title: CcpA_L3vsWT_L3

value: late log


title: Root 3

status: Public on Sep 10 2010

type: RNA

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

hyb_protocol: Samples were hybridized with GeneChip Brassica Exon 1.0 ST Arrays (Affymetrix) at the NASC Microarray Core Facility according to manufacturer's instructions.

scan_protocol: Array scanning was performed using an Affymetrix 3000 7G scanner at the NASC Microarray Core Facility according to manufacturer's instructions (Affymetrix).

data_processing: Data analysis and statistical analysis were performed using the GeneSpring GX 11 program from Agilent Technologies. Raw data was pre-normalised using the RMA algorithm and each gene signal was normalised to the median of the gene signal across all samples. RMA expression values, available in the *.chp file, were derived from Expression Console software.

label: biotin

molecule: total RNA

organism: Brassica rapa

source_name: 11-day-old roots

label_protocol: RNA was amplified, fragmented and labeled using the Ambion WT expression kit.

growth_protocol: Sterilised seeds (washed in 70% ethanol, rinsed in deionised water and surface-sterilised using NaOCl) were sown in large sqaure (20cm x 20 cm) Petri dish plates containing 250ml 0.8% agar with 1x Murashige & Skoog salts adjusted to pH 5.6. Plants were grown under 16 hour photoperiod at 24 C.

extract_protocol: RNA was isolated using a modified TRIzol protocol. To each sample, 1ml of TRIzol was added and total RNA extracted according to the manufacturer's instructions, with the following modifications: (i) after homogenisation the samples were centrifuged and supernatant transferred to a clean Eppendorf tube, and (ii) to aid precipitation of RNA from the aqueous phase, 0.25ml of isopropanol and 0.25ml 1.2M NaCl solution containing 0.8M sodium citrate. Extracted total RNA was then purified using the 'RNA Cleanup' protocol for Qiagen RNeasy columns.

tag: tissue

value: root

tag: line

tag: age

value: 11 days


title: CcpA_L3vsCcpA_L4

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

hyb_protocol: Two individual ,  differentially labeled ,  cDNAs were incubated at  , 95° C for 3' cooled down  , to 68° C and mixed ,  (final-volume 20 µl). To ,  these mixed cDNAs 180 µl  , of pre-heated (68° C) ,  Slidehyb#1 hybridization ,  buffer (Ambion Austin ,  USA) was added and the ,  resulting solution was ,  applied on a pre-heated ,  slide (68° C). Slides were ,  then hybridized at 44° C for  , 16 hours. Subsequently ,  slides were washed at ,  42°C once in 1 x ,  SSC/0.2% SDS and twice  , in 1 x SSC and dried by ,  centrifugation (1 x SSC is ,  0.15 M NaCl and 0.15 M ,  Sodium Citrate).

scan_protocol: Using the Scan Array ,  Express microarray ,  scanner. 1.Turn on the ,  scanner and the computer  , (in this order) 2.Login: ,  scanner 3.Double click the  , 'ScanArray Express' icon  , 4.Switch on lasers 1 and  3 , at least 15 minutes prior  to , scanning arrays 5.Click  the , 'File' button This is to  , prevent you from ,  accidentally turning off the  , laser after the 15 minutes  , warming-up phase  6.Insert , the slide with the  array-side , up and the  label towards , the outside.  On Agilent , slides the  array side is the , side with  the label that has , the  word  Agilent on it ,  7.Press 'Scan | Prescan' ,  8.Put resolution at 50 m ,  select both labels used ,  and set PMT values for ,  both channels 9.Press ,  'Start' 10.Press 'Palette ' ,  'Green' as soon as ,  projection of the image has  , started (first dye) select ,  the red colour as soon as ,  scanning of the second ,  layer (second dye) has ,  started 11.Adjust PMT ,  values to balance signals ,  obtained for both ,  channels. If necessary do ,  a few low-resolution scans  , to obtain a optimal  balance , 12.Click the  'Scan' button , again  13.Select frame for , high  resolution scan adjust ,  resolution (to 10 m) and ,  scan the array for both ,  dyes 14.Press 'File | Save'  , to save the files 'Save all'  , saves both dye layers ,  Create a new folder for ,  each array  'Save all' ,  saves the signals from  both , layers in individual  files , 15.Switch off the  lasers

data_processing: Lowess normalized log2 ratio (Cy3/Cy5). No interslide normalization

organism: Lactiplantibacillus plantarum

label_protocol: Annealing Mix  x µl RNA preparation  (=5µg) y µl  nuclease-free water 1 µl  Random Nonamers 11  µl TOTAL 1. mix  Annealing Mix in a 200  µl PCR tube gently by  pipetting up and down  2. incubate for 5’ 70°C  3. cool at room  temperature for 10’  (annealing) 4. spin down  the mixture to the  bottom of the tube 5.  place on ice Reverse  transcription Reverse  Transcription Mix 4 µl 5x  buffer 2 µl 0.1 M DTT 1  µl dNTP-mix 1 µl  AA-dUTP 1 µl TMIII  (keep only briefly  outside 20°C) 20 µl  TOTAL 1. Mix by very  gently by pipetting up  and down (vigorous  pipetting will denature  the enzyme!) 2.  Incubate for 3 hrs at  42°C (in PCR-machine)  3. Cool on ice for  immediate purification or  place at 20°C for  storage Degradation of  mRNA 1. Add 2 µl 2.5 M  NaOH 2. Mix (vortex)  and spin down 3.  Incubate for 15 min. at  37°C 4. Add 10 µl 2 M  HEPES free acid 5. Mix  (vortex) and spin down  6. Ready for purification  or store at 20°C  Labelling and  purification of cDNA  with cyanine dyes  Followed Ge Healthcare  kit Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA and  Aminoallyl-aRNA code  RPN5661 Labelling of  amino allyl-modified  cDNA with CyDye 1.  Add the amino allyl  modified cDNA (in 0.1 M  sodium bicarbonate)  directly into one aliquot  of CyDye NHS Ester.  Resuspend the ester  completely by pipetting  several times and  transfer the solution to  an amber 1.5 ml tube 2.  Incubate at room  temperature, in the dark  for 60 to 90 minutes 3.  Add 15 µl 4 M  Hydroxylamine to each  coupling reaction 4. Mix  by stirring and incubate  at room temperature, in  the dark, for 15 minutes  5. Proceed directly to  purification of  CyDye-labelled cDNA  Purification of CyDye  labelled cDNA Followed  Ge Healthcare kit  Amersham CyDye  (Cy3/Cy5)Reactive Dye  Protocols for Post  Labelling  Aminoallyl-cDNA

growth_protocol: Cultures were grown in batch fermentation on a chemically defined medium untill an optical density of 1.0 before being stressed with Na-L-lactate

extract_protocol: Collecting  cells Quenching Buffer  66.7 mM HEPES (pH  6.5) 60%Methanol  Extraction Mixture  (Prepared in a  screw-cap tube) -500 µll  phenol/Chloroform -30  µl10% SDS -30 µl3 M  NaAc (pH 5.2) -500 mg  glass-beads (75-150 µm)  -400 µlTE buffer 1.For  each sample prepare a  tube with Extraction  Mixture 2.Harvest cells  and quench them  immediately in  Quenching Buffer. Add  4 volumes of Quenching  Buffer ( 40°C) to 1  volume of cell culture  3.Mix and store the  sample at -40°C  4.Centrifuge cells at -20  C at 9000 rpm for 10  minutes (Centrifuge  RC5B) 5.Discard the  supernatant; keep the  cell pellet cooled and  work quickly to prevent  condensation of water.  Transfer the pellet with  a pre-cooled spatula to  a screw-crap tube with  Extraction Mixture 6.Mix  the cell pellet thoroughly  with Extraction Mixture  by shaking by hand  7.Freeze the tube  immediately in liquid  nitrogen 8.Break cells in  the Savant FastPrep  FP120. Three times 40  seconds at speed 4.0  (cool cells between  steps if necessary)  9.Centrifuge for 5  minutes at 4°C in an  Eppendorf centrifuge at  10.000 rpm 10.Transfer  500 µl of the  supernatant to a new  tube. Add 400 µl  chloroform (chloroform  should be cooled at  4°C) 11.Centrifuge for 2  minutes in an Eppendorf  centrifuge at full speed  (4°C) 5.Continue with  the High Pure RNA  Isolation Kit from  Roche (order # 1 828  665) 6.Incubate for 60  minutes with DnaseI,  elute with 50 µl elution  buffer 7.Store the RNA  in at least 2 aliquots,  one of 20 µl (for  concentration and  quality analysis and  labelling) and one  back-up of 30 µl at  -80°C.

treatment_protocol: Harvested cultures were quenced in extraction mix containing Phenol/Chloroform, SDS, Na-acetate, glass-beads and TE buffer.

tag: genotype

value: CcpA K.O.

tag: growth stage

value: early stationary

tag: treatment

value: Na-L-lactate


title: Human embryonic stem cells, hES-T3, grown on MEF feeder, biological rep1

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: The mRNA profilings of T3MF, T3CM and T3BA cells were analyzed using Affymetrix Human Genome U133 plus 2.0 GeneChip according to the Manufacturer¡¦s protocols (Santa Clara, CA, USA, http://www.affymetrix.com).

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

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

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

organism: Homo sapiens

source_name: hES-T3 cells grown on MEF feeder

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

growth_protocol: Human embryonic stem cell line hES-T3, which is one of the five hES cell lines derived with institutional review board approval from preimplantation embryos donated at IVF clinics in Taiwan, exhibits normal female karyotype (46, XX), and it has been continuously cultured on mitomycin C (10 ug/ml) mitotically inactivated MEF feeder in hES medium under 5% CO2 at 37oC and underwent freezing/thawing processes. The hES culture medium consisted of DMEM/F12 (1:1, GIBCO) supplemented with 20% KSR (Invitrogen), 1% non-essential amino acids, 1 mM L-glutamine, 0.1 mM £]-mercaptoethanol, and 4 ng/ml human basic fibroblast growth factor (bFGF; Life Technologies). Routine passages of hES-T3 cells every 5-7 days were done with collagenase ( type IV, 1 mg/ml, Invitrogen) treatment and mechanical scrape. The hES-T3 cells grown on MEF feeder were designated as T3MF.

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

treatment_protocol: Non

tag: growth conditions

value: hES-T3 cells grown on MEF feeder

tag: gender

value: female

tag: cell line


title: Root 2

institute: Nottingham Arabidopsis Stock Centre (NASC)


title: Root 1


title: Leaf 1

source_name: 23-day-old semi-expanded leaves

growth_protocol: Plants grown in 13-cm pots containing a high-nutrient, medium-grade, peat-based compost, pH; 5.3 - 5.7, N:P:K; 280:160: 350 g m-3. Grown under greenhouse conditions; 16hr photoperiod, 13.3 C - 22.3 C mean temperature range.

value: leaf

value: 23 days


title: Leaf 2


title: Daudi-Luciferase-3

city: Atlanta

first: Xiangxue

last: Guo

state: GA

address: 1365 Clifton Rd, Bld-C, 3rd, B25

country: USA

institute: Emory University

hyb_protocol: Standard Agilent protocol, performed by Agilent

scan_protocol: Agilent 2100 bioanalyser and Agilent MR-2 DNA microarray scaners(Agilent Technolies, Santa Clara, CA)

data_processing: R program/ Bioconductor -Agi4x44PreProcess. Normalization performed using Quantile normalization method.

label_protocol: Standard Agilent protocol

extract_protocol: Qiagen Rneasy mini kit(Cat. 74104)

value: Daudi

tag: sirna

value: Luciferase


title: Leaf 3


title: CD22_Transg_spleen_E4231

city: St. Peter

first: Sanjive

last: Qazi

state: MN

address: 800 west College Av

department: Biology

institute: Gustavus Adolphus College

hyb_protocol: Atlas  cDNA Expression Arrays User Manual, Section VII.B was used and all 68oC incubations were performed at 71oC instead. After discarding prehybridization solution, arrays were hybridized overnight.

scan_protocol: Arrays were washed 4 times by using 2X SSC/1% SDS and 2 times by using 0.1X SSC/0.5% SDS.  Membranes were sealed and exposed to phosphoscreen (Molecular Dynamics).

data_processing: Density readings from the phosphor images were normalized to 5  housekeeping genes (glyceraldehyde-3-phosphate dehydrogenase (G3PDH; GADPH),  myosin I, ornithine decarboxylase (ODC), phospholipase A and hypoxantine-guanine  phosphoribosyltransferase (HPRT)).  The mean signal intensity within  each spot was subtracted from the sub-grid median of the background signal. For  thresholding, the intensities of the duplicate spots for each gene were averaged and  floored to a signal value of 2 units.

organism: Mus musculus

source_name: splenocytes

label_protocol: After DNAase treatment, total RNA was converted into radioactively labeled cDNA using [a-32P] dATP (Amersham) by reverse transcriptase (Clontech). Chroma Spin columns (Clontech) were used to purify labeled cDNA.

extract_protocol: total RNA was isolated using Tripure isolation reagent (Boehringer), a monophasic solution of phenol and guanidine thiocyanate

tag: genetic background

value: FVB

tag: cell type

value: splenocytes

value: CD22DE12 transgenic


title: CcpA_L1vsCcpA_L2

value: mid log

value: early log


title: CcpA_L4vsWT_L4

value: WCFS1- wild type


title: CcpA_L2vsCcpA_L3

value: late log


title: CcpA_R4vsWT_R4


title: PolII CHIP file for + cohesin

type: genomic

city: Bunkyo-ku

first: Katsuhiko

last: Shirahige

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Epigenetic Disease

country: Japan

institute: The University of Tokyo

description: DrosSalivaryGland_Pol-II-ChIP_+cohesin_Rad21TEVnohs (PolII CHIP file for + cohesin (contains non-heat-shocked transgenic TEV-clevable Rad21)

hyb_protocol: Each sample was hybridized to the array in 200 ul containing 1XHybridization buffer (Affymetrix), 50pM Control oligonucleotide (oligo B2, Affymetrix), Herring Sperm DNA (0.1mg/ml), Acetylated BSA (0.5mg/ml), and 7% DMSO. Samples were denatured at 100C for 10 minutes, and then put on ice before being hybridized for 16 hours at 45C in an hybridization oven (GeneChip Hybridization Oven 640, Affymetrix). Washing and scanning protocol provided by Affymetrix was performed automatically on a fluidics station (GeneChip fluidics station 450, Affymetrix).

scan_protocol: Arrays were scanned using the Genechip Scanner3000 7G following the library array description.

data_processing: For the discrimination of positive and negative signals for the binding, we compared ChIP fraction with Sup (supernatant) fraction by using three criteria as follows. First, the reliability of strength of signal was judged by detection p-value of each locus (p-value lower than 0.025 was considered as significant). Secondly, reliability of binding ratio was judged by change p-value (p-value lower than 0.025 was considered as significant). Thirdly, clusters consisted of at least three contiguous loci which filled above two criteria were selected as significantly enriched locus, because it is apparent that a single site of protein-DNA interaction will result in immuno-precipitation of DNA fragments that hybridized not only to the locus of the actual binding site but also to its neighbors. This third criterion is very unique, make the data highly reliable and can be only applicable to the chip data obtained by our high-resolution tiling array.

label: Biotin ddATP

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Pol-II ChIPed DNA from non-heat-shocked hs-TEV TEV-cleavableRad21 (Rad21TEV) salivary glands (genotype: w1118; hs-TEV/+; Rad21ex15 Rad21(TEV)/Rad21ex3)

label_protocol: End labelled with biotin (biotin-11-ddATP) using Terminal Transferase

growth_protocol: larvae were kept at 18C throughout development

extract_protocol: For each Pol-II Chromatin IP, ~50 SG pairs were dissected in cold PBS and fixed in 1% (Pol-II ChIP) formaldehyde for  1.5 - 2 minutes at RT. Crosslinking was terminated by addition of 21.5 μl of 2.5 M  Glycine (0.125 M final concentration) (3 minutes, RT, followed by 5 minutes on ice).  Quenched samples were spun at 4000 rpm for 4 minutes, 4°C. The supernatant was  discarded, and the crosslinked SGs were disintegrated in 100 μl of sonication buffer  (0.5% SDS, 20 mM Tris pH 8, 2 mM EDTA, 0.5 mM EGTA, 0.5 mM PMSF, 1x  complete protease inhibitors (Roche)) by pipetting. After 10 minutes on ice, samples  were sonicated for 15 minutes in a Bioruptor, using the settings “high”, 22 secondsON, 60 seconds OFF, yielding chromatin fragments with an average size of 500 bp.  Sonicated material was spun at 13000 rpm for 5 minutes, 4°C. 85 μl of the  supernatant (100% IP) was used immediately for the IP, and 8.5 μl were stored at -  20°C as 10% Input sample.  Each 85 μl ChIP-sample was diluted 10-fold in IP-Buffer (0.5% Triton X-100, 2 mM  EDTA, 20 mM Tris pH 8, 150 mM NaCl, 10% glycerol, 1x complete protease  inhibitors (Roche)) and precleared for 1-2 hours (4°C, rotating wheel) with 15 μl of  Dynabeads® (Invitrogen) pre-equilibrated in IP-buffer. Beads were removed, and the  supernatant was split in half and incubated with either 2.5 μl of mouse anti-Pol-II  antibody (CTD4H8, Upstate) or 2.5 μl of normal mouse IgG (Millipore) (mock IP)  (o.n., 4°C, rotating wheel). On the next day, 40 μl of pre-equilibrated Dynabeads®  were added for 2-3 hours (4°C, rotating wheel) to capture the immuno-complexes.  The supernatant was removed and the beads were washed in a series of 3-5 minute  washes with cold buffers (1x Low Salt Buffer: 20 mM Tris pH 8, 2 mM ETDA, 0.1%  SDS, 1% Triton X-100, 150 mM NaCl; 3x High Salt Buffer: same as Low Salt Buffer  but 500 mM NaCl; 1x LiCl Buffer: 2 mM EDTA, 10 mM Tris pH 8, 0.25 M LiCl, 1%  NP40, 1% Sodium-deoxycholate; 2x rinse with TE). Immuno-complexes were eluted  and crosslinks were simultaneously reversed in 415 μl of Elution Buffer (100 mM  Sodium-hydrogen-carbonate, 1% SDS, 0.181 M NaCl) for at least 6 hours (or o.n.) at  65°C under vigorous shaking. Crosslinks in Input samples were reversed in parallel  after addition of 207.5 μl of Elution Buffer. Protein and RNA were digested with 14.9  μl (7.5 μl for Input samples) of an enzyme-mix containing 12 μl 1 M Tris pH 8, 1.6 μl  Proteinase K (10 mg/ml) and 1.3 μl DNAse-free RNAse (10 mg/ml) (2 hours, 45°C).  DNA was column-purified (Qiagen PCR-purification kit), eluted in 100 μl water and  stored at -20°C.

treatment_protocol: PolII-ChIP was performed from dissected late third instar Salivary glands

source_name: WCE DNA from non-heat-shocked hs-TEV TEV-cleavableRad21 (Rad21TEV) salivary glands (genotype: w1118; hs-TEV/+; Rad21ex15 Rad21(TEV)/Rad21ex3)


title: PolII CHIP file(s) for - cohesin

description: DrosSalivaryGland_Pol-II-ChIP_-cohesin_Rad21TEVPolII CHIP file for - cohesin (contains transgenic TEV-clevable Rad21)

source_name: Pol-II ChIPed DNA from heat-shocked hs-TEV TEV-cleavableRad21 (Rad21TEV) salivary glands (genotype: w1118; hs-TEV/+; Rad21ex15 Rad21(TEV)/Rad21ex3)

growth_protocol: larvae were heat-shocked for 45 minutes at 37C, then kept for 10-12 hours at RT

source_name: WCE DNA from heat-shocked  hs-TEV transgenicRad21 salivary glands (genotype: w1118; hs-TEV/+; Rad21ex3 tgRad21/Rad21ex3)


title: CcpA_R4vsCcpA_R1


title: CcpA_R1vsCcpA_R2


title: CcpA_R2vsCcpA_R3


title: CcpA_R3vsCcpA_R4


title: PolII CHIP files for + cohesin 2

description: DrosSalivaryGland_Pol-II-ChIP_+cohesin_Rad21.2 (PolII CHIP for + cohesin (contain transgenic wildtype Rad21)

source_name: Pol-II ChIPed DNA from heat-shocked hs-TEV transgenicRad21 salivary glands (genotype: w1118; hs-TEV/+; Rad21ex3 tgRad21/Rad21ex3)

tag: developmental stage

value: Drosophila melanogaster crawling third instar salivary glands


title: CcpA_R2vsWT_R2

value: CcpA K.O.


title: Daudi-Luciferase-1


title: Daudi-P105siRNA-2


title: Daudi-P105siRNA-3


title: Daudi-P105siRNA-1


title: Daudi-P100siRNA-1


title: CcpA_R1vsWT_R1


title: CcpA_R3vsWT_R3


title: Daudi-Luciferase-2


title: Daudi-P100siRNA-3


title: Daudi-P100siRNA-2


title: Oci-Ly3-Luciferase-1


title: PolII CHIP files for + cohesin 1

description: DrosSalivaryGland_Pol-II-ChIP_+cohesin_Rad21.1 (PolII CHIP for + cohesin (contain transgenic wildtype Rad21)

value: w1118; hs-TEV/+; Rad21ex3 tgRad21/Rad21ex3


title: Oci-Ly3-Luciferase-2


title: Oci-Ly3-P105siRNA-2


title: Oci-Ly3-P105siRNA-1


title: p73_ME180_2

city: Boston

first: Kevin

last: Struhl

state: MA

address: 240 Longwood Ave.

department: Dept. Of Biological Chemistry & Molecular Pharmacology

institute: Harvard Medical School

description: p73 ChIP Biological Rep 1-3, chip B

hyb_protocol: Biotinylated DNA was hybridized to the Affymetrix tiled, human whole genome arrays, washed, and stained according to manufacturer's instructions.

scan_protocol: The microarrays were scanned using a custom-built Affymetrix scanner with a laser spot size of 3.5 um and a resolution (pixel size) of 1.0 um.

data_processing: Normalization and two sample comparison analysis were performed using Tiling Analyais Software 1.1.02. Log2(signal) and -10log10(p-value) were reported in BAR files. Supplementary file GSE18650_p73_ME180_BindingSites_hg17.xls contains p73 binding sites at three different significance thresholds.

source_name: p73 ChIP DNA from ME180 cell line

label_protocol: Standard Affymetrix labeling protocol using biotin.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% Fetal Bovine Serum.

extract_protocol:
1. Trypsinized cells were placed into fresh media and cross-linked by the addition of formaldehyde.
2. Cells were then spun down and the cell pellet was then resuspended in micrococcal nuclease (MNase) reaction buffer.
3. The chromatin was then sonicated, spun down and the supernatant was diluted with IP-dilution buffer.
4. Diluted chromatin was precleared with protein A/G sepharose beads, and a portion reserved for control, or 'input', DNA (i.e. omitting immunoprecipitation).
5. The remaining chromatin was incubated with AKp73 anti-p73 antibody-coupled protein A/G seppharose beads.
6. Input and eluted material was de-crosslinked and purified.
Amplified ChIP (or matching input) DNA was fragmented with DNase I, and then biotin-labeled using terminal transferase (TdT).

treatment_protocol: Cells were treated with ethanol (vehicle control) for 24-26 hrs before harvesting by trypsinization.

value: 66 yrs

value: cervical carcinoma

tag: antibody

value: anti-p73 monoclonal antibody (AKp73)

source_name: Input DNA from ME180 cell line


title: p73_ME180_5

description: p73 ChIP Biological Rep 1-3, chip E


title: p73_ME180_7

description: p73 ChIP Biological Rep 1-3, chip G


title: p73_ME180_3

description: p73 ChIP Biological Rep 1-3, chip C


title: p73_ME180_4

description: p73 ChIP Biological Rep 1-3, chip D


title: Oci-Ly3-P100siRNA-3


title: Oci-Ly3-P100siRNA-2


title: Oci-Ly3-P105siRNA-3


title: p73_ME180_1

description: p73 ChIP Biological Rep 1-3, chip A


title: NW3512_Cy5

status: Public on Sep 09 2010

city: Barcelona

first: Anna

last: Antonell

address: C/Casanova, 143

department: Unitat d'Alzheimer i altres transtorns cognitius

country: Spain

institute: Hospital Clínic Barcelona

description: EG__251239129533__NW35.12_Cy5_poolF_Cy3.gpr

hyb_protocol: Hybridization process was performed with the Hybridization Buffer from Agilent for 18h at 60ºC in a rotator oven.

scan_protocol: Image analysis was performed using the Agilent scaner G2565BA.

data_processing: The normalization procedure involves loess without background correction.

source_name: Patient NW35.12

label_protocol: Total RNA (500 ngr) from patients and controls was labeled using the Low Input linear RNA amplification kit and purified with RNeasy (Qiagen) following manufacturer's instructions.

growth_protocol: LCLs were grown in RPMI 1640 medium (GIBCO) supplemented with 10% heat-inactivated fetal bovine serum and 1X antibiotics (penicillin/streptomycin) (Invitrogen), at 37ºC in a humidified 5% CO2 chamber.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

value: Female

value: Lymphoblastoid cell line

tag: genome/variation

source_name: Pool of 5 control cell lines


title: NW10_Cy5

source_name: Patient NW10 E

value: Male


title: SW266_Cy3

description: MO__251239139219__SW26601_Cy3_pool_Cy5_DS.gpr

source_name: Patient SW266.01

tag: disease status

value: Williams-Beuren syndrome


title: SW263_Cy3

description: MO__251239139218__SW26301_Cy3_pool_Cy5_DS.gpr

source_name: Patient SW263.01


title: SW266_Cy5

description: MO__251239139165__SW26601_Cy5_pool_Cy3.gpr


title: NW3512_Cy3

description: EG__251239129534__NW35.12_Cy3_poolF_Cy5_DS.gpr


title: SW5_Cy3

description: MO__251239139217__SW501_Cy3_pool_Cy5_DS.gpr

source_name: Patient SW5.01


title: NW10_Cy3

description: MO__251239139215__NW10_Cy3_pool_Cy5_DS.gpr


title: SW263_Cy5

description: MO__251239139164__SW26301_Cy5_pool_Cy3.gpr


title: SW3_Cy3

description: MO__251239139216__SW301_Cy3_pool_Cy5_DS.gpr

source_name: Patient SW3.01


title: SW5_Cy5

description: MO__251239139163__SW501_Cy5_pool_Cy3.gpr


title: screen 1: TeliA

city: Utrecht

first: Guy

last: Roukens

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Teli cell line repeat 1
4765748037_E
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: in R package beadarray, quantile normalization and VST transformation.

source_name: Primary HUVEC, Tel knockdown

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

growth_protocol: Huvecs were grown in EGM2 medium (Lonza)

extract_protocol: Total RNA was isolated using Trizol according to manufacturers protocol and subsequently purified by using RNEasy minikit (Qiagen)

value: Primary HUVEC (Human Umbilical Vein Endothelial Cells)

tag: knockdown

value: Tel


title: Oci-Ly3-P100siRNA-1


title: screen 1: MockB

description:
Mock cell line repeat 2
4765748037_C
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.

source_name: Primary HUVEC, mock

value: control


title: screen 1: TeliB

description:
Teli cell line repeat 2
4765748037_G
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.


title: screen 1: CtBP2iA

description:
CtBP2i cell line repeat 1
4765748037_F
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.

source_name: Primary HUVEC, CtBP2 knockdown


title: screen 1: CtBP2iB

description:
CtBP2i cell line repeat 2
4765748037_H
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.


title: screen 1: MockA

description:
Mock cell line repeat 1
4765748037_A
Non-normalized data is available in the GSE19335_non-normalized.txt' file, which is linked to the Series GSE19335 record as a supplementary file.


title: SW3_Cy5

description: MO__251239139062__SW301_Cy5_pool_Cy3.gpr

tag: tissue


title: tumor_ID, 16; patient_ID, 4

city: Osaka

first: Kikuya

last: Kato

address: 1-3-3 Nakamichi, Higashinari-ku

institute: Osaka Medical Center for Cancer and Cardiovascular Dieseases

description: comparison of multiple tumors from same patient

hyb_protocol: The samples were hybridized for 24 hours using the Agilent Oligo aCGH Hybridization Kit according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Agilent carousel scanner following maufacturer's instructions. Agilent Feature Extractor software was used to extract the data.

data_processing: Data were extracted using Agilent's Feature Extraction software, version 9.5.3.1 , Cy3 corresponding to the gProcessed Signal column of FE file, Cy5 corresponding to the rProcessedSignal column of FE file. Centralizated Log2Ratio (Cy5/Cy3) was used for the normalization algorithm.　Normalized log10 ratio (Cy5/Cy3) was calculated using CGH-v4_95_Feb07 protocol of FE software.

source_name: human genomic DNA (hepatocellular carcinoma tumor tissue)

label_protocol: The samples were labeled using the Agilent Geomic DNA Labeling Kit PLUS (Agilent p/n 5188-5309) according to manufacturer's instructions. Genomic DNA was fragmented using restriction exzymes. Random hexamers were used to prime an Exo-Klenow fragment DNA polymerase reaction incorporating CyDye labeled dUTP.

growth_protocol:
Human samples obtained with surgecal resection
Human samples obtained with surgecal resection

extract_protocol: Genomic DNA was extracted with QIAamp DNA Micro kit (Qiagen, Valencia, CA).

treatment_protocol: Frozen at minus 70 degrees until DNA extraction

tag: tumor

value: HBs-Ag, negative; HCV-ab, positive

source_name: Human Genomic DNA, MALE (Promega:G1471)

tag: reference

value: Human Genomic DNA, MALE (Promega:G1471)


title: tumor_ID, 42; patient_ID, 15

value: HBs-Ag, positive; HCV-ab, negative


title: tumor_ID, 35; patient_ID, 13


title: tumor_ID, 39; patient_ID, 14


title: tumor_ID, 8; patient_ID, 2


title: tumor_ID, 30; patient_ID, 11

value: HBs-Ag, negative; HCV-ab, negative


title: tumor_ID, 29; patient_ID, 11


title: tumor_ID, 41; patient_ID, 15


title: tumor_ID, 27; patient_ID, 10


title: tumor_ID, 36; patient_ID, 13


title: tumor_ID, 32; patient_ID, 12


title: tumor_ID, 18; patient_ID, 5


title: tumor_ID, 26; patient_ID, 10


title: tumor_ID, 38; patient_ID, 14


title: tumor_ID, 2; patient_ID, 1


title: tumor_ID, 33; patient_ID, 12


title: human tumor 163

city: Paris

first: Laure

last: Gibault

address: 26 rue d'Ulm

country: France

institute: Curie Institute

description: Gene expression data from human tumor samples

hyb_protocol: Samples were then analyzed on Human Genome U133 Plus 2.0 array (Affymetrix®), according to the manufacturer’s procedures.

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

data_processing: All microarray data were simultaneously normalized using the GCRMA algorithm

source_name: Human soft tissue sarcoma

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2005, Affymetrix).

extract_protocol: Total RNA were extracted from frozen tumor samples with TRIzol reagent (Life Technologies, Inc.) and purified using the RNeasy® Min Elute TM Cleanup Kit (Qiagen) according to the manufacturer’s procedures. RNA quality was checked on an Agilent 2100 bioanalyzer (Agilent Technologies)

value: soft tissue sarcoma


title: tumor_ID, 4; patient_ID, 1


title: tumor_ID, 6; patient_ID, 2


title: human tumor 166


title: human tumor 165


title: tumor_ID, 21; patient_ID, 5


title: human tumor 161


title: human tumor 167


title: human tumor 160


title: tumor_ID, 14; patient_ID, 4


title: human tumor 164


title: human tumor 162


title: human tumor 159


title: human tumor 155


title: human tumor 144


title: Oci-Ly3-Luciferase-3

value: Luciferase


title: human tumor 154


title: human tumor 140


title: human tumor 150


title: human tumor 142


title: human tumor 148


title: human tumor 135


title: human tumor 143


title: human tumor 151


title: human tumor 147


title: human tumor 139


title: human tumor 138


title: human tumor 158


title: human tumor 157


title: human tumor 146


title: human tumor 156


title: human tumor 153


title: human tumor 149


title: human tumor 152


title: human tumor 145


title: human tumor 136


title: human tumor 137


title: human tumor 141


title: human tumor 132


title: human tumor 134


title: human tumor 133


title: human tumor 131


title: human tumor 130


title: human tumor 129


title: human tumor 128


title: human tumor 126


title: human tumor 120


title: human tumor 124


title: human tumor 115


title: human tumor 125


title: human tumor 123


title: human tumor 109


title: human tumor 127


title: human tumor 122


title: human tumor 119


title: human tumor 117


title: human tumor 100


title: human tumor 121


title: human tumor 106


title: human tumor 104


title: human tumor 107


title: human tumor 118


title: human tumor 103


title: human tumor 116


title: human tumor 105


title: human tumor 114


title: human tumor 111


title: human tumor 108


title: human tumor 110


title: human tumor 113


title: human tumor 112


title: human tumor 99


title: human tumor 102


title: human tumor 101


title: human tumor 95


title: human tumor 89


title: human tumor 91


title: human tumor 94


title: human tumor 85


title: human tumor 90


title: human tumor 79


title: human tumor 92


title: human tumor 77


title: human tumor 82


title: human tumor 87


title: human tumor 75


title: human tumor 71


title: human tumor 84


title: human tumor 83


title: human tumor 98


title: human tumor 73


title: human tumor 80


title: human tumor 86


title: human tumor 72


title: human tumor 88


title: human tumor 76


title: human tumor 70


title: human tumor 69


title: human tumor 78


title: human tumor 74


title: human tumor 97


title: human tumor 65


title: human tumor 68


title: human tumor 57


title: human tumor 53


title: human tumor 64


title: human tumor 67


title: human tumor 49


title: human tumor 60


title: human tumor 56


title: human tumor 48


title: human tumor 63


title: human tumor 96


title: human tumor 51


title: human tumor 59


title: human tumor 52


title: human tumor 47


title: human tumor 66


title: human tumor 62

description: Gene expression data from human tumor samples.


title: human tumor 61


title: human tumor 45


title: human tumor 44


title: human tumor 58


title: human tumor 54


title: human tumor 50


title: human tumor 93


title: human tumor 46


title: human tumor 55


title: human tumor 42


title: human tumor 37


title: human tumor 33


title: human tumor 41


title: human tumor 29


title: human tumor 38


title: human tumor 34


title: human tumor 43


title: human tumor 30


title: human tumor 39


title: human tumor 18


title: human tumor 26


title: human tumor 21


title: human tumor 35


title: human tumor 31


title: human tumor 23


title: human tumor 22


title: human tumor 40


title: human tumor 19


title: human tumor 24


title: human tumor 32


title: human tumor 15


title: human tumor 81


title: human tumor 28


title: human tumor 25


title: human tumor 36


title: human tumor 27


title: human tumor 17


title: human tumor 20


title: human tumor 13


title: human tumor 12


title: human tumor 11


title: human tumor 14


title: human tumor 10


title: human tumor 16


title: human tumor 7


title: human tumor 8


title: human tumor 9


title: human tumor 6


title: human tumor 4


title: human tumor 1


title: human tumor 3


title: Droughted Bala leaf biologial rep 2

city: Aberdeen

first: Gareth

last: Norton

address: Crucikshank building

institute: University of Aberdeen

description: Gene expression data from droughted rice leaves

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

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

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

organism: Oryza sativa

source_name: Rice leaf from plant droughted for 24 days grown in a field

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed bya RNA clean up step using NucleoSpin® RNA Clean-up kit according to the manufacturer's instructions

tag: cultivar

value: Bala

value: leaf

tag: stress

value: drought

tag: biological rep


title: Droughted Bala leaf biologial rep 3


title: Prdm16 VZ WT3 Rep3

city: Ann Arbor

first: Sean

middle: J

last: Morrison

state: MI

address: 210 Washtenaw Ave

department: HHMI/Department of Internal Medicine

institute: Center for Stem Cell Biology, 5435 Life Sciences Institute University of Michigan

description: Gene expression data from ventricular zone cells of newborn Prdm16+/+ mice

scan_protocol: The chips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language. RMA was used to normalize the data and fit log2 transformed expression values.

label: Biotin

source_name: Brain ventricular zone cells of newborn Prdm16+/+ mice

label_protocol: cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

growth_protocol: The uncultured ventricular zone cells from newborn Prdm16LacZ/LacZ, Prdm16LacZ/+, and Prdm16+/+ mice were dissected from the brains and placed into the Trizol reagent.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by additional purification with RNA Clean & Concentrator™-5 (R1015, Zymo research). Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Applause WT/Amp RNA amplification system (NuGEN Technologies,) following the manufacturer’s instructions.

treatment_protocol: The  ventricular zone cells were processed without treatment. The gene expression comparison is between the different genotypes.

tag: strain

value: C57BL/Ka strain

tag: genotype/variation

value: Newborn mouse Brain ventricular zone


title: Prdm16 VZ KO1 Rep1

description: Gene expression data from ventricular zone cells of newborn Prdm16LacZ/LacZ mice

hyb_protocol: 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.

source_name: Brain ventricular zone cells of newborn Prdm16LacZ/LacZ mice


title: human tumor 5

tag: gender


title: Prdm16 VZ WT2 Rep2


title: Prdm16 VZ HET1 Rep1

description: Gene expression data from ventricular zone cells of newborn Prdm16LacZ/+ mice

source_name: Brain ventricular zone cells of newborn Prdm16LacZ/+ mice


title: Droughted Azucena leaf biologial rep 3

value: Azucena


title: Droughted Bala leaf biologial rep 1


title: Droughted Azucena leaf biologial rep 1


title: Prdm16 VZ HET3 Rep3


title: Prdm16 VZ WT1 Rep1


title: Droughted Azucena leaf biologial rep 2


title: Control Azucena leaf biologial rep 3

description: Gene expression data from control rice leaves

source_name: Rice leaf from control plant grown in a field


title: Control Bala leaf biologial rep 2


title: Prdm16 VZ KO2 Rep2


title: Prdm16 VZ HET2 Rep2


title: Control Azucena leaf biologial rep 1


title: Control Bala leaf biologial rep 1


title: Sex_48h_BioRep2_TechRep2

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

description: SexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate2

hyb_protocol: The slides were prehybridised in 5× SSC, 0.1 % SDS, 1 % BSA for 1 h at 65 C. After washing in distilled water and isopropanol the slides were dried in nitrogen stream. 1.5 µg (ca. 130 pmol) of each labeled RNA was hybridised to the slides using the Agilent ‘60-mer Oligo Microarray Processing’ protocol. The slides were washed and dried in a nitrogen stream.

scan_protocol: Spot intensities were determined using an Agilent G2505B microarray scanner.

data_processing: Microarray intensity data were extracted using the ‘Automatic Image Processing for Microarrays’ software (Katzer et al. 2003). Normalization of the raw intensity data was performed with a non-linear loess regression method using 'R bioconductor'.Differentially expressed genes were identified by an ANOVA fixed effects model (Landgrebe et al. 2004). Normalization and statistical computation with 'R' (Version 2.5) was performed for two independent data sets derived from a high gain and a low gain scan. ‘Contrasts’ refer to log2 normalized intensity ratios between wild type and csnE samples.

organism: Aspergillus nidulans

label_protocol: For each array hybridisation, 1 µg RNA was amplified using the Message Amp II kit (Ambion, Darmstadt, Germany) and 2 µg resulting aRNA was labeled with NHS-activated Cy-3 or Cy-5 dyes (Amersham Bioscience)

growth_protocol: A. nidulans strains were culitvated at 37C in minimal medium and fungal development was induced as described (Clutterbuck 1974). Briefly, asexual sporulation was induced by incubation in continuous white light and cleistothecia formation by oxygen-limiting conditions on plates sealed with cellophane film grown in the dark.

extract_protocol: RNA was extracted from 2 ml of ground fungal mycelium with Trizol (Invitrogen), followed by a double phenol/chlorophorm extraction (Chomczynski 1993). The RNA was then treated with DNAse I for 20 min at 37 °C in the presence of RNAseOUT™ (Invitrogen), extracted with phenol/chlorophorm/isoamyl alcohol and additionally purified using RNeasy columns (Qiagen, Hilden, Germany).

tag: genotype

value: Wildtype

tag: growth type

value: Sexual

tag: age

value: FGSC A4

value: Delta-csnE


title: Prdm16 VZ KO3 Rep3


title: Sex_48h_BioRep2_TechRep4

description: SexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate4


title: Control Bala leaf biologial rep 3

value: control


title: Control Azucena leaf biologial rep 2


title: Asex_48h_BioRep2_TechRep4

description: AsexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate4

value: Asexual


title: Asex_48h_BioRep2_TechRep3

description: AsexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate3


title: Sex_48h_BioRep2_TechRep1

description: SexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate1


title: Sex_48h_BioRep2_TechRep3

description: SexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate3


title: Uterus_estriol_24h_rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
US23502387_251486825759_S01_H.tif
US23502387_251486825759_S01_L.tif
gene expression in ovariectomized E3 24 hour treated uterus

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise.

source_name: uterus, E3 treated 24 hours

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: frozen uterine tissue was pulverized and each uterus was homogenized in 800 ul of Trizol (Invitrogen) with 250 ug/ml glycogen. Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.

treatment_protocol: ovariectomized mice were allowed to rest for 10-14 days, then injected with 100 ul saline or 250 ng estradiol or 250 ng estriol in 100 ul saline ip. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen

tag: agent

value: estriol

tag: time point

tag: replicate

value: adult (10+ weeks)

value: ovariectomized female

value: uterus


title: Uterus_estriol_24h_rep2


title: Asex_48h_BioRep2_TechRep2

description: AsexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate2


title: Uterus_estriol_2h_rep3

description:
US23502387_251486825758_S01_H.tif
US23502387_251486825758_S01_L.tif
gene expression in ovariectomized E3 2 hour treated uterus

source_name: uterus, E3 treated 2 hours


title: Uterus_estriol_2h_rep2


title: Uterus_estradiol_24h_rep3

description:
US23502387_251486825761_S01_H.tif
US23502387_251486825761_S01_L.tif
gene expression in ovariectomized E2 24 hour treated uterus

source_name: uterus, E2 treated 24 hours

value: estradiol


title: Uterus_estriol_24h_rep1


title: Uterus_saline_24h_rep3

description:
US23502387_251486825758_S01_H.tif
US23502387_251486825758_S01_L.tif
gene expression in ovariectomized saline vehicle treated uterus

source_name: uterus, saline control

value: saline


title: Vegetativ_20h_BioRep2_TechRep4

description: VegetativeGrowth_20h_BiologicalReplicate2_TechnicalReplicate4

value: Vegetative


title: Uterus_estriol_2h_rep1


title: Vegetativ_20h_BioRep2_TechRep3

description: VegetativeGrowth_20h_BiologicalReplicate2_TechnicalReplicate3


title: Vegetativ_20h_BioRep2_TechRep2

description: VegetativeGrowth_20h_BiologicalReplicate2_TechnicalReplicate2


title: Asex_48h_BioRep2_TechRep1

description: AsexualGrowth_48h_BiologicalReplicate2_TechnicalReplicate1


title: Vegetativ_14h_BioRep2_TechRep2

description: VegetativeGrowth_14h_BiologicalReplicate2_TechnicalReplicate2


title: Vegetativ_20h_BioRep2_TechRep1

description: VegetativeGrowth_20h_BiologicalReplicate2_TechnicalReplicate1


title: Uterus_estradiol_24h_rep2

description:
US23502387_251486825760_S01_H.tif
US23502387_251486825760_S01_L.tif
gene expression in ovariectomized E2 24 hour treated uterus


title: Sex_48h_BioRep1_TechRep4

description: SexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate4


title: Vegetativ_14h_BioRep2_TechRep3

description: VegetativeGrowth_14h_BiologicalReplicate2_TechnicalReplicate3


title: Sex_48h_BioRep1_TechRep3

description: SexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate3


title: Vegetativ_14h_BioRep2_TechRep4

description: VegetativeGrowth_14h_BiologicalReplicate2_TechnicalReplicate4


title: liver_WT_HFH_rep3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridisation of 10ug cRNA was done overnight for 16 hours at 45ºC in a Hybridisation Oven 640 (Affymetrix). The protocol is conducted as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Target Hybridization) (P/N 701027, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated using GCRMA (v2.2.0) in Bioconductor, applying the emperical Bayes (EB) model for background estimation.

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, high gainer, replicate 3

label_protocol: The Affymetrix GeneChip RNA One cycle Amplification Kit was used to prepare labelled cRNA from 5 μg of total RNA. The protocol was conducted using the reagents provided by Affymetrix in the One-Cycle cDNA synthesis kit (P/N 900431), One-Cycle IVT labelling kit (P/N 90449) and GeneChip Sample Cleanup Module (P/N 900371). A detailed description can be found in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 1 (Eukaryotic Target Preparation) (P/N 701025, revision 6).

growth_protocol: Eight week old male wildtype C57Bl/6 mice were fed LFD (D12450B, Research Diets Inc.) for 3 weeks. Thereafter, mice were either kept on LFD for 21 weeks or put on HFD (D12451, research Diets Inc.) for 21 weeks. Lard in the HFD was replaced by palm oil. Mice were divided into 4 groups based on liver histology. LF-low (LFL) responders displaying normal liver morphology, LF-high (LFH) responders showing benign hepatic steatosis, HF-low (HFL) responders displaying pre-NASH with macrovesicular lipid droplets, and HF-high (HFH) responders exhibiting overt NASH characterized by ballooning of hepatocytes, presence of Mallory bodies, and activated inflammatory cells.

extract_protocol: Total RNA was prepared from mouse livers using TRIzol reagent, followed by purification of total RNA using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Livers were dissected from 18 mice after 21 weeks of diet intervention. Based in liver histology, mice were divided in 4 groups. Liver RNA samples from all mice were used for microarray analysis.

value: liver

tag: diet

value: HFD for 21 weeks

tag: phenotype

value: high gainer


title: Vegetativ_14h_BioRep2_TechRep1

description: VegetativeGrowth_14h_BiologicalReplicate2_TechnicalReplicate1


title: Uterus_saline_24h_rep2

description:
US23502387_251486825757_S01_H.tif
US23502387_251486825757_S01_L.tif
gene expression in ovariectomized saline vehicle treated uterus

tag: tissue


title: liver_WT_HFH_rep4

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, high gainer, replicate 4


title: Uterus_estradiol_24h_rep1


title: liver_WT_HFH_rep1

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, high gainer, replicate 1


title: liver_WT_HFH_rep2

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, high gainer, replicate 2


title: liver_WT_HFL_rep4

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, low gainer, replicate 4

value: low gainer


title: liver_WT_HFL_rep2

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, low gainer, replicate 2


title: Uterus_saline_24h_rep1


title: Asex_48h_BioRep1_TechRep4

description: AsexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate4

value: Wildtype


title: Sex_48h_BioRep1_TechRep1

description: SexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate1

value: Sexual


title: Asex_48h_BioRep1_TechRep3

description: AsexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate3

value: FGSC A4


title: liver_WT_LFH_rep6

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, high gainer, replicate 6

value: LFD for 21 weeks


title: liver_WT_HFL_rep1

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, low gainer, replicate 1


title: liver_WT_HFL_rep3

source_name: liver from C57Bl/6 mouse fed HFD for 21 weeks, low gainer, replicate 3


title: Sex_48h_BioRep1_TechRep2

description: SexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate2

value: Delta-csnE


title: Asex_48h_BioRep1_TechRep2

description: AsexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate2

value: Asexual


title: Asex_48h_BioRep1_TechRep1

description: AsexualGrowth_48h_BiologicalReplicate1_TechnicalReplicate1


title: Vegetativ_20h_BioRep1_TechRep1

description: VegetativeGrowth_20h_BiologicalReplicate1_TechnicalReplicate1


title: Vegetativ_20h_BioRep1_TechRep2

description: VegetativeGrowth_20h_BiologicalReplicate1_TechnicalReplicate2


title: liver_WT_LFH_rep4

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, high gainer, replicate 4


title: Vegetativ_14h_BioRep1_TechRep3

description: VegetativeGrowth_14h_BiologicalReplicate1_TechnicalReplicate3


title: Vegetativ_14h_BioRep1_TechRep4

description: VegetativeGrowth_14h_BiologicalReplicate1_TechnicalReplicate4


title: liver_WT_LFL_rep4

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, low gainer, replicate 4


title: liver_WT_LFH_rep5

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, high gainer, replicate 5


title: Vegetativ_20h_BioRep1_TechRep3

description: VegetativeGrowth_20h_BiologicalReplicate1_TechnicalReplicate3


title: Vegetativ_20h_BioRep1_TechRep4

description: VegetativeGrowth_20h_BiologicalReplicate1_TechnicalReplicate4


title: liver_WT_LFH_rep2

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, high gainer, replicate 2


title: liver_WT_LFH_rep3

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, high gainer, replicate 3


title: liver_WT_LFL_rep3

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, low gainer, replicate 3


title: WN715

city: Merritt Island

first: Wayne

middle: L

last: Nicholson

state: FL

address: 505 Odyssey Way, Rm. 201-B

department: Microbiology and Cell Science

institute: University of Florida

hyb_protocol: Glass microarray slides (Eurogentec) were spotted in duplicate with 4,096 PCR products, each representing an annotated B. subtilis ORF (17).  For hybridization of samples to each slide, both Cy3 and Cy5 labeled samples were re-suspended in 50 µM EDTA and denatured at 98°C for 10 minutes.  140 µl of Hybridization Buffer #3 (Invitrogen) was added to each sample and loaded onto the slides.  Hybridization was performed for 16 hours at 42º C, followed by washes at 50º C for 2 minutes each in medium stringency wash buffer, high stringency wash buffer, and post-wash buffer in a Gene TAC hybridization station using the manufacturer’s reagents.

scan_protocol: Scanning of slides on an Applied Precision Array Worx scanner was performed immediately following hybridization.

data_processing:
Raw and normalized intensities were extracted from scanned images using SoftWorx Tracker.
For each dye channel, background mean intensity was subtracted from spot mean intensity.  The resulting numbers were normalized by multiplying each number by a constant, so that the average of all spots for each channel equalled 100. Constant for W715: 22.6. Constant for W716: 26.4.

organism: Bacillus subtilis

source_name: Strain WN715

label_protocol: WN715 and WN716 cells were labeled with Cy3 and Cy5, respectively using Superscript II Reverse Transcriptase (Invitrogen, Carlsbad, CA), 0.6 µM DTT, and the appropriate volume of 50X Amino allyl-dNTP mix (Sigma) and 5X Superscript II Buffer (Invitrogen) was added.  This mixture was incubated at 42°C for 3 hours and was stopped by adding 10 µM NaOH and 5 µM EDTA and incubating at 65°C for 15 minutes, followed by the addition of 10 µM HCl. Samples were cleaned of all excess primer, enzymes, and dNTP’s using QIAquick purification columns (Qiagen, Valencia, CA) and speed-vacuum dried before coupling of Cy3 or Cy5 dye.  Dye coupling was done by resuspending the cDNA in 0.45 µM Na2CO3 and adding the appropriate dye, followed by a dark incubation for one hour at room temperature.  Dye clean-up was again performed using QIAquick purification columns (Qiagen) and the samples were dried in a speedvac.

growth_protocol: Strains were grown at 37C with aeration in R medium until 1 hour after the end of exponential growth

extract_protocol: RNA was isolated using Tri-Reagent as described by manufacturer

treatment_protocol: Cells were harvested by centrifugation (10,000 xg, 5 min)


title: Normal tail tissue vs. normal tail tissue, replicate 6

status: Public on Sep 08 2010

city: Cambridge

first: Sebastian

last: Hoersch

address: 77 Massachusetts Avenue (E18-366)

department: David H. Koch Institute for Integrative Cancer Research at MIT

institute: Massachusetts Institute of Technology

description:
G2_1-1_NN
Sample is not part of the material presented in the publication (Zhang et al), and is provided for additional context.

hyb_protocol: Agilent aCGH/chip-on-chip hybridization Kit was used for hybridization at 65° celsius, and labeled samples were loaded onto microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially with Agilent Washing buffer A and B.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version v 9.1.3.1).

data_processing:
Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LINEAR normalization.
Agilent control spots and probes were excluded. Normalized log10 ratio (Cy5/Cy3) representing test/reference in original FE output were converted to log2 ratios. Also, probe values for dye-swap samples C_2-2 and G1_1-1 were multiplied by -1 to correct the dye swap, so that data is usable as is.

organism: Danio rerio

source_name: Normal tail from adult fish

label_protocol: 5 µg genomic DNA  was used for probe labeling with DNA polymerase I Klenow exo-. The reactions were carried according to the manufacturer's (Agilent) manual.

growth_protocol: Fish were kept according to standard conditions described in: The Zebrafish Book: A Guide for the Laboratory use of Zebrafish (Danio rerio), Monte Westerfield - 1995 - Univ. of Oregon Press

extract_protocol: Genomic DNA was isolated according to the reference Zhang et al, 2010 (submitted). Briefly, samples were digested in lysis buffer with 10ug/ml proteinase K. Following DNA isolation, the samples were cleaned by phenol-choloroform extraction and ethonal precipitation.

tag: FISH strain

value: Zebrafish TAB strain

value: 8-24 months

value: tail

tag: tumor type

tag: mutation type

source_name: Normal tail from adult fish (reference)


title: human tumor 2

description: Gene expression data from human tumor samples

source_name: Human soft tissue sarcoma

value: soft tissue sarcoma

value: Female


title: Normal tail tissue vs. normal tail tissue, replicate 3

description:
E_2-4_NN
Sample is not part of the material presented in the publication (Zhang et al), and is provided for additional context.


title: Normal tail tissue vs. normal tail tissue, replicate 5

description:
G1_2-1_NN
Sample is not part of the material presented in the publication (Zhang et al), and is provided for additional context.


title: Normal tail tissue vs. normal tail tissue, replicate 4

description:
F_2-4_NN
Sample is not part of the material presented in the publication (Zhang et al), and is provided for additional context.


title: MPNST tumor (p53 mutation) vs normal tail tissue, replicate 3

source_name: Tumor from adult fish

value: Peripheral nerve sheath

value: MPNST

value: p53 mutation


title: MPNST tumor (p53 mutation) vs normal tail tissue, replicate 4


title: Vegetativ_14h_BioRep1_TechRep1

description: VegetativeGrowth_14h_BiologicalReplicate1_TechnicalReplicate1

value: Vegetative


title: Vegetativ_14h_BioRep1_TechRep2

description: VegetativeGrowth_14h_BiologicalReplicate1_TechnicalReplicate2


title: WN716

source_name: Strain WN716


title: MPNST tumor (p53 mutation) vs normal tail tissue, replicate 2


title: MPNST tumor (p53 mutation) vs normal tail tissue, replicate 5


title: Normal tail tissue vs. normal tail tissue, replicate 1

description:
A_2-3_NN
Sample is not part of the material presented in the publication (Zhang et al), and is provided for additional context.


title: Normal tail tissue vs. normal tail tissue, replicate 2

description:
C_1-1_NN
Sample is not part of the material presented in the publication (Zhang et al), and is provided for additional context.


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 31

value: rp mutation


title: MPNST tumor (p53 mutation) vs normal tail tissue, replicate 1


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 30


title: liver_WT_LFL_rep1

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, low gainer, replicate 1

value: liver

value: low gainer


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 25


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 29


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 27


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 26


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 28


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 24


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 21


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 22


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 20


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 23


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 18


title: liver_WT_LFL_rep2

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, low gainer, replicate 2


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 16


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 17


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 19


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 14


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 15


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 12


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 13


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 6


title: Differential RNA (set2∆/SET2)

city: Charlottesville

first: Kunal

last: Poorey

state: VA

address: 1340 Jefferson Park Avenue

department: Biomedical Sciences: Biochemistry, Molecular Biology & Genetics

institute: University of Virginia Health System

description: Differenti RNA(mot1-42/WT)

hyb_protocol: The extraction synthesis and labelling, as well as array hybridisation to Affymetrix GeneChip S.cerevisiae Tiling 1.0R Array were performed as described in the Affymetrix manual.

data_processing:
Data was quantile normalized and analyzed with Tilecore (TAS). Log2(IP/Ctrl) fold changes (fc) were calculated for ChIP-chip samples and log2(expression estimates) for Total RNA single channel analysis. Corresponding pvalues statistics were reported in separate BAR files for one- or two-sample Wilcoxon test over a sliding window.
Results description file: *.bar are generated by TAS software. *.bar files for the ChIP of TBP and TFIIB contains log2(IP/Mock) fold changes for each probe. Total RNA have log2(Expression estimates) from a one sample analysis and for Differential RNA it has log2(IP/Ctrl). The data is a window moving average statistic for each probe (pvalues and signal estimates in separate files.

organism: Saccharomyces cerevisiae

source_name: set2Δ  RNA

label_protocol:
cDNA was synthesized from 7 mg of total RNA using the Affymetrix GeneChip WT Double-Stranded cDNA Synthesis Kit as recommended by the manufacturer, but with the addition 0.4 mM dUTP for subsequent fragmentation and biotin end-labeling.  dsDNA was purified using the GeneChip Sample Cleanup Module (Affymetrix, Inc.). 7.5 μg of amplified sample was fragmented and labeled using the WT double-stranded DNA terminal labeling kit (Affymetrix).
Library preparation and amplification of DNA for both ChIP and mock IP samples were performed using the GenomePlex Complete Whole Genome Amplification Kit (Sigma) as described by O'Green et al (2006) with several modifications:  dUTP was added in equimolar concentration to the dNTP mix (0.4 mM), and a second amplification was performed for both the ChIP and mock samples using 10 ng of the previously amplified material.  Samples were purified with the QIAquick PCR purification kit (QIAGEN) prior to re-amplification and fragmentation. Duplicate samples were combined to obtain 7.5 μg of material for fragmentation and labeling using the WT double-stranded terminal end labeling kit (Affymetrix).

growth_protocol: Cells were grown in YPD media at 30°C to an O.D. of 1.0

extract_protocol: Total RNA was isolated using hot-acid phenol extraction.  ChIP was performed as previously described in Dasgupta et al, 2005.

treatment_protocol: Cells were shifted to 35°C for 45 minutes.

tag: type

value: Yeast Total RNA

source_name: WT RNA (for set2Δ)


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 8


title: Total RNA (SET2)

description: WT Total RNA  Biological Rep 1-2

scan_protocol: The extraction synthesis and labelling, as well as array hybridisation to Affymetrix GeneChip S.cerevisiae Tiling 1.0R Array were performed as described in the Affymetrix manual.

source_name: RNA in WT


title: Total RNA (mot1-42)

description: mot1-42 mutant Total RNA Biological Rep 1-2

source_name: RNA in mot1-42


title: Differential RNA (mot1-42/MOT1)

description: Differential RNA log2(mot1-42/WT)

source_name: mot1-42 RNA

source_name: WT RNA (for mot1-42)


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 11


title: mot1-42 TBP

description: mot1-42 mutant TBP ChIP Biological Rep 1-3

source_name: mot1-42 ChIP for myc-TBP

value: Yeast TBP-myc

source_name: mot1-42 Mock for myc-TBP

value: Mock TBP-myc


title: WT TFIIB

description: WT TFIIB ChIP Biological Rep 1-2

source_name: WT ChIP for TFIIB

value: Yeast TFIIB

source_name: WT Mock for TFIIB


title: WT TBP

description: WT TBP ChIP Biological Rep 1-3

source_name: WT ChIP for myc-TBP

source_name: WT Mock for myc-TBP


title: Total RNA (MOT1)

description: WT Total RNA  Biological Rep 1-2


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 9

source_name: Normal tail from adult fish (reference)


title: Total RNA (set2∆)

source_name: RNA in set2Δ


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 7

source_name: Tumor from adult fish


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 5


title: mot1-42 TFIIB

description: mot1-42 mutant TFIIB ChIP Biological Rep 1-2

source_name: mot1-42 ChIP for TFIIB

source_name: mot1-42 Mock for TFIIB


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 10


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 1


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 3


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 4


title: Spleen_RCSM_21 (Sample 34)

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

description: Sample 34

hyb_protocol: The labeled cRNA was fragmented, diluted into Agilent’s Hi-RPM Gene Expression Hybridization Buffer, applied to the array slide, and sealed with the appropriate gasket slide in an Agilent hybridization chamber. Slides were incubated 16 hours at 65C with rotation in an Agilent hybridization oven and washed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent G2505B Array Scanner. Image files analyzed with Agilent Feature Extraction software (version 9.5.1).

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.

organism: Gallus gallus

source_name: RCSM Spleen tissue Control 21 dpi

label_protocol: RNA was labelled using the Agilent Quick-Amp labelling kit (Agilent Technologies, Santa Clara, CA, USA). In two of the four replicates of each experimental group, the infected samples were labelled with Cy3 and the uninfected two were labelled with Cy5.

extract_protocol: 30~50 mg spleen tissues were homogenized in TRizol Reagent and total RNA extraction was performed according to the manufacturer’s instructions.

tag: inbred line

value: RCSM

value: spleen

tag: infection

value: Control

tag: dpi

source_name: Spleen tissue, Infected, 21 dpi

value: MDV infection


title: volunteer6-oral_intake_dead_bacteria

first: Peter

last: van Baarlen

address: De Elst 1

department: Animal Sciences

hyb_protocol: The labelled RNA was hybridised to a GeneChip Hu133 Plus2 array (Affymetrix, Santa Clara, CA), washed, and stained. Detailed methods for the labelling and subsequent hybridisations to the arrays are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix.

scan_protocol: The GeneChip Hu133 Plus2 array was scanned on an Affymetrix GeneChip 3000 7G scanner. Detailed methods are described in the eukaryotic section of the GeneChip Expression Analysis Technical Manual, Revision 3, from Affymetrix

data_processing: Packages from the Bioconductor project, integrated in an in-house developed on-line management and analysis database for multiplatform microarray experiments, were used for analysing the scanned Affymetrix arrays (Gentleman et al., 2004; Gavai et al, submitted).

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of dead (heat-killed at stationary phase) Lactobacillus rhamnosus (each half-hour)

label_protocol: Total RNA (500 ng) extracted from biopsies was labelled using the Ambion MessageAmp II biotin enhanced single-round amplification kit (cat. no. 1791).

extract_protocol: Total RNA was extracted from biopsies with TRIzol reagent, purified and DNAse treated using the SV Total RNA Isolation System (Promega, Leiden, The Netherlands). RNA integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies, Amsterdam, the Netherlands) with 6000 Nano Chips according to the manufacturer’s instructions. RNA was judged as suitable for array hybridization only if samples showed intact bands corresponding to the 18S and 28S ribosomal RNA subunits, displayed no chromosomal peaks or RNA degradation products, and had a RIN (RNA integrity number) above 8.0.

value: proximal duodenum


title: Spleen_Line72_21 (Sample 19)

description: Sample 19

source_name: Line 72 Spleen tissue Infected 21 dpi

source_name: Spleen tissue, Control, 21 dpi


title: Spleen_RCSM_10 (Sample 31)

description: Sample 31

source_name: RCSM Spleen tissue Infected 10 dpi

source_name: Spleen tissue, Control, 10 dpi


title: volunteer7-oral_intake_dead_bacteria


title: Spleen_Line63_10 (Sample 28)

description: Sample 28

source_name: Line 63 Spleen tissue Control 10 dpi

source_name: Spleen tissue, Infected, 10 dpi


title: Spleen_RCSM_5 (Sample 25)

description: Sample 25

source_name: RCSM Spleen tissue Infected 5 dpi

source_name: Spleen tissue, Control, 5 dpi


title: Spleen_Line72_10 (Sample 32)

description: Sample 32

source_name: Line 72 Spleen tissue Control 10 dpi


title: volunteer5-oral_intake_dead_bacteria


title: Spleen_RCSM_21 (Sample 27)

description: Sample 27

source_name: RCSM Spleen tissue Infected 21 dpi


title: MPNST tumor (rp mutation) vs normal tail tissue, replicate 2

value: Zebrafish TAB strain

value: 8-24 months

source_name: Normal tail from adult fish (reference)

tag: strain

value: tail


title: Spleen_Line63_5 (Sample 33)

description: Sample 33

source_name: Line 63 Spleen tissue Infected 5 dpi


title: Spleen_RCSM_10 (Sample 21)

description: Sample 21


title: liver_WT_LFH_rep1

source_name: liver from C57Bl/6 mouse fed LFD for 21 weeks, high gainer, replicate 1

value: LFD for 21 weeks

value: high gainer


title: Spleen_Line63_10 (Sample 35)

description: Sample 35

source_name: Line 63 Spleen tissue Infected 10 dpi


title: Spleen_Line72_5 (Sample 29)

description: Sample 29

source_name: Line 72 Spleen tissue Infected 5 dpi


title: Spleen_Line63_21 (Sample 16)

description: Sample 16

source_name: Line 63 Spleen tissue Control 21 dpi

source_name: Spleen tissue, Infected, 21 dpi


title: Spleen_RCSM_10 (Sample 24)

description: Sample 24

source_name: RCSM Spleen tissue Control 10 dpi


title: volunteer3-oral_intake_dead_bacteria

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of dead (heat-killed at stationary phase) Lactobacillus rhamnosus (each half-hour)


title: volunteer8-consumption_Lactobacillus_casei_CRL431

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of stationary-phase-grown Lactobacillus casei (each half-hour)


title: Spleen_RCSM_10 (Sample 22)

description: Sample 22


title: Spleen_Line72_21 (Sample 20)

description: Sample 20

source_name: Line 72 Spleen tissue Control 21 dpi


title: volunteer4-oral_intake_dead_bacteria


title: volunteer6-consumption_Lactobacillus_casei_CRL431


title: Spleen_Line63_5 (Sample 36)

description: Sample 36

source_name: Line 63 Spleen tissue Control 5 dpi

source_name: Spleen tissue, Infected, 5 dpi


title: Spleen_Line72_5 (Sample 26)

description: Sample 26

source_name: Line 72 Spleen tissue Control 5 dpi


title: volunteer5-consumption_Lactobacillus_casei_CRL431


title: volunteer5-consumption_Lactobacillus_acidophilus_LaftiL10

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of stationary-phase-grown Lactobacillus acidophilus (each half-hour)


title: volunteer8-oral_intake_dead_bacteria


title: Spleen_Line63_21 (Sample 23)

description: Sample 23

source_name: Line 63 Spleen tissue Infected 21 dpi

source_name: Spleen tissue, Control, 21 dpi


title: volunteer7-consumption_Lactobacillus_casei_CRL431


title: volunteer4-consumption_Lactobacillus_acidophilus_LaftiL10


title: volunteer7-consumption_Lactobacillus_acidophilus_LaftiL10


title: Spleen_Line72_21 (Sample 18)

description: Sample 18

source_name: Line 72 Spleen tissue Infected 21 dpi


title: volunteer6-consumption_Lactobacillus_acidophilus_LaftiL10


title: volunteer3-consumption_Lactobacillus_casei_CRL431


title: volunteer4-consumption_Lactobacillus_casei_CRL431


title: Spleen_Line63_10 (Sample 13)

description: Sample 13

source_name: Spleen tissue, Control, 10 dpi


title: Spleen_RCSM_5 (Sample 10)

description: Sample 10

source_name: RCSM Spleen tissue Control 5 dpi


title: volunteer1-consumption_Lactobacillus_casei_CRL431


title: volunteer3-consumption_Lactobacillus_acidophilus_LaftiL10


title: volunteer3-placebo_control

source_name: biopsy from proximal duodenum, 10-15 cm after pylorus, taken after 6 hrs of oral intake of placebo control (each half-hour)


title: volunteer1-oral_intake_dead_bacteria


title: volunteer8-consumption_Lactobacillus_acidophilus_LaftiL10


title: volunteer1-consumption_Lactobacillus_acidophilus_LaftiL10


title: Spleen_Line72_10 (Sample 17)

description: Sample 17

source_name: Line 72 Spleen tissue Infected 10 dpi


title: Spleen_Line63_10 (Sample 8)

description: Sample 8

source_name: Line 63 Spleen tissue Control 10 dpi

source_name: Spleen tissue, Infected, 10 dpi


title: Spleen_RCSM_21 (Sample 30)

description: Sample 30

source_name: RCSM Spleen tissue Control 21 dpi

source_name: Spleen tissue, Infected, 21 dpi


title: volunteer8-placebo_control


title: Spleen_RCSM_5 (Sample 15)

description: Sample 15

source_name: RCSM Spleen tissue Infected 5 dpi

source_name: Spleen tissue, Control, 5 dpi


title: Spleen_RCSM_21 (Sample 11)

description: Sample 11

source_name: RCSM Spleen tissue Infected 21 dpi


title: Spleen_Line63_21 (Sample 12)

description: Sample 12

source_name: Line 63 Spleen tissue Control 21 dpi


title: volunteer4-placebo_control


title: Spleen_Line72_10 (Sample 7)

description: Sample 7


title: Spleen_Line63_5 (Sample 9)

description: Sample 9

source_name: Line 63 Spleen tissue Infected 5 dpi


title: volunteer5-placebo_control


title: volunteer6-placebo_control


title: volunteer7-placebo_control


title: Spleen_RCSM_5 (Sample 4)

description: Sample 4

source_name: Spleen tissue, Infected, 5 dpi


title: Spleen_Line72_21 (Sample 6)

description: Sample 6

source_name: Line 72 Spleen tissue Control 21 dpi


title: volunteer1-placebo_control


title: Spleen_Line63_5 (Sample 14)

description: Sample 14

source_name: Line 63 Spleen tissue Control 5 dpi


title: Spleen_Line72_5 (Sample 1)

description: Sample 1

source_name: Line 72 Spleen tissue Control 5 dpi


title: Spleen_Line63_21 (Sample 3)

description: Sample 3

source_name: Line 63 Spleen tissue Infected 21 dpi

source_name: Spleen tissue, Control, 21 dpi


title: Spleen_Line72_10 (Sample 2)

description: Sample 2

source_name: Line 72 Spleen tissue Control 10 dpi


title: CC199 S. pneumoniae Disease Isolate_5851-03

status: Public on Sep 07 2010

city: New Haven

first: Jonathan

last: Thomas

state: CT

address: 60 College St.

institute: Yale University

description: CC199 isolate 8

hyb_protocol: Hybridization was done using the MAUI Hybridization Station. After hybridization, slides were washed sequentially. Slides were dried by centrifugation

scan_protocol: Scanned using an Axon GenePix 4200 scanner and GenePix software. Scanned at 625nm and 532nm. PMT was adjusted for the intensity of the fluorescence.

data_processing: Total intensity normalization, LOWESS normalization, standard deviation regularization and low intensity filtering of background subtracted data, log2 ratios. TM4: Microarray Software Suite (TIGR) was used

organism: Streptococcus pneumoniae

source_name: CC199 S. pneumoniae Disease Isolate

label_protocol:
Labelled with Invitrogen's BioPrime Plus Array CGH Indirect Genomic Labeling System
2ug of genomic DNA incubated at 95C for 5mins with random primers, then 37C for 2hrs with Exo-Klenow fragment and a nucleotide mix with aha-dUPT. Stop buffer added at end of 2hrs, product cleaned with the kit's PureLink Spin Columns and eluted in 50uL of DEPC-treated water.
Next, the amino-modified DNA is coupled with fluorescent dye, alexa fluor 555 for reference strain TIGR4 and alexa fluor 647 for the test strain.

growth_protocol: Isolates were grown overnight at 37C in Todd-Hewitt broth

extract_protocol: Genomic DNA extracted using Qiagen 100G kit, following manufacturer's instructions

tag: serotype

value: Blood

source_name: TIGR4 - reference genome strain


title: CC199 S. pneumoniae Disease Isolate_8600-04

description: CC199 isolate 9

value: Cerebrospinal Fluid


title: CC199 S. pneumoniae Carriage Isolate_FG23

description: CC199 isolate 10

source_name: CC199 S. pneumoniae Carriage Isolate

value: Carriage


title: CC199 S. pneumoniae Carriage Isolate_FG59

description: CC199 isolate 11


title: CC199 S. pneumoniae Carriage Isolate_MIB02102

description: CC199 isolate 16


title: CC199 S. pneumoniae Disease Isolate_ME3582

description: CC199 isolate 14

value: Middle Ear Fluid


title: miR-145 overexpressing group, replicate 3

city: Singapore

first: George

middle: W

last: Yip

address: 4 Medical Drive, Block MD10

country: Singapore

institute: National University of Singapore

description: Gene expression data from MDA-MB-231 cells transfected with pre-miR-145

hyb_protocol: Fragmented cRNA was hybridised at 45°C for 16 hours to Affymetrix HG U133 Plus 2.0 GeneChips, followed by washing and staining in an Affymetrix FS450 fluidics station.

scan_protocol: GeneChips were scanned using a GCOS 7000 7G scanner.

data_processing: Data were analysed using GeneSpring GX11.0 with RMA normalisation to median signal intensity.

label_protocol: Biotinylated cRNA was prepared according th the standard Affymetrix protocol from 2.9 μg of total RNA.

growth_protocol: MDA-MB-231 cells were cultured at 37°C in a humidified atmosphere with 5% carbon dioxide.

extract_protocol: Total RNA extracted using the Qiagen RNeasy Kit.

treatment_protocol: Cells were transfected with pre-miR-145 or a negative control pre-miRNA.

value: Breast cancer cells

tag: cell type

value: MDA-MB-231 cells


title: CC199 S. pneumoniae Carriage Isolate_MIC17101

description: CC199 isolate 17


title: CC199 S. pneumoniae Disease Isolate

description: CC199 isolate 2


title: CC199 S. pneumoniae Disease Isolate_ME5846

description: CC199 isolate 15


title: CC199 S. pneumoniae Carriage Isolate_FG67 Repeat 1

description: CC199 isolate 12 - Repeat 1


title: CC199 S. pneumoniae Disease Isolate_ABC20012381

description: CC199 isolate 7


title: CC199 S. pneumoniae Disease Isolate_ME2815

description: CC199 isolate 13


title: Spleen_Line72_5 (Sample 5)

description: Sample 5

source_name: Line 72 Spleen tissue Infected 5 dpi


title: CC199 S. pneumoniae Carriage Isolate

description: CC199 isolate 1


title: CC180 S. pneumoniae Disease Isolate_OR6090-02

description: CC180 isolate included as an outgroup

source_name: CC180 S. pneumoniae Disease Isolate


title: miR-145 overexpressing group, replicate 2

source_name: MDA-MB-231 cells transfected with pre-miR-145


title: Endometrium - pregnant [08-10335-1]

city: Brussel

first: Inge

last: Van Vaerenbergh

address: Laarbeeklaan 103

department: EXPA

country: Belgium

institute: Vrije Universiteit Brussel

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix)

scan_protocol: Scanned on a 2-µm Affymetrix 3000 GeneScanner

data_processing: Affymetrix GeneChip Operating (GCOS) 1.4 was used to analyze the resulting image files. The global scaling technique was used to scale the fluorescence intensity of each chip to a target signal of 150.

source_name: Endometrium on day of oocyte retrieval,  pregnant

label_protocol: Labeled with biotin using the IVT labeling kit (Affymetrix)

extract_protocol: RNA isolation with RNeasy Mini kit (Qiagen) according to manufacturer' s protocol

treatment_protocol: GnRH-antagonist/rec-FSH/ 200 IU hCG stimulated IVF cycle

value: endometrium on day of oocyte retrieval

tag: state

value: pregnant


title: CC199 S. pneumoniae Disease Isolate_ABC20009284

description: CC199 isolate 6


title: CC199 S. pneumoniae Disease Isolate_4564-03

description: CC199 isolate 5


title: Endometrium - not pregnant [08-9292-1]

source_name: Endometrium on day of oocyte retrieval, not pregnant

value: non-pregnant


title: Endometrium - not pregnant [08-10333-3]


title: Endometrium - not pregnant [08-10334-3]


title: Endometrium - pregnant [VE-3]


title: Endometrium - pregnant [08-10662-2]


title: CC199 S. pneumoniae Carriage Isolate_FG67 Repeat 3

description: CC199 isolate 12 - Repeat 3


title: CC199 S. pneumoniae Carriage Isolate_06-01-032NW

description: CC199 isolate 4


title: CC199 S. pneumoniae Disease Isolate_06-01-032LMEF

description: CC199 isolate 3


title: Control group, replicate 3

description: Gene expression data from MDA-MB-231 cells transfected with negative control pre-miRNA


title: CC199 S. pneumoniae Disease Isolate_06-01-003MEF

description: CC199 isolate 2


title: Control group, replicate 1

source_name: MDA-MB-231 cells transfected with negative control pre-miRNA


title: CC199 S. pneumoniae Carriage Isolate_FG67 Repeat 2

description: CC199 isolate 12 - Repeat 2


title: Extra-embryonic membrane_gravid_rep2

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

description: Gene expression in gravid fetal membrane

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v1_95_Feb07 and Grid: 013377_D_20050504) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: extra-embryonic membrane, Gravid side, replicate 2

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the whole of individual follicles using TRizol (Invitrogen) according to the manufacturer's instructions.

tag: tissues

value: extra-embryonic membrane

tag: resion

value: Gravid side


title: CC199 S. pneumoniae Disease Isolate_03AR0753

description: CC199 isolate 1

value: Pleural Fluid


title: Endometrium_gravid_rep1

description: Gene expression in gravid endometrium

source_name: endometrium, Gravid side, replicate 1

value: endometrium


title: Endometrium-d2-3-not pregnant 4

data_processing: Affymetrix GeneChip Operating (GCOS) 1.2 was used to analyze the resulting image files. The global scaling technique was used to scale the fluorescence intensity of each chip to a target signal of 150.

source_name: Endometrium on day of oocyte retrieval,  not pregnant

treatment_protocol: GnRH-antagonist/rec-FSH stimulated IVF cycle

tag: Endometrial dating d2-3, non-pregnant


title: Escherichia coli 8624 wild-type

city: Baltimore

first: David

middle: A

last: Rasko

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

description:
All protocols were done according to manufacturer's specifications:
http://www.affymetrix.com/support/technical/manual/expression_manual.affx

data_processing: Data has not been processed other than those protocols within GCOSv1.4

organism: Escherichia coli

source_name: wild-type

growth_protocol: grown in DMEM to OD600 of 0.5

extract_protocol: Ambion RiboPure RNA Isolation

value: EHEC 8624 wild-type


title: Endometrium_gravid_rep2

description: Gene expression in gravid endometrium

source_name: endometrium, Gravid side, replicate 2


title: Escherichia coli 8624 qseA deletion mutant

hyb_protocol: All protocols were done according to manufacturer's specifications: http://www.affymetrix.com/support/technical/manual/expression_manual.affx

source_name: qseA deletion mutant

value: EHEC 8624 qseA deletion mutant


title: Endometrium_Non-gravid_rep2

description: Gene expression in non-gravid endometrium

source_name: endometrium, Non-gravid side, replicate 2

value: Non-gravid side


title: Endometrium-d2-3-not pregnant 1


title: Endometrium_Non-gravid_rep1

source_name: endometrium, Non-gravid side, replicate 1


title: Endometrium-d2-3-not pregnant 3


title: Extra-embryonic membrane_gravid_rep1

source_name: extra-embryonic membrane, Gravid side, replicate 1


title: Endometrium_gravid_rep3

description: Gene expression in gravid endometrium

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v1_95_Feb07 and Grid: 014127_D_20060125) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: endometrium, Gravid side, replicate 3


title: Endometrium-d2-3- pregnant 4

tag: Endometrial dating d2-3, pregnant


title: Endometrium-d2-3-not pregnant 2


title: miR-145 overexpressing group, replicate 1


title: Extra-embryonic membrane_Non-gravid_rep1

description: Gene expression in non-gravid fetal membrane

source_name: extra-embryonic membrane, Non-gravid side, replicate 1


title: Endometrium-d2-3- pregnant 3


title: naive, biological replicate 2

first: Gabriel

middle: D

last: Victora

address: 9 Cambridge Center

institute: Whitehead Institute

description: Gene expression data from naïve (IgD+) B cells from spleen

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse MOE 430 2.0 gene chips. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Chips were scanned on Affymetrix GeneChip Scanner 3000 using AGCC 2.0 Software

data_processing: The data were analyzed with GeneSpring 11 using Affymetrix default analysis settings and RMA as normalization method.

source_name: naïve splenic B cells

label_protocol: Biotinylated cRNA were prepared using the Affymetrix 3'IVT Express Kit.

growth_protocol: Germinal centers were induced by immunization with ovalbumin in alum followed by transfer of PA-GFP+ B1-8hi B cells and boosting with soluble NP-ovalbumin

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

treatment_protocol: Cells were photoactivated in the dark or light zones of intact lymph nodes and sorted by flow cytometry

value: spleen

value: naive B cells


title: Control B

status: Public on Sep 06 2010

city: Boston

first: Richelle

middle: C.

last: Charles

address: 55 Fruit Street, Gray 504

department: Infectious Diseases

institute: Massachussetts General Hospital

description: Analysis used in vitro RNA with SCOTS as control samples for comparison to the in vitro samples prepared without SCOTS.

hyb_protocol: Labeled products were added to activated Salmonella ORF microarray glass slides (version STv7S; McClelland Laboratory, Vaccine Research Institute of San Diego, CA, http://www.sdibr.org/Faculty/mcclelland/mcclelland-lab), and developed as previously described (Larocque RC et. al. (2005). Infect Immun 73: 4488-4493 [PMID 16040959]).

scan_protocol: Arrays were scanned using a Perkin Elmer scanner and ScanArray Express software version 4.

data_processing: For analyses, we subtracted local background from spot signal intensities, and considered a cDNA for an ORF detected in a particular sample if it met the following criteria: 1) the median signal intensity of at least 2 of its 3 replicate spots on the array was at least ten median absolute deviations greater than the median of spots on the microarray corresponding to genes absent from the S. Paratyphi A genome, and 2) this criteria was met on greater than 75% of slides for that subject.  We then evaluated differences in expression in in vitro versus in vivo grown organisms for all genes detected in in vivo samples.  Using LOESS-normalized, log-transformed data, we employed repeated measures ANOVA (to within slide replicate spots) with fixed type (in vivo versus in vitro) and dye effects with Benjamini-Hochberg correction.  We only considered array features with a coefficient of variation in signal intensity of less than 50% within an array.  We considered significant variations in signal intensity as determined by ANOVA indication of potentially differentially expressed genes.  Since the samples were hybridized to two-channel arrays, the data from different slides were not normalized to have the same median intensities. Instead we used a simple (standard) method of analysis described by Kerr et. al (2001) Genetics Research, 77:123-128 (PMID 11355567) which included a slide effect in the analysis of variance model. Thus, for each gene when comparing in vivo and in vitro levels, the slide effect was adjusted for in the model fit, and there was no need to normalize data to have same median intensities across the slides.

organism: Salmonella enterica subsp. enterica serovar Paratyphi A

source_name: in vitro with SCOTS

label_protocol: We differently labeled in vivo and in vitro SCOTS-cDNAs for each of three patients with S. Paratyphi A bacteremia (Dziejman et. al. (2002) PNAS, 99: 1556-1561 [PMID 11818571]).

growth_protocol: To create cDNA of organisms in the blood of bacteremic patients (in vivo samples), we used TRIzol-preserved blood samples of patients whose day 0 culture subsequently grew S. Paratyphi A.  To generate corresponding in vitro cDNA samples, we grew each patient's bacterial isolate in Luria Bertani (LB) broth until mid-log growth phase (OD600 0.45-0.6), and then immediately placed these samples into TRIzol at a 1 (mid-log culture):2 (TRIzol) volume ratio.

extract_protocol: We recovered total RNA from TRIzol-preserved in vivo and in vitro samples per manufacturer's instructions (Invitrogen), and treated with DNase on RNeasy columns (Qiagen).  We converted 5 µg of total extracted RNA into cDNA using random priming (T-PCR) to obtain a representative cDNA population as described by Froussard (Froussard P. 1992. Nucleic Acids Res 20: 2900 [PMID 1614887]), with modifications as previously described by Graham (Graham JE. 1999. PNAS. 96: 11554-11559 [PMID 10500215]).  We performed three rounds of SCOTS on in vivo and in vitro cDNA samples, as previously described (Graham JE. 1999. PNAS. 96: 11554-11559 [PMID 10500215]).

tag: serovar

value: Paratyphi A

tag: growth condition

value: in vitro (LB media)

tag: scots

value: yes

tag: sample type

value: control

source_name: in vitro without SCOTS

value: no


title: Extra-embryonic membrane_Non-gravid_rep2

source_name: extra-embryonic membrane, Non-gravid side, replicate 2


title: Endometrium_Non-gravid_rep3

source_name: endometrium, Non-gravid side, replicate 3


title: Endometrium-d2-3- pregnant 2

source_name: Endometrium on day of oocyte retrieval,  pregnant


title: Clark 14DAP, Fe sustained, biological rep 3

city: St. Paul

first: Carroll

middle: P

last: Vance

address: 1991 Upper Buford Circle, 411 Borlaug Hall

department: Agronomy and Plant Genetics

institute: USDA-ARS, University of Minnesota

description: Gene expression data from iron sufficiency sustained Clark 14 DAP

hyb_protocol: RNA samples were submited to the University of Minnesota BioMedical Genomics Centerfor hybridization to Soybean Affymetrix GeneChips

scan_protocol: GeneChips were scanned using the Genechip 3000 scanner

data_processing: Data was analyzed using the 'justRMA' command in R.  Data was analyzed for  10DAP roots and 14DAP roots

organism: Glycine max

source_name: Clark 14 day roots, Fe sufficient, biological rep 3

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

growth_protocol: seeds were germinated on germination paper in growth chambers for 1 week.  Seedlings were transferred to hydroponic solutions of 2mM MgSO4*7H2O, 3mM Mg(NO3)2*6H2O, 2.5mM KNO3, 1mM CaCL2*2H2O, 4mM Ca(NO3)2*4H2O, 0.020mM KH2PO4, 542uM KOH, 217uM DTPA, 1.5uM MnCl2 *4H2O, 4.6uM ZnSO4*7H2O, 2uM CuSO4*5H2O, 0.2uM NaMoO4*2H2O, 1uM CoSO4*7H2O, 1uM NiSO4*6H2O, 10uM H3BO3, 20mM HCO3, and either 50 or 100uM Fe(NO3)3.  A daily nutrient solution of 16mM KPO4, 0.287mM H3BO3, and 355mM NH4(NO3)3 maintained stable nutrient conditions.

extract_protocol: RNA was extracted using the TRIzol method, DNAse treated with Ambion DNA-free kit, then further purified using the RNeasy mini kit (QIAGEN)

treatment_protocol: plants were grown in either iron sufficient (100uM Fe(NO3)3) or iron limited (50uM Fe(NO3)3) hydroponic conditions.  After 10 days, the roots of half the plants were collected in liquid nitrogen.  12 days after planting, Iron was added to all remaining hydroponic solutions to either bring the iron levels up to iron sufficient conditions or maintain iron sufficient growth conditions.  14 days after planting, the remaining plant roots were harvested in liquid nitrogen.

tag: isogenic line

value: Clark

tag: time point

value: 14 days

tag: condition

value: Fe sufficient

tag: biological replicate

tag: tissue

value: Total Roots


title: Clark 14DAP, Fe recovery, biological rep 3

description: Gene expression data from iron recovery Clark 14 DAP

source_name: Clark 14 day roots, Fe recovery, biological rep 3

value: Fe recovery


title: Iso 14DAP, Fe sustained, biological rep 3

description: Gene expression data from iron sufficiency sustained IsoClark 14 DAP

source_name: IsoClark 14 day roots, Fe sustained, biological rep 3

value: IsoClark

value: Fe sustained


title: Clark 14DAP, Fe recovery, biological rep 2

source_name: Clark 14 day roots, Fe recovery, biological rep 2


title: Clark 14DAP, Fe recovery, biological rep 1

source_name: Clark 14 day roots, Fe recovery, biological rep 1


title: Control A, dye reversal


title: dark zone, biological replicate 2

description: Gene expression data from sorted B cells photoactivated in the GC dark zone

source_name: day 7 germinal center dark zone cells

value: lymph node

value: germinal center B cells


title: Extra-embryonic membrane_gravid_rep3

source_name: extra-embryonic membrane, Gravid side, replicate 3

value: extra-embryonic membrane

value: Gravid side


title: Hsa embryos 15 wga

city: Miami

first: Ricardo

last: Pastori

department: Diabetes Research Institute

institute: University of Miami

description: The embryonic human pancreas were embeded in 10% volume of RNAlater solution (Ambion).

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Data was processed using the softwares SDS 2.3 and RQ manager 1.2 from Applied Biosystems.
dCt for delta Ct, defined by the formula (Ct of the specific miRNA-Ct of the endogenous control RNU48) for each sample. RQ for relative quantification, defined by the formula 2^-dCt . Small nuclear RNA (RNU48) was used as endogenous control.

label: FAM

source_name: embryonic human pancreas

label_protocol: standard Taqman assay

extract_protocol: Total RNA was isolated using the miRVana microRNA isolation kit (Ambion).

tag: gestational age

value: 15 wk

value: embryonic pancreas


title: Hsa embryos 21 wga

value: 21 wk


title: Iso 14DAP, Fe recovery, biological rep 1

description: Gene expression data from iron recovery IsoClark 14 DAP

source_name: IsoClark 14 day roots, Fe recovery, biological rep 1


title: Iso 14DAP, Fe sustained, biological rep 2

source_name: IsoClark 14 day roots, Fe sustained, biological rep 2


title: Iso 14DAP, Fe sustained, biological rep 1

source_name: IsoClark 14 day roots, Fe sustained, biological rep 1


title: Hsa embryos 22 wga

value: 22 wk


title: Hsa embryos 14 wga N3

value: 14 wk


title: Iso 14DAP, Fe recovery, biological rep 2

source_name: IsoClark 14 day roots, Fe recovery, biological rep 2


title: Iso 14DAP, Fe recovery, biological rep 3

source_name: IsoClark 14 day roots, Fe recovery, biological rep 3


title: Hsa embryos 14 wga N2


title: Clark 10DAP, Fe sufficient, biological rep 3

description: Gene expression data from iron sufficient Clark 10DAP

source_name: Clark 10 day roots, Fe sufficient, biological rep 3

value: 10 days