title: Strain_ypT20_vs_N2

value: hermaphrodite

value: whole animals

value: wild-type


title: JFP41_induced_20.0min_rep1

status: Public on Jan 21 2011

type: RNA

city: Richmond

first: Alejandro

last: Rodriguez

state: VA

address: 521 North 11th Street

department: Dentistry

country: USA

institute: Virginia Commonwealth University

description: Biological replicate 1 of 3. Induced cells 20 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

hyb_protocol: Slides were pretreated for 2 – 3 h at 42ºC in 50µl of prehybridization solution (5x SSC, 0.1% SDS, 1% BSA). Slides were maintained in hybridization cassettes (ArrayIt®, Sunnyvale, CA) throughout the incubation phase. The slides were then washed three times with MilliQ water in a High Throughput Wash Station (ArrayIt®) followed with one wash in isopropanol and dried using a mini-slide centrifuge (Labnet International, Edison, NJ). Dried probes were then resuspended in 50µl hybridization buffer (40% formamide, 5x SSC, 0.1% SDS, 0.6µg/µl salmon sperm DNA). The solution was heated at 95ºC for 10 min while vortexing intermittently and then transferred onto pretreated slides under a LifterSlip™ (Erie Scientific, Portsmouth, NH). The probes were allowed to hybridize for 16 – 20 h at 42ºC in a hybridization cassette. Humidity was maintained with the addition of 15µl of unused hybridization buffer in each well. Slides were washed twice in 2x SSC, 0.1% SDS, 0.1 mM DTT at 55ºC for 10 min, twice at room temperature in 0.1x SSC, 0.1% SDS, 0.1 mM DTT for 5 min, and twice at room temperature in 0.1x SSC, 0.1 mM DTT for 5 min. The slides were then dipped in MilliQ water before being dried in a mini-slide centrifuge. Microarrays were immediately scanned in an Axon GenePix® 4200 scanner (MDS Analytical Technologies).

scan_protocol: Scanned on an Axon Genepix 4200 Scanner Images were quantified using Genepix Pro software (version 5.1)

data_processing: Median normalization of the intensity distributions obtained from log2 of processed Red signal/processed Green signal. Data processed through the Ramhorn Array Database

molecule: total RNA

organism: Streptococcus sanguinis

source_name: 20 min. post-competence induction

label_protocol: 2µg total RNA was annealed to 6µg random hexamers (Invitrogen, Carlsbad, CA) in a total volume of 18.5µl and incubated at 70ºC for 10 min. Samples were snap frozen in ethanol at -80ºC for 30s before addition of 6µl of 5x First Strand Buffer (250 mM Tris-Cl, pH 8.3, 375 mM KCl, 15 mM MgCl2), 3µl 0.1M DTT, and 0.6µl of dNTP solution (25 mM each dATP, dCTP, and dGTP, 15 mM dTTP (Invitrogen) and 10 mM amino allyl-dUTP (Sigma)). The solution was then incubated overnight at 42ºC with 300 U of Superscript III (Invitrogen). The RNA template was then hydrolyzed via the addition of 10µl 0.5 M EDTA and 10µl 1 M NaOH and incubation at 65ºC for 15 min. The mixture was neutralized with 25µl 1 M Tris pH 7.0 and 10µl 3 M NaOAc, and purified using MiniElute® PCR Purification Kit (Qiagen) replacing the Tris buffers with phosphate buffers (5 mM KPO4, pH 8, 80% EtOH) and (4 mM KPO4, pH 8.5) for the wash and elution steps, respectively. The reaction was then dried in a Speed-Vac centrifuge before being resuspended in 4.5µl 0.1 M Na2HCO3, pH 9.3 and 4.5µl of the ester dye (Cy3 or Cy5 (Amersham) for the control and experimental samples, respectively). The coupling reaction proceeded for 1.5 - 2 h at room temperature in the dark before being stopped via the addition of 35µl 100 mM NaOAc pH 5.2 and then purified over Qiagen MiniElute PCR purification columns per the manufacturer's protocol and supplied buffers.

growth_protocol: Overnight cultures of JFP41 grown in Todd Hewitt (TH) broth (Bacto, Sparks, MD) supplemented with 2.5% (v/v) horse serum (TH-HS) (Invitrogen, Grand Island, NY) at 37ºC were diluted 1:200 in pre-warmed TH-HS (7.6). The culture was allowed to incubate until the optical density at 660 nm reached ~0.07.

extract_protocol: Twenty ml of culture was removed and mixed with an equal volume of hot acid phenol containing 0.1 M citrate buffer (pH 4.3, Sigma) and 0.1% (v/v) sodium dodecyl sulfate (SDS, Ambion, Austin, TX). Samples were incubated in a boiling water bath for 10 min, cooled in an ice bath and transferred to Phase Lock Gel™ (PLG) tubes (5 Prime Inc., Gaithersburg, MD). After centrifugation at 1500 x g for 5 min, the supernatant was removed and extracted with an equal volume of acid phenol:chloroform  (1:1), then chloroform. RNA was precipitated from the supernatant by NaOAc/isopropanol precipitation, followed by centrifugation. The resulting RNA pellet was washed with 70% ethanol, dried via tube inversion, and dissolved in 100µl DEPC-treated water. Samples were then treated with DNase I and purified over RNeasy columns (Qiagen, Valencia, CA) according to protocols supplied by the manufacturer.

treatment_protocol: Once an optical density at 660 nm reached ~0.07, cells were treated with Streptococcus sanguinis synthetic CSP (NH2-DLRGVPNPWGWIFGR-COOH) at a concentration of 220 ng/ml and incubated for the appropriate time.

tag: strain

source_name: uninduced cells


title: C38_0_rep_1

city: London

first: Parmjit

last: Jat

address: Queen Square

department: Institute of Neurology

country: United Kingdom

institute: UCL

description: Gene expression data from HMF3A cells grown for 7 days at 38oC

hyb_protocol: According to Affymetrix

scan_protocol: According to Affymetrix

data_processing: The data were analyzed with Bioconductor R packages affy and limma using RMA as normalisation method.

label: biotin

organism: Homo sapiens

source_name: HMF3A cells at 38oC for 7 days

label_protocol: Invitrogen + Enzo

growth_protocol: HMF3A cells and derivatives thereof were maintained in DMEM supplemented with 10% heat inactivated fetal bovine serum, 2mM glutamine, 100 units per ml penicillin and 100 micrograms per ml streptomcyin and cultured in atmosphere of 5% CO2 and 20% O2.

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

treatment_protocol: HMF3A cells were cultured at 34°C ±0.5°C and temperature shift experiments performed at 38°C ±0.5°C. Cells were incubated at 38°C ±0.5°C for 7 days before RNA was extracted.  HMF3A cells were serum starved by culturing in DMEM supplemented with 0.25% heat inactivated fetal bovine serum, 2mM glutamine, 100 units per ml penicillin and 100 micrograms per ml streptomycin.  Cultures were fed with fresh medium the day prior to RNA extraction and were harvested at no greater than 80% confluence.

tag: cell line

value: Human mammary fibroblasts (HMF3A)

tag: treatment

value: 7 days at 38oC


title: JFP41_induced_15.0min_rep1

description: Biological replicate 1 of 3. Induced cells 15 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 15 min. post-competence induction


title: C33_5_rep_2

description: Gene expression data from HMF3A cells grown at 33.5oC

source_name: HMF3A cells at 33.5oC


title: pLPCX_38_0C_7d_rep_2

description: pLPCX (empty vector for introducing genes that can overcome the growth arrest) grown for 7 days at 38oC

source_name: pLPCX vector at 38oC for 7 days


title: JFP41_induced_12.5min_rep2

description: Biological replicate 2 of 3. Induced cells 12.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 12.5 min. post-competence induction


title: JFP41_induced_10.0min_rep2

description: Biological replicate 2 of 3. Induced cells 10 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 10 min. post-competence induction


title: JFP41_induced_12.5min_rep3

description: Biological replicate 3 of 3. Induced cells 12.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_7.5min_rep3

description: Biological replicate 3 of 3. Induced cells 7.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 7.5 min. post-competence induction


title: JFP41_induced_10.0min_rep3

description: Biological replicate 3 of 3. Induced cells 10 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_12.5min_rep1

description: Biological replicate 1 of 3. Induced cells 12.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_10.0min_rep1

description: Biological replicate 1 of 3. Induced cells 10 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_7.5min_rep2

description: Biological replicate 2 of 3. Induced cells 7.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_5.0min_rep2

description: Biological replicate 2 of 3. Induced cells 5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 5.0 min. post-competence induction


title: JFP41_induced_7.5min_rep1

description: Biological replicate 1 of 3. Induced cells 7.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_5.0min_rep1

description: Biological replicate 1 of 3. Induced cells 5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_2.5min_rep3

description: Biological replicate 3 of 3. Induced cells 2.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.

source_name: 2.5 min. post-competence induction


title: JFP41_induced_2.5min_rep2

description: Biological replicate 2 of 3. Induced cells 2.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_uninduced_rep3

description: Biological replicate 3 of 3. Uninduced JFP41 cells. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_2.5min_rep1

description: Biological replicate 1 of 3. Induced cells 2.5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_induced_5.0min_rep3

description: Biological replicate 3 of 3. Induced cells 5 min. after competence induction. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_uninduced_rep2

description: Biological replicate 2 of 3. Uninduced JFP41 cells. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: JFP41_uninduced_rep1

description: Biological replicate 1 of 3. Uninduced JFP41 cells. An overlap extension PCR technique was used to fuse the start codon of the comC gene to the second codon of comD, thus deleting the comC gene and intervening sequence. The resulting mutant can not naturally create a competence stimulating peptide (CSP) and is thus unable to achieve competence without the addition of exogenous CSP.


title: Extraction method 2 Poole_Ex2

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

description: RNA extracted using the Ex2 extraction method

hyb_protocol: Hybridisation was carried out as per the manufacturer's instructions as described in Affymetrix GeneChip Expression analysis technical manual (Affymetrix, www.affymetrix.com)

scan_protocol: GeneChip arrays were scanned with an Affymetrix G2500A GeneArray scanner, as described in the Affymetrix GeneChip Expression Analysis Technical Manual.

data_processing: Following scanning, non-scaled RNA signal intensity (CEL) files were generated using the GeneChip operating system (GCOS version 5.0; Affymetrix) as previously described. Robust Microarray Analysis (RMA) expression values were computed in Bioconductor using the language R.

organism: Solanum lycopersicum

source_name: Extraction method 2 Poole_Ex2

label_protocol: GeneChip arrays were stained with Streptavidin-Phycoerythrin solution as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com).

growth_protocol: Tomato plants were grown in M3 compost under glasshouse conditions at the University of Nottingham, Sutton Bonington Campus (UK, 52o47'N; 1o11'E).   Mean day-time temperatures were maintained at 19°C, whilst night-time temperatures were maintained at 17°C. Side shoots were removed from the plants which were maintained in an upright form using crop supports.

extract_protocol: Approximately 10-12 g was weighed and extracted with 2 ml/g i.e. 20-24 ml of Ex2 buffer ((0.2 M Tris-HCl pH 8.5, 0.2 M sucrose, 30 mM MgCL2, 0.6 M KCl) to which polyvinylpolypyrrolidone (1%) and  beta-mercaptoethanol (0.31% v/v) had been added immediately before use) per g of tissue. Cell debris was removed by centrifugation at 10000 x g for 15 minutes. The pellet was retained for re-extraction using method Ex2. The supernatant was filtered through two layers of muslin, mixed with 0.1 vol 10% SDS and an equal volume of phenol: chloroform. The sample was vortexed vigorously for 45 seconds and centrifuged at 5000 x g for 5 minutes before the aqueous phase was transferred to a fresh tube. The aqueous phase was precipitated overnight at -20oC with an equal volume of isoproanol and 0.1 volumes of 3 M sodium acetate (pH 5.6). Precipitated nucleic acids were collected by centrifugation at 10000 X g for 10 minutes at 4oC. The supernatant was removed and the pellet was suspended again in 500µl of sterile distilled water, which was transferred to a sterile 1.5ml Eppendorf tube and precipitated material was removed by a brief, 3 second, pulse spin in a bench microcentrifuge. RNA was precipitated from the remaining solution by the addition of an equal volume of 8M lithium chloride followed by overnight storage at -20oC. RNA was recovered by centrifugation in a microcentrifuge at 16000 X g for 15 minutes and the supernatant was discarded. The RNA pellet was suspended again in 450µl of sterile distilled water and precipitated material was removed by centrifugation for 2 minutes. The supernatant was precipitated over night at -20oC with three volumes of ethanol and 0.1 volumes of 3 M sodium acetate (pH 5.6). RNA was recovered by centrifugation in a microcentrifuge at 16000 X g for 10 minutes. The pellet was washed with 1 ml of 80% ethanol, dried under vacuum and the RNA suspended in 60 µl of sterile distilled water.

value: Ailsa Craig Solanum lycopersicum

tag: tissue

value: Tomato pericarp


title: Extraction method 2 pellet Poole_Ex2_Pellet

institute: Nottingham Arabidopsis Stock Centre (NASC)

description: 'Cell debris' pellet extracted using the Ex2 extraction method


title: Extraction method 1 Poole_Ex1

description: RNA extracted using the Ex1 extraction method

hyb_protocol: Hybridisation was carried out as per the manufacturer's instructions as described in the Affymetrix GeneChip Expression analysis technical manual (Affymetrix, www.affymetrix.com)

data_processing: Following scanning, non-scaled RNA signal intensity (CEL) files were generated using the GeneChip operating system (GCOS version 5.0; Affymetrix). Robust Microarray Analysis (RMA) expression values were computed in Bioconductor using the language R.

source_name: Extraction method 1 Poole_Ex1

extract_protocol: Approximately 10-12 g was weighed and extracted with 1 ml/g i.e. 10-12 ml of Ex1 buffer (1% Naphthalendisulfonic acid disodium salt [Merck Chemicals], 6% 4-Aminosalicylic acid [Sigma] and 5% (500 g of phenol and 0.5 g 8-hydroxyquinoline in 200 ml water with 70 ml m-cresol)).  An equal volume of phenol/chloroform was added and the mixture vortexed vigorously for 45 seconds. After centrifugation at 10000 x g for 15 minutes, the upper aqueous phase was transferred to a fresh tube.The aqueous phase was precipitated overnight at -20oC with an equal volume of isoproanol and 0.1 volumes of 3 M sodium acetate (pH 5.6). Precipitated nucleic acids were collected by centrifugation at 10000 X g for 10 minutes at 4oC. The supernatant was removed and the pellet was suspended again in 500µl of sterile distilled water, which was transferred to a sterile 1.5ml Eppendorf tube and precipitated material was removed by a brief, 3 second, pulse spin in a bench microcentrifuge. RNA was precipitated from the remaining solution by the addition of an equal volume of 8M lithium chloride followed by overnight storage at -20oC. RNA was recovered by centrifugation in a microcentrifuge at 16000 X g for 15 minutes and the supernatant was discarded. The RNA pellet was suspended again in 450µl of sterile distilled water and precipitated material was removed by centrifugation for 2 minutes. The supernatant was precipitated over night at -20oC with three volumes of ethanol and 0.1 volumes of 3 M sodium acetate (pH 5.6). RNA was recovered by centrifugation in a microcentrifuge at 16000 X g for 10 minutes. The pellet was washed with 1 ml of 80% ethanol, dried under vacuum and the RNA suspended in 60 µl of sterile distilled water.


title: 20min_male_rep5, R GCRMA

city: College Station

first: Ginger

last: Carney

state: TX

address: 3258 TAMU

department: Biology

institute: Texas A&M University

description:
HMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol using an Affymetrix GCS 3000 7G scanner.

data_processing: All 15 chips were analyzed simultaneously by 4 platforms (5 algorithms): dCHIP, GCOS, Bioconductor, GeneSpring GX 7.3.1. dChip uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM and PM procedures under default parameters. Expression values were also computed using the recommended settings in GCOS version 1.2. All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0). We also utilized the GC-RMA model-based algorithm in the R-language platform. Bioconductor provided the open source GCRMA and associated packages. In addition, we used the GCRMA model-based algorithm in GeneSpring GX 7.3.1 (Agilent Technologies). Default normalization was the raw intensity value for each probe set on a chip divided by the overall median intensity value for that chip. This “pre-normalized” value was then divided by the median “pre-normalized” value for that specific probe set across all 15 chips in the experiment.

organism: Drosophila melanogaster

source_name: 20min_male head

label_protocol: Standard Affymetrix protocol.

growth_protocol: Stocks were maintained on cornmeal/sugar media at 25oC.

treatment_protocol: Virgin males were raised in groups of 20 or fewer flies at 25oC. On day 4, they were transferred to individual vials. On day 5, they were exposed to a cauterized virgin female fly and observed for 20 min.

value: isogenized Canton-S

tag: gender

value: male

value: head

tag: age

value: 5 days

value: exposure to a cauterized virgin female fly

tag: treatment time

value: 20 minutes


title: 20min_male_rep4, R GCRMA

description:
FMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM19141_Treat1 cDNA

city: Montreal

first: Tomi

middle: Markku

last: Pastinen

state: Quebec

address: 740, Dr. Penfield Avenue

country: Canada

institute: McGill University and Génome Québec Innovation Centre

description:
duplicate #1 treated with 5uM AZA
set9

hyb_protocol: according to manufacturer's instructions

data_processing: Using GenomeStudio from Illumina

label: Cy3 and Cy5

growth_protocol: The LCLs were grown in T75 flasks in 1X RPMI 1640 Media (invitrogen, Burlington, ON), With 2 mM L-glutamine, 15% fetal bovine serum and 1% penicillin/streptomycin at 37°C with 5% CO2. The Fibroblast primary cell lines were grown in medium containing a-MEM (SigmaAldrich) supplemented with 2 mmol/l L-Glutamine, 100 U/mL penicillin, 100 mg/ml streptomycin, and 10% fetal bovine serum (SigmaAldrich) at 37°C with 5% CO2. At 70%-80% confluence, the cells were harvested.

extract_protocol: total RNA was extracted from cell lysates resuspended in 600 mL RLT lysis buffer using the Rneasy Mini Kit (Qiagen). DNA was extracted from cell lysates resuspended in 200 mL PBS using the GenElute DNA Miniprep Kit (SigmaAldrich).

treatment_protocol: Two cell lines were treated with 1, 5, and 10uM of 5-azadeoxycytidine every 24 hours for three days. A third cell line was treated with 10uM for 5 and 10 days.

value: lymphoblasts

tag: population

value: CEU


title: GM12005 gDNA

type: genomic

description:
pedigree 1420 maternal grandfather
set2

scan_protocol: according to manufacturer's instructions

molecule: genomic DNA


title: GM02640 gDNA

description:
Trio 9 father
set8

label_protocol: according to manufacturer's instructions


title: GM12003 cDNA

description:
pedigree 1420 paternal grandfather
set2


title: GM19141_Treat2 cDNA

description:
duplicate #2 treated with 5uM AZA
set9


title: GM12003 gDNA

description:
pedigree 1420 paternal grandfather
set2


title: GM12005 cDNA

description:
pedigree 1420 maternal grandfather
set2


title: GM12006 gDNA

description:
pedigree 1420 maternal grandmother
set2

value: female


title: GM19238 cDNA

description:
Trio Y117 mother
set9

value: YRI


title: GM19099_2 cDNA

description:
duplicate #2 untreated
set9


title: GM19239 gDNA

description:
Trio Y117 father
set9


title: GM19141_1 gDNA

description:
duplicate #1 untreated
set9


title: GM12004 gDNA

description:
pedigree 1420 paternal grandmother
set2


title: GM12006 cDNA

description:
pedigree 1420 maternal grandmother
set2


title: 20min_male_rep4, GeneSpring GCRMA


title: GM19099_Treat1 cDNA

description:
duplicate #1 treated with 5uM AZA
set9


title: GM01391 cDNA

description:
Trio 6 daughter
set7


title: GM19099_Treat2 cDNA

description:
duplicate #2 treated with 5uM AZA
set9


title: GM19099_1 gDNA

description:
duplicate #1 untreated
set9


title: 20min_male_rep3, GeneSpring GCRMA

description:
EMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM19141_2 gDNA

description:
duplicate #2 untreated
set9


title: GM02640 cDNA

description:
Trio 9 father
set8


title: 20min_male_rep5, GeneSpring GCRMA


title: 20min_male_rep1, GeneSpring GCRMA

description:
AMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 20min_control_rep5, GeneSpring GCRMA

description:
HMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

source_name: 20min_male head_control

value: exposure to no female fly


title: 20min_male_rep2, GeneSpring GCRMA

description:
BMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 20min_control_rep4, GeneSpring GCRMA

description:
FMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM19141_1 cDNA

description:
duplicate #1 untreated
set9


title: 20min_control_rep3, GeneSpring GCRMA

description:
DMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM19099_1 cDNA

description:
duplicate #1 untreated
set9


title: GM19239 cDNA

description:
Trio Y117 father
set9


title: GM02639 gDNA

description:
Trio 9 son
set6


title: GM12004 cDNA

description:
pedigree 1420 paternal grandmother
set2


title: GM01391 gDNA

description:
Trio 6 daughter
set7


title: GM02639 cDNA

description:
Trio 9 son
set6


title: GM19238 gDNA

description:
Trio Y117 mother
set9


title: GM19141_2 cDNA

description:
duplicate #2 untreated
set9


title: 20min_control_rep2, GeneSpring GCRMA

description:
CMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 20min_courtship_rep5, GeneSpring GCRMA

description:
JMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

source_name: 20min_male head_courtship


title: 20min_control_rep1, GeneSpring GCRMA

description:
AMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 20min_courtship_rep4, GeneSpring GCRMA

description:
HMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 20min_courtship_rep2, GeneSpring GCRMA

description:
CMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM02314 cDNA

description:
Trio 7 daughter
set6


title: GM00290 gDNA

description:
Trio 5 mother
set6


title: 20min_courtship_rep1, GeneSpring GCRMA

description:
AMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM19099_2 gDNA

description:
duplicate #2 untreated
set9


title: GM00519 gDNA

description:
Trio 1 daughter
set6


title: 20min_courtship_rep3, GeneSpring GCRMA

description:
DMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM02314 gDNA

description:
Trio 7 daughter
set6


title: GM00935 gDNA

description:
Trio 1 mother
set6


title: GM00519 cDNA

description:
Trio 1 daughter
set6


title: GM00290 cDNA

description:
Trio 5 mother
set6


title: 20min_male_rep3, R GCRMA


title: GM00520 cDNA

description:
Trio 1 father
set6


title: 20min_male_rep2, R GCRMA


title: GM12892_untreated_methylcollector gDNA

description:
untreated_methylcollector
set6


title: GM12892_untreated_fragmented gDNA

description:
untreated_fragmented
set6


title: GM12892_treated_fragmented gDNA

description:
treated_fragmented
set6


title: GM00520 gDNA

description:
Trio 1 father
set6


title: GM02641 cDNA

description:
Trio 9 mother
set5


title: WG2844 gDNA

description:
Trio 4 father
set5


title: 20min_male_rep1, R GCRMA


title: GM02316 gDNA

description:
Trio 7 father
set5


title: GM01392 gDNA

description:
Trio 6 mother
set5


title: GM12892_treated_methylcollector gDNA

description:
treated_methylcollector
set6


title: GM12892_T10_1 cDNA

description:
Duplicate #1 Treated with 10uM AZA for 10 days
set5


title: GM12892_T5_1 cDNA

description:
Duplicate #1 Treated with 10uM AZA for 5 days
set5


title: 20min_control_rep3, R GCRMA


title: WG2844 cDNA

description:
Trio 4 father
set5


title: GM01392 cDNA

description:
Trio 6 mother
set5


title: 20min_control_rep2, R GCRMA


title: 20min_control_rep4, R GCRMA


title: GM02316 cDNA

description:
Trio 7 father
set5


title: GM12892_1 cDNA

description:
Duplicate #1 untreated
set5


title: GM12892_T10_2 cDNA


title: GM12892_T5_2 cDNA


title: 20min_courtship_rep5, R GCRMA


title: 20min_control_rep5, R GCRMA


title: 20min_courtship_rep4, R GCRMA


title: GM00935 cDNA

description:
Trio 1 mother
set6


title: 20min_courtship_rep3, R GCRMA


title: GM12892_2 cDNA

description:
Duplicate #2 untreated
set5


title: 20min_courtship_rep2, R GCRMA


title: GM12892_2 gDNA

description:
Duplicate #2 untreated
set5


title: 20min_control_rep1, R GCRMA


title: 20min_courtship_rep1, R GCRMA


title: GM02641 gDNA

description:
Trio 9 mother
set5


title: GM12892_1 gDNA

description:
Duplicate #1 untreated
set5


title: WG2843 cDNA

description:
Trio 4 mother
set4


title: 20min_male_rep5, MAS5

description:
HMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: WG1656 cDNA

description:
Trio 2 son
set4


title: WG1084 gDNA

description:
Trio 4 son
set4


title: WG1226 cDNA

description:
Trio 3 son
set4


title: WG1657 cDNA

description:
Trio 2 father
set4


title: 20min_male_rep4, MAS5

description:
FMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: WG1084 cDNA

description:
Trio 4 son
set4


title: WG1656 gDNA

description:
Trio 2 son
set4


title: WG1226 gDNA

description:
Trio 3 son
set4


title: GM02455 gDNA

description:
Trio 8 daughter
set4


title: GM02555 gDNA

description:
Trio 8 mother
set4


title: WG1283 cDNA

description:
Trio 3 mother
set4


title: 20min_male_rep1, MAS5


title: 20min_male_rep2, MAS5


title: WG1282 gDNA

description:
Trio 3 father
set4


title: WG1657 gDNA

description:
Trio 2 father
set4


title: 20min_male_rep3, MAS5

description:
EMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM02456 cDNA

description:
Trio 8 father
set4


title: 20min_control_rep5, MAS5


title: GM02455 cDNA

description:
Trio 8 daughter
set4


title: GM02456 gDNA

description:
Trio 8 father
set4


title: WG1658 gDNA

description:
Trio 2 mother
set4


title: WG2843 gDNA

description:
Trio 4 mother
set4


title: GM02555 cDNA

description:
Trio 8 mother
set4


title: 20min_control_rep3, MAS5


title: 20min_control_rep4, MAS5


title: 20min_control_rep2, MAS5


title: GM02317 cDNA

description:
Trio 7 mother
set4


title: GM01393 gDNA

description:
Trio 6 father
set4


title: 20min_control_rep1, MAS5


title: 20min_courtship_rep5, MAS5


title: GM02317 gDNA

description:
Trio 7 mother
set4


title: 20min_courtship_rep4, MAS5


title: GM01393 cDNA

description:
Trio 6 father
set4


title: 20min_courtship_rep3, MAS5


title: GM00292 cDNA

description:
Trio 5 son
set4


title: GM00289 cDNA

description:
Trio 5 father
set4


title: GM00292 gDNA

description:
Trio 5 son
set4


title: 20min_courtship_rep2, MAS5


title: WG1658 cDNA

description:
Trio 2 mother
set4


title: 20min_courtship_rep1, MAS5


title: WG1283 gDNA

description:
Trio 3 mother
set4


title: 20min_male_rep5, dChip PM-MM


title: GM12007 cDNA

description:
pedigree 1420 son
set1


title: GM19240 cDNA

description:
Trio Y117 daughter
set3


title: GM19240 gDNA

description:
Trio Y117 daughter
set3


title: 12hpf StCo 1 vs 12hpf ATG 3

city: Sheffield

first: Michael

last: Harrison

address: Firth Court, Western Bank

department: MRC Centre for Developmental and Biomedical Genetics

institute: University of Sheffield

description: Biological replicate 3 of 3 12hpf Hdac1 ATG injected embryo

hyb_protocol: Two-Color Microarray-Based Gene Expression Analysis Protocol (G4140-90050, Agilent Technologies, Palo Alto, USA)

data_processing: Agilent Feature Extraction Software and Rosetta Resolver was used for background subtraction and normalization.

organism: Danio rerio

source_name: Standard control morphant

label_protocol: Ambion Amino Allyl MessageAmp II aRNA Amplification Kit and Perkin Elmer Cy-dye Coupling

growth_protocol: Embryos injected with morpholino at the one cell stage where cultured in E3 at 28.5°C for 12, 18 or 27 hours

extract_protocol: Total RNA extracted using Trizol, treated with Dnase and purified using QIAgen RNA columns all following manufacturer's instructions

value: Whole embryo

value: 12 hours post fertilisation

tag: morphant

value: Standard control morphant

source_name: hdac1 ATG morphant

value: hdac1 ATG morphant


title: GM12002 cDNA

description:
pedigree 1420 daughter
set1


title: 20min_male_rep4, dChip PM-MM


title: GM12878 gDNA

description:
Trio C1463 daughter
set3


title: GM12007 gDNA

description:
pedigree 1420 son
set1


title: GM12001 gDNA

description:
pedigree 1420 daughter
set1


title: WG1282 cDNA

description:
Trio 3 father
set4


title: 12hpf StCo 1 vs 12hpf ATG 1

description: Biological replicate 1 of 3 12hpf Hdac1 ATG injected embryo

scan_protocol: Two-Color Microarray-Based Gene Expression Analysis Protocol (G4140-90050, Agilent Technologies, Palo Alto, USA)


title: 12hpf StCo 1 vs 12hpf ATG 2

description: Biological replicate 2 of 3 12hpf Hdac1 ATG injected embryo


title: 20min_male_rep2, dChip PM-MM

description:
BMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 18hpf StCo 1 vs 18hpf ATG 3

description: Biological replicate 3 of 3 18hpf Hdac1 ATG injected embryo

value: 18 hours post fertilisation


title: GM12001 cDNA

description:
pedigree 1420 daughter
set1


title: 20min_male_rep3, dChip PM-MM


title: 20min_male_rep1, dChip PM-MM

description:
AMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM12000 gDNA

description:
pedigree 1420 daughter
set1


title: 18hpf StCo 1 vs 18hpf ATG 2

description: Biological replicate 2 of 3 18hpf Hdac1 ATG injected embryo


title: GM11999 gDNA

description:
pedigree 1420 daughter
set1


title: GM11997 gDNA

description:
pedigree 1420 daughter
set1


title: GM10839 cDNA

description:
pedigree 1420 mother
set1


title: GM11998 cDNA

description:
pedigree 1420 daughter
set1


title: 20min_control_rep5, dChip PM-MM

description:
HMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM11997 cDNA

description:
pedigree 1420 daughter
set1


title: 18hpf StCo 1 vs 18hpf ATG 1

description: Biological replicate 1 of 3 18hpf Hdac1 ATG injected embryo


title: GM12000 cDNA

description:
pedigree 1420 daughter
set1


title: HCo 2 vs StCo 2

description: Biological replicate 2 of 2 Hdac1 Control injected embryo

source_name: hdac1 Mismatch control morphant

growth_protocol: Embryos injected with morpholino where cultured in E3 at 28.5°C for 27 hours

value: 27 hours post fertilisation

value: hdac1 Mismatch control morphant


title: 20min_control_rep3, dChip PM-MM

description:
DMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: isogenized Canton-S

value: male


title: GM11998 gDNA

description:
pedigree 1420 daughter
set1


title: GM10839 gDNA

description:
pedigree 1420 mother
set1


title: 20min_control_rep4, dChip PM-MM

description:
FMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: head

value: 5 days


title: GM12878 cDNA

description:
Trio C1463 daughter
set3


title: GM12002 gDNA

description:
pedigree 1420 daughter
set1


title: 20min_control_rep2, dChip PM-MM

description:
CMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: 20 minutes


title: 27hpf StCo 3 vs 27hpf ATG 3

description: Biological replicate 3 of 3 27hpf Hdac1 ATG injected embryo


title: 27hpf ATG 2 vs 27hpf StCo 2

description: Biological replicate 2 of 2 ATG injected embryo


title: 20min_control_rep1, dChip PM-MM

description:
AMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: HCo 1 vs StCo 1

description: Biological replicate 1 of 2 Hdac1 Control injected embryo


title: GM10838 cDNA

description:
pedigree 1420 father
set1

value: lymphoblasts


title: 20min_courtship_rep5, dChip PM-MM

description:
JMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: exposure to a cauterized virgin female fly


title: Splice 1 vs StCo 1 rep2

description: Biological replicate 2 of 2 Hdac1 Splice injected embryo

source_name: hdac1 Splice morphant

value: hdac1 Splice morphant


title: Splice 1 vs StCo 1 rep1

description: Biological replicate 1 of 2 Hdac1 Splice injected embryo


title: 04_Pol2_rep2

city: Worcester

first: Richard

middle: E

last: Baker

state: MA

address: 55 Lake Avenue North

department: Microbiology & Physiological Systems

institute: University of Massachusetts Medical School

description: ChIP-chip wild-type splenic B cells Pol2

hyb_protocol: Arrays were hybridized in Maui hybridization stations following Nimblegen protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Hybridized arrays were scanned on an Agilent Technologies DNA Micraarray Scanner model G2505B.  Two-channel fluorescence intensities were extracted from the resulting TIFF files using NimbleScan v2.4  (Nbs1) or Nimblescan v2.6 (Pol2) software.

data_processing: MA2C (Robust, C=2)

organism: Mus musculus

source_name: Pol2 ChIP DNA from wild-type splenic B cells induced to undergo CSR

label_protocol: DNA samples were amplified using the WGA2 kit (Sigma Corp) according to the provided protocol, except the first fragmentation step was omitted. ChIP samples were amplified undiluted, whereas input control samples were amplified at a starting concentration of 1-2 ng/µl. After amplification, IP and input DNAs were labeled with Cy5 and Cy3 nonamers, respectively (TriLink Biotechnologies) using random primers and linear amplification with Klenow fragment of E. coli DNA Polymerase I (eBioscience Biotechnologies).

growth_protocol: Single-cell suspensions were prepared from spleens of 6 to 12 week old mice

extract_protocol: Cells were washed in PBS and fixed for 10 min at 37°C with 1% formaldehyde. Fixation was quenched by incubating with glycine at a final concentration of 125 mM for 5 minutes at room temperature. Fixed cells were then washed 3 times with PBS and the dried pellet was stored at -80°C. To perform ChIP, the pellet was thawed in Lysis buffer as per the Upstate protocol in the presence of protease and phosphatase inhibitors, and then sonicated 20 times for 10 sec bursts using a VibraCell (Sonics) sonicator at a medium setting. Aliquots containing 2 million cell equivalents of lysate were incubated overnight at 4°C with a mixture of Protein A/Protein G Dynabeads (Invitrogen) coupled with specific antibody. Beads were then washed according to the Upstate protocol and DNA was de-crosslinked and eluted by overnight incubation in elution buffer at 65°C. Eluted DNA and an aliquot of the input DNA were treated with Proteinase K and RNase A (final concentrations of 125 µg/ml) at 55°C overnight. DNA was precipitated in ethanol after phenol/chloroform extraction and resuspended in Tris-EDTA (10/0.1) pH 7 buffer.

treatment_protocol: Cultures induced for 2 days with 50 μg/ml LPS, 100 ng/ml human BLyS, and 25 ng/ml anti–δ-dextran

tag: genotype

value: wild-type

tag: cell type

value: cultured splenic B cells

tag: chip antibody

tag: chip antibody manufacturer

value: Upstate

tag: chip antibody catalog #

tag: chip antibody lot #

source_name: input DNA from wild-type splenic B cells induced to undergo CSR

treatment_protocol: Cultures were induced for 2 days with 50 μg/ml LPS, 100 ng/ml human BLyS, and 25 ng/ml anti–δ-dextran

value: none, input DNA


title: 20min_courtship_rep4, dChip PM-MM

description:
HMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: GM10838 gDNA

description:
pedigree 1420 father
set1

value: CEU


title: GM00289 gDNA

description:
Trio 5 father
set4


title: 20min_courtship_rep3, dChip PM-MM

description:
DMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 04_Pol2_rep1


title: 27hpf ATG 1 vs 27hpf StCo 1

description: Biological replicate 1 of 2 Hdac1 ATG injected embryo

value: Whole embryo

value: hdac1 ATG morphant

value: Standard control morphant


title: 20min_courtship_rep2, dChip PM-MM

description:
CMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 20min_courtship_rep1, dChip PM-MM

description:
AMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: Sibling 2 vs Mutant 2 dye-swap 2

description: Technical replicate of Biological duplicate 2 (dye-swap)

growth_protocol: Embryos where cultured in E3 at 28.5°C for 27 hours when hdac1 mutant embryos could be segragated from there siblings

value: 27 hours post fertilisation

source_name: hdac1 mutant (hi1618)

value: hdac1 mutant (hi1618)


title: Sibling 2 vs Mutant 2 dye-swap 1


title: 20min_male_rep5, dChip PM

description:
HMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: isogenized Canton-S

value: male


title: 20min_male_rep4, dChip PM

description:
FMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: head

value: 5 days


title: Mutant 2 vs Sibling 2 rep2

description: Technical replicate of Biological duplicate 2


title: Mutant 2 vs Sibling 2 rep1


title: GM11999 cDNA

description:
pedigree 1420 daughter
set1

value: female

value: lymphoblasts


title: Sibling 1 vs Mutant 1 dye-swap 2

description: Technical replicate of Biological duplicate 1 (dye-swap)


title: 20min_male_rep3, dChip PM

description:
EMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: exposure to a cauterized virgin female fly

value: 20 minutes


title: 20min_male_rep2, dChip PM

description:
BMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 20min_male_rep1, dChip PM

description:
AMMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: Mutant 1 vs Sibling 1 rep2

description: Technical replicate of Biological duplicate 1


title: 20min_control_rep5, dChip PM

description:
HMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: exposure to no female fly


title: Sibling 1 vs Mutant 1 dye-swap 1


title: Mutant 1 vs Sibling 1 rep1


title: 20min_control_rep4, dChip PM

description:
FMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 04_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3

data_processing: NimbleScan v2.4

source_name: Nbs1 ChIP DNA from aid-/- splenic B cells induced to undergo CSR

value: aid-/-

value: cultured splenic B cells

value: Abcam

source_name: input DNA from aid-/- splenic B cells induced to undergo CSR


title: p68-DDX5-siRNA versus control replicate 1 dye swap

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: HeLa transfection set biological replicate 1 of 3. Technical replicate 2 of 2. p68-DDX5-siRNA versus control comparsion.

hyb_protocol: 2.5 ug of each labelled cDNA were co-hybridized in the presence of 1X Agilent Blocking Agent and 1X Agilent hybridization buffer 17 hours at 60ºC in a rotating chamber at 4 rpm. The arrays were washed with Agilent’s SSPE Wash Protocol 1 minute at room temperature using a solution of 6× SSPE, 0.005% N-lauroylsarcosine,  and 1 minute at room temperature with a solution of 0.06× SSPE, 0.005% N-lauroylsarcosine, followed by 1 minute in acetonitrile and 30 seconds in  Agilent’s Stabilization and Drying Solution. Two biological replicate experiments were performed, each comparing siRNA versus control. For each biological replicate the pair of labelled samples was co-hybridized once on a single microarray with a technical replication with dye swapping. Thus, four  p68-DDX5 RNA interference versus control hybridizations were processed, totalling 4 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Differentially expressed genes for each time point were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .

source_name: pSuper

label_protocol: Indirect labelling was performed according to Exonhit SpliceArray protocol. 10 ug of total RNA were reversed transcribed with random hexamers using the Fair Play II Microarray Labelling kit (Stratagene) in the presence of aminoallyl-UTP. Cy5 or Cy3 labelling was incorporated by coupling NHS-esters.

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS and penicillin (10.000U/ml) and streptomycin (10 mg/ml), at 37ÂºC and 5% CO2 and 100% humidity.

extract_protocol: RNA was extracted using standard total RNA extraction protocol (Nucleospin)

treatment_protocol: For RNA interference experiments, approximately 8x10E6 HeLa cells were electroporated at 250 V and 960 uF with 15 ug of plasmid, obtaining approximately 90% transfection efficiency.

value: Human HeLa Cells

value: transfected with pSuper empty vector

value: transfected with p68 DDX5-interfering RNAi in pSuper


title: p68-DDX5-siRNA versus control replicate 2

description: HeLa transfection set biological replicate 2 of 3. Technical replicate 1 of 2. p68-DDX5-siRNA versus control comparsion.


title: 20min_control_rep2, dChip PM

description:
CMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 02_Pol2_rep2

description: ChIP-chip wild-type splenic B cells Pol2

value: wild-type

value: Upstate

value: none, input DNA


title: 20min_control_rep3, dChip PM

description:
DMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: isogenized Canton-S

value: male


title: 04_Nbs1_WT_rep2

description: ChIP-chip wild-type splenic B cells Nbs2

source_name: Nbs1 ChIP DNA from wild-type splenic B cells induced to undergo CSR


title: p68-DDX5-siRNA versus control replicate 1

description: HeLa transfection set biological replicate 1 of 3. Technical replicate 1 of 2. p68-DSDX5-siRNA versus control comparsion.


title: 20min_control_rep1, dChip PM

description:
AMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: head

value: 5 days


title: 04_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4


title: 02_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4


title: 04_Nbs1_WT_rep1

description: ChIP-chip wild-type splenic B cells Nbs1


title: 20min_courtship_rep3, dChip PM

description:
DMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: p68-DDX5-siRNA versus control replicate 2 dye swap

description: HeLa transfection set biological replicate 2 of 3. Technical replicate 2 of 2. p68-DDX5-siRNA versus control comparsion.


title: 20min_courtship_rep2, dChip PM

description:
CMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: control pneumocytes_48h_rep3

city: Vienna

first: Daniel

last: Schramek

address: Dr. Bohrgasse 3

country: Austria

institute: IMBA

description: control 3

hyb_protocol: Probe- Prehybridisation (TECAN HS4800)   Protocol for 40 domain chips:  Combine: 50µl Labeled DNA 29µl    20x SSPE 4µl 50x Denhardts solution 50µl Form amid 1.5µl   mouse block 3.5µl 20% SDS (last component to be added)   Incubate at 94°C for 2 min Prehybridise probe for at least 1 hour at 50°C  - start prehybridization of the slides  - After prehyb of the samples and the slides pipette 135 µl onto each slide If you have duplicates then pool and use 135µl per slide  - split and pipette 140 µl onto each slide  - Continue with hybridization on TECAN HS4800  for 12hours 45°C

scan_protocol: Scanner: GenePix 4000B

data_processing: Image Analysis: GenPix Pro 6.0

source_name: control pneumocytes + Ad-GFP

label_protocol:
Labeling with a Reactive Fluorescent Dye/ Molecular probes (Alexa 555, 647)

Thoroughly dissolve the amine-modified 4µg DNA in 5µl  nuclease free H2O (warming to 42°C for 5 min if necessary)
Add 3µl  Labeling buffer
(Just before use dissolve one vial of reactive dye in 10-20µl DMSO or use aliquots from ?80°C)
Add 2µl  reactive dye to the samples, vortex briefly to mix (do not spin)
Incubate for 1 hour in the dark at room temperature

growth_protocol: Ham’s F-12 media supplemented with 15 mM HEPES, 0.8 mM CaCl2, 0.25% BSA, ITS (Sigma) and 2% BSA.

extract_protocol: Total RNA extracted using Qiagen Rnaeasy Kit  following manufacturer's instructions followed by MessageAmp II aRNA Amplification   Kit #AM1751 Ambion and Amino-Allyl cDNA Synthesis

treatment_protocol: adenovirus treatment for 8 hours, then wash with PBS and growth in growth medum for 48hours

tag: primary cells

value: pneumocytes derived from lungs (1 passage)

value: Ad-GFP

source_name: control pneumocytes + Ad-Cre-GFP

value: Ad-Cre-GFP


title: MKK7 KO pneumocytes_48h_rep1

description: MKK7 KO 3

source_name: MKK7 KO pneumocytes + Ad-GFP

source_name: MKK7 KO pneumocytes + Ad-Cre-GFP


title: 20min_courtship_rep4, dChip PM

description:
HMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.

value: exposure to a cauterized virgin female fly

value: 20 minutes


title: 20min_courtship_rep5, dChip PM

description:
JMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: MKK7 KO pneumocytes_48h_rep3

description: MKK7 KO d


title: control pneumocytes_48h_rep1

description: control 1


title: 20min_courtship_rep1, dChip PM

description:
AMFMH
Only males who demonstrated robust courtship for 70% of the observation time were collected. Males were randomly pooled in groups of 20 individuals. Heads were removed and used for RNA extraction.


title: 02_Pol2_rep1

value: cultured splenic B cells


title: MKK7 KO pneumocytes_48h_rep2

description: MKK7 KO 2


title: CG-4 cells, untreated, biological replicate 3

status: Public on Jan 20 2011

first: Sean

last: Ryder

address: 364 Plantation Street

department: Biochemistry and Molecular Pharmacology

institute: UMass Medical School

description: untransfected CG-4 cells

hyb_protocol: GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Fluidics protocols for GeneChip ST Arrays (Affymetrix)

data_processing:
CEL files were imported into Partek GS and summarized with RMA with the GC background correction.
RaEx-1_0-st-v1.r2.pgf

organism: Rattus norvegicus

source_name: CG-4 cells, untreated

label_protocol: GeneChip Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix) with ribominus protocol

growth_protocol: CG-4 cells cultured in 30% B104 conditioned medium

extract_protocol: RNA was extracted with Trizol and purified with Qiagen RNeasy.

treatment_protocol: cells were transfected with lipofectamine 2000

value: CG-4 cells, untreated

value: control


title: 02_Nbs1_WT_rep1

value: Abcam


title: control pneumocytes_48h_rep2

description: control 2


title: CG-4 cells, QKI siRNA transfected, biological replicate 1

description: QKI siRNA transfected cells

source_name: CG-4 cells, QKI siRNA transfected

value: transiently transfected CG-4 cells

value: QKI knockdown


title: CG-4 cells, untreated, biological replicate 1

description: untransfected CG-4 cells


title: CG-4 cells, QKI siRNA transfected, biological replicate 2

description: QKI siRNA transfected cells


title: CG-4 cells, QKI siRNA transfected, biological replicate 3

description: QKI siRNA transfected cells


title: CG-4 cells, non-silencing siRNA transfected, biological replicate 2

description: control non-silencing siRNA transfected cells


title: 10_Nbs1_WT_rep1

value: wild-type


title: CG-4 cells, non-silencing shRNA stable line, biological replicate 2

description: control non-silencing shRNA stable line

value: stable CG-4 cells line


title: CG-4 cells, non-silencing siRNA transfected, biological replicate 3


title: CG-4 cells, non-silencing shRNA stable line, biological replicate 3

description: control non-silencing shRNA stable line


title: CG-4 cells, non-silencing siRNA transfected, biological replicate 1


title: CG-4 cells, hnRNP A1 siRNA transfected, biological replicate 2

description: hnRNP A1 siRNA transfected cells

source_name: CG-4 cells, hnRNP A1 siRNA transfected

value: hnRNP A1 knockdown


title: CG-4 cells, untreated, biological replicate 2

description: untransfected CG-4 cells


title: 10_Pol2_rep1

value: Upstate

value: none, input DNA


title: CG-4 cells, non-silencing shRNA stable line, biological replicate 1

description: control non-silencing shRNA stable line


title: 10_Pol2_rep2


title: 02_Nbs1_WT_rep2


title: CG-4 cells, hnRNP A1 siRNA transfected, biological replicate 1

description: hnRNP A1 siRNA transfected cells


title: Tregs purified from MHC II deficient recipient, Biological Rep3

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Gene expression data from CD4 Tregs lacking TCR / MHC class II interactions for 5 days (CD4+ TCRβ+ CD25+ cells purified from Total T cells transferred in CD3e / MHC II double deficient mice)

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip murine Gene from Affymetrix GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were analizing with affy R package (RMA) and statistical analysis were then performed with MeV software (TIGR, Rockville MD)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

extract_protocol: Total RNA was extracted using the Rneasy Mini kit (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: CD4+ TCRβ+ CD25+ cells were isolated by magnetic bead enrichment followed by fluorescence activated cell sorting.

value: 6-8 weeks of age

tag: origin tissue

value: Peripheral lymph nodes and spleen

value: CD4 Tregs lacking TCR


title: CG-4 cells, hnRNP A1 siRNA transfected, biological replicate 3

description: hnRNP A1 siRNA transfected cells


title: 02_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3

value: aid-/-

tag: strain


title: Tregs purified from MHC II competent recipient, Biological Rep1

description: Gene expression data from CD4 Tregs NOT lacking TCR / MHC class II interactions for 5 days (CD4+ TCRβ+ CD25+ cells purified from Total T cells transferred in CD3e deficient mice)

value: CD4 Tregs NOT lacking TCR


title: CG-4 cells, QKI shRNA stable line, biological replicate 3

description: QKI shRNA stable line

source_name: CG-4 cells, QKI shRNA stable line


title: Tregs purified from MHC II competent recipient, Biological Rep3


title: Tregs purified from MHC II deficient recipient, Biological Rep2


title: Ovarian Cancer SO94

city: Boston

last: Birrer

address: 70 Blossom Street

department: Medicine

institute: MGH

description: Gene expression data from late-stage high-grade ovarian cancer

hyb_protocol: A 15 microgram aliquot of amplified biotinylated RNA was hybridized to a Human U133 Plus 2.0 GeneChip array (Affymetrix, Santa Clara, CA).

scan_protocol: Array images were acquired using a GeneChip Scanner 3000 (Affymetrix)

data_processing: Robust Multi-Array Analysis was performed

label: Biotin

source_name: Ovarian tumor

label_protocol: Labeled amplified RNA (aRNA) for microarray analysis was generated from tumor or OSE-derived total RNA using a single round of amplification

extract_protocol: Total RNA was isolated using the RNeasy Micro kit (Qiagen)

treatment_protocol: Tumor specimens were obtained from 185 previously untreated late-stage (III–IV) high-grade ovarian cancer patients. A set of 10 normal ovarian surface epithelium (OSE) cytobrushing specimens were used as control

value: Late-stage high-grade ovarian cancer

tag: surgery outcome

value: Suboptimal

tag: status

value: DOD (dead of disease)

tag: survival years


title: Tregs purified from MHC II deficient recipient, Biological Rep1


title: 10_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3

value: cultured splenic B cells


title: CG-4 cells, QKI shRNA stable line, biological replicate 1

description: QKI shRNA stable line

tag: treatment


title: Ovarian Cancer SO89

tag: tissue

value: AWD (alive with disease)


title: CG-4 cells, QKI shRNA stable line, biological replicate 2

description: QKI shRNA stable line


title: Ovarian Cancer SO86


title: Ovarian Cancer SO88

value: NED (no evidence of disease)


title: Ovarian Cancer SO83


title: 06_Pol2_rep2


title: Ovarian Cancer SO87

value: Optimal


title: Ovarian Cancer SO85


title: Ovarian Cancer SO84


title: 10_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4

value: Abcam


title: 06_Nbs1_aid_rep1

description: ChIP-chip aid-/- splenic B cells Nbs3


title: 06_Pol2_rep1

value: wild-type


title: 10_Nbs1_WT_rep2


title: 06_Nbs1_WT_rep2


title: 06_Nbs1_aid_rep2

description: ChIP-chip aid-/- splenic B cells Nbs4


title: Ovarian Cancer SO77


title: Ovarian Cancer SO74


title: Ovarian Cancer SO80


title: Ovarian Cancer SO73


title: Ovarian Cancer SO8


title: Ovarian Cancer SO76


title: Ovarian Cancer SO78


title: Ovarian Cancer SO604


title: Ovarian Cancer SO67


title: Ovarian Cancer SO79


title: Ovarian Cancer SO91


title: Ovarian Cancer SO613


title: Ovarian Cancer SO71


title: Ovarian Cancer SO607


title: Ovarian Cancer SO68


title: Ovarian Cancer SO609


title: Ovarian Cancer SO69


title: Ovarian Cancer SO70


title: Ovarian Cancer SO511


title: Ovarian Cancer SO603


title: Ovarian Cancer SO58


title: Ovarian Cancer SO60


title: Ovarian Cancer SO57


title: Ovarian Cancer SO59


title: Ovarian Cancer SO501


title: Tregs purified from MHC II competent recipient, Biological Rep2

tag: age


title: Ovarian Cancer SO500


title: Ovarian Cancer SO7


title: Ovarian Cancer SO61


title: Ovarian Cancer SO489


title: Ovarian Cancer SO600


title: Ovarian Cancer SO490


title: Ovarian Cancer SO504


title: Ovarian Cancer SO479


title: Ovarian Cancer SO505


title: Ovarian Cancer SO506


title: Ovarian Cancer SO509


title: Ovarian Cancer SO5


title: Ovarian Cancer SO507


title: Ovarian Cancer SO82


title: Ovarian Cancer SO502


title: Ovarian Cancer SO475


title: Ovarian Cancer SO487


title: Ovarian Cancer SO610


title: 06_Nbs1_WT_rep1


title: epidermis5_4J/m2

city: Rennes

first: Nicolas

last: Mouchet

state: Bretagne

address: 2 Av du Professeur Leon Bernard

department: Institut genetique et developpement de Rennes

institute: CNRS UMR6290

hyb_protocol: Hybridization was performed using an Agilent oligonucleotide microarray in situ Hybridisation-Plus kit, following manufacturer's instructions.

scan_protocol: Scanned with th dynamic autofocus Agilent G2565A microarray scanner

data_processing:
Agilent feature extraction software version 9.1 and the Bioconductor package Limma were used to extract and normalized the data.
Script under R (bioconductor with Limma package)
MA = normalizeWithinArrays(RGb,method=loess)
MA.q=normalizeBetweenArrays(MA,method=Gquantile)

[Data filtering criteria]

Flagged-signals excluded:
-Saturated in the 2 channels
-Non uniform
-SNR< 2,6 and not significantly different from local background

And only genes with less than 30% of missing values were selected

source_name: epidermis irradiated 4J/m2

label_protocol: Total RNA (350ng) were amplified and labelled using a two color labelling protocol with the low input linear amplification kit according to the manufacturer's recommandations (Agilent)

extract_protocol: Skin homogenisation was carried out with the Precellys 24 device (Bertin), using ceramic beads (CK14), in the presence of 350microlitres of RA1 buffer (Macherey-Nagel) supplemented with 3.5 microlitres of beta-mercaptoethanol. Th e device was set at a speed of 6300 rpm, with a cycle duration of 23 seconds and an interval time between 2 cycles of 2 minutes at 4°C. Six cycles were required for complete homogenisation. Tri-reagent (400 microlitres) was added followed by 150 microlitres of chloroform. The aqueous phase was recovered, mixed with 500 microlitres of 70% ethanol and transferred to a nucleospin RNA II colomn. RNA was recovered from the column following the manufacturer's instructions.

treatment_protocol: Irradiation with a solar simulated radiation five hours before recovering the samples

value: epidermis

tag: dose

source_name: Pool of all samples (control)

tag: reference

value: Pool of all samples


title: Ovarian Cancer SO481


title: Ovarian Cancer SO46


title: Ovarian Cancer SO483


title: Ovarian Cancer SO428


title: epidermis3_4J/m2


title: epidermis3_control

source_name: epidermis control

value: control (0J/m2)


title: Ovarian Cancer SO44


title: epidermis4_control


title: epidermis4_2J/m2

source_name: epidermis irradiated 2J/m2


title: Ovarian Cancer SO420


title: epidermis4_4J/m2


title: epidermis1_control


title: Ovarian Cancer SO421


title: Ovarian Cancer SO428b


title: Ovarian Cancer SO420b


title: epidermis3_2J/m2


title: epidermis2_4J/m2


title: Ovarian Cancer SO422b


title: Ovarian Cancer SO422


title: epidermis1_2J/m2


title: Ovarian Cancer SO429


title: Ovarian Cancer SO404


title: Ovarian Cancer SO402


title: epidermis2_2J/m2


title: Ovarian Cancer SO393


title: Ovarian Cancer SO418


title: Ovarian Cancer SO401


title: Ovarian Cancer SO395


title: epidermis2_control


title: epidermis5_control


title: Ovarian Cancer SO409


title: Ovarian Cancer SO396


title: Ovarian Cancer SO400


title: Ovarian Cancer SO426


title: Ovarian Cancer SO388


title: Ovarian Cancer SO423


title: epidermis5_2J/m2


title: Ovarian Cancer SO387


title: Ovarian Cancer SO38


title: Ovarian Cancer SO367


title: Ovarian Cancer SO312


title: Ovarian Cancer SO36


title: Ovarian Cancer SO362


title: Ovarian Cancer SO322


title: Ovarian Cancer SO325


title: Ovarian Cancer SO4


title: Ovarian Cancer SO342


title: Ovarian Cancer SO347


title: Ovarian Cancer SO434


title: Ovarian Cancer SO300


title: Ovarian Cancer SO299


title: Ovarian Cancer SO295


title: Ovarian Cancer SO31


title: Ovarian Cancer SO375


title: Ovarian Cancer SO283


title: CG-4 cells, QKI siRNA transfected, biological replicate 3

description: QKI siRNA transfected cells

data_processing:
CEL files were imported into Partek GS and summarized with RMA with the GC background correction. Winsorized mean was determined for transcripts.
RaEx-1_0-st-v1.r2.pgf
RaEx-1_0-st-v1.r2.dt1.rn3.extended.mps

value: transiently transfected CG-4 cells

value: QKI knockdown


title: CG-4 cells, QKI siRNA transfected, biological replicate 2

description: QKI siRNA transfected cells


title: CG-4 cells, QKI siRNA transfected, biological replicate 1

description: QKI siRNA transfected cells


title: CG-4 cells, untreated, biological replicate 3

description: untransfected CG-4 cells

value: CG-4 cells, untreated

value: control


title: CG-4 cells, non-silencing shRNA stable line, biological replicate 3

description: control non-silencing shRNA stable line

value: stable CG-4 cells line


title: CG-4 cells, non-silencing siRNA transfected, biological replicate 1


title: CG-4 cells, untreated, biological replicate 2

description: untransfected CG-4 cells


title: CG-4 cells, non-silencing siRNA transfected, biological replicate 2


title: Ovarian Cancer SO303

value: Late-stage high-grade ovarian cancer


title: Ovarian Cancer SO290


title: Ovarian Cancer SO308


title: epidermis1_4J/m2


title: Ovarian Cancer SO334

value: Suboptimal


title: Ovarian Cancer SO282

value: DOD (dead of disease)


title: Ovarian Cancer SO267


title: Ovarian Cancer SO278


title: Ovarian Cancer SO279


title: Ovarian Cancer SO301


title: Ovarian Cancer SO285


title: Ovarian Cancer SO268


title: Ovarian Cancer SO258


title: CG-4 cells, non-silencing shRNA stable line, biological replicate 2

description: control non-silencing shRNA stable line


title: CG-4 cells, non-silencing shRNA stable line, biological replicate 1

description: control non-silencing shRNA stable line


title: Ovarian Cancer SO265


title: Ovarian Cancer SO263


title: CG-4 cells, hnRNP A1 siRNA transfected, biological replicate 3

description: hnRNP A1 siRNA transfected cells

value: hnRNP A1 knockdown


title: Ovarian Cancer SO257


title: CG-4 cells, hnRNP A1 siRNA transfected, biological replicate 2

description: hnRNP A1 siRNA transfected cells


description: QKI shRNA stable line


title: CG-4 cells, hnRNP A1 siRNA transfected, biological replicate 1

description: hnRNP A1 siRNA transfected cells


description: QKI shRNA stable line


title: CG-4 cells, non-silencing siRNA transfected, biological replicate 3


title: Ovarian Cancer SO256


title: Ovarian Cancer SO262


title: Ovarian Cancer SO273


title: Ovarian Cancer SO250


title: Ovarian Cancer SO244


title: Ovarian Cancer SO246


title: CG-4 cells, QKI shRNA stable line, biological replicate 3

description: QKI shRNA stable line


title: CG-4 cells, untreated, biological replicate 1

description: untransfected CG-4 cells


title: Ovarian Cancer SO247


title: Ovarian Cancer SO249


title: Ovarian Cancer SO261


title: MCF-7

city: Parkville

last: Saffery

state: Victoria

address: Flemington Rd

department: Cancer, Disease and Developmental Epigenetics

country: Australia

institute: Murdoch Children's Research Institute

hyb_protocol: Hybridized as per manufacturer's instructions at Service XS (www.servicexs.com)

scan_protocol: Scanned as per manufacturer's instructions at Service XS (www.servicexs.com)

data_processing: Data was extracted and background normalized using the Illumina GenomeStudio Methylation (M) Module 1.0

label: Cy5 and Cy3

source_name: Solid cancer cell line

label_protocol: Labelled as per manufacturer's instructions at Service XS (www.servicexs.com). DNA is whole-genome amplified, hybridised to locus-specific DNA oligomers linked to individual bead types. There are two bead types that correspond to the methylated (C) and the the unmethylated (T) state. Allele-specific primer annealing is followed by single-base extension using DNP- and Biotin-labeled ddNTPs. After extension, the array is fluorescently stained, scanned, and the intensities of the unmethylated and methylated bead types measured.)

extract_protocol: Genomic DNA was extracted using the standard Phenol-Chloroform extraction protocol. DNA purity was determined using the 260/280 ratio, with all samples showing good quality. DNA was bisulphite converted using the MethylEasy Bisulphite Modification kit (Human Genetic Signatures, Australia).

tag: cell line

value: Solid cancer cell line, breast cancer


title: Ovarian Cancer SO236

value: NED (no evidence of disease)


title: Ovarian Cancer SO241


title: Ovarian Cancer SO23

value: Optimal


title: Ovarian Cancer SO237


title: CB_2029.1

source_name: Non-transformed cord blood mononuclear cells

tag: cell type


title: Ovarian Cancer SO229


title: CB_1012.1

value: Non-transformed cord blood mononuclear cells


title: Ovarian Cancer SO231


title: Ovarian Cancer SO228


title: Ovarian Cancer SO218


title: Ovarian Cancer SO243


title: TEV1

source_name: Placenta-derived cell line

value: transformed trophoblasts


title: REH

source_name: Blood cancer cell line

value: REH

value: blood cancer cell line


title: AC1M32

source_name: Trophoblast-derived cell line

value: trophoblast-derived cell line


title: F58_HLAplus

source_name: HLAG+ extravillous trophoblasts

value: extravillous trophoblasts


title: Ovarian Cancer SO272


title: Ovarian Cancer SO217


title: Ovarian Cancer SO227


title: Ovarian Cancer SO225


title: SWAN

value: SWAN


title: Sample863_4

source_name: CK7+ cytotrophoblasts

value: villous cytotrophoblast population


title: SW48

value: Solid cancer cell line


title: Ovarian Cancer SO216


title: BEWO

value: BEWO


title: Ovarian Cancer SO235

value: Late-stage high-grade ovarian cancer


title: Ovarian Cancer SO214

value: Suboptimal


title: Ovarian Cancer SO211

value: DOD (dead of disease)


title: Primary patient sample_MMRC0445_1_GEP

city: Cambridge

middle: Anthony

last: Chapman

address: 7 Cambridge Center

institute: Broad Institute

description: Gene expression data from untreated cells

hyb_protocol: Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer.

data_processing: Data were extracted from CEL files by GenePattern ExpressionFileCreator version 8, using RMA with quantile normalization and background correction.

source_name: Sample from patient MMRC0445

label_protocol: 1-2 ug of Total RNA was labeled using the One-Cycle Target Labeling kit from Affymetrix as per the manufacturers suggestion.

growth_protocol: After informed consent bone marrow aspirates were collected in sodium citrate tubes at MMRC member institutions and shipped by overnight courier to the MMRC Tissue Bank (Scottsdale, Arizona).  White blood cells were collected after red cell lysis using ACK reagent.  Plasma cells were selected using CD138 and the RoboSep (StemCell Technologies) as per the manufacturers protocol.  The purified plasma cells were lysed in 1 ml of TRIzol Reagent (Life Technologies).

extract_protocol: RNA was extracted from the TRIzol suspension using the manufacturers protocol..  The RNA was subsequently cleaned-up with a Qiagen RNeasy mini or micro kit as per the manufacturers suggestion..  RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer.

treatment_protocol: No post collection treatment was performed.

value: CD138-selected bone marrow cells


title: Ovarian Cancer SO242


title: Primary patient sample_MMRC0442_1_GEP

source_name: Sample from patient MMRC0442


title: Primary patient sample_MMRC0441_1_GEP

source_name: Sample from patient MMRC0441


title: Ovarian Cancer SO201

value: AWD (alive with disease)


title: Ovarian Cancer SO25


title: Ovarian Cancer SO200


title: Primary patient sample_MMRC0444_1_GEP

source_name: Sample from patient MMRC0444


title: HTR8

value: placenta-derived cell line


title: Primary patient sample_MMRC0438_1_GEP

source_name: Sample from patient MMRC0438


title: Ovarian Cancer SO205

source_name: Ovarian tumor

value: Optimal

value: NED (no evidence of disease)


title: Ovarian Cancer SO203


title: Primary patient sample_MMRC0437_1_GEP

source_name: Sample from patient MMRC0437


title: Primary patient sample_MMRC0443_1_GEP

source_name: Sample from patient MMRC0443


title: Primary patient sample_MMRC0435_1_GEP

source_name: Sample from patient MMRC0435


title: Ovarian Cancer SO2


title: Ovarian Cancer SO21


title: Ovarian Cancer SO224


title: F58_HLAminus

source_name: HLAG- extravillous trophoblasts


title: Ovarian Cancer SO230


title: Primary patient sample_MMRC0439_1_GEP

source_name: Sample from patient MMRC0439


title: Primary patient sample_MMRC0434_1_GEP

source_name: Sample from patient MMRC0434


title: RV-control-C3

city: Kansas City

first: Douglas

middle: C

last: Bittel

state: MO

address: 2401 Gillham Rd

department: Genetics research

institute: Childrens Mercy Hospital

description:
C3
Donor tissues from right ventricle of normally developing infants.

hyb_protocol: The microarrays were CodeLink Human Whole Genome Bioarray (Applied Microarrays Inc. Tempe, AZ), which contain > 54,000 probes. Hybridization was performed overnight in a temperature-controlled shaking incubator with buffers supplied in the kit. Post-hybridization processing includes a stringent wash to remove unbound and non-specifically hybridized target molecules, a staining step with a Cy5-Streptavidin conjugate, and several non-stringent washing steps to remove unbound conjugate. Following a final rinse, the microarrays were dried by centrifugation.

scan_protocol: Scanned using an Agilent G2505B Microarray scanner (Agilent Inc. Santa Clara CA) according to the CodeLink protocol for scanning Human Whole genome arrays.

data_processing: Analysis of the microarrays was done with CodeLink Expression Analysis software (Applied Microarrays) and results were transferred to GeneSpring analytical software (Agilent Inc.) for further analysis. Signal intensities less than 0 were converted to a positive value (i.e., 0.01). Normalization to the median baseline signal was accomplished using a global scaling process for all probe sets. Essentially, all microarrays were normalized to the median value of the control samples such that each measurement for each probe, in each microarray, was divided by the median of that probe’s measurement in the corresponding control samples.  Each measurement was then divided by the 50th percentile of all measurements in that sample.The inclusion criteria for further analysis required a ‘‘present’’ or ‘‘marginal’’ signal in at least three of five control arrays or three fourths of the arrays from the subjects with TOF. We chose to include only those probes that had a two-fold difference between the TOF samples and controls since these are more likely to achieve robust differences.  Furthermore, within the TOF group, all values for the probe had to be in the same direction (up or down) relative to the control group. Differences between mean probe signal intensity were evaluated using a Welsh t-test without assuming equal variances and with a false discovery rate (fdr) of 5% or less using Bonferroni correction for multiple testing as undertaken in other studies.

label_protocol: The detailed microarray processing protocol can be found at http://www.appliedmicroarrays.com.  Briefly, the poly(A)+ RNA subpopulation (within the total RNA population) is primed for reverse transcription using an oligonucleotide containing a T7 RNA polymerase promoter 5' to an oligo d(T)24 sequence. After second-strand cDNA synthesis, the cDNA serves as the template for an in vitro transcription (IVT) reaction to produce target cRNA. The IVT is performed in the presence of biotinylated nucleotides to label the target cRNA. This produces an approximate 1000-fold to 5000-fold linear amplification of the input mRNA. A set of bacterial control mRNAs is included in the CodeLink™ Expression Assay Reagent Kit (Applied Microarrays, Tempe AZ) as controls for the cDNA synthesis and the IVT reactions.

extract_protocol: RNA was extracted from frozen tissues using the PerfectPure RNA fibrous tissue Kit (5 Prime GmbH, Hamburg), according to the manufacturer’s protocol.

treatment_protocol:
Controls: For the control samples, if the donor was placed in a refrigerated morgue within 12 hours of asystole, tissues were recovered for up to 24 hours and placed in a 1-10C sterile isotonic solution; if the donor was not refrigerated, tissues were recovered for up to 15 hours and placed in a 1-10C sterile isotonic solution. The control tissues (cryopreserved pulmonary homografts) were thawed per protocol in sterile conditions.  One author (JEO) aseptically dissected samples from the control tissue from the right ventricle matching what was done in surgery.

TOF: All subjects enrolled in this study were undergoing surgical correction of TOF. Tissue samples obtained during patient surgery (attending surgeons JEO and GKL) were immediately de-identified and frozen.  All tissue samples removed during surgery were excised by the performing surgeon for clinical indications utilizing standard of care procedures.

value: right ventricle

value: 2 months

tag: Sex

value: female

tag: disease state

value: control


title: RV-control-C2

description:
C2
Donor tissues from right ventricle of normally developing infants.

value: 4 months

value: male


title: JAR

value: JAR

value: hybrid cell line


title: JEG-3

value: primary choriocarcinoma tumour, hybrid cell line


title: Primary patient sample_MMRC0431_1_GEP

source_name: Sample from patient MMRC0431


title: Primary patient sample_MMRC0440_1_GEP

source_name: Sample from patient MMRC0440


title: Primary patient sample_MMRC0436_1_GEP

source_name: Sample from patient MMRC0436


title: Primary patient sample_MMRC0433_1_GEP

source_name: Sample from patient MMRC0433


title: RV-control-C5

description:
C5
Donor tissues from right ventricle of normally developing infants.

value: 12 months


title: Ovarian Cancer SO194

value: Late-stage high-grade ovarian cancer


title: Primary patient sample_MMRC0432_1_GEP

source_name: Sample from patient MMRC0432


title: Ovarian Cancer SO196

value: DOD (dead of disease)


title: Ovarian Cancer SO193


title: RV-control-C1

description:
C1
Donor tissues from right ventricle of normally developing infants.

value: 1 months


title: Ovarian Cancer SO190


title: RV-control-C4

description:
C4
Donor tissues from right ventricle of normally developing infants.


title: Primary patient sample_MMRC0420_1_GEP

source_name: Sample from patient MMRC0420

value: CD138-selected bone marrow cells


title: Ovarian Cancer SO197

value: AWD (alive with disease)


title: Primary patient sample_MMRC0421_1_GEP

source_name: Sample from patient MMRC0421


title: Primary patient sample_MMRC0418_1_GEP

source_name: Sample from patient MMRC0418


title: RV-TOF-T13

description:
T13
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

source_name: excess tissue from right ventricle, TOF

value: 3 months

value: Tetralogy of Fallot (TOF)


title: RV-TOF-T14

description:
T14
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: right ventricle

value: 6 months


title: Primary patient sample_MMRC0417_1_GEP

source_name: Sample from patient MMRC0417


title: Ovarian Cancer SO185

source_name: Ovarian tumor

value: Optimal

value: NED (no evidence of disease)


title: Primary patient sample_MMRC0414_1_GEP

source_name: Sample from patient MMRC0414


title: Primary patient sample_MMRC0422_1_GEP

source_name: Sample from patient MMRC0422


title: Ovarian Cancer SO184


title: Primary patient sample_MMRC0413_1_GEP

source_name: Sample from patient MMRC0413


title: RV-TOF-T15

description:
T15
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: 7.5 months

value: female


title: Primary patient sample_MMRC0410_1_GEP

source_name: Sample from patient MMRC0410


title: Primary patient sample_MMRC0409_1_GEP

source_name: Sample from patient MMRC0409


title: Primary patient sample_MMRC0412_1_GEP

source_name: Sample from patient MMRC0412


title: Primary patient sample_MMRC0408_1_GEP

source_name: Sample from patient MMRC0408


title: Ovarian Cancer SO18


title: RV-TOF-T12

description:
T12
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: 13 months


title: Primary patient sample_MMRC0430_1_GEP

source_name: Sample from patient MMRC0430


title: Primary patient sample_MMRC0411_1_GEP

source_name: Sample from patient MMRC0411


title: RV-TOF-T16

description:
T16
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: male


title: Primary patient sample_MMRC0404_1_GEP

source_name: Sample from patient MMRC0404


title: Ovarian Cancer SO181


title: Ovarian Cancer SO187


title: Primary patient sample_MMRC0419_1_GEP

source_name: Sample from patient MMRC0419


title: RV-TOF-T8

description:
T8
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: 5 months


title: Ovarian Cancer SO174

value: Suboptimal


title: Ovarian Cancer SO189

value: Late-stage high-grade ovarian cancer


title: Primary patient sample_MMRC0403_1_GEP

source_name: Sample from patient MMRC0403


title: Primary patient sample_MMRC0406_1_GEP

source_name: Sample from patient MMRC0406


title: RV-TOF-T9

description:
T9
Excess tissue from right ventricle obtained at the time of reconstructive surgery.


title: Primary patient sample_MMRC0401_1_GEP

source_name: Sample from patient MMRC0401


title: Primary patient sample_MMRC0405_1_GEP

source_name: Sample from patient MMRC0405


title: Primary patient sample_MMRC0400_1_GEP

source_name: Sample from patient MMRC0400


title: Primary patient sample_MMRC0402_1_GEP

source_name: Sample from patient MMRC0402


title: RV-TOF-T6

description:
T6
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

source_name: excess tissue from right ventricle, TOF


title: RV-TOF-T10

description:
T10
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: 8 months


title: Primary patient sample_MMRC0416_1_GEP

source_name: Sample from patient MMRC0416


title: Ovarian Cancer SO173

source_name: Ovarian tumor


title: Primary patient sample_MMRC0399_1_GEP

source_name: Sample from patient MMRC0399


title: Ovarian Cancer SO16

value: DOD (dead of disease)


title: Primary patient sample_MMRC0397_1_GEP

source_name: Sample from patient MMRC0397

value: CD138-selected bone marrow cells


title: Primary patient sample_MMRC0393_1_GEP

source_name: Sample from patient MMRC0393


title: RV-TOF-T4

description:
T4
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: 7 months


title: Primary patient sample_MMRC0392_1_GEP

source_name: Sample from patient MMRC0392


title: RV-TOF-T5

description:
T5
Excess tissue from right ventricle obtained at the time of reconstructive surgery.


title: RV-TOF-T3

description:
T3
Excess tissue from right ventricle obtained at the time of reconstructive surgery.


title: RV-TOF-T7

description:
T7
Excess tissue from right ventricle obtained at the time of reconstructive surgery.


title: Primary patient sample_MMRC0396_1_GEP

description: Gene expression data from untreated cells

source_name: Sample from patient MMRC0396


title: Ovarian Cancer SO166

description: Gene expression data from late-stage high-grade ovarian cancer


title: Ovarian Cancer SO154

value: AWD (alive with disease)


title: Primary patient sample_MMRC0395_1_GEP

source_name: Sample from patient MMRC0395


title: RV-TOF-T2

description:
T2
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: Tetralogy of Fallot (TOF)


title: Primary patient sample_MMRC0389_1_GEP

source_name: Sample from patient MMRC0389


title: RV-TOF-T11

description:
T11
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

value: right ventricle

value: 2 months


title: Primary patient sample_MMRC0387_1_GEP

source_name: Sample from patient MMRC0387


title: Primary patient sample_MMRC0394_1_GEP

source_name: Sample from patient MMRC0394


title: Primary patient sample_MMRC0391_1_GEP

source_name: Sample from patient MMRC0391


title: Ovarian Cancer SO148


title: Primary patient sample_MMRC0386_1_GEP

source_name: Sample from patient MMRC0386


title: Ovarian Cancer SO17


title: Primary patient sample_MMRC0384_1_GEP

source_name: Sample from patient MMRC0384


title: Primary patient sample_MMRC0382_1_GEP

source_name: Sample from patient MMRC0382


title: Ovarian Cancer SO131

value: Optimal


title: Ovarian Cancer SO143


title: Normal_9

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Gene expression ratios were obtained from human kidney tumor cell lines.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with MBNI re-mapped CDF files, version 12.

source_name: Homo Sapiens

label_protocol: 10 ug of Qiagen-purified total RNA

value: normal tissue

tag: mutation

value: unknown


title: Primary patient sample_MMRC0383_1_GEP

source_name: Sample from patient MMRC0383


title: Ovarian Cancer SO137


title: Primary patient sample_MMRC0364_1_GEP

source_name: Sample from patient MMRC0364


title: Primary patient sample_MMRC0390_1_GEP

source_name: Sample from patient MMRC0390


title: Primary patient sample_MMRC0365_1_GEP

source_name: Sample from patient MMRC0365


title: Normal_3


title: Ovarian Cancer SO134

source_name: Ovarian tumor


title: Primary patient sample_MMRC0362_1_GEP

source_name: Sample from patient MMRC0362


title: Normal_8


title: Primary patient sample_MMRC0359_1_GEP

source_name: Sample from patient MMRC0359


title: Ovarian Cancer SO13

value: NED (no evidence of disease)


title: Primary patient sample_MMRC0360_1_GEP

source_name: Sample from patient MMRC0360


title: Primary patient sample_MMRC0361_1_GEP

source_name: Sample from patient MMRC0361


title: RV-TOF-T1

description:
T1
Excess tissue from right ventricle obtained at the time of reconstructive surgery.

source_name: excess tissue from right ventricle, TOF

value: 10 months

value: female


title: Primary patient sample_MMRC0381_1_GEP

source_name: Sample from patient MMRC0381


title: Primary patient sample_MMRC0372_1_GEP

source_name: Sample from patient MMRC0372


title: Primary patient sample_MMRC0380_1_GEP

source_name: Sample from patient MMRC0380


title: Normal_4


title: Ovarian Cancer SO141


title: Primary patient sample_MMRC0379_1_GEP

source_name: Sample from patient MMRC0379


title: Ovarian Cancer SO135


title: Primary patient sample_MMRC0373_1_GEP

source_name: Sample from patient MMRC0373


title: Primary patient sample_MMRC0357_1_GEP

source_name: Sample from patient MMRC0357


title: Normal_7

source_name: Homo Sapiens


title: Primary patient sample_MMRC0353_1_GEP

source_name: Sample from patient MMRC0353


title: Primary patient sample_MMRC0358_1_GEP

source_name: Sample from patient MMRC0358


title: Primary patient sample_MMRC0375_1_GEP

source_name: Sample from patient MMRC0375


title: Primary patient sample_MMRC0356_1_GEP

source_name: Sample from patient MMRC0356


title: Primary patient sample_MMRC0355_1_GEP

source_name: Sample from patient MMRC0355


title: Ovarian Cancer SO122

source_name: Ovarian tumor


title: Primary patient sample_MMRC0351_1_GEP

source_name: Sample from patient MMRC0351


title: Normal_13


title: Ovarian Cancer SO12


title: Primary patient sample_MMRC0343_1_GEP

source_name: Sample from patient MMRC0343


title: Primary patient sample_MMRC0340_1_GEP

source_name: Sample from patient MMRC0340


title: Ovarian Cancer SO118


title: Normal_11


title: Normal_12


title: Normal_10


title: Normal_6


title: Normal_5


title: Normal_2


title: Primary patient sample_MMRC0330_1_GEP

source_name: Sample from patient MMRC0330


title: VARI365T

value: clear cell

value: VHL


title: Ovarian Cancer SO121

value: Late-stage high-grade ovarian cancer


title: VARI361T


title: Primary patient sample_MMRC0374_1_GEP

source_name: Sample from patient MMRC0374


title: Normal_1


title: Ovarian Cancer SO124


title: Primary patient sample_MMRC0329_1_GEP

source_name: Sample from patient MMRC0329


title: Ovarian Cancer SO129


title: Ovarian Cancer SO117


title: VARI352T


title: Primary patient sample_MMRC0335_1_GEP

source_name: Sample from patient MMRC0335


title: Ovarian Cancer SO116


title: Primary patient sample_MMRC0352_1_GEP

source_name: Sample from patient MMRC0352


title: Primary patient sample_MMRC0332_1_GEP

source_name: Sample from patient MMRC0332


title: Primary patient sample_MMRC0334_1_GEP

source_name: Sample from patient MMRC0334


title: Ovarian Cancer SO108


title: Primary patient sample_MMRC0307_1_GEP

source_name: Sample from patient MMRC0307


title: VARI194T

source_name: Homo Sapiens


title: Ovarian Cancer SO11


title: Ovarian Cancer SO115


title: Ovarian Cancer SO113


title: Primary patient sample_MMRC0299_1_GEP

source_name: Sample from patient MMRC0299


title: Primary patient sample_MMRC0286_1_GEP

source_name: Sample from patient MMRC0286


title: Primary patient sample_MMRC0328_1_GEP

source_name: Sample from patient MMRC0328


title: Ovarian Cancer SO10


title: Ovarian Cancer SO103


title: Ovarian Cancer SO100


title: Primary patient sample_MMRC0287_1_GEP

source_name: Sample from patient MMRC0287


title: VARI200T


title: VARI216T


title: Primary patient sample_MMRC0318_1_GEP

source_name: Sample from patient MMRC0318


title: VARI268T


title: Primary patient sample_MMRC0324_1_GEP

source_name: Sample from patient MMRC0324


title: VARI256T


title: VARI274T


title: Primary patient sample_MMRC0302_1_GEP

source_name: Sample from patient MMRC0302


title: Ovarian Cancer SO106

source_name: Ovarian tumor


title: VARI245T


title: Primary patient sample_MMRC0308_1_GEP

source_name: Sample from patient MMRC0308


title: Primary patient sample_MMRC0331_1_GEP

source_name: Sample from patient MMRC0331


title: Primary patient sample_MMRC0309_1_GEP

source_name: Sample from patient MMRC0309


title: Normal HOSE2234

description: Gene expression data from ovarian surface epithelial cells

source_name: Ovarian surface epithelial cells

value: Normal ovarian surface epithelium


title: Primary patient sample_MMRC0291_1_GEP

source_name: Sample from patient MMRC0291


title: Primary patient sample_MMRC0303_1_GEP

source_name: Sample from patient MMRC0303


title: Primary patient sample_MMRC0285_1_GEP

source_name: Sample from patient MMRC0285


title: VARI139T


title: Primary patient sample_MMRC0284_1_GEP

source_name: Sample from patient MMRC0284


title: Normal HOSE2230


title: Normal HOSE2228


title: Normal HOSE2085