title: Erythroid GATA

description: Images generated at 635 and 532 nm as per NimbleGen ChIP protocol.

data_processing: Images processed and data generated using NimbleScan v2 exactly as described in NimbleChip Arrays User's Guide. The Scaled Log2-ratio is the ratio of the input signals for the experimental and test samples co-hybridised to the array. The log2-ratio is computed and scaled to cenre the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

source_name: GATA1 Erythroid d10 ChIP input sample

growth_protocol: Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. GATA1 ChIP study. Sample precessed as ChIP input.

source_name: GATA1 Erythroid d10 ChIP test sample

growth_protocol: Human adult male erythroid cells grown in standard 2-phase culture and harvested at d10. GATA1 ChIP study. Sample precessed as ChIP test.


title: 12 hours with HGF n13 h12hgf1n13 experiment TR5

status: Public on Jun 10 2009

type: RNA

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

description:
Advanced ovarian cancers are initially responsive to
chemotherapy with platinum drugs but develop drug
resistance in most cases. We showed recently that
hepatocyte growth factor (HGF) enhances death of human
ovarian cancer cell lines treated with cisplatin (CDDP) and
that this effect is mediated by the p38 mitogen-activated
protein kinase. In this work, we integrated genome-wide
expression profiling, in silico data survey, and functional
assays to identify transcripts regulated in SK-OV-3 ovarian
cancer cells made more responsive to CDDP by HGF.
Using oligonucleotide microarrays, we found that HGF
pretreatment changes the transcriptional response to
CDDP. Quantitative reverse transcription-PCR not only
validated all the 15 most differentially expressed genes
but also confirmed that they were primarily modulated by
the combined treatment with HGF and CDDP and reversed
by suppressing p38 mitogen-activated protein kinase
activity. Among the differentially expressed genes, we
focused functional analysis on two regulatory subunits of
the protein phosphatase 2A, which were down-modulated
by HGF plus CDDP. Decrease of each subunit by RNA
interference made ovarian cancer cells more responsive to
CDDP, mimicking the effect of HGF. In conclusion, we
show that HGF and CDDP modulate transcription in
ovarian cancer cells and that this transcriptional response
is involved in apoptosis regulation. We also provide the
proof-of-concept that the identified genes might be
targeted to either increase the efficacy of chemotherapeutics
or revert chemotherapy resistance.

hyb_protocol: arrays were hybridized as suggested by manufacturer

scan_protocol: arrays were scanned as suggested by manufacturer

data_processing:
Two of the time-course experiments, done independently, were analyzed. From digitized image data
files of raw data, background-normalized image data (CEL
files) were generated. Microarray quality control and
statistical validation was done using Bioconductor.
The presence of hybridization/construction artifacts was
evaluated with the fitPLM function (Bioconductor package
affyPLM). The probes (PM) intensity distribution was
evaluated using hist function (Bioconductor package affy).
Only two arrays, CDDP 6 hours and CDDP/HGF 6 hours
in TR7 experiment were discarded due to low quality. TR5
and TR7 experiments were then analyzed separately. Probe
set intensities were obtained by robust multiarray average (RMA), and normalization was done according to quantiles
method. Probe sets in TR5 and
TR7 were filtered separately to have an interquantile range
for each probe set greater than 0.4.
TR5 and TR7, represented as ratio with
respect to probe sets mean across the experiments, were
combined in a unique exprSet object. The identification of
differentially expressed genes associated to the HGF effect
was addressed using linear modeling approach. For
assessing differential expression, an empirical Bayes
method was used to moderate the SE of the estimated
log-fold changes together with the BH correction of the
false discovery rate.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SK-OV-3 ovarian carcinoma cells

label_protocol: cRNAs were generated as suggested by Affymetrix

extract_protocol:
Total RNA was extracted and purified from SK-OV-3 cell
lines at each time point using the Concert Cytoplasmic
RNA Purification Reagent (Invitrogen, Carlsbad, CA) as
suggested by the manufacturer

treatment_protocol:
Exponentially growing cells were cultured for 48 hours in
the presence of pure recombinant HGF (R&D Systems,
Minneapolis, MN) at the concentration of 50 ng/mL or
control medium. Apoptosis was then induced by adding
fresh medium, with or without HGF, supplemented with
10 Amol/L CDDP.

tag: cell line


title: Non-pregnant female whole blood 5A

city: Hong Kong

first: Yuk Ming

middle: Dennis

last: Lo

address: The Prince of Wales Hospital

department: Department of Chemical Pathology

country: China

institute: The Chinese University of Hong Kong

description: All RNA samples had a 28S/18S ratio over 1.5 with no evidence of degradation. All scanned images were visually inspected for surface defects. Hybridization and Poly-A controls were within expected parameters, and 3'/5' ratios for actin and GAPDH were below 3 (mean Beta Actin 3'/5' = 1.53 and mean GAPDH 3'/5' = 1.02).

hyb_protocol: Aliquots of each sample were hybridized to U133A/B oligonucleotide microarray using standard Affymetrix protocols.

scan_protocol: The chips were scanned using the GeneArray scanner (Affymetrix) using standard Affymetrix protocols.

data_processing: The CEL files generated by the Affymetrix Microarray Suite (MAS 5.0) were processed by Robust Multi-chip Average, with GC-content background correction (GC-RMA) using Genespring v.7.2 (Agilent Technologies, Palo Alto, CA).

source_name: Non-pregnant female whole blood

label_protocol: cRNA probes were generated using standard Affymetrix protocols

extract_protocol: Peripheral whole blood were collected in PAXgene blood RNA tubes (PreAnalytiX, Hombrechtikon, Switzerland) and total RNA was isolated following the manufacturer's instruction.

tag: tissue

value: whole blood

tag: condition

value: non-pregnant

tag: gender

value: female


title: Non-pregnant female whole blood 3A


title: 0 hours no HGF n3 h0hgf0n3 TR7


title: 0 hours no HGF n1 h0hgf0n1 experiment TR5


title: 12 hours no HGF n11 h12hgf0n11 experiment TR5


title: 0 hours with HGF n6bis h0hgf1n6bis experiment TR7


title: 12 hours with HGF n14 h12hgf1n14 experiment TR7


title: 0 hours with HGF n5 h0hgf1n5 experiment TR5


title: Aug101cx71a

city: Fargo

first: Steve

last: Travers

state: ND

address: 218 Stevens Hall

department: Biological Sciences

country: USA

institute: North Dakota State University

hyb_protocol: The labeled cDNA was hybridized overnight at 50C to cDNA microarrays, followed by a second hybridization of the dye molecules with the specific primers on the cDNAs.

scan_protocol: Microarray chips were scanned with an Axon Genepix 4000B scanner at two wavelengths, 652 and 532 nm, using GenePix software (v. 6) producing two-channel images.

data_processing: We then loaded the GAL file for the SAM 1.1 maize microarray, aligned the spots using a template grid and the irregular spot function and optimized to the two channel gain levels to yield a whole array count ratio of approximately one. Obvious anomalies in the grids were flagged as bad spots and then fluorescence intensity was assessed with GenePix. These results were queried for quality control. Features with signal to noise ratios less than three were flagged bad and those greater than three good. All data flagged bad were then removed from further analysis. The intensity values on each array were then normalized with the ratio of medians protocol. Prior to the high-throughput regression analysis we normalized the fluorescence values by conducting mixed model ANOVAs with array and dye included as fixed effects: yij=X+Ai+Dj+(AxD)ij+Eij, where yij is the fluorescence intensity on the ith array and labeled with the jth dye, X is the mean, Ai is the effect of the ith array (i = 1-16), Dj is the effect of the jth dye, (AxD)ij is the array–dye interaction and Eij is the stochastic error.

organism: Andropogon gerardi

source_name: 101c Aug

label_protocol: Genisphere kit (Array 900)

extract_protocol: RNeasy kit (Qiagen)

tag: type

value: Big bluestem

source_name: 71a Aug


title: 0 hours no HGF n2 h0hgf0n2 experiment TR5


title: 12 hours no HGF n12 h12hgf0n12 experiment TR7


title: Non-pregnant female whole blood 2A


title: Non-pregnant female whole blood 4A


title: 0 hours with HGF n4 h0hgf1n4 experiment TR5


title: Aug74bx104d

source_name: 74b Aug

source_name: 104d Aug


title: Non-pregnant female whole blood 1A


title: Aug111cx121c

source_name: 111c Aug

source_name: 121c Aug


title: Aug24bx32d


title: Third trimester maternal whole blood 5A

source_name: Third trimester maternal whole blood

value: pregnant, third trimester


title: Aug64bx94a


title: Aug41cx51a

source_name: 41c Aug


title: Aug112dx122c

source_name: 112d Aug

source_name: 122c Aug


title: Aug42dx54c

source_name: 42d Aug


title: Aug131ax151c

source_name: 131a Aug


title: Sample_shGATA2_3

city: Chicago

first: Zan

last: Huang

state: IL

address: 303 E Superior St

department: Med

institute: Northwestern University

description: GATA-1-deficient megakaryocytic cells G1ME were transduced with Banshee control vector or Banshee vector producing short hairpin RNA specific to mouse GATA-2 gene. The transduced cells were sorted based on GFP+ on the next day. Use Qiagen RNeasy Mini Kit.

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.7.18). It was vst transformed and quantile normalized

organism: Mus musculus

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina


title: Third trimester maternal whole blood 4A


title: Aug132dx152d

source_name: 132d Aug

source_name: 152d Aug


title: Third trimester maternal whole blood 1A


title: Sample_shGATA2_1


title: Aug61ax91c

source_name: 61a Aug

source_name: 91c Aug


title: Aug31ax21a

source_name: 31a Aug

source_name: 21a Aug


title: JulyB42dx54c

source_name: 54c  JulyB


title: Third trimester maternal whole blood 3A


title: Sample_Banshee_3


title: JulyB64ax94b

source_name: 64a JulyB

source_name: 94b JulyB


title: JulyB41ax51c

source_name: 41a JulyB

source_name: 51c JulyB


title: Non-pregnant female whole blood 5B

source_name: Non-pregnant female whole blood


title: TIL #83 CD8+CD28+

city: houston

first: yufeng

last: li

state: TX

address: 7455 Fannin

department: Melanoma

institute: MDACC

description: RNA from sorted TIL sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using BeadStudio software from Illumina

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

growth_protocol: TIL was isolated out of melanoma tumor fragment during 5 weeks culture in presence of IL-2; then subjected to rapid expansion protocol where CD3 stimulation and high dose IL-2 provided; TIL were harvested and sorted based on their CD8+ and CD28 expression. Isolation (5 weeks) -> expansion (2 weeks) -> sorting.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: FACS sorting

tag: cell type

value: human melanoma tumor infiltrating lymphocytes


title: JulyA61ax91c

source_name: 61a JulyA

source_name: 91c JulyA


title: JulyB61ax91c

source_name: 61a JulyB

source_name: 91c JulyB


title: TIL #59 CD8+CD28+

description: RNA from sorted TIL sample


title: TIL #83 CD8+CD28-

description: RNA from sorted TIL sample


title: JulyA64bx94a

description: 64bx94a JulyA

source_name: 94a JulyA


title: Sample_shGATA2_2


title: Sample_Banshee_1


title: JulyA41cx51c

source_name: 41c JulyA


title: JulyA42dx54c

source_name: 42d JulyA


title: Third trimester maternal whole blood 2A

source_name: Third trimester maternal whole blood


title: TIL #22 CD8+CD28+

description: RNA from sorted TIL sample


title: Non-pregnant female whole blood 4B


title: TIL #22 CD8+CD28-

description: RNA from sorted TIL sample


title: JulyB31cx21c

source_name: 31c JulyB

source_name: 21C JulyB


title: TIL #59 CD8+CD28-

description: RNA from sorted TIL sample


title: Non-pregnant female whole blood 3B


title: JulyB32bx24b

source_name: 32b JulyB

source_name: 24b JulyB


title: Erbb2 overexpression in NIH3T3 cells_4

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: RNA isolation, Labelling, Hybridisation and Scanning procedure are described in the fields above

hyb_protocol: This hybridization mixture was placed on a prehybridised microarray, under a cover slip, placed into a hybridization chamber (Genetix) and immersed in a thermostatic bath at 42°C for at least 16 hours. After hybridization slides were washed in 40ml of 3x , 1x, 0.25x and 0.1x SSC at room temperature. For drying slides were placed in an empty 50 ml Falcon tube (Becton Dickinson, USA) and centrifuged at 4000m/s2. Beckers, J., Herrmann, F., Rieger, S., Drobyshev, A., Horsch, M., Hrabé de Angelis, M. and Seliger, B. (2005): Identification and validation of novel ERBB2 (Her2, NEU) targets including genes involved in angiogenesis. Int. J. Cancer 114: 590-597. Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

scan_protocol: Dried slides were scanned with a GenePix 4000A microarray scanner and the images were analyzed using the GenePix Pro3.0 image processing software (Axon Instruments, USA) Greenwood AD, Horsch M, Stengel A, Vorberg I, Lutzny G, Maas E, Schädler S, Erfle V, Beckers J, Schätzl H and Leib-Mösch C (2005): Cell Line Dependent RNA Expression Profiles of Prion-infected Mouse Neuronal Cells. JMB 349: 487-500 Seltmann M, Horsch M, Drobyshev A, Chen Y, Hrabé de Angelis M, Beckers J (2005): Assessment of a Systematic Expression Profiling. Approach in ENU-Induced Mouse Mutant Lines. Mam Genome 16 (1): 1-10

data_processing: Gene Pix 6.1

source_name: Erbb2 transfected NIH3T3 cells

label_protocol:
For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye.
HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562

extract_protocol: Total RNA was isolated just before processing for expression profiling. For preparation of total RNA individual organs were thawed in buffer containing chaotropic salt (RLT buffer, Qiagen) and homogenised using a Polytron homogeniser. Total RNA from individual samples was obtained according to manufacturer’s protocols using RNeasy Midi kits (Qiagen). The concentration was calculated from OD260/280 measurement and 2 µg RNA aliquots were run on a formaldehyde agarose gel to check for RNA integrity. The RNA was stored at -80°C in RNase free water (Qiagen).

value: Erbb2 transfected NIH3T3 cell line with Erbb2 overexpression

source_name: NIH3T3 cells

value: NIH3T3 cell line with normal Erbb2 expression


title: JulyA24bx32d

source_name: 24b JulyA

source_name: 32d JulyA


title: Sample_Banshee_2


title: JulyA21cx31c

source_name: 21c JulyA

source_name: 31c JulyA


title: Erbb2 overexpression in NIH3T3 cells_2

label_protocol: For labeling 20 µg of total RNA were used for reverse transcription and indirectly labeled with Cy3 or Cy5 fluorescent dye according the TIGR protocol (Hedge et al., 2000). Labeled cDNA was dissolved in 30 µl hybridization buffer (6x SSC, 0.5% SDS, 5x Denhardt’s solution and 50% formamide) and mixed with 30 µl of reference cDNA solution (pool from six control animals) labeled with the second dye. HegdeP, Qi R, Abernathy R, Gay C, Dharap S, et al (2000): A concise guide to cDNA microarray analysis-II. Biotechniques 29: 548-562


title: Erbb2 overexpression in NIH3T3 cells_3


title: Non-pregnant female whole blood 2B

source_name: Non-pregnant female whole blood


title: June13d

source_name: 131d June


title: Non-pregnant female whole blood 1B


title: June112dx122c

source_name: 122c June


title: Erbb2 overexpression in NIH3T3 cells


title: Third trimester maternal whole blood 5B


title: June104bx74d


title: wild-type treated with fludioxonil vs atfA mutant treated with fludioxonil (Exp.5) Dye-swapped

city: Sendai

first: Daisuke

last: Hagiwara

state: Miyagi

address: 6-6-10 Aoba Aramaki

department: New Industry Creation Hatchery Center

country: Japan

institute: Tohoku university

description: Gene expression was considered to be significantly higher or lower whenever the spot intensity changed by at least 2-fold in all four replicates.

hyb_protocol: DNA microarray slides were hybridized in a Slide Booster (Advalytix) at 42ºC overnight (16-18 h). Then, the slides were washed twice in wash buffers (first in a buffer containing 2×SSC and 0.1 % SDS for 15 min, then in a buffer containing 1×SSC and 0.1% SDS for 5 min at room temperature. Finally, the slides were rinsed with 0.2×SSC at room temperature for 5 min and dried by centrifugation.

scan_protocol: The slides were scanned using GenePix4000B scanner (Molecular Devices).

data_processing: The resulting TIFF images were imported into GenePix Pro and fluorescent intensity of spots were calculated for each of the Cy3 and Cy5 channels. Global normalization was applied to analysis. Following normalization, spots whose Cy3 or Cy5 intensity was less than 0 were removed from the data set (the exceptional case was that intensity of the other channel was more than 100). The dye-swap replicates and in-slide replicates were subjected to all analyses. Finally, gene expression ratios (Cy5/Cy3) were calculated for each replicates.

organism: Aspergillus nidulans

source_name: wild-type treated with fludioxonil

label_protocol: Cy3- and Cy5-labeled cDNA probes were prepared using the Amersham CyScribe Post-Labelling Kit (GE Healthcare). Initially, amino allyl-dUTP (AA-dUTP) was incorporated into cDNA in a reverse transcriptase reaction, in which 1 μg mRNA was used as the template for each sample. The AAdUTP-modified cDNA samples were labeled with Cy3 or Cy5 using CyDye NHS-esters, resulting in Cy3- or Cy5-labeled cDNA probes. The Cy3 and Cy5 probes were purified using the CyScribe GFX Purification Kit (GE Healthcare) and evaporator-dried. Samples were then dissolved in 28 μL of hybridization buffer (50% formamide, 5×SSC, 0.1% SDS, 0.6 μg/μL Salmon Sperm DNA).

growth_protocol: 10 8 conidia of each strain were added into 100 ml of standard A. nidulans minimal media, Czapek-Dox (CD) medium (adjusted pH 6.5 with KOH) containing 2% glucose and appropriate requirements, and were cultured for 18 hours in a rotated shaker (160 rpm) at 37ºC. After this, fludioxonil was added (final concentration, 10ug/ml). After 15min, mycelia were harvested, frozen in liquid nitrogen, ground to powder, and used for RNA preparation.

extract_protocol: Total RNA was purified using the Qiagen RNeasy plant mini kit according to the manufacturer's instructions (QIAGEN).

tag: strain

tag: genotype

value: (biA1, pyrG89, wA3, argB2, pyroA4, argB+)

source_name: atfA mutant treated with fludioxonil

value: atfA mutant (BPU1)

value: (biA1, pyrG89, wA3, argB2, pyroA4, atfA::argB)


title: June132dx152b

source_name: 132d june

source_name: 152b June


title: Third trimester maternal whole blood 4B

source_name: Third trimester maternal whole blood


title: wild-type treated with fludioxonil vs atfA mutant treated with fludioxonil (Exp.5)


title: June111cx121c

source_name: 111c June

source_name: 121c June


title: Third trimester maternal whole blood 3B


title: wild-type treated with fludioxonil vs hogA mutant treated with fludioxonil (Exp.4)

source_name: hogA mutant treated with fludioxonil

value: hogA mutant (BPU1)

value: (biA1, pyrG89, wA3, argB2, pyroA4, hogA::argB)


title: Third trimester maternal whole blood 1B


title: Third trimester maternal whole blood 2B


title: June61ax91c

source_name: 61a June

source_name: 91c June


title: June71ax101c

source_name: 101c June


title: June64bx94a

source_name: 64b June


title: wild-type treated with fludioxonil vs srrA mutant treated with fludioxonil (Exp.3) Dye-swapped

source_name: srrA mutant treated with fludioxonil

value: srrA mutant (BPU1)

value: (biA1, pyrG89, wA3, argB2, pyroA4, srrA::argB)


title: June42bx54a

description: June 42b 54a


title: wild-type treated with fludioxonil vs srrA mutant treated with fludioxonil (Exp.3)


title: wild-type treated with fludioxonil vs sskA mutant treated with fludioxonil (Exp.2) Dye-swapped

data_processing: The resulting TIFF images were imported into GenePix Pro and fluorescent intensity of spots were calculated for each of the Cy3 and Cy5 channels. Global normalization was applied to  analysis. Following normalization, spots whose Cy3 or Cy5 intensity was less than 0 were removed from the data set (the exceptional case was that intensity of the other channel was more than 100). The dye-swap replicates and in-slide replicates were subjected to all analyses. Finally, gene expression ratios (Cy5/Cy3) were calculated for each replicates.

source_name: sskA mutant treated with fludioxonil

value: sskA mutant (BPU1)

value: (biA1, pyrG89, wA3, argB2, pyroA4, sskA::argB)


title: June41dx51d

description: June 41d51d

source_name: June 51d


title: June24dx32b

description: June 24d32b


title: June21ax31c

source_name: 21a June


title: wild-type treated with fludioxonil vs wild-type treated with DMSO (Exp.1) Dye-swaped

source_name: wild-type treated with DMSO

growth_protocol: 10 8 conidia of each strain were added into 100 ml of standard A. nidulans minimal media, Czapek-Dox (CD) medium (adjusted pH 6.5 with KOH) containing 2% glucose and appropriate requirements, and were cultured for 18 hours in a rotated shaker (160 rpm) at 37ºC. After this, DMSO was added. After 15min, mycelia were harvested, frozen in liquid nitrogen, ground to powder, and used for RNA preparation.


title: wild-type treated with fludioxonil vs hogA mutant treated with fludioxonil (Exp.4) Dye-swapped

source_name: wild-type treated with fludioxonil


title: wild-type treated with fludioxonil vs wild-type treated with DMSO (Exp.1)


title: wild-type treated with fludioxonil vs sskA mutant treated with fludioxonil (Exp.2)


title: N1_2058, non-leukemia, DS

status: Public on Jun 09 2009

city: Pleasanton

first: Wei-Min

last: Liu

state: CA

address: 4300 Hacienda Drive

institute: Roche Molecular Systems

description: Microarray classification of myelodysplastic syndrome identifies patients with high risk of AML transformation

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: Data pre-processing included a summarization and quantile normalization step to generate probe set level signal intensities for each microarray experiment and was performed as previously published by Liu WM et al. PQN and DQN: algorithms for expression microarrays. J.Theor.Biol. 2006;243:273-278.

source_name: Salamanca

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

growth_protocol: not applicable

extract_protocol: The total RNA was purified either with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) or with TRIzol-based protocols

treatment_protocol: Samples are from untreated patients.

tag: disease state

value: none-of-the-targets


title: N1_2022, MDS, DS

source_name: Cardiff

value: MDS


title: N1_2016, MDS, DS

source_name: Munich


title: N1_2005, MDS, DS


title: N1_1992, MDS, DS


title: N1_1984, MDS, DS


title: N1_1974, MDS, DS


title: N1_2019, MDS, DS


title: N1_2000, MDS, DS


title: N1_1970, MDS, DS

source_name: Berlin


title: N1_2055, non-leukemia, DS


title: N1_1979, MDS, DS


title: N1_1985, MDS, DS


title: N1_1982, MDS, DS


title: N1_1971, MDS, DS


title: N1_2001, MDS, DS


title: N1_1967, MDS, DS


title: N1_1972, MDS, DS


title: N1_1939, MDS, DS


title: N1_1946, MDS, DS


title: N1_1906, MDS, DS


title: N1_1954, MDS, DS


title: N1_1929, MDS, DS


title: N1_1922, MDS, DS


title: N1_1961, MDS, DS


title: N1_1949, MDS, DS


title: N1_1955, MDS, DS


title: N1_1945, MDS, DS


title: N1_1901, MDS, DS


title: N1_1914, MDS, DS


title: N1_1963, MDS, DS


title: N1_1902, MDS, DS


title: N1_1947, MDS, DS


title: N1_1937, MDS, DS


title: N1_1920, MDS, DS


title: N1_2011, MDS, DS


title: N1_1931, MDS, DS


title: N1_1944, MDS, DS


title: N1_1917, MDS, DS


title: N1_1907, MDS, DS


title: N1_1900, MDS, DS


title: N1_1898, MDS, DS


title: N1_1878, MDS, DS


title: N1_1891, MDS, DS


title: N1_1883, MDS, DS


title: N1_1936, MDS, DS


title: N1_1854, MDS, DS


title: N1_1845, MDS, DS


title: N1_1877, MDS, DS


title: N1_1855, MDS, DS


title: N1_1925, MDS, DS


title: N1_1884, MDS, DS


title: N1_1857, MDS, DS


title: N1_1847, MDS, DS


title: N1_1874, MDS, DS


title: N1_1849, MDS, DS


title: N1_1885, MDS, DS


title: N1_1844, MDS, DS


title: N1_1887, MDS, DS


title: N1_1896, MDS, DS


title: N1_1868, MDS, DS


title: N1_1842, MDS, DS


title: N1_1841, MDS, DS


title: N1_1889, MDS, DS


title: N1_1867, MDS, DS


title: N1_1848, MDS, DS


title: N1_1828, MDS, DS


title: N1_1836, MDS, DS


title: N1_1820, MDS, DS


title: N1_1819, MDS, DS


title: N1_1822, MDS, DS


title: N1_1824, MDS, DS


title: N1_1817, MDS, DS


title: N1_1818, MDS, DS


title: N1_1122, AML, DS

value: AML


title: N1_2075, non-leukemia, DQN3


title: N1_1148, AML, DS


title: N1_2018, MDS, DQN3


title: N1_2017, MDS, DQN3


title: N1_2031, non-leukemia, DQN3


title: N1_1826, MDS, DS


title: N1_2020, MDS, DQN3


title: N1_1208, AML, DS


title: N1_2023, MDS, DQN3


title: N1_1165, AML, DS


title: N1_0917, AML, DS


title: N1_1053, AML, DS


title: N1_1064, AML, DS


title: N1_2012, MDS, DQN3


title: N1_2014, MDS, DQN3


title: N1_2009, MDS, DQN3


title: N1_2008, MDS, DQN3


title: N1_2007, MDS, DQN3


title: N1_2004, MDS, DQN3


title: N1_1999, MDS, DQN3


title: N1_1998, MDS, DQN3


title: N1_2003, MDS, DQN3


title: N1_1997, MDS, DQN3


title: N1_1996, MDS, DQN3


title: N1_1995, MDS, DQN3


title: N1_1987, MDS, DQN3


title: N1_1991, MDS, DQN3


title: N1_1994, MDS, DQN3


title: N1_1986, MDS, DQN3


title: N1_1978, MDS, DQN3


title: N1_1962, MDS, DQN3


title: N1_1957, MDS, DQN3


title: N1_1981, MDS, DQN3


title: N1_1973, MDS, DQN3


title: N1_1956, MDS, DQN3


title: N1_1959, MDS, DQN3


title: N1_1980, MDS, DQN3


title: N1_1968, MDS, DQN3


title: N1_1969, MDS, DQN3


title: N1_1966, MDS, DQN3


title: N1_1977, MDS, DQN3


title: N1_1958, MDS, DQN3


title: N1_1953, MDS, DQN3


title: N1_1952, MDS, DQN3


title: N1_1950, MDS, DQN3


title: N1_1930, MDS, DQN3


title: N1_1935, MDS, DQN3


title: N1_1943, MDS, DQN3


title: N1_1926, MDS, DQN3


title: N1_1932, MDS, DQN3


title: N1_1927, MDS, DQN3


title: N1_1928, MDS, DQN3


title: N1_1933, MDS, DQN3


title: N1_1915, MDS, DQN3


title: N1_1923, MDS, DQN3


title: N1_1934, MDS, DQN3


title: N1_1916, MDS, DQN3


title: N1_1908, MDS, DQN3


title: N1_1941, MDS, DQN3


title: N1_1921, MDS, DQN3


title: N1_1912, MDS, DQN3


title: N1_1924, MDS, DQN3


title: N1_1942, MDS, DQN3


title: N1_1909, MDS, DQN3


title: N1_1919, MDS, DQN3


title: N1_1910, MDS, DQN3


title: N1_1899, MDS, DQN3


title: N1_1895, MDS, DQN3


title: N1_1905, MDS, DQN3


title: N1_1951, MDS, DQN3


title: N1_1882, MDS, DQN3


title: N1_1893, MDS, DQN3


title: N1_1879, MDS, DQN3


title: N1_1892, MDS, DQN3


title: N1_1864, MDS, DQN3


title: N1_1870, MDS, DQN3


title: N1_1858, MDS, DQN3


title: N1_1875, MDS, DQN3


title: N1_1865, MDS, DQN3


title: N1_1862, MDS, DQN3


title: N1_1890, MDS, DQN3


title: N1_1869, MDS, DQN3


title: N1_1851, MDS, DQN3


title: N1_1843, MDS, DQN3


title: N1_1853, MDS, DQN3


title: N1_1860, MDS, DQN3


title: N1_1846, MDS, DQN3


title: N1_1850, MDS, DQN3


title: N1_1837, MDS, DQN3


title: N1_1831, MDS, DQN3


title: N1_1839, MDS, DQN3


title: N1_1830, MDS, DQN3


title: N1_1821, MDS, DQN3


title: N1_1833, MDS, DQN3


title: N1_1838, MDS, DQN3


title: N1_1823, MDS, DQN3


title: N1_1829, MDS, DQN3


title: Control slide_LP chip

city: Addlestone, Surrey

first: Akbar

last: Dastjerdi

address: Woodham Lane

department: Virology

country: United Kingdom

institute: Animal and Plant Health Agency

description: Genotyping of lyssaviruses, control sample

hyb_protocol: Hybridised according to previously published protocol: 1. Burton, J.E., et al., Development of a multi-pathogen oligonucleotide microarray for detection of Bacillus anthracis. Mol Cell Probes, 2005. 19(5): p. 349-57.

scan_protocol: Slides were scanned using a GenePix scanner

data_processing: Fluorescence was quantified using GenePix Pro software. Statistical analysis of the data was done with DetectiV software (Watson et al., 2007).  DetectiV is implemented as a package for R, a powerful and open access statistical programming package (http://www.R-project.org).  The median and array methods of normalization were used in the statistical analysis of the results.  In the median method, DetectiV software calculates the mean fluorescence for each set of probes and normalised against background fluorescence of all probes except the landing lights, which are used to align the array, assuming that most probes are not hybridized.  The array method utilizes an entire control array, e.g. RNA from a known uninfected animal, as the negative control and all probe values are divided by their respective elements from the control array. DetectiV ouputs only the mean, t stat, and p -value of top hits.

label: Alexa flour 555 (Invitrogen)

organism: unidentified

source_name: Amplified RNA from mouse brain

label_protocol: Superscript reverse transcriptase (Invitrogen) and random amplification followed by indirect labelling with amino allyl dUTP and Alexa flour 555. Primers used:GTT TCC CAG TCA CGA TAN NNN NNN NN and GTT TCC CAG TCA CGA TA

extract_protocol: Total RNA was extracted from mouse brain using the TRIzol reagents (Invitrogen)

tag: infection

value: brain


title: Lyssavirus genotype 7_LP chip

description: Genotyping of lyssaviruses

organism: Lyssavirus australis

source_name: Amplified RNA from mouse brain infected with lyssaviruses

value: Lyssavirus genotype 7


title: N1_1840, MDS, DQN3


title: Lyssavirus genotype 6_LP chip

description: Genotyping of lyssaviruses

organism: European bat lyssavirus 2

value: Lyssavirus genotype 6


title: Lyssavirus genotype 5_LP chip

description: Genotyping of lyssaviruses

organism: European bat lyssavirus 1

value: Lyssavirus genotype 5


title: Lyssavirus genotype 3_LP chip

description: Genotyping of lyssaviruses

organism: Lyssavirus mokola

value: Lyssavirus genotype 3


title: Lyssavirus genotype 4_LP chip

description: Genotyping of lyssaviruses

organism: Lyssavirus duvenhage

value: Lyssavirus genotype 4


title: Lyssavirus genotype 1_LP chip

description: Genotyping of lyssaviruses

organism: Lyssavirus rabies

value: Lyssavirus genotype 1


title: Lyssavirus genotype 2_LP chip

description: Genotyping of lyssaviruses

organism: Lyssavirus lagos

value: Lyssavirus genotype 2


title: N1_1827, MDS, DQN3


title: Coded sample F_lyssavirus_LP chip

description: Detection of lyssaviruses in the coded samples


title: N1_1210, AML, DQN3


title: Coded sample E_lyssavirus_LP chip


title: N1_1162, AML, DQN3


title: Coded sample D_lyssavirus_LP chip


title: N1_1261, AML, DQN3


title: Coded sample C_lyssavirus_LP chip

source_name: Water

extract_protocol: Total RNA was extracted from the water sample with TRIzol reagents (Invitrogen)

tag: Water sample was subjected to RT, random amplification, labelling and microarray analysis


title: Coded sample B_lyssavirus_LP chip


title: Coded sample A_lyssavirus_LP chip


title: Testis-Spleen_HpaII_male_rep1

type: genomic

city: Seattle

first: Barbara

middle: J.

last: Trask

state: WA

address: 1100 Fairview Avenue N., C3-168, P.O. Box 19024

department: Division of Human Biology

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Labeled test and reference samples were mixed with 85 micrograms of Cot-1 DNA (Invitrogen) and hybridized to arrays under conditions described elsewhere (P.G. Buckley et al., Cancer Res., 2005).

scan_protocol: Image acquisition was performed using an Axon 4000B scanner and hybridization intensities were analyzed with the GenePixPro image analysis software (both Axon Instruments). For each spot, GenePixPro gave raw intensity values with the surrounding background subtracted for each wavelength scanned (635 nm and 532 nm for red and green channels, respectively).

data_processing: A custom R script was used to log2-transform raw intensity values, calculate the ratio of red to green fluorescence intensities, and apply a block-based loess normalization procedure based on GC content of the BACs on the array (see file bacGCcontents.txt), as BAC GC content strongly affects reported log ratios in this assay. We identified and eliminated clones whose duplicate spots reported significantly different normalized log2 ratios from each other (i.e., with SD >0.28) or had been flagged by GenePixPro as bad spots. The log2 ratios for the two spots for each remaining clone were averaged, and the median of all the clone averages was calculated and set to zero. We also eliminated results for subtelomeric clone RP5-857K21, as it appeared as an outlier on almost every array.

molecule: genomic DNA

source_name: Testis

label_protocol: Random priming using the Bioprime DNA Labeling System (Invitrogen) and Cy3-dCTP (GE Healthcare)

extract_protocol: DNA was phenol-chloroform precipitated and digested to completion with methylation-sensitive restriction enzyme HpaII (New England Biolabs). After digestion, DNA was fractionated on 5% to 30% sucrose gradients by using a Beckman SW-40TI swing-out rotor as previously described (R. Tompa, et al., Curr. Biol., 2002). Fractions containing fragments smaller than 2.5 kb and greater than 80 bp as judged by gel electrophoresis were selected, pooled, and precipitated with isopropanol. One microgram each of digested, size-selected test and reference DNA was labeled and hybridized to arrays

tag: Tissue

value: male

tag: Gender

source_name: Spleen

label_protocol: Random priming using the Bioprime DNA Labeling System (Invitrogen) and Cy5-dCTP (GE Healthcare)


title: Testis-Spleen_HpaII_male_rep2


title: Pons-Spleen_HpaII_male_rep1

source_name: Pons


title: Testis-Spleen_HpaII_male_rep3


title: Pons-Spleen_HpaII_male_rep2


title: Pons-Spleen_HpaII_male_rep3


title: Pons-Spleen_HpaII_female_rep2

value: female


title: N1_1048, AML, DQN3


title: Pons-Spleen_HpaII_female_rep1


title: Ovary-Spleen_Genomic_female

data_processing: A custom R script was used to log2-transform raw intensity values, calculate the ratio of red to green fluorescence intensities, and apply a block-based loess normalization procedure. For regular CGH arrays (not HpaII-digested), we normalized data based on intensity. We identified and eliminated clones whose duplicate spots reported significantly different normalized log2 ratios from each other (i.e., with SD >0.28) or had been flagged by GenePixPro as bad spots. The log2 ratios for the two spots for each remaining clone were averaged, and the median of all the clone averages was calculated and set to zero.

source_name: Ovary

extract_protocol: standard genomic DNA extraction procedure


title: OneKD-HCT116_HpaII_OneKD

source_name: OneKD

growth_protocol: McCoy's 5A medium supplemented with 10% FCS

tag: Cell line

value: HCT116 colorectal cancer


title: Ovary-Spleen_HpaII_female_rep2


title: Pons-Spleen_Genomic_female


title: Ovary-Spleen_HpaII_female_rep1


title: Ovary-Spleen_HpaII_female_rep3


title: OneKD-HCT116_Genomic_OneKD


title: H4K12ac ChIP, biological replicate 2, chip2

city: Leeds

first: David

last: Miller

address: Clarendon Way

department: Leeds Institute for Genetics and Health Therapeutics

institute: Leeds University

description: For chip array, purified IP-probe (Qiaquick Purification Kit, Qiagen, Hilden, Germany) and 10 ng of input material (total chromatin) was prepared by adapting the protocol for whole genome amplification using Sigma GenomePlex WGA kit (http://www.sigmaldrich.com) as described in O’Green et al. {O'Geen, 2006 #170}. The initial random amplification step of the WGA protocol was omitted due to previous defragmentation of sperm chromatin after sonification. The required amount of DNA for microarray analysis (4 µg per sample) was generated using WGA Reamplifikation Kit (Sigma, Munich, Germany). Amplicons were applied to the HG18 human 5 kb promoter array from NimbleGen System (http://www.nimblegen.com).

hyb_protocol: Hybridization was conducted at the manufacturer's facility

scan_protocol: Scanning was conducted at the manufacturer's facility

data_processing: Fluorescence signal intensity data were extracted from the scanned images of each array using Nimblegen data extraction software. Each feature on the array has a corresponding scaled log2-ratio that was calculated from the input signal (Cy3 for total chromatin) and IP-probe (Cy5) which were co-hybridized to the array. The log2 ratio was computed and scaled to center the ratio data around zero.

source_name: DNA associated with histone H4 acetylated at lysine 12 (H4K12ac)

label_protocol: Labeling and hybridisation of the probes for ChIP-on-chip analysis was performed by NimbleGen Service ImaGenes GmbH (Berlin, Germany)

extract_protocol: Approximately 107 cells from fertile donors were separated from seminal plasma and washed twice in 1x Dulbecco’s PBS by 5 min centrifugation at 300 x g. Chromatin crosslinking was carried out by addition of formaldehyde to a final volume of 1% and 10 min incubation on a rotating platform at room temperature followed by 10 min incubation with 125 mM glycine to quench the crosslinking reaction. After fixation, sperm was pelleted by 10 min centrifugation at 300 x g and resuspended in 200 µl cold PBS containing protease inhibitors (Roche, Mannheim, Germany). To separate heads from tails, cells were homogenised with 20 strokes in an UltraTurrax homogeniser (IKA, Staufen, Germany). After adding 2 ml lysis buffer, the sample was sonicated 10 times on ice with a Branson 250 sonifier on setting 3, duty cycle 50 % for 30 sec to obtain an average fragment length of 200-1000 bp. Chromatin was then diluted 10-fold with the provided dilution buffer. 1 ml of the probe was precleared with 40 µl of salmon sperm DNA/protein A agarose solution before overnight incubation at 4°C with primary antibodies purchased from Abcam (Cambridge, UK). These included a polyclonal antibody recognising histone H4 acetylated at lysine 12 (H4K12ac) (ab1761); a non-specific rabbit polyclonal IgG (ab46540) was used as a negative control and a polyclonal recognising unmodified histone H3 (abcam ab1791) was used as a positive control. 10 % of sonicated chromatin (100 µl) was retained from each sample to determine the amount of input DNA. After addition of 40 µl salmon sperm DNA/protein A agarose solution, samples were incubated for 2 hrs. Beads were then washed with the provided buffers and the chromatin was eluted twice with 250 µl elution buffer (1 % SDS in 0.1 M NaHCO3). Crosslinks were reversed by addition of 5 M NaCl and incubation at 65 °C for 4 hrs followed by proteinase K digestion at 45 °C for 1 hr. DNA was extracted by phenol/chloroform using ethanol precipitation with 3 µl glycogen as inert carrier, resuspended in 30 µl nuclease free water and stored at –20 °C.

tag: antibody

value: spermatozoa

source_name: Total Unfractionated Chromatin

treatment_protocol: Chromatin immunoprecipitation (ChIP) was performed using ChIP assay kit (Cat¹17-295) provided by UpstateMillipore (http://www.millipore.com) with modifications due to the relatively low quantity of histones in spermatozoa.


title: H4K12ac ChIP, biological replicate 0, chip2


title: OccipitalLobe-Spleen_HpaII_male_rep2

source_name: Occipital lobe


title: Pons-Spleen_HpaII_female_rep3


title: OccipitalLobe-Spleen_HpaII_male_rep1


title: H4K12ac ChIP, biological replicate 1, chip2

treatment_protocol: Chromatin immunoprecipitation (ChIP) was performed using ChIP assay kit (Cat¹17-295) provided by UpstateMillipore (http://www.millipore.com) with modifications due to the relatively low quantity of histones in spermatozoa


title: OccipitalLobe-Spleen_HpaII_male_rep3


title: OccipitalLobe-Spleen_Genomic_male


title: OccipitalLobe-Spleen_HpaII_female_rep3


title: OccipitalLobe-Spleen_HpaII_female_rep2


title: N1_1030, AML, DQN3


title: OccipitalLobe-Spleen_Genomic_female


title: Medulla-Spleen_HpaII_male_rep2

source_name: Medulla


title: Medulla-Spleen_HpaII_male_rep3


title: Medulla-Spleen_Genomic_male


title: Medulla-Spleen_HpaII_female_rep3


title: N1_1271, AML, DQN3


title: OccipitalLobe-Spleen_HpaII_female_rep1


title: Medulla-Spleen_HpaII_female_rep1


title: Medulla-Spleen_HpaII_female_rep2


title: Medulla-Medulla_HpaII_female


title: Lung-Spleen_HpaII_male_rep2

source_name: Lung


title: Lung-Spleen_HpaII_male_rep1


title: Lung-Spleen_HpaII_female_rep3


title: Liver-Spleen_HpaII_male_rep3

source_name: Liver


title: Lung-Spleen_HpaII_female_rep2


title: Lung-Spleen_Genomic_male


title: Lung-Spleen_Genomic_female


title: Liver-Spleen_HpaII_male_rep2


title: Liver-Spleen_HpaII_male_rep1


title: Liver-Spleen_HpaII_female_rep3


title: Lung-Spleen_HpaII_female_rep1


title: Lung-Spleen_HpaII_male_rep3


title: Liver-Spleen_Genomic_male


title: Medulla-Spleen_Genomic_female


title: Liver-Spleen_HpaII_female_rep2


title: Medulla-Spleen_HpaII_male_rep1


title: Liver-Spleen_HpaII_female_rep1


title: Liver-Spleen_Genomic_female


title: Heart-Spleen_HpaII_male_rep3

source_name: Heart


title: Heart-Spleen_HpaII_male_rep1


title: Heart-Spleen_HpaII_female_rep2


title: Heart-Spleen_HpaII_male_rep2


title: Heart-Spleen_HpaII_female_rep1


title: Heart-Spleen_Genomic_male


title: Heart-Spleen_Genomic_female


title: Cervix vs pool 3 of 6

first: Amit

middle: V

last: Kulkarni

address: 401 Terry Ave N

department: Genomics

institute: Rosetta Inpharmatics / Merck Pharmaceuticals

description: Cervix vs pool

hyb_protocol: Microarrays are incubated at 40°C for 48 hours in a rotating carousel.  Hybridizations to custom Agilent microarrays are completed as previously described (Hughes et al.Nat Biotech (2001), 19(4):342-7).  Microarrays are washed to remove non-specific hybridized sample. Afterwards, microarrays are dried in an ozone-free nitrogen chamber.

scan_protocol: Microarrays are scanned using the Agilent LP2 laser scanner. The scanner output is a Tiff file, which contains the quantitative hybridization data from each individual microarray. The Tiff files are then processed using Rosetta custom feature extraction software.

data_processing: Data were processed using the Rosetta Resolver® system. Rosetta's custom feature extraction software performs error modeling before data are loaded into the Resolver system. The Resolver system performs a squeeze operation that combines replicates of the same sequence in an array while applying error weighting. The error weighting consists of adjusting for additive and multiplicative noise. A P-value is generated and propagated throughout the system. The P-value represents the probability that a gene is expressed. The Resolver system allows users to set thresholds, below which genes of a P-value are considered to be significantly expressed. The Resolver system also combines multiple arrays using a squeezing process. If multiple spots reference one sequence, summarization is performed using an error-weighted average as described in Roland Stoughton and Hongyue Dai, Statistical Combining of Cell Expression Profiles. US Patent #6,351,712, February 26, 2002.

source_name: Cervix

label_protocol: custom automated version of the aminoallyl MessageAmp II kit from Ambion.

extract_protocol: Qiagen RNeasy spin columns with DNAse treatment

value: Cervix

source_name: pool

value: adult tissue pools


title: Cervix vs pool 2 of 6

description: Cervix vs pool


title: Blood CD8plus activated  T cells vs pool 3 of 6

description: Blood CD8plus activated  T cells vs pool

source_name: Blood CD8plus activated  T cells

value: Blood CD8plus activated  T cells


title: Cerebellum-Spleen_HpaII_male_rep2

source_name: Cerebellum


title: Heart-Spleen_HpaII_female_rep3


title: Blood CD4plus activated T cells vs pool 3 of 6

description: Blood CD4plus activated T cells vs pool

source_name: Blood CD4plus activated T cells

value: Blood CD4plus activated T cells


title: Cerebellum-Spleen_HpaII_male_rep3


title: Bladder vs pool 3 of 6

description: Bladder vs pool

source_name: Bladder

value: Bladder


title: Lymph node vs pool 3 of 6

description: Lymph node vs pool

source_name: Lymph node

value: Lymph node


title: Blood CD4plus activated T cells vs pool 2 of 6

description: Blood CD4plus activated T cells vs pool


title: Blood CD8plus activated  T cells vs pool 2 of 6


title: Cerebellum-Spleen_HpaII_male_rep1

source_name: Spleen


title: Lymph node vs pool 5 of 6

description: Lymph node vs pool


title: lung_AIRmax_male_saline_mice24

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

institute: IRCSS Istituto Nazionale Tumori

description: no additional information

data_processing:
The data were normalised using cubic spline normalization with Illumina's BeadStudio Gene Expression Module v3.4, July 2008 (see VALUE column below).
The data were then filtered by detection p-value (p<0.05).  A matrix of the normalized, filtered data is linked as supplementary file at the foot of the Series record.

source_name: lung from AIRmax male treated with saline

extract_protocol: Total RNA was extracted with RNeasy Midi kit (Qiagen, Valencia, CA) from normal lung parenchyma and purified with RNeasy MinElute CleanUP Kit (Qiagen). RNA concentration was determined with a Nanodrop spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA)

treatment_protocol: two intraperitoneal injections of 1 mg/g body weight urethane or saline solution

value: lung

value: AIRmax

value: M

tag: agent

value: saline


title: N1_0944, AML, DQN3

source_name: Cardiff

value: AML


title: lung_AIRmax_male_saline_mice21

description: no additional information


title: Bladder vs pool 2 of 6

description: Bladder vs pool


title: DNA packaging in human spermatozoal chromatin investigated by micrococcal nuclease digestion (MND)

description: Spermatozoal DNA from a healthy human donor was digested via micrococcal nuclease to profile histone and protamine binding of the chromatin.

hyb_protocol: For hybridisation, equal quantities of labelled DNA (500 - 1000 ng) were mixed with Cot-1 DNA (1 mg/ml) and incubated at 95°C for 3 minutes and then re-incubated at 37°C for 30 minutes. The DNAs were applied to either Agilent's 44K (100 μl) or 244K (490 μl) arrays, sealed and then incubated for 40 hours (244K arrays) or 24 hours (44K arrays) at 65°C with constant rotation (20 rpm).

scan_protocol: Scanning was conducted an accordance with the Agilent protocol.

data_processing:
Data was processed for feature extraction, background subtraction and normalized in the Agilent CGH analytics software package.
The default settings for the Agilent Analytics CGH v9.1 protocols were used (selection of a subset of rank invariant probes and using these for a linear median normalization between channels).

source_name: Spermatozoal DNA digested with micrococcal nuclease (MNDI; insoluble fraction)

label_protocol:
Labelling with cy3 or cy5 (GE Healthcare, Amersham UK) was accomplished using a
random priming method in the presence of Klenow DNA polymerase (Invitrogen,
Paisley, UK) according to the suggested Agilent protocol. Unincorporated nucleotides
were removed by passing the reaction mixture through a sephadex G50 column.

extract_protocol:
CGH profiling was carried out according to the manufacturer's (Agilent) instructions.
Prior to processing, all DNA samples (including those pre-digested with EcoR1 and
BamH1 or MNase were double re-digested with 10 units each of Alu1 and Rsa1
(New England Biolabs, Hitchin, UK) that generates fragments of 500 bp or less.

treatment_protocol:
Semen was
washed free of seminal plasma in HSOF buffer as described above and pellets
resuspended in 10mM Tris-Cl pH 8.0 containing 0.05% w/v PMSF and 1% w/v CTAB
to detach principal pieces. Following centrifugation, pellets containing ~108 nuclei
were resuspended in Mg2+ and Ca2+ free phosphate buffered saline (PBS) containing
0.5% v/v Triton X-100 and incubated for 10 minutes at 4°C. Following centrifugation,
the pellets were resuspended in 1 ml PBS containing 0.5% PMSF, 10 mM DTT and
incubated for 30 minutes at 37°C. CaCl2 was added to a final concentration of 0.6
mM and 5 units of micrococcal nuclease (Fermentas,, York, UK) added. Digestion
was stopped after 3 minutes incubation at 37°C by the addition of EDTA to 5 mM.
Following centrifugation at 5000g for 10 minutes, the supernatants (representing the soluble, histone-enriched fraction) and pellets (protamine-enriched) were processed.

value: Spermatozoa

tag: donor

value: healthy human donor

source_name: Spermatozoal DNA digested with micrococcal nuclease (MNDS; soluble Fraction)


title: Blood CD8plus activated  T cells vs pool 5 of 6


title: Lymph node vs pool 2 of 6

description: Lymph node vs pool


title: Cerebellum-Spleen_Genomic_male

value: male


title: Cerebellum-Spleen_HpaII_female_rep3

value: female


title: Cerebellum-Cerebellum_HpaII_male


title: Blood CD4plus activated T cells vs pool 5 of 6

description: Blood CD4plus activated T cells vs pool


title: Cerebellum-Spleen_HpaII_female_rep1


title: lung_AIRmax_male_urethane_mice16

description: no additional information

source_name: lung from AIRmax male treated with urethane

value: urethane


title: Cerebellum-Spleen_HpaII_female_rep2


title: lung_AIRmin_female_saline_mice3

description: no additional information

source_name: lung from AIRmin female treated with saline

value: AIRmin

value: F


title: lung_AIRmin_female_saline_mice20

description: no additional information


title: Cervix vs pool 5 of 6

description: Cervix vs pool

value: Cervix

value: adult tissue pools


title: lung_AIRmin_male_saline_mice10

description: no additional information

source_name: lung from AIRmin male treated with saline


title: lung_AIRmax_female_saline_mice22

description: no additional information

source_name: lung from AIRmax female treated with saline


title: Lymph node vs pool 4 of 6

description: Lymph node vs pool


title: Blood CD4plus activated T cells vs pool 4 of 6

description: Blood CD4plus activated T cells vs pool

value: Blood CD4plus activated T cells


title: DNA packaging in mouse spermatozoal chromatin investigated by micrococcal nuclease digestion (MND)

description: Spermatozoal DNA from mouse was digested via micrococcal nuclease to profile histone and protamine binding of the chromatin.

hyb_protocol: For hybridisation, equal quantities of labelled DNA (500 - 1000 ng) were mixed with Cot-1 DNA (1 mg/ml) and incubated at 95°C for 3 minutes and then re-incubated at 37°C for 30 minutes. The DNAs were applied to either Agilent's 44K (100 µl) or 244K (490 µl) arrays, sealed and then incubated for 40 hours (244K arrays) or 24 hours (44K arrays) at 65°C with constant rotation (20 rpm).

data_processing: Data was processed for feature extraction, background subtraction and normalized in the Agilent CGH analytics software package. The default settings for the Agilent Analytics CGH v9.1 protocols were used (selection of a subset of rank invariant probes and using these for a linear median normalization between channels).

label_protocol: Labelling with cy3 or cy5 (GE Healthcare, Amersham UK) was accomplished using a random priming method in the presence of Klenow DNA polymerase (Invitrogen, Paisley, UK) according to the suggested Agilent protocol. Unincorporated nucleotides were removed by passing the reaction mixture through a sephadex G50 column.

extract_protocol:
DNA obtained from spermatozoa released into HEPES buffered synthetic oviduct fluid from the dissected epididymides of CD1 mice
CGH profiling was carried out according to the manufacturer's (Agilent) instructions. Prior to processing, all DNA samples (including those pre-digested with EcoR1 and BamH1 or MNase were double re-digested with 10 units each of Alu1 and Rsa1 (New England Biolabs, Hitchin, UK) that generates fragments of 500 bp or less.

treatment_protocol: Semen was washed free of seminal plasma in HSOF buffer and pellets resuspended in 10mM Tris-Cl pH 8.0 containing 0.05% w/v PMSF and 1% w/v CTAB to detach principal pieces. Following centrifugation, pellets were resuspended in Mg2+ and Ca2+ free phosphate buffered saline (PBS) containing 0.5% v/v Triton X-100 and incubated for 10 minutes at 4°C. Following centrifugation, the pellets were resuspended in 1 ml PBS containing 0.5% PMSF, 10 mM DTT and incubated for 30 minutes at 37°C. CaCl2 was added to a final concentration of 0.6 mM and 5 units of micrococcal nuclease (Fermentas,, York, UK) added. Digestion was stopped after 3 minutes incubation at 37°C by the addition of EDTA to 5 mM. Following centrifugation at 5000g for 10 minutes, the supernatants (representing the soluble, histone-enriched fraction) and pellets (protamine-enriched) were processed.

tag: fraction

value: MNDI (insoluble fraction)

extract_protocol:
DNA obtained from spermatozoa released into HEPES buffered synthetic oviduct fluid from the dissected epididymides of CD1 mice
Prior to processing, all DNA samples (including those pre-digested with EcoR1 and BamH1 or MNase were double re-digested with 10 units each of Alu1 and Rsa1 (New England Biolabs, Hitchin, UK) that generates fragments of 500 bp or less.

value: MNDS (soluble fraction)


title: Blood CD8plus activated  T cells vs pool 4 of 6

tag: tissue

value: Blood CD8plus activated  T cells


title: Cerebellum-Spleen_Genomic_female


title: lung_AIRmin_female_urethane_mice17

description: no additional information

source_name: lung from AIRmin female treated with urethane

value: lung


title: Cervix vs pool 4 of 6

description: Cervix vs pool

source_name: Cervix


title: lung_AIRmin_male_saline_mice18

description: no additional information

value: M


title: lung_AIRmax_female_saline_mice11

description: no additional information

value: AIRmax

value: saline


title: Trachea vs pool 3 of 3

description: Trachea vs pool

source_name: Trachea

value: Trachea

source_name: pool


title: lung_AIRmin_male_urethane_mice13

description: no additional information

source_name: lung from AIRmin male treated with urethane


title: Epididymis vs pool 2 of 3

description: Epididymis vs pool

source_name: Epididymis

value: Epididymis


title: lung_AIRmin_female_saline_mice23

description: no additional information


title: Epididymis vs pool 3 of 3

description: Epididymis vs pool


title: Spleen vs pool 3 of 3

description: Spleen vs pool

value: Spleen


title: Lymph node vs pool 6 of 6

description: Lymph node vs pool

value: Lymph node


title: Brain cerebral cortex vs pool 2 of 3

description: Brain cerebral cortex vs pool

source_name: Brain cerebral cortex

value: Brain cerebral cortex


title: lung_AIRmax_male_urethane_mice1

description: no additional information

value: urethane


title: Spleen vs pool 2 of 3

description: Spleen vs pool


title: Cervix vs pool 6 of 6

description: Cervix vs pool


title: Trachea vs pool 2 of 3

description: Trachea vs pool


title: DNA packaging in human spermatozoal chromatin:SRDI versus SRDS (44K3)-dye swap

description: Spermatozoal DNA from a healthy human donor was partitioned through a salt extraction to profile protamine associated DNA relative to histone associated DNA.

hyb_protocol: For hybridisation, equal quantities of labelled DNA (500 - 1000 ng) were mixed with Cot-1 DNA (1 mg/ml) and incubated at 95°C for 3 minutes and then re-incubated at 37°C for 30 minutes. The DNAs were applied to Agilent's 44K (100 µl) arrays, sealed and then incubated for 24 hours at 65°C with constant rotation (20 rpm).

source_name: Spermatozoal DNA partitioned into a Salt Insoluble (SRDI) Fraction

extract_protocol: CGH profiling was carried out according to the manufacturer's (Agilent) instructions. Prior to processing, all DNA samples (including those pre-digested with EcoR1 and BamH1 or MNase were double re-digested with 10 units each of Alu1 and Rsa1 (New England Biolabs, Hitchin, UK) that generates fragments of 500 bp or less.

treatment_protocol: Semen was washed free of seminal plasma by diluting the semen 1:1 with HEPES buffered HSOF and centrifuging for 10 minutes at 500 x g. Pellets were resuspended in HSOF and pelleted as before. This was repeated until the supernatants were clear. Pellets were resuspended in STE buffer (100mM NaCl, 10 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.2 mM phenylmethylsulphonylfluoride (PMSF) and re-pelleted to remove HSOF. Pellets were subsequently processed with sequential extraction in 10% (w/v) mixed CTAB (alkly-trimethylammonium bromide), which removes the flagella, including principal pieces, thus ensuring no contamination of the samples with non-genomic DNA followed by sequential incubation in 1% w/v CTAB in 10 mM Tris-Cl pH 8.0 containing 0.05% w/v digitonin; Tris buffered saline (TBS) containing 0.05% w/v digitonin, 10 mM Tris-Cl pH 8.0 containing 1mM EDTA, 0.05% w/v digitonin, EDTA-free protease inhibitor cocktail (Roche) and finally extraction in 0.65M NaCl to release soluble histones. Nuclear pellets were re-suspended in BamH1 buffer containing 0.05% digitonin and digested with ~150 units each of BamH1 and EcoR1 (Invitrogen, Paisley, UK: 2,000 U per 5 x 108 nuclei) for 90 minutes at 37°C. Suspensions were centrifuged at 3,000 x g for 5 minutes and the supernatants removed. STOP buffer comprising proteinase K (Bioline: - 200 µg/ml) in TBS, 0.5% w/v sodium dodecyl sulphate (SDS) was added to this suspension and incubated for 10 hours at 55°C. Pellets were also resuspended in STOP buffer and concurrently digested under identical conditions. DNA was isolated from the insoluble fraction by incubation in STOP buffer containing RNAse A at 10mg/ml for 1 hour at 37°C and extraction in phenol chloroform (1:1) followed by ethanol precipitation. Precipitated DNA was dissolved in TE buffer and stored at 4°C.

value: Spermatozoa

value: healthy human donor

source_name: Spermatozoal DNA partitioned into a Salt Soluble (SRDS) Fraction

treatment_protocol: Semen was washed free of seminal plasma by diluting the semen 1:1 with HEPES buffered HSOF and centrifuging for 10 minutes at 500 x g. Pellets were resuspended in HSOF and pelleted as before. This was repeated until the supernatants were clear. Pellets were resuspended in STE buffer (100mM NaCl, 10 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.2 mM phenylmethylsulphonylfluoride (PMSF) and re-pelleted to remove HSOF. Pellets were subsequently processed with sequential extraction in 10% (w/v) mixed CTAB (alkly-trimethylammonium bromide), which removes the flagella, including principal pieces, thus ensuring no contamination of the samples with non-genomic DNA followed by sequential incubation in 1% w/v CTAB in 10 mM Tris-Cl pH 8.0 containing 0.05% w/v digitonin; Tris buffered saline (TBS) containing 0.05% w/v digitonin, 10 mM Tris-Cl pH 8.0 containing 1mM EDTA, 0.05% w/v digitonin, EDTA-free protease inhibitor cocktail (Roche) and finally extraction in 0.65M NaCl to release soluble histones.The supernatant following salt extraction was retained. DNA was isolated from the soluble fraction by incubation in STOP buffer containing RNAse A at 10mg/ml for 1 hour at 37°C and extraction in phenol chloroform (1:1) followed by ethanol precipitation. Precipitated DNA was dissolved in TE buffer and stored at 4°C.


title: lung_AIRmax_female_saline_mice12

description: no additional information

value: F


title: Bladder vs pool 4 of 6

description: Bladder vs pool

source_name: Bladder

value: Bladder

value: adult tissue pools


title: Trachea vs pool 1 of 3

description: Trachea vs pool


title: lung_AIRmax_male_saline_mice9

description: no additional information

source_name: lung from AIRmax male treated with saline


title: Blood CD8plus activated  T cells vs pool 6 of 6

source_name: Blood CD8plus activated  T cells


title: Duodenum vs pool 2 of 3

description: Duodenum vs pool

source_name: Duodenum

value: Duodenum


title: Brain cerebral cortex vs pool 3 of 3

description: Brain cerebral cortex vs pool


title: lung_AIRmax_female_urethane_mice4

description: no additional information

source_name: lung from AIRmax female treated with urethane


title: Spleen vs pool 1 of 3

description: Spleen vs pool

source_name: Spleen


title: Bladder vs pool 6 of 6

description: Bladder vs pool


title: Epididymis vs pool 1 of 3

description: Epididymis vs pool


title: lung_AIRmin_female_urethane_mice8

description: no additional information

value: AIRmin


title: DNA packaging in human spermatozoal chromatin:SRDI versus SRDS (44K2)-dye swap


title: lung_AIRmin_female_urethane_mice7

description: no additional information

value: lung


title: lung_AIRmin_male_urethane_mice15

description: no additional information

value: M


title: Lymph node vs pool 1 of 6

description: Lymph node vs pool

source_name: Lymph node


title: DNA packaging in human spermatozoal chromatin:SRDI versus SRDS (44K3)

description: Spermatozoal DNA from a healthy human donor was partitioned through a salt extraction to profile histone associated DNA relative to protamine associated DNA.

treatment_protocol: Semen was washed free of seminal plasma by diluting the semen 1:1 with HEPES buffered HSOF and centrifuging for 10 minutes at 500 x g. Pellets were resuspended in HSOF and pelleted as before. This was repeated until the supernatants were clear. Pellets were resuspended in STE buffer (100mM NaCl, 10 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.2 mM phenylmethylsulphonylfluoride (PMSF) and re-pelleted to remove HSOF. Pellets were subsequently processed with sequential extraction in 10% (w/v) mixed CTAB (alkly-trimethylammonium bromide), which removes the flagella, including principal pieces, thus ensuring no contamination of the samples with non-genomic DNA followed by sequential incubation in 1% w/v CTAB in 10 mM Tris-Cl pH 8.0 containing 0.05% w/v digitonin; Tris buffered saline (TBS) containing 0.05% w/v digitonin, 10 mM Tris-Cl pH 8.0 containing 1mM EDTA, 0.05% w/v digitonin, EDTA-free protease inhibitor cocktail (Roche) and finally extraction in 0.65M NaCl to release soluble histones.The supernatant following salt extraction was retained. DNA was isolated from the soluble insoluble fraction by incubation in STOP buffer containing RNAse A at 10mg/ml for 1 hour at 37°C and extraction in phenol chloroform (1:1) followed by ethanol precipitation. Precipitated DNA was dissolved in TE buffer and stored at 4°C.


title: Bladder vs pool 5 of 6

description: Bladder vs pool


title: 9311_young panicle 2cm, biological rep3

city: Mishima

first: Nori

last: Kurata

address: 1111 Yata

institute: National Institute of Genetics

description: Gene expression data from rice young panicle

hyb_protocol: According to Affymetrix standard procedure, 10 micrograms of fragmented cRNA were hybridized to an array for 16-18 hours at 45°C with constant rotation at 60 rpm. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray 3000 scanner.

data_processing: The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Oryza sativa Indica Group

source_name: young panicle 2cm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA was isolated and purified by RNeasy Plant Mini Kit (QIAGEN)

value: young panicle

tag: cultivar


title: 9311_young panicle 2cm, biological rep5


title: DNA packaging in human spermatozoal chromatin: Unfractionated (NF) & Insoluble (44K4)-dye swap

description: Spermatozoal DNA from a healthy human donor was partitioned through a salt extraction to profile protamine associated DNA relative to an unfractionated DNA sample.

source_name: Unfractionated (NF) Spermatozoal DNA

treatment_protocol: Semen was washed free of seminal plasma by diluting the semen 1:1 with HEPES buffered HSOF and centrifuging for 10 minutes at 500 x g. Pellets were resuspended in HSOF and pelleted as before. This was repeated until the supernatants were clear. Pellets were resuspended in STE buffer (100mM NaCl, 10 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.2 mM phenylmethylsulphonylfluoride (PMSF) and re-pelleted to remove HSOF. Pellets were subsequently processed with sequential extraction in 10% (w/v) mixed CTAB (alkly-trimethylammonium bromide), which removes the flagella, including principal pieces, thus ensuring no contamination of the samples with non-genomic DNA followed by sequential incubation in 1% w/v CTAB in 10 mM Tris-Cl pH 8.0 containing 0.05% w/v digitonin; Tris buffered saline (TBS) containing 0.05% w/v digitonin, 10 mM Tris-Cl pH 8.0 containing 1mM EDTA, 0.05% w/v digitonin, EDTA-free protease inhibitor cocktail (Roche)


title: DNA packaging in human spermatozoal chromatin: Unfractionated (NF) & Soluble (44K4)-dye swap

description: Spermatozoal DNA from a healthy human donor was partitioned through a salt extraction to profile histone associated DNA relative to an unfractionated DNA sample.

source_name: Unfractionated  (NF) Spermatozoal DNA


title: 9311_young panicle 2cm, biological rep2


title: Blood CD4plus activated T cells vs pool 6 of 6

description: Blood CD4plus activated T cells vs pool

source_name: Blood CD4plus activated T cells

value: Blood CD4plus activated T cells


title: DNA packaging in human spermatozoal chromatin:SRDI versus SRDS (44K2)


title: 9311_young panicle 2cm, biological rep4


title: lung_AIRmax_female_urethane_mice6

description: no additional information

value: AIRmax

tag: gender


title: Cervix vs pool 1 of 6

description: Cervix vs pool

source_name: Cervix

value: Cervix

source_name: pool


title: Duodenum vs pool 3 of 3

description: Duodenum vs pool


title: Brain cerebral cortex vs pool 1 of 3

description: Brain cerebral cortex vs pool


title: Duodenum vs pool 1 of 3

description: Duodenum vs pool


title: DNA packaging in human spermatozoal chromatin:SRDI versus SRDS (44K1)-dye swap


title: Blood CD8plus activated  T cells vs pool 1 of 6

value: Blood CD8plus activated  T cells


title: lung_AIRmin_male_urethane_mice14

description: no additional information

source_name: lung from AIRmin male treated with urethane


title: DNA packaging in human spermatozoal chromatin:SRDI versus SRDS (44K1)

description: Spermatozoal DNA from a healthy human donor was partitioned through a salt extraction to profile protamine associated DNA relative to an unfractionated sample.

source_name: Spermatozoal DNA partitioned into a Soluble (SRDS) Fraction

source_name: Spermatozoal DNA partitioned into an Insoluble (SRDI) Fraction


title: lung_AIRmax_female_urethane_mice5

description: no additional information


title: 9311_young panicle 2cm, biological rep1


title: lung_AIRmin_male_saline_mice19

description: no additional information

source_name: lung from AIRmin male treated with saline

value: saline


title: lung_AIRmax_male_urethane_mice2

description: no additional information

source_name: lung from AIRmax male treated with urethane


title: DNA packaging in human spermatozoal chromatin: Unfractionated (NF) & insoluble (44K4)

source_name: Unfractionated Spermatozoal DNA (NF)

treatment_protocol: Semen was washed free of seminal plasma by diluting the semen 1:1 with HEPES buffered HSOF and centrifuging for 10 minutes at 500 x g. Pellets were resuspended in HSOF and pelleted as before. This was repeated until the supernatants were clear. Pellets were resuspended in STE buffer (100mM NaCl, 10 mM Tris-Cl, pH 8.0, 1 mM EDTA) containing 0.2 mM phenylmethylsulphonylfluoride (PMSF) and re-pelleted to remove HSOF. Pellets were subsequently processed with sequential extraction in 10% (w/v) mixed CTAB (alkly-trimethylammonium bromide), which removes the flagella, including principal pieces, thus ensuring no contamination of the samples with non-genomic DNA followed by sequential incubation in 1% w/v CTAB in 10 mM Tris-Cl pH 8.0 containing 0.05% w/v digitonin; Tris buffered saline (TBS) containing 0.05% w/v digitonin, 10 mM Tris-Cl pH 8.0 containing 1mM EDTA, 0.05% w/v digitonin, EDTA-free protease inhibitor cocktail (Roche).

source_name: Spermatozoal DNA partitioned into a Salt Insoluble (SRDI) Fraction


title: Nipponbare_young panicle 2cm, biological rep5

organism: Oryza sativa Japonica Group

value: Nipponbare


title: Nipponbare_young panicle 2cm, biological rep4


title: Nipponbare_young panicle 2cm, biological rep3


title: DNA packaging in human spermatozoal chromatin: Unfractionated (NF) & Soluble (44K4)

description: Spermatozoal DNA from a healthy human donor was partitioned through a salt extraction to profile histone associated DNA relative to an unfractionated sample.

source_name: Spermatozoal DNA partitioned into a Salt Soluble (SRDS) Fraction


title: Blood CD4plus activated T cells vs pool 1 of 6

description: Blood CD4plus activated T cells vs pool


title: Gene expression profiling of SMA III patient (H) compared with age-matched normal muscle (Array B)

status: Public on Jun 08 2009

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

description: We performed microarray competitive hybridizations with RNA from muscle samples of single SMA III (Patient H) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).

hyb_protocol: Microarray hybridization was carried on overnight at 48°C by submerging microarrays closed in a sealed chamber (HybChamber, GeneMachines, San Carlos, CA, USA) in a high-precision water bath (W28 Grant, Cambridge, UK). Post-hybridization washing was performed according to the protocol suggested in the Amino Allyl kit.

scan_protocol: Fluorescence signals were detected by analyzing the microarrays in a Perkin-Elmer LITE dual confocal laser scanner guided by ScanArray Microarray Analysis Software, and raw microarray images were analyzed with QuantArray Analysis Software (GSI Lumonics, Ottawa, Canada).

data_processing: Intensity values were processed with the gene expression data analysis tool MIDAS (www.tigr.org/software/tm4/). Normalized values were converted to a logarithmic scale.

source_name: Normal skeletal muscle (Reference)

label_protocol: Total RNA, 1 μg, was retro-transcribed and labelled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to manufacturer's protocol.

extract_protocol: Total RNA from biopsies was purified following the standard Trizol standard protocol. The RNA 6000 LabChip kit (Agilent Technologies) was used for RNA quantification and quality control in conjunction with an Agilent Bioanalyzer 2001.

tag: Biopsy of quadriceps femoralis normal skeletal muscles.

source_name: SMAIII patient H (Test)

tag: Biopsy of SMA III patient (H) quadriceps femoralis skeletal muscles.


title: Nipponbare_young panicle 2cm, biological rep1


title: Bladder vs pool 1 of 6

description: Bladder vs pool

source_name: Bladder


title: Gene expression profiling of SMA III patient (H) compared with age-matched normal muscle (Array A)


title: Gene expression profiling of SMA III patient (F) compared with age-matched normal muscle (Array B)

description: We performed microarray competitive hybridizations with RNA from muscle samples of single SMA III (Patient E) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).

source_name: SMAIII patient F (Test)

tag: Biopsy of SMA III patient (F) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA III patient (E) compared with age-matched normal muscle (Array B)

source_name: SMAIII patient E (Test)

tag: Biopsy of SMA III patient (E) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA III patient (I) compared with age-matched normal muscle (Array A)

description: We performed microarray competitive hybridizations with RNA from muscle samples of single SMA III (Patient I) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).

source_name: SMAIII patient I (Test)

tag: Biopsy of SMA III patient (I) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA III patient (E) compared with age-matched normal muscle (Array A)


title: Gene expression profiling of SMA I patient (C) compared with age-matched normal muscle (Array B)

description: We performed microarray competitive hybridizations with RNA from muscle samples of single SMA I (Patient C) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).

source_name: SMAI patient C (Test)

tag: Biopsy of SMA I patient (C) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA III patient (G) compared with age-matched normal muscle (Array B)

source_name: SMAIII patient G (Test)

tag: Biopsy of SMA III patient (G) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA I patient (C) compared with age-matched normal muscle (Array A)


title: Gene expression profiling of SMA I patient (D) compared with age-matched normal muscle (Array A)

description: We performed microarray competitive hybridizations with RNA from muscle samples of single SMA I (Patient D) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).

source_name: SMAI patient D (Test)

tag: Biopsy of SMA I patient (D) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA I patient (B) compared with age-matched normal muscle (Array B)

description: We performed microarray competitive hybridizations with RNA from muscle samples of single SMA I (Patient B) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).

source_name: SMAI patient B (Test)

tag: Biopsy of SMA I patient (B) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA I patient (D) compared with age-matched normal muscle (Array B)


title: Gene expression profiling of SMA I patient (B) compared with age-matched normal muscle (Array A)


title: Gene expression profiling of SMA III patient (I) compared with age-matched normal muscle (Array B)


title: H4K12ac ChIP, biological replicate 0, chip1

description: For chip array, purified IP-probe (Qiaquick Purification Kit, Qiagen, Hilden, Germany) and 10 ng of input material (total chromatin) was prepared by adapting the protocol for whole genome amplification using Sigma GenomePlex WGA kit (http://www.sigmaldrich.com) as described in O’Green et al. {O'Geen, 2006 #170}. The initial random amplification step of the WGA protocol was omitted due to previous defragmentation of sperm chromatin after sonification. The required amount of DNA for microarray analysis (4 µg per sample) was generated using WGA Reamplifikation Kit (Sigma, Munich, Germany). Amplicons were applied to the HG18 human 5 kb promoter array from NimbleGen System (http://www.nimblegen.com).

source_name: DNA associated with histone H4 acetylated at lysine 12 (H4K12ac)

tag: cell type

value: spermatozoa

source_name: Total Unfractionated Chromatin


title: Gene expression profiling of SMA I patient (A) compared with age-matched normal muscle (Array B)

description: We performed microarray competitive hybridizations with RNA from muscle samples of single SMA I (Patient A) and age-matched muscle control. These samples were labeled and hybridized to muscle specific microarrays produced by our group (Human Array 2.0, GPL2011).

source_name: SMAI patient A (Test)

tag: Biopsy of SMA I patient (A) quadriceps femoralis skeletal muscles.


title: Gene expression profiling of SMA III patient (G) compared with age-matched normal muscle (Array A)


title: H4K12ac ChIP, biological replicate 1, chip1

tag: antibody


title: Gene expression profiling of SMA III patient (F) compared with age-matched normal muscle (Array A)


title: Seedling_BAP treated_rep1

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

description: Rice seedlings were kept in 50 micromolar solution of benzyl aminopurine (BAP) for 1h and 3h to serve as BAP-treated sample and equal amount was pooled before RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

data_processing: Signal intensity was calculated by GCOS1.4 under default parameters

label: Biotin

organism: Oryza sativa

source_name: 7-day-old light-grown rice seedlings

growth_protocol: Seedlings were grown on cotton saturated with reverse-osmosis water at 28 degree centigrade in a culture room with a daily photoperiodic cycle of 14h light and 10h dark

extract_protocol: TRIzol reagent

treatment_protocol: seedlings were kept in 50 micromolar solution of benzyl aminopurine (BAP) for 1h and 3h and pooled together in equal amount before RNA isolation

tag: Subspecies

value: indica

tag: Variety

tag: Tissue

value: light-grown seedlings

tag: Stage


title: Gene expression profiling of SMA I patient (A) compared with age-matched normal muscle (Array A)


title: Seedling_BAP treated_rep2


title: Seedling_IAA treated_rep2

description: Rice seedlings were kept in 50 micromolar solution of indole-3-acetic acid (IAA) for 1h and 3h to serve as IAA-treated sample and equal amount was pooled before RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

treatment_protocol: seedlings were kept in 50 micromolar solution of indole-3-acetic acid (IAA) for 1h and 3h and pooled together in equal amount before RNA isolation


title: Seedling_IAA treated_rep1


title: H4K12ac ChIP, biological replicate 2, chip1


title: Seedling_Control_rep1

description: Rice seedlings were mock-treated for 1h and 3h to serve as control and equal amount was pooled before RNA isolation. The high-quality total RNA (260/280 ratio between 1.9-2.1 and 260/230 ratio >2.0) was used for microarray analysis

treatment_protocol: seedlings were mock-treated with dimethyl sulfoxide (final concentration 0.1%) for 1h and 3h and pooled together in equal amount before RNA isolation


title: OneKD-HCT116_HpaII_Nim_rep3

description: DNMT1 defective cell line (reference is parental cell line HCT116)

hyb_protocol: Hybridization performed at Nimblegen (see R.R. Selzer et al., Genes Chromosomes Cancer, 2005)

scan_protocol: Image acquisition performed at Nimblegen (see R.R. Selzer et al., Genes Chromosomes Cancer, 2005)

data_processing: Signal intensity ratios are log2 transformed and normalized by the cubic spline method (C. Workman et al., Genome Biol., 2002)

source_name: OneKD

label_protocol: Labeling performed at Nimblegen (see R.R. Selzer et al., Genes Chromosomes Cancer, 2005)

extract_protocol: DNA was phenol-chloroform precipitated and digested to completion with methylation-sensitive restriction enzyme HpaII (New England Biolabs). After digestion, DNA was fractionated on 5% to 30% sucrose gradients by using a Beckman SW-40TI swing-out rotor as previously described (R. Tompa, et al., Curr. Biol., 2002). Fractions containing fragments smaller than 2.5 kb and greater than 80 bp as judged by gel electrophoresis were selected, pooled, and precipitated with isopropanol.

tag: Cell line

value: HCT116 colorectal cancer


title: HeLa cells treated for 6 h

city: Shanghai

first: Zhixiang

last: Zhang

address: Rd. Zuchongzhi

institute: SIMM

description: Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: The data were analyzed with GCOS software

source_name: HeLa cells

label_protocol: Standard Affymetrix protocol.

growth_protocol: HeLa cells were grown in RPMI1640 plus 10% fetal bovine serum as the supplier's instruction

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: HeLa cells treated with 5 mM MT7 for 0(control), 1.5(Time1), 3(Time2), 6(Time3) and 12(Time4) hours, respectively, were then washed three times with PBS and the total RNA was isolated and processed for Affymetrix U133A 2.0 hybridizations.

tag: agent

tag: time

value: 6 h


title: HeLa cells treated for 1.5 h

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.


title: HeLa cells treated for 12 h


title: OneKD-HCT116_HpaII_Nim_rep1


title: HeLa cells treated for 3 h

value: 3 h


title: 1984902_635

city: Boston

first: Mark

last: Pomerantz

state: MA

address: 44 Binney St.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: RNA-normalized signal intensity; a probe was considered positive in the cDNA array when its intensity was higher (> 1) than its genomic DNA probe value.

hyb_protocol: The Cy3- and Cy5-labeled samples were combined (5 ug each) in hybridization buffer, denatured, and hybridized to the custom 8q24 385K feature array using standard hybridization conditions for gene expression (NimbleGen Expression User Guide, Roche NimbleGen, Madison, WI).  Slides were then washed and dried using standard conditions per the Roche NimbleGen protocol.

scan_protocol: Slides were scanned with a GenePix 4000B Scanner. Initial pre-scannig was performed at PMT Gain = 500 and Power (%) = 100. After the pre-scan, the PMT was adjusted to avoid saturated spots.

data_processing: Initially, data generated from each group of microarray scans (cDNA and genomic DNA) were normalized separately. Quantile normalization of probe intensities was carried out using the Multi-Array quantile normalization module, part of the NMPP 1.01 package with the two-step normalization option as described by Wang and colleagues (Wang, X. et al. NMPP: a user-customized NimbleGen microarray data processing pipeline. Bioinformatics 2006 22, 2955-7). First, replicate slides within each set were normalized, followed by a global normalization to adjust both sets to an average baseline.

source_name: histologically normal human colon tissue obtained from surgery for adenocarcinoma of the colon

label_protocol: RNA was converted to double-stranded cDNA (SuperScript Double Strand cDNA Synthesis Kit, Invitrogen USA, Carlsbad, CA) with oligo-dT primer (Promega USA) according to the manufacturer’s protocol. Resultant ds-cDNA was labeled using cy3-tagged random 9mers and Klenow fragment for 2h at 37°C, prior to denaturation and hybridization to a microarray.  Genomic DNA was labeled using cy5-tagged random 9mers.

extract_protocol: From the frozen tissue, 5 micron thick cryosections were cut, mounted on glass slides, and stained with Hematoxylin and Eosin.  Sections were reviewed by a pathologist to confirm the diagnoses of prostatic adenocarcinoma and benign tissue.  Areas of tumor were selected where >60% of cells consisted of tumor cells.  Areas of benign tissue were selected where >50% of cells consisted of non-neoplastic epithelium.  From these areas, two 2 mm punch biopsy cores of frozen tissue were removed from the frozen block and processed for DNA and RNA extraction using a modified Qiagen Allprep DNA/RNA protocol.  Briefly, tissue was homogenized in Qiagen buffer RLT with b-mercaptoethanol.  Lysates were passed through Allprep DNA columns for purification of DNA.  All washes and elution of DNA from the Allprep column were performed per manufacturer’s protocol.  Initial flow through from the column was mixed with 3 volumes of Trizol LS reagent (Invitrogen) and processed per manufacturer’s protocol to yield total RNA.

tag: individual

tag: tissue

value: colon


title: HeLa cells untreated

value: untreated

value: control


title: 1967402_635


title: Endogenous small RNAs from rice - Run2

type: other

city: Davis

first: Venkatesan

last: Sundaresan

address: One Shields Ave

department: Plant Biology

institute: University of California Davis

description: 18-34nt small RNAs

data_processing: 5' and 3' adapter sequences were identified by alignment, and RNA sequences between these were extracted. Sometimes more than one RNA sequence could be obtained from a single 100nt sequence read.

molecule: other

extract_protocol: Small RNA libraries were constructed using a method that requires the 5’ end of the small RNAs to be phosphorylated  [Lau, N.C., Lim, L.P., Weinstein, E.G., Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science, 294, 858–862].  Total cellular RNA was fractionated on a 15% acrylamide gel run in 8M urea and 1X TBE, and the region of the gel containing 16 to 28 nt RNAs was excised.  The small RNAs were eluted in 0.3 M NaCl and ethanol precipitated with 2.8 volumes of ethanol.     Mixed tissues from unstressed plants. Library prepared from equal amounts of adult root, adult stem and inflorescence from unstressed plants. Amplified with Standard primers (5' ATCGTAGGCACCTGAAA - smRNA - CTGTAGGCACCATCAAT 3').     Seedlings stressed by cold, salt desiccation, heat and dark. Tissues were mixed in a 2:2:1:1:1:1 ratio.  Amplified with A primers (5' AGCTATCGTAGGCACCTGAAA - smRNA - CTGTAGGCACCATCAATACTG 3').     Kinase library. RNA was isolated from tissues used in 'Adult whole plant' (~30%), 'Stressed' (~25%), from unstressed seedlings of various ages (~15%) from 30 and 60 day leaves (20%) and from immature inflorescence (~10%).  RNA isolated from tissues from unstressed plants were treated with polynucleotide kinase before second ligation.  This eliminates the dependence of a 5` phosphate as for all the other libraries.  Amplified with B primers (5' CAGTATCGTAGGCACCTGAAA - smRNA - CTGTAGGCACCATCAATAGCT 3').  The small RNAs were ligated in a reaction containing 20 uM 3´-adaptor, 50 mM Hepes pH 8.3, 5 mM MgCl2, 3 mM DTT, 5 ug/ ml BSA and 8% glycerol for 2 hr.  The ligated small RNAs were gel isolated as described above and ligated to an RNA 5’ adaptor and subsequently gel isolated.  The resulting RNAs were reversed transcribed and amplified by PCR.  The resulting DNAs were gel purified and sequenced by 454 Life Sciences.

value: mixed


title: 1964902_635


title: 1967402_532


title: U1A pulldown experiment

status: Public on Jun 07 2009

city: San Francisco

first: Esther

middle: T

last: Chan

state: California

address: 1500 Owens Street, Suite 500

institute: Celgene Corporation

description: Pulldown RNA sample labeled with Cy5 from non-organism specfic custom-designed RNA pool versus control RNA sample labeled with Cy3 from non-organism specfic custom-designed RNA pool.

hyb_protocol: Hybridizations were carried out for 20 hours at 42°C and washed for 30 seconds in 6 x SSPE, 0.005% sarcosine and 30 seconds in 0.06x SSPE in a HS4800 Pro Hybridization Station (Tecan).

scan_protocol: Arrays were scanned on an Agilent microarray scanner at 5 micron resolution. Images were quantified using Imagene 3.0.

data_processing:
Data was normalized using variance stabilization, each channel was adjusted with an offset and multiplicative constant and spots with low signal intensity in either channel were removed. We subtracted from each spot ratio the median value (among non-flagged spots) across all ten experiments.
NOTE: The "N" in the headers of the raw data file (linked below as a supplementary file) stands for "Normalized". The image quantification software (Imagene) automatically places the data under those headings, regardless of whether we ask it to normalize the data or not. In our case, we did not ask the program to normalize the data, so the data under the headings should be interpreted without the "N" (i.e. just as the Signal Mean, rather than a Normalized Signal Mean).

organism: synthetic construct

source_name: Pool control sample labeled with Cy3

label_protocol: Manufacturer's recommended protocol (Kreatech)

extract_protocol: An RNA pool is synthesized from the array and subsequently stripped from the array and PCR-amplified to create a dsDNA pool. This pool is then used as a template for in vitro T7 RNA polymerase-mediated RNA transcription to generate an RNA pool control.

tag: protocol

source_name: Pulldown RNA sample labeled with Cy5

extract_protocol: An RNA pool is synthesized from the array and subsequently stripped from the array and PCR-amplified to create a dsDNA pool. This pool is then used as a template for in vitro T7 RNA polymerase-mediated RNA transcription to generate an RNA pool used for pull-down experiments using GST-tagged RNA binding proteins.

value: GST-tagged RNA binding protein pulldown


title: OneKD-HCT116_HpaII_Nim_rep2


title: 1984902_532


title: Seedling_Control_rep2


title: SLM2 pulldown experiment


title: YB1 pulldown experiment


title: RBM4 pulldown experiment


title: 1944902_635


title: Endogenous small RNAs from rice - Run1

description: 18-34nt small RNAs

extract_protocol: Small RNA libraries were constructed using a method that requires the 5’ end of the small RNAs to be phosphorylated  [Lau, N.C., Lim, L.P., Weinstein, E.G., Bartel, D.P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science, 294, 858–862].  Total cellular RNA was fractionated on a 15% acrylamide gel run in 8M urea and 1X TBE, and the region of the gel containing 16 to 28 nt RNAs was excised.  The small RNAs were eluted in 0.3 M NaCl and ethanol precipitated with 2.8 volumes of ethanol.  A small RNA library was generated from whole cell RNA isolated from inflorescence, 30 and 60 day leaves, 10 and 25 day seedlings and from seedling polysomes using Bartel primers (5' ATCGTAGGCACCTGAAA - smRNA - CTGTAGGCACCATCAAT 3').  This was combined with a library derived from whole cell RNA isolated from 30 and 60 day leaves and 10 and 25 day seedlings using Bartel A primers (5' AGCTATCGTAGGCACCTGAAA - smRNA - CTGTAGGCACCATCAATACTG 3').  The small RNAs were ligated in a reaction containing 20 uM 3´-adaptor, 50 mM Hepes pH 8.3, 5 mM MgCl2, 3 mM DTT, 5 ug/ ml BSA and 8% glycerol for 2 hr.  The ligated small RNAs were gel isolated as described above and ligated to an RNA 5’ adaptor and subsequently gel isolated.  The resulting RNAs were reversed transcribed and amplified by PCR.  The resulting DNAs were gel purified and sequenced by 454 Life Sciences.


title: SF2/ASF pulldown experiment


title: Vts1 pulldown experiment


title: Fusip1 pulldown experiment


title: HuR pulldown experiment


title: H3Core_LF2_4d-atRA

status: Public on Jun 06 2009

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: ChIP-chip LF2 ES cells

hyb_protocol: The labeled ChIP DNA (Cy5) and genomic DNA (Cy3) was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized simultaniously with the Cy5 and Cy3 labeled material in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction; Raw data was used for visualisations. Each feature on the array has a corresponding scaled log2-ratio. This is the ratio of the input signals for the experimental and test samples that were co-hybridized to the array. The log2-ratio is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value.

source_name: H3Core ChIP DNA from LF2 4d atRA treated ES cells

label_protocol: 1 µg ChIP DNA (or cDNA) was directly labeled by Klenow (New England Biolabs) random priming with Cy5 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). 1 µg genomic DNA was labeled similarly using Cy3 and used as Input.

growth_protocol: ES cells grown on gelatin coated plates with LIF and ES grade serum

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode). It was immunoprecipitated using the indicated antisera. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input by phenol extraction and ethanol precipitation. The ChIP material was amplified using two rounds of lineair T7 amplification. All further details were performed as indicated by http://www.nimblegen.com/products/lit/lit.html

treatment_protocol: treated for 4 days with atRA

tag: gender

value: female

tag: strain

source_name: Input genomic DNA from LF2 4d atRA treated ES cells

tag: reference

value: input genomic DNA


title: H3Core_E14_undiff

description: ChIP-chip E14 ES cells

source_name: H3Core ChIP DNA from E14 undifferentiated ES cells

treatment_protocol: undifferentiated cells

value: male

source_name: Input genomic DNA from E14 undifferentiated ES cells


title: 1944902_532


title: PTB pulldown experiment


title: H3Core_LF2_10d-EB

description: ChIP-chip LF2 ES cells

source_name: H3Core ChIP DNA from LF2 10d EB ES cells

treatment_protocol: grown to embryoid bodies for 10 days

source_name: Input genomic DNA from LF2 10d EB ES cells


title: 1964902_532


title: H3Core_LF2_undiff

description: ChIP-chip LF2 ES cells

source_name: H3Core ChIP DNA from LF2 undifferentiated ES cells

source_name: Input genomic DNA from LF2 undifferentiated ES cells


title: H3K9me2_E14_10d-EB

description: ChIP-chip E14 ES cells

source_name: H3K9me2 ChIP DNA from E14 10d EB ES cells

source_name: Input genomic DNA from E14 10d EB ES cells


title: GST pulldown experiment

value: GST protein pulldown


title: H3K9me2_E14_4d-atRA

description: ChIP-chip E14 ES cells

source_name: H3K9me2 ChIP DNA from E14 4d atRA treated ES cells

source_name: Input genomic DNA from E14 4d atRA treated ES cells


title: H3K9me2_LF2_undiff

description: ChIP-chip LF2 ES cells

source_name: H3K9me2 ChIP DNA from LF2 undifferentiated ES cells


title: H3Core_E14_10d-EB

description: ChIP-chip E14 ES cells

source_name: H3Core ChIP DNA from E14 10d EB ES cells


title: H3K9me2_LF2_4d-atRA

description: ChIP-chip LF2 ES cells

source_name: H3K9me2 ChIP DNA from LF2 4d atRA treated ES cells


title: H3Core_E14_4d-atRA

description: ChIP-chip E14 ES cells

source_name: H3Core ChIP DNA from E14 4d atRA treated ES cells


title: 1945002_532

source_name: histologically normal human colon tissue obtained from surgery for adenocarcinoma of the colon