immunology

country: USA

institute: Stanford University

description: Gene expression data from SL-29s infected with indicated T. gondii strain, 24 hpi

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridizedl on GeneChip Chicken Genome Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

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

label: biotin

molecule: total RNA

organism: Gallus gallus

source_name: SL-29 chicken embryonic fibroblasts infected with Toxoplasma gondii of indicated strain, 24 hpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for one-cycle amplification from 5 ug total RNA (GeneChip Expression Analysis Technical Manual, P/N 702232 Rev. 3, Affymetrix).

growth_protocol: SL-29 (ATCC CRL-1590) chicken embryonic fibroblast cells were grown to confluence in Dulbecco’s modified Eagle’s medium (30-2002; ATCC, Manassas, VA) supplemented with 5% FCS (Hyclone, Logan, UT) and 5% tryptose phosphate broth (Sigma, St. Louis, MO).  Passage #<10 for all experiments performed.

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

tag: cell line

value: SL-29 (chicken embryonic fibroblasts)

tag: parasite strain

value: ME49 (Type II)

tag: time point

value: 24hr post-infection


title: SL29-S21-1

data_processing: The data were normalized using Robust Multichip Average normalization and analyzed using MeV v. 4.6.1 from the TM4 software suite.

treatment_protocol: SL-29 cells were infected with Toxoplasma gondii tachyzoites (prepared by syringe-lysis from infected HFFs and extensive washing in PBS) of the indicated strain at multiplicity of infection ~3; 24 hours post-infection, the supernatant was removed and cells were lysed in Trizol for RNA extraction.


title: SL29-mock-1


title: SL29-CL13-1


title: SL29-ME49-1


title: SL29-C96E7-1


title: TS(Ki4) cells -2

city: Chapel Hill

first: Gary

last: Johnson

state: NC

address: 120 Mason Farm Drive,4009 Genetic Medicine Building,CB#7365

department: Pharmacology

institute: UNC-Chapel Hill

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-133

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with an Agilent Scanner

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

organism: Mus musculus

source_name: reference: TS(WT) cells

extract_protocol: total RNA

tag: cell type

value: trophoblast stem (TS) cells

tag: protocol

value: wild-type control (TS^WT)

source_name: test: TS(Ki4) cells-2

extract_protocol: Qiagen Rneasy Kit

value: inactive MAP3K4 (TS^KI4)


title: SL29-S28-1


title: CEF_ROP16KO_2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on GeneChip Chicken Genome Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

source_name: SL-29 chicken embryonic fibroblasts infected with Toxoplasma gondii of indicated strain, 5 hpi

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug starting total RNA (3' IVT Express Kit, Affymetrix).

growth_protocol: Primary chicken embryonic fibroblasts (CEFs) were derived from specific pathogen-free fertilized eggs purchased from Charles River (Wilmington, MA).  Fibroblasts were prepared from 12-day old embryos and maintained in complete DMEM, comprised of Dulbecco’s modified Eagle’s medium (Invitrogen, Carlsbad, CA) supplemented with 10% heat-inactivated fetal calf serum (FCS; Hyclone, Logan, UT), 2 mM L-glutamine, 100 U/mL penicillin and 100 μg ml−1 streptomycin.   For CEF maintenance, complete DMEM was additionally supplemented with 1% heat-inactivated chicken serum (Invitrogen, Carlsbad, CA), and 1 mM sodium pyruvate (Invitrogen, Carlsbad, CA).

treatment_protocol: SL-29 cells were infected with Toxoplasma gondii tachyzoites (prepared by syringe-lysis from infected HFFs and extensive washing in PBS) of the indicated strain at multiplicity of infection ~3; 5 hours post-infection, the supernatant was removed and cells were lysed in Trizol for RNA extraction.

value: 5hr post-infection


title: T(Diff) cells -3

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-127

source_name: test: T(Diff) cells-3

value: differentiated for 4 days (T^Diff)


title: CEF_RH_2

value: RH


title: SL29-CL16-1


title: SL29-C96A5-1


title: SL29-STE10-1


title: SL29-CEP-1

value: CEP (Type I)


title: SL29-CEP-2


title: Lsd1 vs. input

type: genomic

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

hyb_protocol: Samples were hybridized to Human Promoter 1.0R  Genechip arrays (Affymetrix). Hybridization and washing conditions were carried out following Affymetrix instructions.

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner (7G upgrade). The data extraction was done by the Affymetrix GCOS software v.1.4.

data_processing: Three LSD1 immunoprecipitated samples and two inputs were hybridized and normalized using quantile normalization. Two-sample analysis was performed and log2 signal intensity ratios corresponding to ChIP DNA/genomic DNA were calculated. To identify potential enriched regions the following TAS parameters were used: bandwidth=100, max gap=120, min run=250. For the two-sample analysis the threshold for the peak selection was set to the minimum 1.5 fold change (log2 0.58) of ChIP DNA/genomic DNA.

molecule: genomic DNA

organism: Homo sapiens

source_name: ESC line transfected with LSD1 short hairpin

label_protocol: The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer's protocols (Affymetrix, Santa Clara, CA). We were using a modification of the labeling protocol first described in "Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays. Auer H, Newsom DL, Nowak NJ, McHugh KM, Singh S, Yu CY, Yang Y, Wenger GD, Gastier-Foster JM, Kornacker K. BMC Genomics. 2007;8:111.".  6ug of amplified ChIP DNA  was fragmented and biotin labeled by terminal transferase using GeneChip Mapping 10K Xba Assay Kit (Affymetrix).

extract_protocol: The human embryonic stem cell lines ES[4] and ES[2] were grown in matrigel coated plates and in the presence of irradiated MEFs conditioned media supplemented with FGF. About 15x106 of ES[4] cells were used per immunoprecipitation. The immunoprecipitated material was amplified using the WGA2 kit from Sigma and purified using the QIAquick PCR purification kit (Qiagen).

tag: modification

value: transfected with LSD1 short hairpin

source_name: Input DNA


title: T(Inv) cells -1

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-128

source_name: test: T(Inv) cells-1

value: differentiated for 4-days and isolated following invasion through Matrigel (T^Inv)


title: I_SUM149:RMF (1:1 ratio, 48hrs, replicate2)

first: Melissa

last: Troester

address: 135 Dauer Drive, CB 7435

department: Epidemiology

institute: University of North Carolina at Chapel Hill

hyb_protocol: Standard Agilent hybridization protocol.

scan_protocol: Fluorescent array images were collected using an Agilent scanner and intensity data were extracted with Agilent software.

data_processing: Data for both channels were Lowess-normalized (University of North Carolina Microarray Database) and then the log(2) ratio was calculated.

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

label_protocol: Described in Hu et al. 2005, BioTechniques, 38:121-124 (PMID 15679094).

extract_protocol: Total RNA isolated by Stratagene.

tag: sample type

value: reference

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, basal-like

extract_protocol: Qiagen Rneasy Kit.

value: basal-like breast cancer cells:fibroblasts


title: I_SUM102:RMF (1:1 ratio, 48hrs, replicate1)


title: I_SUM149:RMF (1:1 ratio, 48hrs, replicate1)


title: I_SUM102:RMF (1:1 ratio, 48hrs, replicate2)


title: I_RMF:SUM102 (1:1, 48 hrs, replicate1)

description: I_RMF:SUM102 (1:1, 48 hrs, replicate1)

value: fibroblasts:basal-like breast cancer cells


title: I_Sum149 (F12, 48 hrs, replicate 2)

description: I_Sum149 (F12, 48 hrs, replicate 2)

source_name: Human breast cancer cell line, basal-like

value: basal-like breast cancer cells


title: I_RMF:T47D (1:1 ratio, 48 hrs, replicate 1)

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, luminal

value: fibroblasts:luminal breast cancer cells


title: I_RMF:SUM149 (1:1, 48 hrs, replicate 1)

description: I_RMF:SUM149 (1:1, 48 hrs, replicate 1)


title: I_RMF:SUM102 (1:1, 48 hrs, replicate 2)

description: I_RMF:SUM102 (1:1, 48 hrs, replicate 2)


title: I_MCF7( RPMI, 48 hrs, replicate 1)

description: I_MCF7( RPMI, 48 hrs, replicate 1)

source_name: Human breast cancer cell line, luminal

value: luminal breast cancer cells


title: I_MCF7:RMF (1:1 ratio, 48hrs, replicate2)

value: luminal breast cancer cells:fibroblasts


title: I_Sum102 (HuMec, 48 hrs, replicate 1)

description: I_Sum102 (HuMec, 48 hrs, replicate 1)


title: I_RMF:MCF7 (1:1, 48h, replicate 2)

description: I_RMF:MCF7 (1:1, 48h, replicate 2)


title: I_RMF:T47D (1:1 ratio, 48 hrs, replicate 2)


title: I_RMF in SUM102 media (1:1, 48 hrs, replicate 2)

source_name: Reduction mammoplasty-derived fibroblast cell line

value: RMF

value: fibroblasts


title: I_T47D:RMF (1:1 ratio, 48hrs, replicate2)


title: I_RMF in SUM149 media (1:1, 48 hrs, replicate 2)


title: I_T47D:RMF (1:1 ratio, 48hrs, replicate1)


title: I_RMF:MCF7 (1:1, 48h, replicate 1)

description: I_RMF:MCF7 (1:1, 48h, replicate 1)


title: C_RMF:HCC1937(2:1,48h)


title: C_RMF:HCC1937(1:4,48h)


title: I_MCF7:RMF (1:1 ratio, 48hrs, replicate1)


title: I_RMF in SUM149 media (1:1, 48 hrs, replicate 1)


title: I_RMF:SUM149 (1:1, 48 hrs, replicate 2)

description: I_RMF:SUM149 (1:1, 48 hrs, replicate 2)


title: I_RMF (RPMI, 48h, replicate 2)

description: I_RMF (RPMI, 48h, replicate 2)


title: C_RMF:HCC1937(1:2,48h)


title: I_RMF (RPMI, 48h, replicate 1)

description: I_RMF (RPMI, 48h, replicate 1)


title: C_RMF:HCC1937(1:1,48h)


title: I_RMF in SUM102 media (1:1, 48 hrs, replicate 1)


title: C_RMF:HCC1937(1:0,48h)


title: C_RMF:MDAMB468(2:1,48h)_rep1


title: C_RMF:MDAMB468(1:2,48h)_rep1


title: C_RMF:SUM159(2:1,48h)_rep1


title: C_RMF:MDAMB468(0:1,48h)_rep1


title: OregonR^TOW Stage 9/10 ORC2 ChIP

city: Cambridge

first: Terry

middle: L.

last: Orr-Weaver

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Slides were hybridized to custom Agilent tiling arrays and washed as per Agilent recommendations

scan_protocol: Arrays were scanned on an Agilent scanner per manufacturer's protocol

data_processing: The value is log2 median normalized

organism: Drosophila melanogaster

source_name: ORC2 ChIP DNA from OregonR^TOW Stage 9/10 egg chambers

label_protocol: DNA was labeled using Invitrogen's BioPrime Total for Agilent aCGH labeling kit

growth_protocol: Drosophila were grown on standard cornmeal, molasses agar media

extract_protocol: Staged egg chambers were fixed with 2% formaldehyde in Grace's medium for 15 min at room temperature followed by quenching with 0.125 M glycine for 5 min (4 samples of 300 egg chambers each). The cells were washed twice with TBS and placed in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate). The crosslinked chromatin was sheared to an average size of 300-1000 bp by three 12-second pulses using a Branson 250 sonicator. The lysate was then centrifuged to remove cell debris. 50 uL was saved for the input DNA from each sample. The chromatin supernatant was then incubated overnight with 2 uL of antibody at 4C. After incubation with 30 uL protein G Dynabeads beads (Invitrogen) for 2h at 4C, the immune complexes were collected using the Dynal magnetic strip and washed with the following buffers at room temperature for 5 minutes each: 2X ChIP lysis buffer, 2X high salt (500mM NaCl) ChIP lysis buffer, 1X ChIP lysis buffer, 1X TE. The protein-DNA complexes were eluted from the beads in 100 uL ChIP elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA/1% SDS) at 65C for 15 min followed by another wash with 150 uL TE/0.67% SDS. Eluates were pooled and incubated at 65C for at least 6 hours. Input DNAs were similarly subject to reversal of crosslinks with 200 µL TE/1% SDS. DNAs from four samples were pooled together. Samples were treated with 100 ug proteinase K at 37C for 2 hours. DNA samples were phenol chloroform extracted twice and ethanol precipitated.

treatment_protocol: Stage 9 and early stage 10 egg chambers were hand sorted from 2-3 day fattened female flies

tag: developmental stage

value: stage 9 and 10

value: egg chambers

tag: strain

value: OregonR^TOW

tag: chip antibody

source_name: Input DNA from OregonR^TOW Stage 9/10 egg chambers

treatment_protocol: stage 9 and early stage 10 egg chambers were hand sorted from 2-3 day fattened female flies

value: none; input DNA


title: C_RMF:MDAMB468(1:0,48h)_rep1


title: C_RMF:SUM159(1:0,48h)_rep1


title: C_RMF:SUM102(2:1,48h)


title: C_RMF:SUM159(1:1,48h)_rep1


title: C_RMF:SUM102(1:2,48h)


title: 42D Overnight 10.0 PZQ Female C

city: Albuquerque

first: Jarrett

last: Hines-Kay

state: NM

address: 1 University of New Mexico

department: Biology

institute: University of New Mexico

description: The sample name identifies the charecteristics with the following code: “28D” or “42D” refers to the days post exposure of the schistosomes; “60min” or “Overnight” refers to the length of the exposure; “0,” “1,” or “10” refers the amount of praziquantel (PZQ) the worms were exposed to; “Female” or “Male” refers to the worm sex, however the 28 DPE worms were mixed sex so there is no identification based on sex for the 28D treatment groups; “A,” “B,” or “C” refers to the biological replicate; and, “g” and “r” refer to green and red respectively, the color of the cyanine dyes with green representing Cy-3, the dye used for the reference sample and red representing Cy-5, the dye for the experimental samples.  All reference samples used in every reaction are the same and made of RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ.

hyb_protocol: A fragmentation mix was made by adding 825 ng total Cy-3 and Cy-5 labeled cRNA to 10X blocking agent and a 25X Fragmentation Buffer. This was then incubated at 60 oC for 30 min.  The reaction was then placed on ice and a stop buffer was added to halt the reaction.  Each sample was then pipetted onto a gasket slide sitting in a hybridization chamber and an array slide was then placed over the gasket slide sandwiching the samples into four separate chambers. The top of the hybridization chamber was then fitted to the samples and the whole apparatus was placed in an oven and rotated at 10 rpm and 65 oC for 17 h. After hybridization, the slides were washed in Agilent wash buffers and stabilized against ozone deterioration in Agilent’s Stabilization Buffer.

scan_protocol: The slides were then scanned with Agilent’s Microarray G2505C scanner and extracted using Agilent’s Feature Extraction software by the University of California San Francisco’s Viral Diagnostics and Discovery Center, China Basin Landing Facility.

data_processing: The array data was analyzed using GeneSpring GX version 11 by first creating five separate experimental groupings: 28 DPE mixed sex 1 h PZQ exposures, 42 DPE male 1 h PZQ exposures, 28 DPE mixed sex 20 h PZQ exposures, 42 DPE male 20 h PZQ exposures and 42 DPE female 20 h PZQ exposures. A baseline transformation to the median of the control for each grouping (Table 1) was then performed.  Features that were not positive, not significant, not above background noise, not uniform, saturated or a population outlier were not considegreen for analysis.  Replicates in each grouping were then grouped based on PZQ concentration and only features with signal in all three replicates were retained.  The signal from the replicates was averaged in each of the 14 treatment groups.  The signal from these groups was log2 transformed.  Differential analysis evaluated features that had fold change values greater than a magnitude of two.  Analyses of significance compagreen the PZQ exposed groups to the control in each grouping with an unpaigreen, unequal variance t-test.  Significant features had p-values < 0.05.

organism: Schistosoma mansoni

source_name: 42D Overnight 10.0 PZQ Female C.txt:rProcessedSignal(raw)

label_protocol: cDNA was reverse transcribed from mRNA according to the kit protocol by adding a T7 Promoter Primer to the spiked samples and denaturing them at 65oC for 10 min.  A master mix containing a 5X first strand buffer, dithiothreitol (DTT), dNTPs and Affinity Script RNase Block Mix containing Affinity Script reverse transcriptase (Agilent Technologies) was then added to the samples and the mixture incubated at 40 oC for 2 h.  The enzyme was then inactivated by incubation at 70 oC for 15 min. cDNA was transcribed to cRNA and amplified according to manufacturers instructions by adding a transcription master mix containing 5X transcription buffer, DTTs, NTPs and a blend of enzymes (Agilent Technologies) to the sample.  The cyanine dye Cy-3 (Invitrogen) was then added to the reference samples and Cy-5 (Invitrogen) to the experimental samples and incubated at 40 oC for 2 h. After the incubation period, the cRNA was purified using Qiagen’s RNeasy Mini Kit and the RNA quantified. Calculations for labeling efficiency were performed using manufacturer recommendations and only samples which met the manufacturer’s suggested minimum activity for hybridization were processed further (Agilent Technologies)

growth_protocol: Schistosome infected mice and snails were supplied by Dr. Fgreen A. Lewis, NIAID Schistosomiasis Resource Center at the Biomedical Research Institute (Rockville, MD). The abdomens of female Swiss Webster mice were exposed to 125 PR-1 S. mansoni  cercariae.

extract_protocol: The worms were harvested immediately after the exposure period by placing them in separate 1.5mL tubes with 600 µL of RLT Buffer (Qiagen) containing 1% (v/v) β-mercaptoethanol (Sigma) (RLT/β-ME buffer) and homogenizing them using a RNase-Free Pellet Pestle (VWR International; Aragon et al., 2009).  The homogenate was then frozen at −80 °C until RNA was extracted. Total RNA was isolated from thawed worm homogenates using an RNeasy® Mini kit (Qiagen) including a DNase step according to the manufacturer's specifications, eluted with 100 μL of RNase free distilled water (dH2O) and quantified using a NanoDrop® ND-1000 spectrophotometer with ND-1000 3.3 software (NanoDrop Technologies). In addition, RNA integrity was evaluated using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano LabChip® Kit (Agilent Technologies).

tag: days post exposure

tag: length of exposure

value: Overnight

tag: treatment

value: 10.0 ug/ml PZQ

tag: gender

value: female

tag: tissue

value: whole organism

source_name: Reference used in reaction with sample 42D Overnight 10.0 PZQ Female C

tag: components


title: 42D Overnight 10.0 PZQ Female A

source_name: 42D Overnight 10.0 PZQ Female A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 10.0 PZQ Female A

value: RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ


title: C_RMF:SUM102(1:0,48h)

value: reference


title: C_RMF:SUM102(1:1,48h)

value: fibroblasts:basal-like breast cancer cells


title: C_RMF:MDAMB468(1:1,48h)_rep1


title: C_RMF:SUM102(1:4,48h)


title: 42D Overnight 1.0 PZQ Male A

source_name: 42D Overnight 1.0 PZQ Male A.txt:rProcessedSignal(raw)

value: 1.0 ug/ml PZQ

value: male

source_name: Reference used in reaction with sample 42D Overnight 1.0 PZQ Male A


title: C_RMF:SUM159(0:1,48h)_rep1

value: basal-like breast cancer cells


title: 42D Overnight 10.0 PZQ Female B

source_name: 42D Overnight 10.0 PZQ Female B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 10.0 PZQ Female B


title: C_RMF:HCC1937(0:1,48h)


title: C_RMF:SUM159(1:2,48h)_rep1


title: 42D Overnight 1.0 PZQ Male B

source_name: 42D Overnight 1.0 PZQ Male B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 1.0 PZQ Male B


title: 42D Overnight 1.0 PZQ Female C

source_name: 42D Overnight 1.0 PZQ Female C.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 1.0 PZQ Female C


title: 42D Overnight 0 PZQ Male C

source_name: 42D Overnight 0 PZQ Male C.txt:rProcessedSignal(raw)

value: 0 ug/ml PZQ

source_name: Reference used in reaction with sample 42D Overnight 0 PZQ Male C


title: C_RMF:SUM102(0:1,48h)

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

source_name: Human breast cancer cell line, basal-like


title: 42D Overnight 1.0 PZQ Female B

source_name: 42D Overnight 1.0 PZQ Female B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 1.0 PZQ Female B


title: C_RMF:SKBR3(2:1,48h)

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, HER2+

value: fibroblasts:HER2+ breast cancer cells


title: 42D Overnight 1.0 PZQ Female A

source_name: 42D Overnight 1.0 PZQ Female A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 1.0 PZQ Female A


title: 42D Overnight 1.0 PZQ Male C

source_name: 42D Overnight 1.0 PZQ Male C.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 1.0 PZQ Male C


title: C_RMF:SKBR3(1:4,48h)


title: C_RMF:SKBR3(1:1,48h)


title: 42D Overnight 0 PZQ Female A

source_name: 42D Overnight 0 PZQ Female A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 0 PZQ Female A


title: C_RMF:SKBR3(1:2,48h)


title: 42D Overnight 0 PZQ Female B

source_name: 42D Overnight 0 PZQ Female B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 0 PZQ Female B


title: 42D 60M 1.0 PZQ Male C

source_name: 42D 60M 1.0 PZQ Male C.txt:rProcessedSignal(raw)

value: 60 min

source_name: Reference used in reaction with sample 42D 60M 1.0 PZQ Male C


title: C_RMF:SKBR3(1:0,48h)

source_name: Reduction mammoplasty-derived fibroblast cell line

value: RMF

value: fibroblasts


title: C_RMF:SKBR3(0:1,48h)

source_name: Human breast cancer cell line, HER2+

value: HER2+ breast cancer cells


title: 42D Overnight 0 PZQ Male A

source_name: 42D Overnight 0 PZQ Male A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 0 PZQ Male A


title: 42D 60M 10.0 PZQ Male C

source_name: 42D 60M 10.0 PZQ Male C.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D 60M 10.0 PZQ Male C


title: C_RMF:T47D(1:2,48h)

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, luminal

value: fibroblasts:luminal breast cancer cells


title: C_RMF:T47D(1:4,48h)


title: C_RMF:T47D(2:1,48h)


title: 42D 60M 10.0 PZQ Male B

source_name: 42D 60M 10.0 PZQ Male B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D 60M 10.0 PZQ Male B


title: OregonR^MOD Stage 10 ORC2 ChIP

source_name: ORC2 ChIP DNA from OregonR^MOD Stage 10 egg chambers

treatment_protocol: Stage 10 egg chambers were hand sorted from 2-3 day fattened female flies

value: stage 10

value: egg chambers

value: OregonR^MOD

source_name: Input DNA from OregonR^MOD Stage 10 egg chambers

treatment_protocol: stage 10 egg chambers were hand sorted from 2-3 day fattened female flies

value: none; input DNA


title: 42D Overnight 0 PZQ Female C

source_name: 42D Overnight 0 PZQ Female C.txt:rProcessedSignal(raw)

value: Overnight

value: female

value: whole organism

source_name: Reference used in reaction with sample 42D Overnight 0 PZQ Female C

value: RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ


title: 42D 60M 1.0 PZQ Male A

source_name: 42D 60M 1.0 PZQ Male A.txt:rProcessedSignal(raw)

value: 1.0 ug/ml PZQ

value: male

source_name: Reference used in reaction with sample 42D 60M 1.0 PZQ Male A


title: C_RMF:T47D(0:1,48h)

value: reference

source_name: Human breast cancer cell line, luminal

value: luminal breast cancer cells


title: C_RMF:T47D(1:1,48h)


title: 42D 60M 0 PZQ Male C

source_name: 42D 60M 0 PZQ Male C.txt:rProcessedSignal(raw)

value: 60 min

value: 0 ug/ml PZQ

source_name: Reference used in reaction with sample 42D 60M 0 PZQ Male C


title: 42D 60M 10.0 PZQ Male A

source_name: 42D 60M 10.0 PZQ Male A.txt:rProcessedSignal(raw)

value: 10.0 ug/ml PZQ

source_name: Reference used in reaction with sample 42D 60M 10.0 PZQ Male A


title: Fezf1-/- 3

city: Santa Cruz

first: Matthew

middle: Joseph

last: Eckler

address: 434 Sinsheimer Labs, UCSC

department: MCDB

institute: UCSC

hyb_protocol: Labeled cRNA were fragmented and hybridized according to the standard Affymetrix protocol (GeneChip Whole Transcript (WT) Sense Target Laebeling Assay Manuel Version 4, 2007, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: GC-RMA normalization using Affymetrix Expression Console

source_name: FACS isolated Fezf1 expressing cells from Fezf1-/- MOE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip Whole Transcript (WT) Sense Target Laebeling Assay Manuel Version 4, 2007, Affymetrix).

extract_protocol: Qiagen Rneasy Plus Micro Kit according to manufacture's protocol

tag: genotype

value: Fezf1 -/-

tag: age

value: Fezf1 -/- cells from Main Olfactory Epithelium

tag: genetic background


title: Fezf1+/- 2

source_name: FACS isolated Fezf1 expressing cells from Fezf1+/- MOE

value: Fezf1 +/-

value: Fezf1 +/- cells from Main Olfactory Epithelium


title: 42D 60M 0 PZQ Male A

source_name: 42D 60M 0 PZQ Male A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D 60M 0 PZQ Male A


title: C_RMF:ZR75-1(1:2,48h)

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, luminal

tag: cell line

value: fibroblasts:luminal breast cancer cells


title: Fezf1+/- 1

tag: cell type


title: Fezf1-/- 1


title: 42D 60M 0 PZQ Male B

source_name: 42D 60M 0 PZQ Male B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D 60M 0 PZQ Male B


title: C_RMF:ZR75-1(2:1,48h)


title: Fezf1-/- 2


title: 42D 60M 1.0 PZQ Male B

source_name: 42D 60M 1.0 PZQ Male B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D 60M 1.0 PZQ Male B


title: C_RMF:ZR75-1(1:1,48h)


title: 42D Overnight 0 PZQ Male B

source_name: 42D Overnight 0 PZQ Male B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 42D Overnight 0 PZQ Male B


title: Fezf1+/- 3


title: 28D Overnight 10.0 PZQ A

source_name: 28D Overnight 10.0 PZQ A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D Overnight 10.0 PZQ A


title: C_RMF:ZR75-1(0:1,48h)_rep2

source_name: Human breast cancer cell line, luminal


title: C_RMF:ZR75-1(0:1,48h)_rep1


title: 28D Overnight 10.0 PZQ B

source_name: 28D Overnight 10.0 PZQ B.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D Overnight 10.0 PZQ B


title: 28D Overnight 10.0 PZQ C

source_name: 28D Overnight 10.0 PZQ C.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D Overnight 10.0 PZQ C


title: C_RMF:ME16C(1:4,48h)

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, basal-like

value: fibroblasts:basal-like breast cancer cells


title: Total Cell Population, GFP +/-, biological rep 1

city: Cuernavaca

first: Leonor

last: Perez-Martinez

state: Morelos

address: Avenida Universidad 2001

department: Medicina Molecular y Bioprocesos

country: Mexico

institute: University of Mexico

description: Primary cultures of E17 hypotalamic neurons were transfected with a GFP TRH-promoter drived vector. RNA from total population (GFP+/- cells) was used

hyb_protocol: Resulting target cRNA was collected on RNAeasy columns (QIAGEN, Valencia, CA) and then fragmented for hybridization on the microarrays. Biotinylated target cRNA (15 µg) was hybridized to the array and then processed using the Affymetrix GeneChip Fluidics Workstation 400

scan_protocol: After binding with phycoerythrin-coupled avidin, microarrays were scanned on a Hewlett-Packard Gene Array Scanner (Hewlett-Packard Co., Palo Alto, CA).

data_processing: Results were analyzed using Affymetrix MAS 5.0 software. Individual microarrays were scaled to produce a mean signal intensity of 125. Iterative comparisons of different microarray datasets were done with MAS 5.0 comparison analysis.

label: Biotin

organism: Rattus norvegicus

source_name: TRH-GFP Transfected Hypothalamic Neurons, Total Population GFP+/-

label_protocol: RNA was reverse-transcribed into double-stranded cDNA with a T7 promoter-containing primer using SuperScript II Reverse Transcriptase, RNase H, and DNA polymerase (Invitrogen). After precipitation with 5M NH4OAc and ethanol, the cDNA was used as a template in a biotin-labeled in vitro transcription reaction (Enzo BioArray, Affymetrix).

growth_protocol: Animals used were Wistar rats raised at the animal facility of the Instituto de Biotecnología, UNAM. Animals were maintained in standard environmental conditions (lights on between 0700-1900 h, temperature 21 ± 2 oC) and received rat chow and tap water ad libitum. Animal care and protocols were approved by the Animal Care and Ethics Committee of the Institute following the guidelines for the use of animals in neuroscience research of the Society for Neuroscience, USA.

extract_protocol: Total RNA (10 µg) was extracted from three different cell populations: i) sorted TRH-GFP+ cells (GFP+); ii) TRH-GFP+ and GFP- mixed cells (GFP+/-) passed through the FACS but not sorted, and iii) non transfected cells (NT). To obtain a sufficient amount of RNA for each cell population, the number of independent experiments pooled for the GFP+ sample was higher than for the other samples. Therefore, a pool of six independent experiments was used to prepare total RNA from the GFP+ and three independent experiments for GFP+/- or NT cells.

treatment_protocol: Twenty-four hours after seeding, cells were transfected essentially as described before. In general, 8 mg of branched polyethylenimine (PEI) (600-1000 KDa; Fluka) solution was diluted in 10 ml of water, pH adjusted to 6.9 with 0.2 N HCl and the solution filtered (Millipore, 0.22 µm). PEI (30 µl) and plasmid DNA (10 µg) were separately diluted to adjust NaCl to 150 mM in a final volume of 50 µl, vortexed and incubated for 10 min at room temperature; subsequently, the polymer solution was added to the DNA, vortexed-mixed, incubated for 10 min at room temperature followed by the addition of 900 µl of serum-free DMEM. The supplemented DMEM was removed from the culture dishes and the transfection mixture was added. After 3 hours incubation, transfection mix was removed and fresh supplemented DMEM was added.

value: Hypothalamus

value: Wistar

value: Embryo


title: Non transfected Cells

description: Primary cultures of E17 hypotalamic neurons.

source_name: Non-transfected Hypothalamic Neurons

value: Non-transfected Hypothalamic Neurons


title: 28D Overnight 1.0 PZQ B

source_name: 28D Overnight 1.0 PZQ B.txt:rProcessedSignal(raw)

value: Overnight

value: 1.0 ug/ml PZQ

value: whole organism

source_name: Reference used in reaction with sample 28D Overnight 1.0 PZQ B

value: RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ


title: OregonR^TOW Stage 10 ORC2 ChIP

source_name: ORC2 ChIP DNA from OregonR^TOW Stage 10 egg chambers

value: stage 10

value: egg chambers

value: OregonR^TOW

source_name: Input DNA from OregonR^TOW Stage 10 egg chambers

value: none; input DNA


title: Sorted TRH, GFP+, biological rep 2

description: Primary cultures of E17 hypotalamic neurons were transfected with a GFP TRH-promoter drived vector. The culture was sorted afterwards in order to obtain only GFP positive cells

source_name: TRH-GFP Transfected Hypothalamic Neurons, Sorted GFP+


title: 28D Overnight 1.0 PZQ C

source_name: 28D Overnight 1.0 PZQ C.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D Overnight 1.0 PZQ C


title: C_RMF:ME16C(1:2,48h)

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

value: reference


title: C_RMF:ME16C(2:1,48h)


title: Total Cell Population, GFP +/-, biological rep 2

value: TRH-GFP Transfected Hypothalamic Neurons, Total Population GFP+/-


title: C_RMF:ME16C(1:0,48h)

source_name: Reduction mammoplasty-derived fibroblast cell line

value: RMF

value: fibroblasts


title: C_RMF:ME16C(1:1,48h)

value: fibroblasts:basal-like breast cancer cells


title: Sorted TRH, GFP+, biological rep 1

value: TRH-GFP Transfected Hypothalamic Neurons, Sorted GFP+

value: Hypothalamus


title: C_RMF:ME16C(0:1,48h)

source_name: Human breast cancer cell line, basal-like

value: basal-like breast cancer cells


title: 28D Overnight 0 PZQ C

source_name: 28D Overnight 0 PZQ C.txt:rProcessedSignal(raw)

value: 0 ug/ml PZQ

source_name: Reference used in reaction with sample 28D Overnight 0 PZQ C


title: C_RMF:MCF7(1:3,48h)_rep1

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, luminal

value: fibroblasts:luminal breast cancer cells


title: 28D Overnight 1.0 PZQ A

source_name: 28D Overnight 1.0 PZQ A.txt:rProcessedSignal(raw)

value: Overnight

value: 1.0 ug/ml PZQ

source_name: Reference used in reaction with sample 28D Overnight 1.0 PZQ A


title: C_RMF:MCF7(2:1,48h)_rep1


title: C_RMF:MCF7(1:2,48h)_rep1


title: 28D Overnight 0 PZQ B

source_name: 28D Overnight 0 PZQ B.txt:rProcessedSignal(raw)

value: whole organism

source_name: Reference used in reaction with sample 28D Overnight 0 PZQ B

value: RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ


title: 28D Overnight 0 PZQ A

source_name: 28D Overnight 0 PZQ A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D Overnight 0 PZQ A


title: WBiOV vs WBiTT_3

city: Pathumthani

first: nitsara

last: karoonuthaisiri

state: Pathumthani

address: Paholyothin

department: Central

country: Thailand

institute: BIOTEC

hyb_protocol: The probe was resuspended in hybridization solution (50% Formamide; 5x SSC; 0.1% SDS; 1 mg/ml Human Placental DNA; 10mM Tris, pH 7.5) and placed onto the post-processed slides.  The slides were hybridized at 420C for 16 hrs before they were washed according to Corning’s protocol.

scan_protocol: The slides were scanned with GenePix 4000B (Molecular Devices, Sunnyvale, CA).  Microarray spots on scanned images are located using GenePix Pro version 6.1.

data_processing: All “empty” and “bad” spots were removed from the analysis.  “Empty” spots were failed PCR products whereas “bad” spots were flagged by visual inspection of the spot images.  From the remaining spots, only the spots with intensities more than one standard deviation above the background intensity were further analyzed.  The processed data were normalized within each array by the median-nomalization method, and across arrays, using the Aroma package (Bengtsson, available from: http://www.maths.lth.se/help/R/aroma/) run in R project environment (http://cran.r-project.org).  Data from replicated spots were averaged before clustering.  Logarithmic base 2 values of intensities from both Cy3- and Cy5- samples (M values) were used as inputs for clustering.  Cluster program was used to perform hierarchical clustering and Treeview program was used to visualized the clustered results (Eisen et al., 1998)

organism: Penaeus monodon

source_name: individual ovary from wild-broodstock from west coast of Thailand

label_protocol: RNA samples were extracted from both testes and ovaries of pooled juveniles (4 month-old, pooled from n=114 ), individual juvenile and broodstocks from West sides of Thailand. The RNA from ovaries were labeled with Cy3 dye as a reference and those of testes were labeled with Cy5 dye.  The Cy3- and Cy5-samples were mixed together and hybridized onto the arrays overnight. The hybridized slides were washed according to Corning’s instruction.

extract_protocol: RNA samples were extracted from both testes and ovaries of juvenile shrimp and wild broodstock. Contaminated genomic DNA was removed by treatment with DNase I at 0.15 U/μg total RNA at 37°C for 30 min.

value: individual ovary sample from 1 wild broodstock from west coast of Thailand

source_name: individual testis from wild-broodstock from west coast of Thailand

value: individual testis sample from 1 wild broodstock from west coast of Thailand


title: C_RMF:SUM149(2:1,48h)

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, basal-like


title: C_RMF:MCF7(1:0,48h)_rep1


title: C_RMF:SUM149(1:4,48h)


title: C_RMF:SUM149(1:1,48h)


title: WBiOV vs WBiTT_2


title: C_RMF:MCF7(1:1,48h)_rep1


title: WBiOV vs WBiTT_1


title: C_RMF:SUM149(1:2,48h)


title: C_RMF:MCF7(0:1,48h)_rep1

source_name: Human breast cancer cell line, luminal

value: luminal breast cancer cells


title: OregonR^TOW dissected Stage 10 RNAPII ChIP

source_name: RNAPII ChIP DNA from OregonR^TOW dissected Stage 10 egg chambers

extract_protocol: Staged egg chambers were dissected to remove the nurse cells and fixed with 2% formaldehyde in Grace's medium for 15 min at room temperature followed by quenching with 0.125 M glycine for 5 min (4 samples of 300 egg chambers each). The cells were washed twice with TBS and placed in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate). The crosslinked chromatin was sheared to an average size of 300-1000 bp by three 12-second pulses using a Branson 250 sonicator. The lysate was then centrifuged to remove cell debris. 50 uL was saved for the input DNA from each sample. The chromatin supernatant was then incubated overnight with 2 uL of antibody at 4C. After incubation with 30 uL protein G Dynabeads beads (Invitrogen) for 2h at 4C, the immune complexes were collected using the Dynal magnetic strip and washed with the following buffers at room temperature for 5 minutes each: 2X ChIP lysis buffer, 2X high salt (500mM NaCl) ChIP lysis buffer, 1X ChIP lysis buffer, 1X TE. The protein-DNA complexes were eluted from the beads in 100 uL ChIP elution buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA/1% SDS) at 65C for 15 min followed by another wash with 150 uL TE/0.67% SDS. Eluates were pooled and incubated at 65C for at least 6 hours. Input DNAs were similarly subject to reversal of crosslinks with 200 µL TE/1% SDS. DNAs from four samples were pooled together. Samples were treated with 100 ug proteinase K at 37C for 2 hours. DNA samples were phenol chloroform extracted twice and ethanol precipitated.

treatment_protocol: Stage 10 egg chambers were hand sorted from 2-3 day fattened female flies, and the nurse cells were manually removed

value: egg chambers

value: stage 10

value: OregonR^TOW

value: RNAPII (Upstate clone CTD4H8)

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #

source_name: Input DNA from OregonR^TOW dissected Stage 10 egg chambers

treatment_protocol: stage 10 egg chambers were hand sorted from 2-3 day fattened female flies, and the nurse cells were manually removed

value: none; input DNA

tag: deveopmental stage


title: 28D 60min 10.0 PZQ A

source_name: 28D 60min 10.0 PZQ A.txt:rProcessedSignal(raw)

value: 60 min

value: 10.0 ug/ml PZQ

source_name: Reference used in reaction with sample 28D 60min 10.0 PZQ A

tag: sample type


title: 28D 60min 10.0 PZQ C

source_name: 28D 60min 10.0 PZQ C.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D 60min 10.0 PZQ C


title: 28D 60min 1.0 PZQ C

source_name: 28D 60min 1.0 PZQ C.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D 60min 1.0 PZQ C


title: C_RMF:SUM149(1:0,48h)

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

value: reference

source_name: Reduction mammoplasty-derived fibroblast cell line

value: RMF

value: fibroblasts


title: C_RMF:MCF7(1:2,48h)

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, luminal

value: fibroblasts:luminal breast cancer cells


title: C_RMF:SUM149(0:1,48h)

source_name: Human breast cancer cell line, basal-like

value: basal-like breast cancer cells


title: JNpOV vs JNpTT_3

source_name: pooled ovary from juvenile shrimp

value: pooled ovary samples from 114 juvenile shrimp

source_name: pooled testes from juvenile shrimp

value: pooled testes samples from 114 juvenile shrimp


title: #757-1 [Embryonic stem cell line, ECAT11EGFP/EGFP]

city: Kyoto

first: Shinya

last: Yamanaka

address: 53 Kawahara-machi, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Applicaton (CiRA), Kyoto University

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: Data were analyzed with GeneSpring GX 11. The parameters for normalization are as follows: Data transformation: Normalize to 75th percentile

source_name: #757-1 (Embryonic stem cell line, ECAT11EGFP/EGFP)

label_protocol: Agilent standard protocol

growth_protocol: Culture of ESCs in DMEM supplemented with 20% FBS, 0.1 mM non-essential amino acids, 2 mM L-glutamine, 50 U/ml penicillin-streptomycin, 0.11 mM 2-mercaptoethanol and LIF on gelatin coated dishes.

extract_protocol: Total RNA was isolated with Trizol

value: Embryonic stem cell

tag: strain

value: C57BL6/129sv origin

tag: genotype/variation

value: ECAT11EGFP/EGFP Knock-in ESCs

tag: modification

value: ECAT11 disrupted

value: male


title: #757-2 [Embryonic stem cell line, ECAT11EGFP/EGFP]

source_name: #757-2 (Embryonic stem cell line, ECAT11EGFP/EGFP)


title: C_RMF:MCF7(1:0,48h)


title: C_RMF:MCF7(2:1,0Gy,48h)


title: JNpOV vs JNpTT_2


title: OregonR^TOW Stage 10 tetraH4 ChIP

data_processing: MA2C normalized

source_name: tetraH4 ChIP DNA from OregonR^TOW Stage 10 egg chambers

value: egg chambers

tag: developmental stage

value: stage 10

value: OregonR^TOW

tag: chip antibody

value: tetraH4 (Active Motif 39179)

value: Active Motif

source_name: Input DNA from OregonR^TOW Stage 10 egg chambers


title: OregonR^MOD Stage 10 tetraH4 ChIP

source_name: tetraH4 ChIP DNA from OregonR^MOD Stage 10 egg chambers

value: OregonR^MOD

source_name: Input DNA from OregonR^MOD Stage 10 egg chambers

value: none; input DNA


title: 28D 60min 1.0 PZQ B

source_name: 28D 60min 1.0 PZQ B.txt:rProcessedSignal(raw)

tag: days post exposure

tag: length of exposure

value: 60 min

tag: treatment

value: 1.0 ug/ml PZQ

value: whole organism

source_name: Reference used in reaction with sample 28D 60min 1.0 PZQ B

value: RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ


title: #620-6 [Embryonic stem cell line, ECAT11EGFP/EGFP]

source_name: #620-6 (Embryonic stem cell line, ECAT11EGFP/EGFP)

tag: gender

value: female


title: C_RMF:MCF7(1:4,0Gy,48h)

value: reference

value: fibroblasts:luminal breast cancer cells


title: JNpOV vs JNpTT_1

tag: tissue

value: pooled ovary samples from 114 juvenile shrimp

value: pooled testes samples from 114 juvenile shrimp


title: #620-2 [Embryonic stem cell line, wild type]

source_name: #620-2 (Embryonic stem cell line, wild type)

value: Embryonic stem cell

value: C57BL6/129sv origin

value: wild type Embryonic stem cell(control)


title: C_RMF:MCF7(1:1,48h)


title: C_RMF:MCF7(0:1,48h)

source_name: Human breast cancer cell line, luminal

value: luminal breast cancer cells


title: C_RMF:MDA-MB-231(2:1,48h)

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, basal-like

value: fibroblasts:basal-like breast cancer cells


title: 28D 60min 10.0 PZQ B

source_name: 28D 60min 10.0 PZQ B.txt:rProcessedSignal(raw)

value: 10.0 ug/ml PZQ

source_name: Reference used in reaction with sample 28D 60min 10.0 PZQ B

tag: components


title: C_RMF:MCF7(1:3,48h)

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, luminal

tag: cell line


title: JNiOV vs JNiTT_3

source_name: individual ovary from juvenile shrimp

value: individual ovary sample from 1 juvenile shrimp

source_name: individual testis from juvenile shrimp

value: individual testis sample from 1 juvenile shrimp


title: 28D 60min 0 PZQ C

source_name: 28D 60min 0 PZQ C.txt:rProcessedSignal(raw)

value: 60 min

value: 0 ug/ml PZQ

source_name: Reference used in reaction with sample 28D 60min 0 PZQ C


title: C_RMF:MDA-MB-231(1:1,48h)

tag: cell type


title: JNiOV vs JNiTT_2


title: RF8 [Embryonic stem cell line, wild type]

source_name: RF8 (Embryonic stem cell line, wild type)

value: 129sv origin

value: male


title: C_RMF:MCF7(1:1,0Gy,48h)


title: 28D 60min 0 PZQ B

source_name: 28D 60min 0 PZQ B.txt:rProcessedSignal(raw)

value: whole organism

source_name: Reference used in reaction with sample 28D 60min 0 PZQ B

value: RNA derived from 100 mixed sex, unexposed 42 DPE schistosomes spiked with 0.5 % (v/v) RNA isolated from 42 DPE mixed sex worms exposed to 10 µg/mL PZQ, 0.5 % (v/v) RNA isolated from 28 DPE worms exposed to 10 µg/mL PZQ and 0.5 % (v/v) RNA isolated from 28 DPE worms unexposed to PZQ


title: C_RMF:MCF7(1:0,0Gy,48h)

value: reference

source_name: Reduction mammoplasty-derived fibroblast cell line

value: RMF

value: fibroblasts


title: 28D 60min 0 PZQ A

source_name: 28D 60min 0 PZQ A.txt:rProcessedSignal(raw)

source_name: Reference used in reaction with sample 28D 60min 0 PZQ A


title: C_RMF:MDA-MB-231(1:4,48h)


title: C_RMF:MCF7(2:1,48h)

value: fibroblasts:luminal breast cancer cells


title: C_RMF:MDA-MB-231(1:2,48h)


title: 28D 60min 1.0 PZQ A

source_name: 28D 60min 1.0 PZQ A.txt:rProcessedSignal(raw)

value: 1.0 ug/ml PZQ

source_name: Reference used in reaction with sample 28D 60min 1.0 PZQ A


title: Buccal DNA_1

status: Public on May 26 2011

city: Setagaya

first: Kazuhiko

last: Nakabayashi

state: Tokyo

department: Department of Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

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

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Normal buccal cells

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted using  the standard phenol/chloroform extraction method or the QIAamp DNA Blood Midi Kit (Qiagen)

value: buccal cells

tag: disease state

value: normal


title: Leukocyte_2

source_name: Normal leukocytes

value: leukocytes (whole blood)


title: Leukocyte_5


title: Leukocyte_1

value: leukocytes


title: Fat_1

source_name: Normal fat tissue

value: fat


title: JNiOV vs JNiTT_1

value: individual ovary sample from 1 juvenile shrimp

value: individual testis sample from 1 juvenile shrimp


title: Placenta_1

source_name: Normal placenta

value: placenta


title: Leukocyte_4


title: mUPD_1_leukocytes

source_name: Genome-wide maternal uniparental disomy (mUPD), leukocytes

value: Silver-Russell syndrome-like phenotype


title: Leukocyte_3


title: pUPD_3_leukocytes

source_name: Genome-wide paternal uniparental disomy (pUPD), leukocytes


title: Brain_1

source_name: Normal brain

value: brain


title: C_RMF:MCF7(1:2,0Gy,48h)

source_name: Stratagene Human Universal Reference B containing 1/10 added MCF7 and ME16C RNAs

source_name: Reduction mammoplasty-derived fibroblast cell line and human breast cancer cell line, luminal


title: Muscle_1

source_name: Normal muscle

value: muscle


title: C_RMF:MDA-MB-231(0:1,48h)

source_name: Human breast cancer cell line, basal-like

value: basal-like breast cancer cells


title: PON3

city: Iowa City

first: Alejandro

middle: A

last: Pezzulo

state: IA

address: 169 Newton Rd 6334 PBDB

department: Internal Medicine

institute: University of Iowa

description: This sample is of Drosophila melanogaster with third chromosome tubulin driver and third chromosome PON1 transgene.

hyb_protocol: Hybridization of Roche Nimblegen 12plex HD2 (080813_Dmel_exp_HX12) was performed following the Roche Nimblegen Gene Expression Protocol v.3.2.

scan_protocol: Arrays were scanned on an Axon GenePix 4000B microarray scanner (Molecular Devices).

data_processing: RMA expression values were computed using Partek Genomics Suite v6.5.

source_name: Drosophila melanogaster whole body, tubulin driver and PON1 transgene

label_protocol: Labeling with Cy3 was performed following the Roche Nimblegen Gene Expression Protocol v.3.2.

growth_protocol: Drosophila stocks were reared on standard cornmeal-agar-molasses medium at room temperature.

extract_protocol: RNA was extracted from pools of 30 flies using pestle and mortar disruption in Trizol reagent, followed by column RNA extraction using the Invitrogen PureLink RNA Mini Kit. Double-stranded cDNA was generated following the Roche Nimblegen Gene Expression Protocol v.3.2.

tag: genotype

value: whole body


title: C_RMF:MDA-MB-231(1:0,48h)

value: reference

source_name: Reduction mammoplasty-derived fibroblast cell line

value: RMF


title: PON4


title: pUPD_2_leukocytes


title: C_RMF:MCF7(0:1,0Gy,48h)

source_name: Human breast cancer cell line, luminal

value: luminal breast cancer cells


title: pUPD_1_leukocytes


title: PON2


title: Placenta_2


title: PON1


title: Tub4

description: This sample is of Drosophila melanogaster with third chromosome tubulin driver.

source_name: Drosophila melanogaster whole body, tubulin driver


title: Tub3


title: CD34+CD45RA+Lin- HPCs overexpressing A2M cultured onto 5 µg of Delta1ext-IgG

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

country: France

institute: Centre hospitalier de Versailles

description:
BCE_06
Gene expression data from Notch-activated (5 µg) cells transduced with A2M lentiviral vector

hyb_protocol: cRNAs were then hybridized to Affymetrix HG-U133 plus 2.0 GeneChip arrays

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner 2500A

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: CD34+CD45RA-Lin- HPCs

label_protocol: RNA samples were subjected to linear amplification using the MessageAMP Ambion amplification kit

growth_protocol: Cell were cultured under serum free condtion in the presence of  SCF, FL and TPO with 0, 2 or 5µg of plastic-immobilized Delta1ext-IgG

extract_protocol: RNA were extracted using the RNeasy Micro Kit

treatment_protocol: CD34+CD45RA-Lin-HPCs were exposed to A2M or control lentiviral vectors, and sorted again based on GFP expression. After 72-hr culture with 0, 2 or 5 µg of Delta1-ext-IgG, cells were harvested and processed for RNA extraction

value: umbilical cord blood

value: hematopoietic progenitors

value: transduced with A2M

tag: treatment group

value: Notch-activated (5 µg)


title: WT1

description: This sample is of wild-type Drosophila melanogaster.

source_name: Drosophila melanogaster whole body, wild-type


title: NaCl 2M-rep4

city: Jeongeup

first: Im

last: Seong Hun

address: Jeongeup 580-185, Republic of KoreaInstitute

country: South Korea

institute: Korea Atomic Energy Research Institute

description: 2M NaCl vs Control

hyb_protocol: The labeled cDNA pools were mixed, dried, and dissolved with hybridization buffer. The probes were denatured by heating and hybridized simultaneously to a prehybridized DNA microarray slide for 16 h at 42°C in a MAUI Hybridization System (BioMicro Systems, Salt Lake City, UT, USA) with gentle mixing, After hybridization, slides were washed sequential

scan_protocol: Scanned on an Genepix Pro 4000B scanner. Images were quantified using Genepix Pro Software (version 6.0).

data_processing: LOWESS normalized, performed in GeneSpringGX 11 software, Agilent.

organism: Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539

source_name: D.radiodurans R1 exposed to 2M NaCl

label_protocol: 50 µg of total RNA were primed with 2 µl of 3 µg/µl random primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 2 µl of 50X aminoallyl-dNTP mix, 25 µM Cy3-labeling dye

extract_protocol: Total RNA extracted using RiboEX (GeneAll biotechnology, Korea) following manufacturer's instructions

tag: stress treatment

value: exposed to 2M NaCl

source_name: untreated wild type

value: none (reference)


title: WT2


title: CD34+CD45RA+Lin- HPCs transduced with empty vector cultured onto 5 µg of Delta1ext-IgG

description:
BCE_05
Gene expression data from Notch-activated (5 µg) cells transduced with empty vector

value: transduced with empty vector


title: NaCl 2M-rep7

description: Control vs 2M NaCl


title: CD34+CD45RA+Lin- HPCs transduced with empty vector cultured onto BSA

description:
BCE_01
Gene expression data from control cells transduced with empty vector

value: control


title: CD34+CD45RA-Lin- HPCs transduced with A2M

description:
CD45RA-M
Gene expression data from cell transduced with nuclear-trapped AF1q/MLLT11 (A2M)

growth_protocol: Cell were cultured under serum free condition in the presence of  SCF, FL and TPO

treatment_protocol: CD34+CD45RA-Lin- and CD34+CD45RA+Lin- HPCs were sorted differentially by FACS, exposed to A2M or control lentiviral vectors, and sorted again based on GFP expression. After 72-hr culture with SCF, FL and TPO, cells were harvested, and processed for RNA extraction


title: NaCl 2M-rep5

description: Control vs 2M NaCl


title: CD34+CD45RA+Lin- HPCs transduced with empty vector cultured onto 2 µg of Delta1ext-IgG

description:
BCE_03
Gene expression data from Notch-activated (2 µg) cells transduced with empty vector

value: Notch-activated (2 µg)


title: WT3


title: NaCl 2M-rep6

description: Control vs 2M NaCl


title: NaCl 2M-rep8

description: Control vs 2M NaCl


title: CD34+CD45RA+Lin- HPCs  transduced with A2M cultured onto BSA

description:
BCE_02
Gene expression data from control cells transduced with A2M lentiviral vector


title: CD34+CD45RA+Lin- HPCs transduced with A2M cultured onto 2 µg of Delta1ext-IgG

description:
BCE_04
Gene expression data from Notch-activated (2 µg) cells transduced with A2M lentiviral vector


title: CD34+CD45RA+Lin- HPCs transduced with empty vector

description:
CD45RA+P
Gene expression data from cell transduced with empty vector

source_name: CD34+CD45RA+Lin- HPCs


title: CD34+CD45RA-Lin- HPCs transduced with empty vector

description:
CD45RA-P
Gene expression data from cell transduced with empty vector


title: WT4


title: NaCl 2M-rep3

description: 2M NaCl vs Control


title: CD34+CD45RA+Lin- HPCs transduced with A2M

description:
CD45RA+M
Gene expression data from cell transduced with nuclear-trapped AF1q/MLLT11 (A2M)


title: Tub1


title: ctrl+ rep2

city: Lyon

first: Cedric

last: Hesling

address: 24 rue Laënnec

institute: CRCL

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Operating Software (GCOS)

data_processing: CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix GeneChip Operating Software (GCOS)

source_name: HMEC-TR, SiRNA scramble, 5 ng/ml TGFβ1 for 24h

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Human mammary epithelial cells (HMEC-TR) kindly provided by RA Weinberg have been previously described (Elenbaas B. et al. 2001 and Morel A.P. et al. 2008). These cells were cultured in 1:1 Dulbecco’s Modified Eagle’s Medium DMEM/HAMF12 medium (Invitrogen) complemented with 10% FBS (Cambrex) and 100 U/ml penicillin-streptomycin (Invitrogen), 2 mM L glutamine (Invitrogen), 10 ng/ml human epidermal growth factor (hEGF, PromoCell), 0.5 mg/ml hydrocortisone (Sigma) and 10 mg/ml insulin (Sigma).

extract_protocol: Total RNA from the transfected HMEC-TR cells was isolated by Trizol and miRNeasy Mini extraction kit (Qiagen). RNA quality was assessed by an Agilent Bioanalyzer (model 2100; Agilent Technologies).

treatment_protocol: We performed transcriptomic microarrays analysis on control HMEC-TR cells (transfected by scramble si-RNA) and cells inactivated for TIF1γ or Smad4 (SiRNA strategy) and treated or not with TGFβ1 for 24 hours. Inactivation of TIF1γ and Smad4 expression was checked by Western Blot.

value: Human mammary epithelial cells infected with retrovirus carrying hTERT and the oncogenic allele of H-Ras, H-RasV12 described in (Elenbaas B, Spirio L, Koerner F, Fleming MD, Zimonjic DB, Donaher JL, Popescu NC, Hahn WC, and Weinberg RA (2001) Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells. Genes Dev 15:50-65)


title: SiS4+ rep2

source_name: HMEC-TR, SiRNA anti-Smad4, 5 ng/ml TGFβ1 for 24h


title: SiTIF- rep2

source_name: HMEC-TR, SiRNA anti-TIF1γ


title: SiTIF+ rep2

source_name: HMEC-TR, SiRNA anti-TIF1γ, 5 ng/ml TGFβ1 for 24h


title: SiS4-

source_name: HMEC-TR, SiRNA anti-Smad4


title: NaCl 2M-rep2

description: 2M NaCl vs Control


title: NaCl 2M-rep1

description: 2M NaCl vs Control


title: NaCl 0.3M-rep8

description: Control vs 0.3M NaCl

source_name: D.radiodurans R1 exposed to 0.3M NaCl

value: exposed to 0.3M NaCl


title: NaCl 0.3M-rep7

description: Control vs 0.3M NaCl


title: NaCl 0.3M-rep2

description: 0.3M NaCl vs Control


title: NaCl 0.3M-rep3

description: 0.3M NaCl vs Control


title: astrocytoma_RISC-IP microRNA (02_H11.0_092343)

city: Calgary

first: Joanna

last: Moser

state: AB

address: 3330 Hospital Drive N.W.

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description: The concentration of RNA samples was determined using Nanodrop ND-1000 Spectrophotometer and the RNA quality of 2 samples was checked on RNA Nano chip using Agilent 2100 Bioanalyzer. All RNA samples displayed no degradation with two sharp ribosomal peaks.  The microarray assay was performed using a 5 µg total RNA sample, which was fractionated using a YM-100 Microcon centrifugal filter (Millipore, Billerica, MA) to isolate small RNAs (< 300 nt).  Small RNAs were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining with Cy5.

hyb_protocol: Hybridizations were performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies, Houston, TX).  Each detection probe on the microfluidic chip consisted of a chemically modified nucleotide coding segment complementary to 6211 target human miRNAs (Sanger miRBase version 11, http://microrna.sanger.ac.uk/sequences/) or control RNAs (array hybridization controls and single-base mismatch targets), and a polyethylene glycol spacer segment to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using photogenerated reagent chemistry and were replicated seven times within each microarray chip [46].  The hybridization melting temperatures of the probes were balanced by chemical modifications of the detection probes. Hybridization was performed at 34 °C using 100 µL of 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA pH 6.8) containing 25% formamide.

scan_protocol: After washing, the hybridized fluorescent Cy5 signals were detected with a laser scanner (GenePix 4000B, Molecular Devices, Sunnyvale, CA) and digitized by Array-Pro image analysis software (Media Cybernetics, Bethesda, MA).

data_processing:
Data were further processed by subtracting the background followed by signal normalization with a LOWESS (locally weighted regression) filter.
For a miRNA transcript to be classified as reliably detectable, it had to satisfy the following criteria: overall signal intensity >3× background standard deviation, spot coefficient of variation <0.5, and >50% of the repeated probes had signal intensities above detection level.

source_name: human U-87 MG astrocytoma/glioblastoma cell line (ATCC, cat# HTB-14)

growth_protocol: Primary human cerebral cortex astrocyte cells were cultured in cell specific astrocyte medium containing 2% fetal bovine serum, 1% astrocyte growth supplement and 1% penicillin/streptomycin (ScienCell Research Laboratories). Adherent human U-87 MG astrocytoma/glioblastoma cells were cultured under 5% CO2 in DMEM F12 + 1% L-glutamine (2 mM) (Cambrex, Walkersville, MD) supplemented with 10% fetal calf serum (Gibco, Burlington, ON, Canada), 1% penicillin-streptomycin (Gibco), 1% sodium pyruvate (1 mM) (Gibco) and 1% non-essential amino acids (0.1 mM) (Gibco) at 37°C.

extract_protocol: Total RNA enriched with small RNAs was isolated from the RISC-IP complex and the global cellular fraction using the mirVana kit (Ambion) according to the procedures outlined in the manufacturer’s protocol.

tag: passage number

value: between 18 - 22

tag: cell fraction

value: RISC-immunoprecipitated

tag: antibody

value: anti-RISC


title: NaCl 0.3M-rep1

description: 0.3M NaCl vs Control


title: NaCl 0.3M-rep6

description: Control vs 0.3M NaCl


title: NaCl 0.3M-rep4

description: 0.3M NaCl vs Control


title: astrocyte_RISC-IP microRNA (01_H11.0_092342)

source_name: primary human cerebral cortex astrocyte cell line (ScienCell Research Laboratories, cat#1800)

label_protocol: The microarray assay was performed using a 5 µg total RNA sample, which was fractionated using a YM-100 Microcon centrifugal filter (Millipore, Billerica, MA) to isolate small RNAs (< 300 nt).  Small RNAs were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining with Cy5.

value: between 4 - 6


title: Tub2

value: whole body


title: SiTIF+ rep1


title: astrocyte_global mRNA (S803681.H52)

description: The concentration of RNA samples was determined using Nanodrop ND-1000 Spectrophotometer and the RNA quality of 2 samples was checked on RNA Nano chip using Agilent 2100 Bioanalyzer. All RNA samples displayed no degradation with two sharp ribosomal peaks. Affymetrix’s GeneChip IVT Express kit was used for cDNA synthesis and in vitro transcription.

hyb_protocol: A hybridization cocktail is prepared, including the fragmented target, and probe array controls. It is then hybridized to the probe array during a 16-hour incubation.  As outlined in detail in http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf

scan_protocol: Once the probe array has been hybridized, washed, and stained, it is scanned. Each workstation running Affymetrix Microarray Suite or GCOS can control one scanner. The software defines the probe cells and computes an intensity for each cell. Each complete probe array image is stored in a separate data file identified by the experiment name and is saved with a data image file (.dat) extension.

data_processing:
The data were processed by Affymetrix Software Command Console and Expression Console using RMA algorithms which consisted of three steps: background correction, quantile normalization (each performed at the individual probe level), and robust linear model fit using log-transformed intensities (at the probe set level).  The RMA normalized expression values in the Matrix are the average of 4 replicates for each of the 4 samples.
The overall selection criteria for presence used genes with expression values larger than a threshold 3.5 in more than 50% of samples (2 out of 4).

label_protocol: Double-stranded cDNA is synthesized from total RNA isolated from cells. Affymetrix’s GeneChip IVT Express kit was used for cDNA synthesis and in vitro transcription to produce biotin-labeled cRNA from the cDNA. The cRNA is fragmented before hybridization. As outlined in detail in http://www.affymetrix.com/support/downloads/manuals/expression_analysis_technical_manual.pdf

value: primary human cerebral cortex astrocyte cell line (ScienCell Research Laboratories, cat#1800)

value: global cellular fraction


title: astrocytoma_RISC-IP mRNA (S905515.K439)

value: human U-87 MG astrocytoma/glioblastoma cell line (ATCC, cat# HTB-14)


title: SiS4+ rep1


title: ctrl- rep2

source_name: HMEC-TR, SiRNA scramble


title: CDM 3

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

hyb_protocol: The labeled RNAs were hybridized to Human miRNA V2 8x15K microarrays (G4470B, Agilent) at 55°C for 20 h in a Agilent rotating oven.

scan_protocol: After washing, the arrays were scanned with an Agilent Microarray Scanner (G2565B) using extended dynamic range as specified by the manufacturer.

data_processing: Agilent Feature Extraction 9.5 Software was used to extract the microarray data using default parameters (protocol miRNA-v1_95_May07 and Grid: 019118_D_20080214)

source_name: muscle primary culture cells

label_protocol: Each sample was prepared using Agilent’s “miRNA Complete Labeling and Hyb” Kit (5190-0456) according to the Manufacturer’s protocol. Total RNA (100 ng) was dephosphorylated with Calf Intestinal Alkaline Phosphatase at 37°C for 30 min, denatured with DMSO at 100°C for 10 min, and labelled with Cyanine3-pCp using T4 RNA ligase at 16°C for 2 h.

growth_protocol: Myoblasts were grown in HAM’s F10 medium (Gibco) supplemented with 50 µg/ml gentamycine (Biomedia) and 20% fetal calf serum (Biomedia). All cultures were incubated at 37°C in a humid atmosphere containing 5% CO2. For myoblast differentiation, growth medium was removed from sub-confluent cultures and replaced by Dulbecco’s modified Eagle’s medium (Gibco) containing 10 µg/ml insulin and 100 µg/ml transferrin (Sigma)

extract_protocol: TRIZOL

treatment_protocol: Biopsies from quadriceps muscles were obtained during autopsies of control or age-matched  CDM1 patient.

value: myotube

value: congenital myotonic dystrophy


title: ctrl+ rep1


title: SiTIF- rep1


title: ctrl- rep1


title: minimal media DvH LS4D

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

description: Mid-log phase DvH in LS4D, 1 biological replicate

hyb_protocol: Slides were hybridized using Nimblegen's standard protocol.

scan_protocol: Nimblegen slides were scanned on an Axon Gene Pix 4200A scanner with 100% gain

data_processing: Slides were analyzed with Nimblescan, with no local alignment and a border value of -1. Data from potentially cross-hybridizing probes (matching at 50 or more of 60 nucleotides to a second location in the genome) was removed.

label: Alexa 555

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: DvH grown in minimal media

label_protocol: First-strand cDNA was synthesized with random hexamer primers using SuperScript indirect cDNA labeling system (Invitrogen); the reaction buffer was supplemented with actinomycin D to inhibit second-strand synthesis.  First-strand cDNA was labeled with Alexa 555.  About 2 ug of labeled first-strand cDNA was hybridized to the array. For the genomic control, we used DNA from cells in stationary phase to minimize copy number variation across the chromosome.  Genomic DNA was extracted using the DNeasy blood tissue kit (Qiagen) and labeled with Nimblegen's comparative genomic hybridization protocol. Briefly, genomic DNA was sonicated to 200-1000 bp and amplified using Klenow fragment and Cy3-labeled random nonamer primers.

extract_protocol: Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyzer; only samples with an RNA integrity number of around 9 or better were used.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads coated with oligonucleotides that hybridize to ribosomal RNA.

tag: media


title: 7113_TSC10A_controlpool

city: St. Louis

first: Ivan

last: Baxter

state: MO

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

description: The control pool from the F2s segregating from a 7113 x ler cross used for BSQA mapping.

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

organism: Arabidopsis thaliana

source_name: leaves

label_protocol: Invitrogen Bioprime labelling kit

extract_protocol: Qiagen DNeasy kit

tag: age

value: ~6 weeks

value: Leaves


title: astrocytoma_global mRNA (S803681.H42.1)


title: 7113_TSC10A_phenotypepool

description: The phenotype pool from the F2s segregating from a 7113 x ler cross used for BSQA mapping.


title: CDM 2


title: NC_DM4_HuEx

description: Primary culture of skeletal muscle cells of a CDM1 fetus, differentiation of 10 days

hyb_protocol: 5 micrograms of biotinylated cDNA were hybridized on GeneChip® Human Exon 1.0 ST array at 45°C for 16 hours

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G

data_processing: Raw data (.CEL Intensity files) were generated using the Affymetrix GeneChip® Operating Software (GCOS) version 1.4. We then used Xray version 2.5 (BIOTIQUE Systems) to analyze the data on the core probe-sets at the exon level. The input files were normalized with quantile method. We applied the GC background correction and the expression score for each probe-set was derived via application of median-polish (ExonRMA). We filtered out probes with GC count less than 6 and greater than 17 and non-expressed probes using the DABG Filter Non Expressed Probes option.  Nested Analysis of Variance was used to identify genes with alternative splicing.

source_name: CDM1 primary muscle cells culture 3

label_protocol: Samples were labeled according to GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual, Affymetrix P/N 701880 Rev.2

growth_protocol: Skeletal muscle cell cultures derived from control and age-matched CDM1 fetus (36 weeks)  were differentiated into myotubes for 10 days in D-MEM (Invitrogen) + 5µg/ml gentamycin + 10μg/ml insulin and 100μg/ml of transferrin

extract_protocol: Total RNA was extracted by Trizol protocol


title: rich media DvH LS

description: Mid-log phase DvH in LS, 2 biological replicates

source_name: DvH grown in lactate/sulfate media supplemented with yeast extract (LS)

value: LS


title: NC_DM3_HuEx

source_name: CDM1 primary muscle cells culture 2


title: Ler_tilingTray810

description: Ler array for identification of SFPs

tag: ecotype

value: Ler


title: Ler_tilingTray811

description: Ler array for identification of SFPs


title: Ler_tilingTray809

description: Ler array for identification of SFPs


title: astrocytoma_global microRNA (01_H11.0_081771)


title: Col-0_tilingTray811

description: Col-0 array for identification of SFPs


title: astrocyte_global microRNA (02_H11.0_081772)


title: Col-0_tilingTray810

description: Col-0 array for identification of SFPs


title: astrocyte_RISC-IP mRNA (S905515.K438)


title: Col-0_tilingTray809

description: Col-0 array for identification of SFPs


title: CDM 1


title: NC_DM2_HuEx

source_name: CDM1 primary muscle cells culture 1


title: Control 2

value: control


title: Control 3


title: NC_CTL4_HuEx

description: Primary culture of skeletal muscle cells of a control fetus, differentiation of 10 days

source_name: Control primary muscle cells culture 3

value: Control


title: NC_CTL2_HuEx

source_name: Control primary muscle cells culture 1


title: Malignant cervical carcinoma cell line_CaSki #1

status: Public on May 25 2011

middle: Jonathan

last: Murray

address: Box 197, Hills Road

department: MRC/Hutchison Research Centre

country: United Kingdom

institute: MRC Cancer Cell Unit

description:
CaSki #1
Biological replicate 9 of 10

hyb_protocol: Test and reference RNA samples were mixed pair-wise and hybridized to the miRCURY LNA array platform version 8.0 (Exiqon, Vedbaek, Denmark), according to the manufacturer's instructions.

scan_protocol: As described in Muralidhar et al 2007, PMID 17471471

data_processing: The resultant raw .txt files were processed using the Bioconductor package limma in the statistical software environment R. For most experimental conditions, microRNA profiling was performed on two experimental replicates, which were mean summarized. Mean foreground signal intensities were corrected for background noise using exponential-normal convolution model, while inter-array normalization was performed using variance stabilization algorithm vsn2. Drosha over-expression was defined as levels ≥2.0 fold greater than in normal cervical keratinocytes (as described in Muralidhar et al 2007, PMID 17471471). We used limma to fit a linear model with empirical Bayes moderated t-statistics, adjusting p-values for false discovery using the Benjamini-Hochberg method and applying a significance threshold of alpha=0.01.

source_name: Cluster 2: Drosha over-expressing cell line (CaSki); replicate 1

label_protocol: Total RNA from each sample and the reference (the latter pooled First Choice Human RNA Survey Panel, Ambion, Austin, TX, USA) were labeled with Hy3 and Hy5 fluorescent label, respectively, using the miRCURY LNA Array power labeling kit (Exiqon, Vedbaek, Denmark).

growth_protocol: Cell lines cultured under standard tissue culture conditions - incubated at 37C and in 5% CO2.

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

treatment_protocol: Nil; pre-treatment

value: malignant cervical carcinoma cell line CaSki

tag: cluster

value: Cluster 2

tag: drosha expression

value: over-expression

tag: reference

value: Pooled human RNA from 20 anatomical sites


title: Malignant cervical carcinoma cell line_CaSki #2

description:
CaSki #2
Biological replicate 10 of 10

source_name: Cluster 2: Drosha over-expressing cell line (CaSki); replicate 2

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX


title: Malignant cervical carcinoma cell line; manipulated_SW756.v #1

description:
SW756-v #1
Biological replicate 7 of 10

source_name: Cluster 2: Drosha over-expressing cell line (SW756) with empty vector; replicate 1

value: malignant cervical carcinoma cell line SW756

tag: protocol

value: empty vector


title: Malignant cervical carcinoma cell line; manipulated_SW756.v #2

description:
SW756-v #2
Biological replicate 8 of 10

source_name: Cluster 2: Drosha over-expressing cell line (SW756) with empty vector; replicate 2


title: NC_CTL3_HuEx

source_name: Control primary muscle cells culture 2


title: Malignant cervical carcinoma cell line; manipulated_SW756 #2

description:
SW756 #2
Biological replicate 6 of 10

source_name: Cluster 2: Drosha over-expressing cell line (SW756); replicate 2


title: Malignant cervical carcinoma cell line; manipulated_SW756 #1

description:
SW756 #1
Biological replicate 5 of 10

source_name: Cluster 2: Drosha over-expressing cell line (SW756); replicate 1


title: Malignant cervical carcinoma cell line; manipulated_MS751.v

description:
MS751-v
Biological replicate 3 of 8

source_name: Cluster 1: Drosha under-expressing cell line (MS751) with empty vector

value: malignant cervical carcinoma cell line MS751

value: Cluster 1

value: under-expression


title: Malignant cervical carcinoma cell line_ME180 #1

description:
ME180 #1
Biological replicate 3 of 10

source_name: Cluster 2: Drosha over-expressing cell line (ME180); replicate 1

value: malignant cervical carcinoma cell line ME180


title: Malignant cervical carcinoma cell line_MS751

description:
MS751
Biological replicate 4 of 8

source_name: Cluster 1: Drosha under-expressing cell line (MS751)


title: Malignant cervical carcinoma cell line_ME180 #2

description:
ME180 #2
Biological replicate 4 of 10

source_name: Cluster 2: Drosha over-expressing cell line (ME180); replicate 2


title: Malignant cervical carcinoma cell line; manipulated_SW756.mut3.dup2kd #1

description:
SW756 mut3 dup2kd #1
Biological replicate 5 of 8

source_name: Cluster 1: Drosha under-expressing cell line due to siRNA duplex #2 knockdown with mutation to duplex #3 binding site; replicate 1


title: NaCl 0.3M-rep5

description: Control vs 0.3M NaCl

source_name: D.radiodurans R1 exposed to 0.3M NaCl

value: exposed to 0.3M NaCl

source_name: untreated wild type

value: none (reference)


title: Malignant cervical carcinoma cell line; manipulated_SW756.mut3.dup3kd #2

description:
SW756 mut3 dup3kd #2
Biological replicate 2 of 10

source_name: Cluster 2: Drosha over-expressing cell line due to siRNA duplex #3 knockdown but mutation to duplex #3 binding site; replicate 2


title: Malignant cervical carcinoma cell line; manipulated_SW756.mut3.dup2kd #2

description:
SW756 mut3 dup2kd #2
Biological replicate 6 of 8

source_name: Cluster 1: Drosha under-expressing cell line due to siRNA duplex #2 knockdown with mutation to duplex #3 binding site; replicate 2


title: Malignant cervical carcinoma cell line; manipulated_SW756.mut3.dup3kd #1

description:
SW756 mut3 dup3kd #1
Biological replicate 1 of 10

source_name: Cluster 2: Drosha over-expressing cell line due to siRNA duplex #3 knockdown but mutation to duplex #3 binding site; replicate 1


title: Malignant cervical carcinoma cell line; manipulated_MS751.pcDNA3.1.zeo.Drosha #2

description:
MS751 pcDNA3.1 zeo Drosha #2
Biological replicate 8 of 8

source_name: Cluster 1: Drosha under-expressing cell line: construct to over-express Drosha in MS751 cell line; levels only reached 1.996x reference; miRNA profiles still clustered with Drosha under-expressing samples; replicate 2

value: pcDNA3.1 zeo Drosha construct


title: Malignant cervical carcinoma cell line; manipulated_MS751.pcDNA3.1.zeo.Drosha #1

description:
MS751 pcDNA3.1 zeo Drosha #1
Biological replicate 7 of 8

source_name: Cluster 1: Drosha under-expressing cell line: construct to over-express Drosha in MS751 cell line; levels only reached 1.996x reference; miRNA profiles still clustered with Drosha under-expressing samples; replicate 1

source_name: First Choice Human RNA Survey Panel, Ambion, Austin, TX


title: Malignant cervical carcinoma cell line; manipulated_CaSki.dup2kd

description:
CaSki dup2kd
Biological replicate 1 of 8

source_name: Cluster 1: Drosha under-expressing cell line due to siRNA duplex #2 knockdown

value: siRNA duplex #2 knockdown


title: Malignant cervical carcinoma cell line; manipulated_CaSki.dup3kd

description:
CaSki dup3kd
Biological replicate 2 of 8

source_name: Cluster 1: Drosha under-expressing cell line due to siRNA duplex #3 knockdown

value: siRNA duplex #3 knockdown


title: Control 1

source_name: muscle primary culture cells

value: myotube

value: control


title: Aspergillus nidulans + ors-2 (array 2)

city: Jena

first: Fabian

last: Horn

address: Beutenbergstr. 11a

department: Systems Biology / Bioinformatics

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology e.V. Hans-Knöll-Institute (HKI)

hyb_protocol: febit GmbH proprietary standard hybridization buffer (15µl pre array) was added and took place in the Geniom RT Analyzer

scan_protocol: Geniom RT Analyzer using the febit's Consecutive Signal Enhancement procedure

data_processing: Background correction with help of control spots and subsequent quantile normalization. Fold-Changes were calculated and p-values determined using the „t-statistics“.

organism: Aspergillus nidulans

source_name: fungal pellet

label_protocol: For each Array 1µg of total RNA was labelled with MessageAmp(TM)II-Biotin Enhanced kit from Ambion (including reverse transcription into cDNA).

growth_protocol: A.nidulans incubation over night in liquid Aspergillus minimal media (AMM). S. rapamycinicus was cultivated in M79 medium. Protocoll according to Schroeckh 2009 (PMID:19666480)

extract_protocol: Total RNA was isolated using RiboPure-Yeast Kit (Applied Biosystems).

treatment_protocol: A.nidulans was shifted into fresh 100ml AMM. Either 5ml of the S.rapamycinicus culture or orsellinic/lecanoric acid was added. 3 hours incubation at 37°C with 200rpm.

tag: strain

tag: treatment

value: orsellinic acid


title: Aspergillus nidulans + lec-1 (array 2)

value: lecanoric acid


title: Aspergillus niculans + lec-2 (array 2)


title: Aspergillus nidulans-2 (array 2)


title: Aspergillus nidulans + Streptomyces rapamycinicus-1 (array 1)

value: S. rapamycinicus


title: Aspergillus nidulans + Streptomyces rapamycinicus-1 (array 2)


title: Aspergillus nidulans + ors-1 (array 2)


title: Aspergillus nidulans-2 (array 1)


title: Aspergillus niculans + lec-2 (array 1)


title: Aspergillus nidulans + Streptomyces rapamycinicus-2 (array 2)


title: Aspergillus nidulans-1 (array 1)


title: Active EBF replicate 1

city: Salt Lake City

first: Monica

last: Vetter

state: UT

address: 50 N. Medical Dr. 517 Wintrobe

department: Neurobiology and Anatomy

institute: University of Utah

description: Active EBF

hyb_protocol: Agilent Two-color Gene Expression Hyb/Wash Protocol

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

data_processing: Images where processed using Agilent Feature Extraction software version 9.1.3.1. Lowess normalized log base 10 ratios of Cy3/Cy5 intensity were obtained.

organism: Xenopus laevis

label_protocol: Agilent Two-Color LRILAK Labeling Protocol

growth_protocol: 1ng of hGR-XEBF3 mRNA and 0.2ng noggin mRNA were co-injected into Xenopus embryos at the one-cell stage. Alternatively, 0.4ng hGR mRNA and 0.2ng noggin mRNA were co-injected in control embryos. At stage 9, animal caps were dissected from the embryo, using either a Gastromaster or a hypodermic needle tip.

extract_protocol: Total RNA was isolated from animal caps with the RNeasy mini kit following manufacturer's instructions (Qiagen).

treatment_protocol: Animal caps were treated with 30μM DEX in 1x MMR for 4.5 hours before harvesting of total RNA. For condition 1, animal caps were incubated in 1X MMR for 4.5 hours without any treatment

value: hGR-Xebf3 with DEX treatment

value: hGR-Xebf3 without DEX treatment


title: Control for DEX

description: Control for DEX

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Images where processed using Agilent Feature Extraction software version 8.1.1.1. Lowess normalized log ratios of Cy3/Cy5 intensity were obtained.

source_name: hGR+DEX

growth_protocol: 1ng of hGR-XEBF3 mRNA  was injected into Xenopus embryos at the one-cell stage. Alternatively, 0.4ng hGR mRNA  was injected in control embryos. At stage 9, animal caps were dissected from the embryo, using either a Gastromaster or a hypodermic needle tip.

value: hGR with DEX treatment


title: Aspergillus nidulans + Streptomyces rapamycinicus-2 (array 1)


title: Active EBF

description: Active EBF


title: BW+CCL-1/2

city: Brussels

first: Amel

last: Tounsi

address: 74 avenue hippocrate

country: Belgium

institute: LICR

description: Gene expression data from  BW5147 cells simulated with 100 U/ml of CCL-1.

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse expression Array 430A. GeneChips were washed and stained in the Affymetrix genechip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

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

source_name: BW5147 cells obtained from the American Type Culture Collection (Rockville, MD)

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

growth_protocol: The thymic lymphoma cell line BW5147 was obtained from the American Type Culture Collection (Rockville, MD) and were cultured in Iscove-Dulbeco’s medium supplemented with 10% fetal calf serum, 0.24 mM asparagine, 1.5 mM glutamine, 0.55 mM arginine, and 50 μM 2-mercapthoethanol

extract_protocol: RNA was extracted using Tripure isolation reagent (Roche) according to the manufacturer’s instructions.

treatment_protocol: one million BW5147 cells were stimulated with 100 ng/ml of dexamethasone and/or with 100 U/ml of IL-9 or CCL1 for eight hours.

tag: mouse T cell lymphomas sensitive to glucocorticoids


title: Aspergillus nidulans-1 (array 2)


title: Aspergillus nidulans + ors-1 (array 1)


title: Aspergillus nidulans + ors-2 (array 1)


title: Active EBF replicate 2

description: Active EBF


title: Gastric_mucosa_MNU+H. pylori

city: Tokyo

first: Takeshi

last: Toyoda

address: 1-18-1 Kamiyoga, Setagaya-ku

department: Division of Pathology

institute: National Institute of Health Sciences

description: We followed manufacturer's protocol.

hyb_protocol: We followed manufacturer's protocol. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

scan_protocol: We followed manufacturer's protocol, and used GenePix 4000B. http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

source_name: Mouse gastric mucosa, N-methyl-N-nitrosourea-treated, Helicobacter pylori-infected, 40 weeks

extract_protocol: QIAGEN RNeasy Plus Mini Kit was used.

tag: stress

tag: gender

value: male

value: 45 or 46 weeks

tag: tissue

value: gastric mucosa of glandular stomach


title: Gastric_mucosa_MNU

description: We followed manufacturer's protocol.

source_name: Mouse gastric mucosa, N-methyl-N-nitrosourea-treated, 40 weeks

label_protocol:
We followed manufacturer's protocol.
http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf

value: MNU (control)


title: Aspergillus nidulans + lec-1 (array 1)


title: Control for DEX replicate 2

description: Control for DEX


title: Active EBF replicate 4

description: Active EBF


title: Control for DEX replicate 4

description: Control for DEX


title: Control for DEX replicate 1

description: Control for DEX


title: Gastric_mucosa_MNU+NaCl

description: We followed manufacturer's protocol.

source_name: Mouse gastric mucosa, N-methyl-N-nitrosourea and high-salt diet-treated, 40 weeks

value: MNU+NaCl


title: Gastric_mucosa_MNU+NaCl+H. pylori

description: We followed manufacturer's protocol.

source_name: Mouse gastric mucosa, N-methyl-N-nitrosourea and high-salt diet-treated, Helicobacter pylori-infected, 40 weeks


title: Active EBF replicate 3

description: Active EBF


title: CD34+CD45+(CD7-CD10-CD19-) donor-3

description:
SP3
Gene expression data from luympho-granulo-macrophagic precursors

hyb_protocol: cRNAs were then hybridized to Affymetrix HG-U133A GeneChip arrays

label_protocol: RNA samples were subjected to double linear amplification using the GeneChip Eukaryotic Small Sample Target Labeling Assay Version II  (Affymetrix).

growth_protocol: CD34+ HPCs were isolated from Umbilical cord blood  midiMACS system (Miltenyi)

treatment_protocol: CD34+ PCs were labelled with CD34, CD45RA, CD7, CD10 and CD19  antibodies before the corresponding population were sorted by FACS

value: umbilical cord blood

tag: cell type

value: hematopoietic progenitors


title: CD34+CD45+(CD7-CD10-CD19-) donor-2

description:
SP2
Gene expression data from luympho-granulo-macrophagic precursors


title: CD34+CD45+(CD7-CD10-CD19-) donor-1

description:
SP1
Gene expression data from luympho-granulo-macrophagic precursors


title: CD34+CD45RA+CD7+(CD10-)  donor-2

description:
DP2
Gene expression data from prothymocytes

source_name: CD34+CD45RA+CD7+(CD10-)  HPCs


title: CD34+CD45RA+CD10+(CD7-CD19-) donor-2

description:
Galy2
Gene expression data from pre-proB cells

source_name: CD34+CD45RA+CD10+(CD7-CD19-)  HPCs


title: Control for DEX replicate 3

description: Control for DEX


title: 13969294 - Fci.Salk11 vs Col-0

city: Evry

first: Eddy

last: Blondet

address: 2 rue Gaston crémieux

department: URGV

institute: INRA

description: The At3g49120 gene codes for the peroxidase 34 (PRX 34), an enzyme potentially involved in the polymérisation of monolignols, the lignin precursors. This enzyme is expressed in primary floral stem and its absence has an impact on the lignin quantity and biomass (at the young stage). Here, its question to characterize several mutants.

hyb_protocol: Col-0 Cy5 / Fci.Salk11 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 using R version 2.8.1 (2008-12-22) (ISBN 3-900051-07-0). 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.

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: stem - Media : compost  hygrometry : 40% to 60%  Temperature : 21°C Day / 18°C Night  Light : Long days

extract_protocol: Col-0:12ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

value: wassilewskija

tag: genotype/variation

value: mutant (fci.c)

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

value: boyes 6.20

extract_protocol: Fci.Salk11:12ug. (Qiagen_RNeasy.pdf)

value: columbia

value: mutant (gabi728f08)


title: 13969303 - Ws vs FCI.89

hyb_protocol: FCI.89 Cy5 / Ws 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.

growth_protocol: stem - media : compost  hygrometry : 40% to 60%  temperature : 21°C Day / 18°C Night  light : Long days

extract_protocol: FCI.89:15ug. (Qiagen_RNeasy.pdf)

value: mutant (fci.89)

source_name: Ws

extract_protocol: Ws:15ug. (Qiagen_RNeasy.pdf)

value: wild type


title: CD34+CD45RA+CD10+(CD7-CD19-) donor-1

description:
Galy1
Gene expression data from pre-proB cells

extract_protocol: RNA were extracted using the RNeasy Micro Kit


title: BW+Dex+CCL-1/1

description: Gene expression data from  BW5147 cells simulated with 100ng/ml of Dex and 100 U/ml of CCL-1.


title: BW+Dex+CCL-1/2


title: BW+IL-9/2

description: Gene expression data from  BW5147 cells simulated with 100 U/ml of IL-9.