title: plasma patient 4727

description: miRNA expression in plamsa

value: patient 4727


title: Strain p17 isolated from lettuce infection rep. 2

status: Public on Sep 20 2011

type: RNA

city: Braunschweig

first: Piotr

last: Bielecki

address: Inhoffenstr 7

department: Cell Biology

country: Germany

institute: Helmholtz Centre for Infection Research

description: In vivo P. aeruginosa gene expression from lettuce infection

hyb_protocol: Standard affymetrix

scan_protocol: Standard affymetrix

data_processing: Data analysis was performed using the R version 2.6.0 and Bioconductor version 2.1. The quality of all chips was assessed by fitting a linear model to the probe level data using the function “fitPLM” from the “affyPLM” package. Subsequently, the distribution (boxplots) of RLE (Relative Log Expression) and NUSE (Normalised Unscaled Standard Errors) was manually analysed.

label: biotin

molecule: total RNA

organism: Pseudomonas aeruginosa

label_protocol: Biotin incorporation during amplification

growth_protocol: Burn wound - collection from wound and stabilization in RNAprotect (QIAGEN), Murine tumore - 5 mice with tumor per strain infected intravenously with P. aeruginosa, Tumors extracted after 24h homogenized with stabilization of the RNA, Plant - Lettuce leaves infected with P. aeruginosa, infection sites stabilized and RNA extracted after 5 days of incubations, Planktonic LB - early stationary phase - RNAprotect, Biofilm - 24h biofilm on plastic slide and 10% LB - RNAprotect

extract_protocol: QIAGEN RNAmini, Ambion MicrobEnrich, Ambion MessageAMP

treatment_protocol: RNAprotect QIAGEN, human sample collected with sterile swab which was deepen in RNAprotect

tag: strain

tag: initial isolate source

value: burn wound isolate

tag: infection model isolate source

value: lettuce infection


title: EWS knock-down replicate 1

city: barcelona

first: BELEN

last: MINANA

state: barcelona

address: dr aiguader 88

department: GENE REGULATION, STEM CELLS AND CANCER

country: Spain

institute: Center for genomic regulation

description: Mean foreground and background intensities were extracted from the red (Cy5) and green (Cy3) channels for every spot on the microarray. The background intensities are used to correct the foreground intensities for local variation on the array surface, resulting in corrected red and green intensities.

hyb_protocol: Slides were hybridized following manufacturer protocol, with the exception that we hybridized 6 micrograms of each amplified cRNA sample and the Agilent hybridization oven was set to 60ºC.

scan_protocol: Fluorescent images were obtained using the G2565BA Microarray Scanner System (Agilent) with 100% laser power and 100% PMT settings and 16-bit TIFF images, one for each channel, were quantified using GenePix Pro 6.0 microarray analysis software (Molecular Devices, www.moleculardevices.com).

data_processing: Raw data were processed using SAPO (http://bioinfo.ciberehd.org/SAP.ang.htm) and CGEM (http://bioinfo.ciberehd.org/CGEM.ang.html) alternative splicing analysis tools, obtaining lowess normalized log2ratios.

organism: Homo sapiens

source_name: EWS siRNA knock-down in HeLa cell line replicate 1

label_protocol: Sample was labeled using the Quick-Amp labeling kit, no dye (Agilent 5190-0447) and cyanine 5-CTP and cyanine 3-CTP (Perkin-Elmer NEL580, NEL581). Purified using Quiagen RNeasy mini kit. Quality control assessed by Agilent Bioanalyzer 2100.

growth_protocol: Cell were grown in complete media (DMEM + 10% FBS + penicillin/streptomycin). Before transfection, HeLa cells were plated the day before at 4X10E3 per well in 35mm plates in DMEM 10%FBS without antibiotics.

extract_protocol:
RNeasy mini kit (QUIAGEN, cat.no. 74104) and DNase treated on-column with DNase RNase-free (QUIAGEN, cat no. 79254)
Quality assesment of Total RNA samples were analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay.

treatment_protocol: HeLa cells were plated the day before transfection at 4X10E3 per well in 35mm plates in DMEM 10%FBS without antibiotics and transfected with 20micromolar of a scrambled RNA or EWS siRNA oligonucleotides using Lipofectamine RNA iMAX (Cat. No 13778-150, Invitrogen) in optimem media (Invitrogen). Five hours after transfection, the media was removed and replaced by complete media (DMEM + 10% FBS + penicillin/streptomycin). Cell were harvested after 72 hours after transfection.

tag: cell line

value: HeLa

tag: genotype/variation

value: knockdown with a EWS siRNA oligo

source_name: HeLa siRNA control of trasfection replicate 1

value: transfected with a scrambled oligo


title: genomic DNA of BSG014T, brainstem LGG

status: Public on Sep 21 2011

type: genomic

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

country: USA

institute: St Jude Children's Research Institute

description: Gene expression data from pediatric brainstem LGG patient.

hyb_protocol: Hybridizations were performed according the standard Affymetrix protocol

scan_protocol: Scanning performed according to the standard Affymetrix protocol

data_processing:
Affymetrix CEL files for the tumor and normal samples in the collection were analyzed using Genotyping Console software for initial quality control, followed by use of "Birdseed" algorithm to generate the SNP call files. The CEL and CHP files were first analyzed with dChipSNP to extract un-normalized signal intensity.  The intensity data was then normalized using reference normalization with selected diploid chromosomes within each sample.

Please contact Suzanne Baker at Suzanne.Baker@stjude.org for CEL files and genotype calls.

molecule: genomic DNA

source_name: brainstem of pediatric LGG patient collected Pretreatment

label_protocol: According to Affymetrix protocol

extract_protocol: Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.

tag: disease

value: brainstem LGG

tag: age at diagonosis (years)

tag: survival (years)

tag: histology

value: Pilocytic Astrocytoma

tag: sample collection

value: Pretreatment


title: plasma patient 4724

city: shanghai

first: xiaonan

last: zhang

address: caolang road 2901, Jinshan district

department: research unit

country: China

institute: Shanghai public health clinical center

description: miRNA expression in plamsa

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction software 10.7(Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT 100%，10%.

source_name: plasma, before treatment

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: reponse to therapy

value: Rapid response

tag: sample type

value: plasma

tag: disease state

value: hepatatis B

tag: individual

value: patient 4724


title: plasma patient 4725

description: miRNA expression in plamsa

value: patient 4725


title: plasma patient 4723

description: miRNA expression in plamsa

value: No response

value: patient 4723


title: Strain p17 isolated from lettuce infection rep. 1


title: genomic DNA of BSG011W, matched normal to BSG011T

description: Normal samples

source_name: white blood cell matched to BSG011T

value: Normal


title: plasma patient 4722

description: miRNA expression in plamsa

value: patient 4722


title: plasma patient 4720

description: miRNA expression in plamsa

value: patient 4720


title: Strain p17 isolated from murine tumor rep. 1

description: In vivo P. aeruginosa gene expression from murine tumor infection

value: burn wound isolate

value: murine tumor


title: genomic DNA of BSG018W, matched normal to BSG018T

description: Normal samples

source_name: white blood cell matched to BSG018T


title: plasma patient 4719

description: miRNA expression in plamsa

value: patient 4719


title: plasma patient 4718

description: miRNA expression in plamsa

value: patient 4718


title: Strain p17 isolated from murine tumor rep. 2


title: Strain p17 isolated from in vitro biofilm rep. 2

description: In vitro P. aeruginosa gene expression from biofilm

value: in vitro biofilm


title: plasma patient 4717

description: miRNA expression in plamsa

value: patient 4717


title: plasma patient 4715

description: miRNA expression in plamsa

value: patient 4715


title: plasma patient 4716

description: miRNA expression in plamsa

value: Rapid response

value: patient 4716


title: Urothelial cancer cell line RT112 replicate 2

city: Sheffield

first: Ewa

last: Dudziec

address: Beech Hill Road

department: ICS

country: United Kingdom

institute: The University of Sheffield

description: RT112 3

hyb_protocol: Hybridization was performed according to the Agilent protocol. Hybridisation took place in a rotating hybridisation platform at 67°C for 40 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Agilent instructions

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version v 9.5.3).

data_processing: Agilent Feature Extraction Software (v 9.5.3) was used for background subtraction and LOWESS normalization.

source_name: Bladder cancer cell line, 5-methylcystosine enriched DNA (IP)

label_protocol: The samples were fluorescently labelled with Cyanine 3-dUTP (the reference samples) and Cyanine 5-dUTP (immunoprecipitated DNA samples) according to Agilent’s recommendations

growth_protocol: Cancer cell lines (EJ, RT112) were grown in Dulbecco's medium with 10% FCS, and normal human urothelial (NHU) cell line was maintained in keratinocyte serum–free medium containing bovine pituitary extract, epidermal growth factor (Invitrogen), and cholera toxin

extract_protocol: DNA was extracted with DNeasy Blood and Tissue extraction kit from Qiagen, as per manufacturer's instructions. For MeDIP, genomic DNA is extracted and purified from the cells and sheared by sonication to yield 200-600bp fragments. DNA is incubated with antibody raised against 5-methylcytosine. At the same time, a negative mouse IgG control is used in order to rule out non specific binding of antibodies. The antibody-antigen complex is captured with magnetic beads conjugated to anti-mouse-IgG. In extensive washes, unbound and non specific DNA are removed and methylated DNA is purified. Enrichment of methylated DNA in the immunoprecipitated fraction can be determined by PCR with primers designed to the known methylated gene.

tag: cell type

value: Human bladder carcinoma, fast growing tumour

source_name: Bladder cancer cell line (non-IP)


title: Normal urothelium cell line NHU Replicate 1

description: NHU 14.7.10

source_name: Normal human urothelial cell line, 5-methylcystosine enriched DNA (IP)

value: NHU

value: Normal human urothelial cell line, moderate growth

source_name: Normal human urothelial cell line (non-IP)


title: genomic DNA of BSG006T, brainstem LGG

value: brainstem LGG

value: Pilocytic Astrocytoma

value: Pretreatment


title: Urothelial cancer cell line RT112 replicate 1

description: RT112 30.4.10


title: Urothelial cancer cell line EJ replicate 2

description: EJ 2 14.7.10

value: EJ


title: Strain p17 isolated from burn wound rep. 1

description: In vivo P. aeruginosa gene expression from burn wound

value: burn wound


title: genomic DNA of BSG008T, brainstem LGG


title: genomic DNA of BSG011T, brainstem LGG


title: plasma patient 4730

description: miRNA expression in plamsa

value: No response

value: plasma

value: hepatatis B

value: patient 4730


title: plasma patient 4711

description: miRNA expression in plamsa

value: patient 4711


title: Strain p17 isolated from in vitro biofilm rep. 1

value: burn wound isolate

value: in vitro biofilm


title: plasma patient 4705

description: miRNA expression in plamsa

value: Rapid response

value: patient 4705


title: plasma patient 4707

description: miRNA expression in plamsa

value: patient 4707


title: plasma patient 4708

description: miRNA expression in plamsa

value: patient 4708


title: plasma patient 4713

description: miRNA expression in plamsa

value: patient 4713


title: Strain p17 isolated from in vitro planktonic culture rep. 1

description: In vitro P. aeruginosa gene expression from sessile growth

value: in vitro planktonic culture


title: plasma patient 4712

description: miRNA expression in plamsa

value: patient 4712


title: plasma patient 4710

description: miRNA expression in plamsa

value: patient 4710


title: plasma patient 4703

description: miRNA expression in plamsa

value: patient 4703


title: plasma patient 4709

description: miRNA expression in plamsa

value: patient 4709


title: Strain p11 isolated from lettuce infection rep. 1

value: lettuce infection


title: Strain p11 isolated from lettuce infection rep. 2


title: plasma patient 4702

description: miRNA expression in plamsa

value: plasma

value: patient 4702


title: plasma patient 4704

description: miRNA expression in plamsa

value: No response

value: hepatatis B

value: patient 4704


title: Urothelial cancer cell line EJ replicate 1

description: EJ 25.6.10

value: EJ

value: Human bladder carcinoma, fast growing tumour


title: genomic DNA of BSG002T, brainstem LGG

value: brainstem LGG

value: Pilocytic astrocytoma

value: Pretreatment


title: Normal urothelium cell line NHU Replicate 2

description: NHU 2 18.8.10

value: NHU

value: Normal human urothelial cell line, moderate growth


title: genomic DNA of BSG006W, matched normal to BSG006T

description: Normal samples

source_name: white blood cell matched to BSG006T

value: Normal


title: plasma patient 4701

description: miRNA expression in plamsa

value: patient 4701


title: genomic DNA of BSG002W, matched normal to BSG002T

description: Normal samples

source_name: white blood cell matched to BSG002T


title: Strain p17 isolated from in vitro planktonic culture rep. 2

value: burn wound isolate

value: in vitro planktonic culture


title: genomic DNA of BSG010T, DIPG

description: Gene expression data from pediatric DIPG patient.

source_name: brainstem of pediatric DIPG patient collected Postmortem

value: DIPG

value: Glioblastoma

value: Postmortem


title: Strain p11 isolated from burn wound rep. 2

value: burn wound


title: Strain p11 isolated from in vitro biofilm rep. 1

value: in vitro biofilm


title: plasma patient 4664

description: miRNA expression in plamsa

value: No response

value: plasma

value: hepatatis B

value: patient 4664


title: plasma patient 4663

description: miRNA expression in plamsa

value: patient 4663


title: plasma patient 4662

description: miRNA expression in plamsa

value: Rapid response

value: patient 4662


title: Strain p11 isolated from murine tumor rep. 1

value: murine tumor


title: plasma patient 4666

description: miRNA expression in plamsa

value: patient 4666


title: plasma patient 4660

description: miRNA expression in plamsa

value: patient 4660


title: Strain p11 isolated from burn wound rep. 1

value: burn wound isolate


title: plasma patient 4714

description: miRNA expression in plamsa

value: patient 4714


title: TRA1 vs. tra1_SRR3413_L3733A (array 3)

city: London

first: Christopher

last: Brandl

state: Ontario

address: 1151 Richmond St.

department: Biochemistry

country: Canada

institute: University of Western Ontario

description: Experiment was performed to analyze the effects of the tra1_SRR3413_L3733A allele on gene expression. This array is one of three replicates including one dye-swap.

hyb_protocol: Hybridization was performed at MOgene LC (St. Louis, MO).  Labeled material was fragmented according to the protocol described in the Agilent processing manual and hybridized overnight with the array in a rotating oven at 60 degrees Celsius in an ozone-free environment.  Wash conditions used were as outlined in the Agilent processing manual.

scan_protocol: Scanning was performed at MOgene LC (St. Louis, MO) using an Agilent scanner.

data_processing: Data processing was performed at MOgene LC (St. Louis, MO).  Feature extraction, normalization and background subtraction of reported values were performed using Agilent software.

organism: Saccharomyces cerevisiae

source_name: Cy3: CY2706(TRA1::Tn10LUK with 1980(myc9-TRA1-YCplac111))

label_protocol: Labeling was performed at MOgene LC (St. Louis, MO).  Total RNA from yeast was amplified using Agilent's low input linear amplification kit according to the process outlined by the manufacturer (Agilent Technologies).  1-5ug of amplified target cRNA was labeled using the Micromax kit (PerkinElmer, Inc.).  The labeled material was passed through a zymo RNA Clean-up Kit-5 column (Zymo Research Corp., CA) to remove un-incorporated label and eluted in 15-20ul of RNase-free water (Ambion, Inc.).  All of the labeling and post-labeling procedures were conducted in an ozone-free environment to ensure the integrity of the label.

extract_protocol: RNA extraction was performed as described in Mutiu AI, and Brandl CJ (2005) RNA isolation from yeast using silica matrices. J Biomol Tech 16:316-317.

tag: Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.

source_name: Cy5: CY3015(TRA1::Tn10LUK with IB157(myc9-tra1_SRR3413_L3733A-YCplac111))


title: plasma patient 4667

description: miRNA expression in plamsa

value: patient 4667


title: plasma patient 4665

description: miRNA expression in plamsa

value: patient 4665


title: plasma patient 4659

description: miRNA expression in plamsa

value: patient 4659


title: TRA1 TRA1 vs. TRA1 tra1_G3745 (array 2)

description: Experiment was performed to analyze the effects of the tra1_G3745 allele on gene expression. This array is one of three replicates including one dye-swap.

source_name: Cy3: CY3020(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB160(myc9-TRA1-YCplac111))

tag: Yeast cells were grown to A600=1.5 in 15 ml SC-trp media containing 50 ug/ml methionine.  Cells were then washed three times with 30 ml water, resuspended in 30 ml SC-trp media containing 2 ug/ml methionine and grown for 12 hours.

source_name: Cy5: CY3019(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB162(myc9-tra1_G3745-YCplac111))


title: Strain p11 isolated from murine tumor rep. 2

tag: strain


title: Strain p11 isolated from in vitro biofilm rep. 2

tag: initial isolate source


title: tra1_SRR3413_L3733A vs. TRA1 (array 2)

source_name: Cy3: CY3015(TRA1::Tn10LUK with IB157(myc9-tra1_SRR3413_L3733A-YCplac111))

source_name: Cy5: CY2706(TRA1::Tn10LUK with 1980(myc9-TRA1-YCplac111))


title: TRA1 TRA1 vs. TRA1 tra1_G3745 (array 3)


title: plasma patient 4657

description: miRNA expression in plamsa

value: patient 4657


title: TRA1 tra1_G3745 vs. TRA1 TRA1 (array 1)

source_name: Cy3: CY3019(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB162(myc9-tra1_G3745-YCplac111))

source_name: Cy5: CY3020(TRA1::Tn10LUK with 1259(myc-TRA1-YCplac111) and IB160(myc9-TRA1-YCplac111))


title: Strain p11 isolated from in vitro planktonic culture rep. 2

tag: infection model isolate source

value: in vitro planktonic culture


title: plasma patient 4656

description: miRNA expression in plamsa

source_name: plasma, before treatment

value: No response

value: patient 4656


title: plasma patient 4661

description: miRNA expression in plamsa

value: plasma

value: hepatatis B

value: patient 4661


title: plasma patient 4655

description: miRNA expression in plamsa

value: patient 4655


title: plasma patient 4654

description: miRNA expression in plamsa

value: Rapid response

value: patient 4654


title: TRA1 vs. tra1_SRR3413_L3733A (array 1)


title: plasma patient 4653

description: miRNA expression in plamsa

value: patient 4653


title: Strain p11 isolated from in vitro planktonic culture rep. 1


title: Strain p10 isolated from lettuce infection rep. 2

value: lettuce infection


title: plasma patient 4658

description: miRNA expression in plamsa

value: patient 4658


title: plasma patient 4645

description: miRNA expression in plamsa

value: patient 4645


title: TRA1 vs. tra1_L3733A (array 3)

description: Experiment was performed to analyze the effects of the tra1_L3733A allele on gene expression. This array is one of three replicates including one dye-swap.

source_name: Cy5: CY3003(TRA1::Tn10LUK with IB150(myc9-tra1_L3733A-YCplac111))


title: plasma patient 4648

description: miRNA expression in plamsa

value: patient 4648


title: plasma patient 4649

description: miRNA expression in plamsa

value: patient 4649


title: plasma patient 4647

description: miRNA expression in plamsa

value: patient 4647


title: Strain p17 isolated from burn wound rep. 2

value: burn wound isolate

value: burn wound


title: plasma patient 4646

description: miRNA expression in plamsa

value: patient 4646


title: Ctnnb1_Kras_1

city: Houston

first: JoAnne

last: Richards

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: gene expression data

hyb_protocol: cRNA were hybridized on GeneChip Mouse Genome 430 2.0 Array using Hybridization Oven 640. The GeneChip® Fluidics Station 450 automates the delivery, timing and temperature control of reagents for staining and washing of the probe arrays.

scan_protocol: GeneChips were scanned using GeneArray™ Scanner 3000 and quantified with Affymetrix GCOS 1.4.

data_processing: The data were analyzed using affy package from Bioconductor version 1.8 with RMA method.

organism: Mus musculus

source_name: whole ovary from beta-Catenin;Kras(G12D) double mutant

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

growth_protocol: Animals were housed under a 16-h light/8-h dark schedule in the Center for Comparative Medicine at Baylor College of Medicine and provided food and water ad libitum.

extract_protocol: Total RNA extraction by RNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Animals were treated in accordance with the NIH Guide for the Care and Use of Laboratory Animals, as approved by the Animal Care and Use Committee at Baylor College of Medicine.

tag: tissue

value: whole ovary

value: mixed background (includes C57BL/6)

tag: genotype

value: Krastm4Tyj/ Krastm4Tyj ; Ctnnb1 tm1Mmt /Ctnnb1 tm1Mmt; Tg(CYP19A1-cre)1jri/+ (Ctnnb1;Kras;C-cre)

tag: age

value: 4 weeks


title: Ctnnb1_Pten_1

description: gene expression data

source_name: whole ovary from beta-Catenin;Pten double mutant

value: Ptentm1Hwu/ Ptentm1Hwu; Ctnnb1 tm1Mmt /Ctnnb1 tm1Mmt; Tg(CYP19A1-cre)1jri/+ (Ctnnb1;Pten;C-cre)


title: plasma patient 4652

description: miRNA expression in plamsa

value: No response

value: plasma

value: hepatatis B

value: patient 4652


title: Strain p10 isolated from in vitro biofilm rep. 2

value: in vitro biofilm


title: Strain p10 isolated from lettuce infection rep. 1

value: lettuce infection


title: Strain p10 isolated from murine tumor rep. 2

value: murine tumor


title: plasma patient 4650

description: miRNA expression in plamsa

value: patient 4650


title: Strain p10 isolated from murine tumor rep. 1


title: plasma patient 4644

description: miRNA expression in plamsa

value: Rapid response

value: patient 4644


title: Strain p10 isolated from in vitro biofilm rep. 1

value: burn wound isolate


title: plasma patient 4642

description: miRNA expression in plamsa

value: patient 4642


title: plasma patient 4643

description: miRNA expression in plamsa

value: patient 4643


title: wt_ave

description: gene expression data

source_name: whole ovary from wild type mice (average from previous samples GSM403220 and GSM403221)

value: whole ovary

value: mixed background (includes C57BL/6)

value: wild type

value: 26 days


title: plasma patient 4640

description: miRNA expression in plamsa

value: patient 4640


title: Ctnnb1_OV_1

description: gene expression data

source_name: whole ovary from beta-Catenin constitutively active mutant

value: Ctnnb1 tm1Mmt /Ctnnb1 tm1Mmt; Tg(CYP19A1-cre)1jri/+ (Ctnnb1;C-cre)

value: 4 weeks


title: Strain p10 isolated from burn wound rep. 2

value: burn wound


title: plasma patient 4641

description: miRNA expression in plamsa

value: No response

value: plasma

value: hepatatis B

value: patient 4641


title: Strain p10 isolated from burn wound rep. 1


title: plasma patient 4639

description: miRNA expression in plamsa

value: patient 4639


title: plasma patient 4638

description: miRNA expression in plamsa

value: patient 4638


title: plasma patient 4635

description: miRNA expression in plamsa

value: Rapid response

value: patient 4635


title: plasma patient 4634

description: miRNA expression in plamsa

value: patient 4634


title: plasma patient 4636

description: miRNA expression in plamsa

value: patient 4636


title: plasma patient 4637

description: miRNA expression in plamsa

value: patient 4637


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [73]

city: lleida

first: angela

last: canovas

state: lleida

address: 191, rovira roure

institute: irta

description: LD/LW x Duroc pigs cross

hyb_protocol: Hybridisation protocol as recommented by Affymetrix using the Porcine Genome Array from Affymetrix.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A, as recommended by Affymetrix

data_processing: Data pre-processing, normalisation and class comparison analysis were carried out with the BRB-ArrayTools software version 3.7.1, which is available online at http://linus.nci.nih.gov/BRB-ArrayTools.html, as follows: microarray data normalisation was performed using the gcRMA algorithm, which corrects the intensity of each probe by its GC content; genes showing minimal variation across the set of arrays were excluded from the analysis, that is, only genes whose expression differed above 1.5 fold from the median in at least 20% of the arrays were retained. From the total 23937 spots of the array, 4299 spots passed these filtering conditions. For each probe, expression fold-change was calculated as the ratio between median values in both groups.

organism: Sus scrofa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A total of 75 animals from a LD/LW x Duroc cross were raised together in an experimental farm. 60 piglets were selected randomly after the postweaning period. During the feeding period, they were feed ad libitum. One piglet died during this time and was excluded from further studies.  Tissue samples were collected at slaughter, snap froxen in LN2 and stored at -80ºC until analysis

extract_protocol: total RNA was extracted from longissimus dorsi muscle using RNeasy Protect Mini kit (QIAGEN, Hamburg, Germany) following the manufacturer's protocol

treatment_protocol: After slaughter, controled animals were ranked based in 33 composition, conformation and meat quality and compositional traits.

tag: breed

value: LD/LW x Duroc

tag: selection

value: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits

value: 170 days-old

value: Longissimus Dorsi muscle


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [72]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [9]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [70]

description: LD/LW x Duroc pigs cross


title: plasma patient 4633

description: miRNA expression in plamsa

value: patient 4633


title: plasma patient 4631

description: miRNA expression in plamsa

value: patient 4631


title: Strain p10 isolated from in vitro planktonic culture rep. 1

value: burn wound isolate

value: in vitro planktonic culture


title: Strain p10 isolated from in vitro planktonic culture rep. 2


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [69]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [68]

description: LD/LW x Duroc pigs cross


title: plasma patient 4632

description: miRNA expression in plamsa

value: plasma

value: hepatatis B

value: patient 4632


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [74]

description: LD/LW x Duroc pigs cross


title: plasma patient 4629

description: miRNA expression in plamsa

value: No response

value: patient 4629


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [71]

description: LD/LW x Duroc pigs cross


title: plasma patient 4628

description: miRNA expression in plamsa

value: Rapid response

value: patient 4628


title: plasma patient 4626

description: miRNA expression in plamsa

value: patient 4626


title: plasma patient 4627

description: miRNA expression in plamsa

value: patient 4627


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [67]

description: LD/LW x Duroc pigs cross

value: LD/LW x Duroc


title: plasma patient 4625

description: miRNA expression in plamsa

value: patient 4625


title: plasma patient 4630

description: miRNA expression in plamsa

value: patient 4630


title: plasma patient 4624

description: miRNA expression in plamsa

value: patient 4624


title: BT474-J4_Lap-GSK089_24-2

city: Collegeville

first: Yuan

last: Liu

state: PA

address: 1250 South Collegeville Rd

department: Biomarker

institute: GlaxoSmithKline

description: Gene expression data of a breast cancer cell line.

hyb_protocol: Experiment conducted at Response Genetics, Inc.

data_processing: RNA microarray signals were normalized by MAS5. QC and data analysis were performed using Omicsoft microarray analysis tools (http://www.omicsoft.com/).

source_name: BT474-J4 breast cancer cell line, lapatinib and foretinib

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Response Genetics, Inc.)

growth_protocol: Cells were plated in RPMI medium containing 10% FBS overnight at 37ºC, 5%CO2.

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

treatment_protocol: Cells were treated with vehicle (DMSO), 1 µM lapatinib, 0.1 µM GSK1363089 (foretinib) or a combination of 1µM lapatinib and 0.1 µM foretinib for 24h.

tag: cell line

value: breast cancer

tag: lapatinib sensitivity

value: acquired lapatinib-resistant

tag: her2 status

tag: treatment

value: lapatinib and foretinib


title: BT474-J4_Lap-GSK089_24-3

scan_protocol: Experiment conducted at Response Genetics, Inc.


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [66]

description: LD/LW x Duroc pigs cross

value: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits

value: 170 days-old

value: Longissimus Dorsi muscle


title: plasma patient 4622

description: miRNA expression in plamsa

tag: reponse to therapy

tag: sample type

value: plasma

tag: disease state

value: hepatatis B

value: patient 4622


title: BT474-J4_Lap_24-3

source_name: BT474-J4 breast cancer cell line, lapatinib

tag: cell type

value: lapatinib


title: plasma patient 4623

description: miRNA expression in plamsa

value: Rapid response

tag: individual

value: patient 4623


title: BT474-J4_Lap-GSK089_24-1


title: plasma patient 4621

description: miRNA expression in plamsa

value: No response

value: patient 4621


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [63]

description: LD/LW x Duroc pigs cross

value: LD/LW x Duroc


title: plasma patient 4620

description: miRNA expression in plamsa

value: patient 4620


title: plasma patient 4617

description: miRNA expression in plamsa

value: patient 4617


title: plasma patient 4616

description: miRNA expression in plamsa

value: patient 4616


title: plasma patient 4615

description: miRNA expression in plamsa

value: patient 4615


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [60]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [58]

description: LD/LW x Duroc pigs cross


title: plasma patient 4614

description: miRNA expression in plamsa

value: patient 4614


title: plasma patient 4618

description: miRNA expression in plamsa

value: patient 4618


title: BT474-J4_Lap_24-2

value: breast cancer

value: acquired lapatinib-resistant


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [64]

description: LD/LW x Duroc pigs cross

value: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits

value: 170 days-old

value: Longissimus Dorsi muscle


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [59]

description: LD/LW x Duroc pigs cross


title: BT474-J4_Lap_24-1

value: lapatinib


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [57]

description: LD/LW x Duroc pigs cross


title: plasma patient 4619

description: miRNA expression in plamsa

value: Rapid response

value: plasma

value: hepatatis B

value: patient 4619


title: plasma patient 4613

description: miRNA expression in plamsa

value: No response

value: patient 4613


title: plasma patient 4612

description: miRNA expression in plamsa

value: patient 4612


title: BT474-J4_GSK089_24-2

source_name: BT474-J4 breast cancer cell line, foretinib

value: foretinib


title: BT474-J4_GSK089_24-3


title: BT474-J4_GSK089_24-1


title: plasma patient 4608

description: miRNA expression in plamsa

value: patient 4608


title: plasma patient 4610

description: miRNA expression in plamsa

value: patient 4610


title: BT474-J4_DMSO_24-3

source_name: BT474-J4 breast cancer cell line, DMSO

value: DMSO


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [54]

description: LD/LW x Duroc pigs cross

value: LD/LW x Duroc


title: plasma patient 4609

description: miRNA expression in plamsa

value: patient 4609


title: plasma patient 4607

description: miRNA expression in plamsa

value: patient 4607


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [56]

description: LD/LW x Duroc pigs cross

value: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits

value: 170 days-old


title: plasma patient 4611

description: miRNA expression in plamsa

value: patient 4611


title: BT474-J4_DMSO_24-2

value: breast cancer

value: acquired lapatinib-resistant


title: plasma patient 4606

description: miRNA expression in plamsa

value: Rapid response

value: plasma

value: hepatatis B

value: patient 4606


title: plasma patient 4605

description: miRNA expression in plamsa

value: No response

value: patient 4605


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [51]

description: LD/LW x Duroc pigs cross

value: Longissimus Dorsi muscle


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [52]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [50]

description: LD/LW x Duroc pigs cross


title: plasma patient 4602

description: miRNA expression in plamsa

value: patient 4602


title: plasma patient 4604

description: miRNA expression in plamsa

value: patient 4604


title: plasma patient 4603

description: miRNA expression in plamsa

value: patient 4603


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [5]

description: LD/LW x Duroc pigs cross

value: LD/LW x Duroc


title: BT474_Lap_24-2

source_name: BT474 breast cancer cell line, lapatinib

value: lapatinib-sensitive

value: lapatinib


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [49]

description: LD/LW x Duroc pigs cross

value: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits

value: 170 days-old


title: BT474-J4_DMSO_24-1

value: breast cancer

value: DMSO


title: BT474_Lap_24-1


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [48]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [47]

description: LD/LW x Duroc pigs cross


title: BT474_Lap_24-3


title: 96hr BMP6 treatment, 10d culture, replicate 2

city: Cold Spring Harbor

first: Weijun

last: Luo

state: NY

address: 1 Bungtown Rd

institute: Cold Spring Harbor Lab

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

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

data_processing: The raw data (.CEL file) were processed by using FARMS with a custom CDF file (version 8) based on Entrez Gene sequences as described by Dai et al, PMID: 16284200.

source_name: mesenchymal stem cells treated 96 hours with BMP6, and harvested at 10 days

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

growth_protocol: Passage 5 human MSC (5x105) were plated in 24-well dishes and cultured for 3 days. The cells were subsequently placed in serum free media supplemented with ITS for 24 hours.

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

treatment_protocol: 20 nM BMP6 (R&D Systems) was then added for the pre-designed time periods and then removed. To remove BMP6, cells were rinsed 2 times and fresh media without BMP was added.

value: vertebral bone marrow mesenchymal stem cell

tag: gender

value: male

tag: time

tag: culture age


title: 10d BMP6 treatment, 10d culture, replicate 2

source_name: mesenchymal stem cells cultured 10 days without BMP6


title: plasma patient 4601

description: miRNA expression in plamsa

value: Rapid response

value: plasma

value: hepatatis B

value: patient 4601


title: 96hr BMP6 treatment, Control culture, replicate 2

source_name: mesenchymal stem cells cultured 96 hours without BMP6


title: BT474_DMSO_24-3

source_name: BT474 breast cancer cell line, DMSO


title: BT474_DMSO_24-2


title: 96hr BMP6 treatment, 96hr culture, replicate 2

source_name: mesenchymal stem cells treated 96 hours with BMP6, and harvested at 96 hours


title: NHU

hyb_protocol: 15µg of cRNA molecules were heat fragmented and applied to the Affymetrix Human Genome U133 Plus 2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

source_name: Normal human urothelial cell line

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol: Total RNA was extracted using the MirVana kit (Ambion, TX) according to manufacturer's instructions

value: NHU

value: Normal human urothelial cell line, moderate growth


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [45]

description: LD/LW x Duroc pigs cross

tag: tissue

value: Longissimus Dorsi muscle


title: LN308_CCI+Rad_Cy3_rep3

city: Heidelberg

first: Jan

last: Gronych

address: Im Neuenheimer Feld 280

department: Molecular Genetics

institute: German Cancer Research Center

description: bological replicate 3

hyb_protocol: Labeled samples werehybridized on Agilent microarrays according to manufacturer´s protocol using SureHyb chambers and incubated rotating at 65°C for 16h. Subsequently, slides were washed in GE wash buffer 1 and 2, respectively.

scan_protocol: Two-color Agilent Scanner G25505B with 5 µm resolution  was used for slide scanning according to manufacturer’s specification. Scans were performed with a 100% PMT voltage for each channel. Values were extracted using Feature Extraction software version 9.1.3.1 (Agilent)

data_processing: The in-house developed R-based platform was used for data fitlering, normalization and joining of dye swaps using the following parameters. Filtering: Minimal raw signal=90; signal-to-noise-ratio>1.5; mean-to-median sd<=(75% quantile+0.2*IQR) (all rules applied for single channels). Normalization per chip: printtiploess. Joining of dye swaps: max NA per probe=0.4; max NA per sample=0.6

label_protocol: 1µg of total RNA was used for cDNA and subsequent cRNA synthesis according to Agilent Manual (Part No. G4140-90050). Dye swap experiments were performed using the same total RNA as input but inverse cRNA labeling.

extract_protocol: Total RNA was extracted using Qiagen RNeasy Mini kit according to manufacturer´s protocol

value: CCI-779 + 4 Gy Radiation

source_name: LN308 untreated

value: untreated


title: 24hr BMP6 treatment, 10d culture, replicate 2

source_name: mesenchymal stem cells treated 24 hours with BMP6, and harvested at 10 days


title: 24hr BMP6 treatment, 96hr culture, replicate 2

source_name: mesenchymal stem cells treated 24 hours with BMP6, and harvested at 96 hours


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [44]

description: LD/LW x Duroc pigs cross

value: LD/LW x Duroc


title: LN308_CCI_Cy3_rep3

description: bological replicate 3


title: RT112

source_name: Bladder cancer cell line

value: Human bladder carcinoma, relatively fast growing tumour


title: LN308_CCI+Rad_Cy5_rep3

description: bological replicate 3


title: EJ1

value: Human bladder carcinoma, fast growing tumour


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [43]

description: LD/LW x Duroc pigs cross

value: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits

value: 170 days-old


title: BT474_DMSO_24-1

value: breast cancer

value: lapatinib-sensitive

value: DMSO


title: LN308_CCI_Cy5_rep3

description: bological replicate 3


title: LN308_DMSO_Cy5_rep3

description: bological replicate 3


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [46]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [42]

description: LD/LW x Duroc pigs cross


title: 24hr BMP6 treatment, 24hr culture, replicate 2

source_name: mesenchymal stem cells treated 24 hours with BMP6, and harvested at 24 hours

value: vertebral bone marrow mesenchymal stem cell

value: male


title: LN308_DMSO_Cy3_rep3

description: bological replicate 3


title: LN308_DMSO+Rad_Cy5_rep3

description: bological replicate 3

value: DMSO + 4 Gy Radiation


title: 8hr BMP6 treatment, 10d culture, replicate 2

source_name: mesenchymal stem cells treated 8 hours with BMP6, and harvested at 10 days


title: 24hr BMP6 treatment, Control culture, replicate 2

source_name: mesenchymal stem cells cultured 24 hours without BMP6


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [41]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [38]

description: LD/LW x Duroc pigs cross


title: NHEK-10

city: New York

first: Mayte

last: Suarez-Farinas

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: GeneChip Affymetrix protocol

scan_protocol: Hewlett–Packard Gene Array Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor). Each platform was preprocess separately, then merged. An extra quantile normalization was needed to normalized across platforms.

source_name: normal human epidermal keratinocyte

label_protocol: GeneChip Affymetrix protocol

growth_protocol: Primary keratinocytes were cultured in Epilife medium (Cascade Biologics, Portland, OR, U.S.A.) with EDGS (Cascade Biologic) and Penicillin Streptomycin (100 IU mL-1 and 0.1 mg mL-1, respectively) (Gibco, Carlsbad, CA, U.S.A.) at 37 °C. Once 80% confluent, the medium was supplemented with or without the following cytokines: recombinant human (rh)-IL-17 (R&D System, Minneapolis, MN, U.S.A.) 200 ng mL-1 and TNF-α (Sigma-Aldrich Corp, St. Louis, MO, USA) (1 ng mL-1 or 10 ng mL-1) for 24 h before harvesting for other analyses.

extract_protocol: Qiagen RNeasy Kit protocol

tag: group

value: KC vitro

tag: type

value: Vitro


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [4]

description: LD/LW x Duroc pigs cross

tag: breed

tag: age


title: 8hr BMP6 treatment, 24hr culture, replicate 2

source_name: mesenchymal stem cells treated 8 hours with BMP6, and harvested at 24 hours


title: NHEK-9


title: 8hr BMP6 treatment, 8hr culture, replicate 2

source_name: mesenchymal stem cells treated 8 hours with BMP6, and harvested at 8 hours


title: LN308_DMSO_Cy3_rep2

description: bological replicate 2

tag: cell line


title: LN308_DMSO_Cy5_rep2

description: bological replicate 2


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [40]

description: LD/LW x Duroc pigs cross

tag: selection


title: 8hr BMP6 treatment, 96hr culture, replicate 2

source_name: mesenchymal stem cells treated 8 hours with BMP6, and harvested at 96 hours


title: NHEK-6


title: NHEK-8


title: NHEK-7


title: 10d BMP6 treatment, 10d culture, replicate 1


title: LN308_DMSO+Rad_Cy3_rep3

description: bological replicate 3


title: NHEK-4


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [37]

description: LD/LW x Duroc pigs cross


title: LN308_DMSO+Rad_Cy3_rep2

description: bological replicate 2


title: LN308_CCI_Cy5_rep2

description: bological replicate 2


title: 96hr BMP6 treatment, 10d culture, replicate 1

source_name: mesenchymal stem cells treated 96 hours with BMP6, and harvested at 10 days


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [36]

description: LD/LW x Duroc pigs cross


title: 96hr BMP6 treatment, 96hr culture, replicate 1


title: NHEK-3


title: NHEK-5


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [35]

description: LD/LW x Duroc pigs cross


title: LN308_DMSO+Rad_Cy5_rep2

description: bological replicate 2


title: 8hr control culture, replicate 2

source_name: mesenchymal stem cells cultured 8 hours without BMP6

value: control


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [34]

description: LD/LW x Duroc pigs cross

value: Longissimus Dorsi muscle


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [33]

description: LD/LW x Duroc pigs cross


title: NHEK-2


title: NHEK-1


title: 24hr BMP6 treatment, 10d culture, replicate 1


title: 96hr BMP6 treatment, Control culture, replicate 1

source_name: mesenchymal stem cells cultured 96 hours without BMP6


title: 24hr BMP6 treatment, 96hr culture, replicate 1


title: sorted KC-10

source_name: sorted kereatinocyte

value: KC sorted

value: Vivo


title: LN308_CCI_Cy3_rep2

description: bological replicate 2

value: untreated


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [31]

description: LD/LW x Duroc pigs cross

value: LD/LW x Duroc


title: LN308_CCI+Rad_Cy3_rep2

description: bological replicate 2

value: CCI-779 + 4 Gy Radiation


title: 24hr BMP6 treatment, 24hr culture, replicate 1


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [32]

description: LD/LW x Duroc pigs cross

value: Animals selected by composition and conformation traits (intramuscular fat, content of several fatty acids, ratio of saturated, monounsaturated and polyunsaturated fatty acids, and protein and humidity contents) and meat quality (pH24, pH45, Lab colour coordinates, curing yield and exudation at three different times) traits


title: sorted KC-8


title: sorted KC-9


title: sorted KC-7


title: 24hr BMP6 treatment, Control culture, replicate 1


title: LN308_CCI+Rad_Cy5_rep2

description: bological replicate 2


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [30]

description: LD/LW x Duroc pigs cross

value: 170 days-old


title: LN308_CCI_Cy3_rep1

description: bological replicate 1


title: LN308_CCI_Cy5_rep1

description: bological replicate 1


title: LN308_CCI+Rad_Cy5_rep1

description: bological replicate 1


title: sorted KC-6


title: LN308_DMSO_Cy5_rep1

description: bological replicate 1


title: LN308_CCI+Rad_Cy3_rep1

description: bological replicate 1


title: 8hr BMP6 treatment, 96hr culture, replicate 1


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [29]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [28]

description: LD/LW x Duroc pigs cross


title: sorted KC-5


title: 8hr BMP6 treatment, 10d culture, replicate 1


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [25]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [26]

description: LD/LW x Duroc pigs cross


title: sorted KC-4


title: sorted KC-3


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [21]

description: LD/LW x Duroc pigs cross


title: sorted KC-2


title: LN308_DMSO+Rad_Cy3_rep1

description: bological replicate 1


title: 8hr BMP6 treatment, 8hr culture, replicate 1


title: sorted KC-1


title: 8hr control culture, replicate 1


title: 8hr BMP6 treatment, 24hr culture, replicate 1


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [2]

description: LD/LW x Duroc pigs cross


title: LN308_DMSO_Cy3_rep1

description: bological replicate 1


title: LN308_DMSO+Rad_Cy5_rep1

description: bological replicate 1


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [20]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [19]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [18]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [16]

description: LD/LW x Duroc pigs cross


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [14]

description: LD/LW x Duroc pigs cross


title: 18_p53-_TX

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

description: 13_PD7_katie_02-19-11_(MoGene-1_0-st-v1)_2

hyb_protocol: Arrays were hybridized with fragmented and biotin-labeled target (2.5 µg) in 110 µl of hybridization cocktail. Target denaturation was performed a 99oc for 2 min. and then 45oc for 5 min., followed by hybridization for 18 hrs. Arrays then were washed and stained using Genechip Fluidic Station 450, and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA, USA).

scan_protocol: Arrays were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: RMA summarization, PM BG correction, and quantile normalization were performed in Affymetrix Expression Console 1.1

source_name: frozen liver tissue

label_protocol: Labeling was performed by the WT-Ovation Pico RNA amplification system (NuGen Technologies, Inc.)

extract_protocol: RNA was harvested from frozen liver tissue using RNeasy Blood and Tissue kit (Qiagen, Inc., Valencia, CA) according to the manufacturer's suggested protocols, and quantified on a Nanodrop ND-100 spectrophotometer. RNA quality was assessed by analysis on an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Fourteen-day-old mice were given a single interperitoneal (i.p.) injection of diethylnitrosamine (DEN) dissolved in 0.9% saline at a dose of 20 mg/kg body weight.

tag: strain

value: DEN

tag: p53 status

value: KO

tag: rb status

value: WT


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [13]

description: LD/LW x Duroc pigs cross


title: 16_p53-_TX

description: 12_PD6_katie_02-19-11_(MoGene-1_0-st-v1)

tag: treatment


title: R12_Rb-_TX


title: 25_p53-RB-_TX

description: 20_ND7_katie_02-19-11_(MoGene-1_0-st-v1)


title: 13_p53-_TX

description: 11_PD5_katie_02-19-11_(MoGene-1_0-st-v1)


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [15]

description: LD/LW x Duroc pigs cross


title: tra1_L3733A vs. TRA1 (array 2)

source_name: Cy3: CY3003(TRA1::Tn10LUK with IB150(myc9-tra1_L3733A-YCplac111))

tag: Yeast cells were grown in YP media containing 2% glucose to an A600=2.0.

source_name: Cy5: CY2706(TRA1::Tn10LUK with 1980(myc9-TRA1-YCplac111))


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [12]

description: LD/LW x Duroc pigs cross


title: R09_WT_TX


title: Control sample 2

hyb_protocol: Labeled DNA was hybridized to Agilent Mouse Genome 244A CGH Microarrays and arrays were washed according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned with the Agilent Technologies Scanner G2505C at 5 micron resolution.

data_processing: Data was extracted from imaged sample TIFF files using Agilent Feature Extraction v10.5.1.1 using the CGH_105_Dec08 extraction protocol.

source_name: Promega Mouse gDNA

label_protocol: 1ug of genomic DNA digested with Alu I and Rsa I restriction enzymes at 37C for 2 hours. Enzymes were inactivated to stop the reaction by heating the mixture to 65C for 20 minutes. 5ul of Random Primers were added to 24ul of digested gDNA randomly primed at 95C for 3 minutes. 19ul of Cy3/Cy5 labeling master mix was added to each reaction for a final volume of 50ul, Cy3 and Cy5 modified nucleotides were then incorporated by Exo-Klenow fragment at 37C for 2 hours.

extract_protocol: 1ug of each sample at approximately 200ng/ul concentration was used for labeling, hybridization and scanning.

treatment_protocol: Fourteen-day-old mice were given a single interperitoneal (i.p.) injection of diethylnitrosamine (DEN) dissolved in 0.9% saline at a dose of 20 mg/kg body weight. Mouse liver tissues were analyzed 6-months post-treatment for CGH analysis.

tag: reference

value: common reference DNA

value: Pooled genomic DNA from normal mouse liver tissue


title: R10_WT_TX


title: 24_p53-RB-_TX

description: 19_ND6_katie_02-19-11_(MoGene-1_0-st-v1)


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [10]

description: LD/LW x Duroc pigs cross


title: Vibrio vulnificusSmcR transcriptome analysis 3 down

city: Seoul

first: Seung Min

last: Kim

address: 1 Gwanakro

country: South Korea

institute: Seoul National University

hyb_protocol: 1) Activate slide in pre-Hybridization buffer for 30-60 min at 42°C.  2) Wash the slide with D.W..  3) Dry the slide with centrifugation (700 rpm) for 5 min.  4) Add the 35 µl of hybridization buffer into the dried labeled sample tube.  5) Denaturation (95°C, 5min).  6) Centrifuge for 2 min at 11,000 rpm.  7) Mix two labeled samples well.  8) Attach the MAUI lid (heating 65°C).  9) Inject the labeled samples.   10) Sealing.   11) Mix in Lid + slide MAUI Hybridization system (42°C, 16 hrs).

scan_protocol: After hybridization, the arrays were washed, dried and scanned using GenePix 4000B (Axon Instruments, Foster City, CA).

data_processing: Data from three independent experiments were normalized and then analyzed using the GenePix Pro 3.0 software (Axon Instruments).

organism: Vibrio vulnificus

source_name: Total cellular RNA from the wild-type V. vulnificus strains

label_protocol: To synthesize aminoallyl-cDNA, reactions were performed with an Amino Allyl cDNA Labeling Kit (Ambion, Austin, TX) according to the manufacturer’s procedures with 50 µg of total RNA. The aminoallyl-cDNA from the smcR mutant and wild type were respectively labeled with Cy3 or Cy5 (Ambion), and equal amounts of the labeled cDNA were combined.

growth_protocol: The V. vulnificus strains were grown in Luria-Bertani medium supplemented with 2.0% (w/v) NaCl (LBS). All of the media components were purchased from Difco.

extract_protocol: Total cellular RNA from the V. vulnificus strains grown to OD600 1.5 was isolated using an RNeasy® Mini Kit (Qiagen, Valencia, CA) and any residual DNA was removed using DNase I (NEB, Ipswich, MA).

tag: genotype/variation

value: wild type

source_name: Total cellular RNA from the smcR mutant V. vulnificus strains

value: smcR mutant


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [11]

description: LD/LW x Duroc pigs cross


title: Vibrio vulnificusSmcR transcriptome analysis 3 up


title: Tumor sample 5

value: Genomic DNA from dissected mouse liver tumor


title: Tumor sample 2


title: 18_p53-RB-_TX


title: R08_WT_NT


title: TRA1 vs. tra1_L3733A (array 1)

source_name: Cy3: CY2706(TRA1::Tn10LUK with 1980(myc9-TRA1-YCplac111))

source_name: Cy5: CY3003(TRA1::Tn10LUK with IB150(myc9-tra1_L3733A-YCplac111))


title: Tumor sample 3


title: Tumor sample 1


title: Tumor sample 4


title: Vibrio vulnificusSmcR transcriptome analysis 2 down


title: Vibrio vulnificusSmcR transcriptome analysis 2 up


title: 17_p53-RB-_TX


title: Longissimus Dorsi muscle from LD/LW x Duroc pigs cross [1]

description: LD/LW x Duroc pigs cross


title: Control sample 1


title: 15_Rb-_TX


title: 16_p53-RB-_TX


title: Vibrio vulnificusSmcR transcriptome analysis 1 up


title: 14_Rb-_TX


title: A2780 TRT1

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

country: Italy

institute: Nerviano Medical Sciences srl

description: Gene expression data from cell line

hyb_protocol: Extracted RNAs were hybridized to Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array (900466).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (GCS 3000)

data_processing: Microarray data analysis was performed using Bioconductor libraries (www.bioconductor.org). Probe set intensity were calculated using the RMA algorithm.

source_name: A2780 cell line treated with the compound for 24 hrs, biological rep1

label_protocol: Total RNAs extracted from treated and untreated samples were processed according to the manufacturers recommended protocols.

growth_protocol: Human cell lines MCF7, MDA-MB-468, Colo205, HCT116 and A2780 were grown in RMPI 1640 or McCoy’s (HCT116) or MEM (MCF7) + 10% FCS + 2mM Glutamine, and maintained at 37C in an atmosphere of 5% CO2 and 95% room air.

extract_protocol: Total RNA was extracted from each sample using the RNeasy Mini Kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.

treatment_protocol: Compound was dissolved in DMSO at a concentration of 10 mM. Cells were plated at 2x106 cells/100mm plate and after 24 hrs were untreated or exposed to 1uM of the compound for 24 hrs. Two biological replicates were performed for each  treatment.

tag: agent

value: Danusertib

tag: tissue origin

value: Ovary

tag: tp53 status


title: 13_Rb-_TX


title: Vibrio vulnificusSmcR transcriptome analysis 1 down


title: Cy3-Breast, Labeling #1

city: Santa Clara

first: Robert

last: Ach

state: CA

address: 5301 Stevens Creek Boulevard

department: Agilent Laboratories

institute: Agilent Technologies

description: Cy3-Breast, Labeling #1

hyb_protocol: Hybridized 17h at 65C according to Agilent hyb protocol (www.agilent.com)

scan_protocol: G2505A scanner

data_processing: Feature extracted using Agilent Feature Extraction software, v10.2.1.3

source_name: Human Breast tissue

label_protocol: 500ng samples labeled with Agilent Low-Input Linear Amplification Kit, according to manufacturer's protocol (www.agilent.com)

extract_protocol: Total RNA prepared by Ambion (ABI). According to the manufacturer, RNA was prepared using a modified version of Ambion's ToTALLY RNA Kit for RNA isolation. Tissues were stored in RNAlater stabilization solution or frozen until processed. RNA was DNase-treated to minimize DNA contamination.

tag: tissue

value: Breast

tag: commercial provider

value: Ambion (ABI) (Life Technologies)

tag: lot number

tag: gender

value: female


title: A2780 CTRL2

description: Gene expression data from cell line

source_name: A2780 cell line untreated 24 hrs, biological rep2


title: Cy3-Brain, Labeling #1

description: Cy3-Brain, Labeling #1

source_name: Human Brain tissue

value: Brain

value: male

tag: age


title: A2780 TRT2

description: Gene expression data from cell line

source_name: A2780 cell line treated with the compound for 24 hrs, biological rep2

tag: cell line


title: A2780 CTRL1

description: Gene expression data from cell line

source_name: A2780 cell line untreated 24 hrs, biological rep1


title: Bingchenggensis_120hr

city: Haerbin

first: zhang

last: bo

state: Heilongjiang

address: Mucai street 59#

department: Life Sciences

institute: Northeast Agricultural University

description: gene expression after 120hr in mycelium

hyb_protocol: the labelled cDNAs were then rolling hybridized in the  hybridization oven G2545A (Agilent) for 17 h at 65°C and 10rpm on individual GeneChips.After hybridization, GeneChips were washed by using the Gene Expression Wash Buffer Kit (Agilent, 5188-5327).

scan_protocol: Fluorescent images of the microarrays were acquired using a GeneChip Scanner G2565BA (Agilent) in the resolution of 5μm, auto in 100% and 10%PMT.

data_processing: Agilent's Feature Extraction Software was used for array image analysis and the calculation of  spot  intensity  measurements  which  are  considered  to  be  raw  data  for  the  purposes  of   this study. The raw data files which contain  “ProcessedSignal  ”were processed using the limma package developed within the Bioconductor project  in  the  R  statistical  programming environment. After log transformation, the data normalized using “quantile” method. Whole expressional data results were filtered, and the processed data was used to statistically analyze the data with absolute log2 fold change value cut off  at 1.

organism: Streptomyces bingchenggensis

source_name: mycelium, 120hr, replicate 1

label_protocol: The protocol consists in cDNA synthesis by reverse transcription (starting with 2 µg RNA), followed by cDNA fragmentation with DNase I and labeling with Cy3 and purified by the RNeasy® Mini Kit (QIAGEN),

growth_protocol: The seed for preculture was spores. The medium for sporulation contained sucrose 4.0 g, yeast extract 2.0 g, malt extract 5.0 g and skimmed milk powder 1.0 g in 1l water. The pH was adjusted to 7.0 with 1 M NaOH, 20 g of agar was added and this mixture was sterilized at 121 ℃ for 30 min. The spore suspension was prepared from agar plates incubated at 28℃ for 7–8 days. A spore suspension of the culture of strain S.bingchenggensis, 1.0 ml, was transferred to a 250-ml Erlenmeyer ﬂask that contained 25 ml of the seed medium containing sucrose 0.25 g, polypepton 0.0875 g, yeast extract 0.125 g and K2HPO4 1.25 mg.Then 0.8 ml of the culture was transferred into a 250-ml Erlenmeyer ﬂask containing 25 ml of the producing medium consisting of sucrose 8.0%, soybean powder (boil and filter) 1.0%, yeast extract 0.2%, meat extract 0.1%, CaCO3 0.3%, K2HPO4 0.03%, MgSO4•7H2O 0.1% and FeSO4•7H2O 0.005%. The medium pH was 7.2 before sterilization.

extract_protocol: RNA was extracted from mycelium pellets deriving from 1-ml culture samples using the mirVana TM RNA Isolation Kit (Applied Biosystem p/n AM1556) recovering it in 50 µl of Elution Solution.The extracted RNAs were purified by using RNeasy® Kit (QIAGEN) to be for suitable microarray  hybridization.

tag: time point

value: mycelium


title: Bingchenggensis_144hr

description: gene expression after 144hr in mycelium

source_name: mycelium, 144hr, replicate 1


title: Colo205 TRT1

description: Gene expression data from cell line

source_name: Colo205 cell line treated with the compound for 24 hrs, biological rep1

value: Colon

value: mut


title: 10_p53-_TX

source_name: frozen liver tissue

tag: strain

value: DEN

value: KO


title: Colo205 TRT2

description: Gene expression data from cell line

source_name: Colo205 cell line treated with the compound for 24 hrs, biological rep2


title: 12_p53-_TX

tag: p53 status

value: WT


title: Cy3-Thymus, Lableing #2

description: Cy3-Thymus, Lableing #2

source_name: Human Thymus tissue

value: Thymus


title: Cy3-Testes, Labeling #2

description: Cy3-Testes, Labeling #2

source_name: Human Testes tissue

value: Testes


title: Bingchenggensis_96hr

description: gene expression after 96hr in mycelium

source_name: mycelium, 96hr, replicate 1


title: Cy3-Placenta, Labeling #2

description: Cy3-Placenta, Labeling #2

source_name: Human Placenta tissue

value: Placenta


title: 09_WT_TX

tag: rb status


title: Cy3-Ovary, Labeling #2

description: Cy3-Ovary, Labeling #2

source_name: Human Ovary tissue


title: Colo205 CTRL1

description: Gene expression data from cell line

source_name: Colo205 cell line untreated 24 hrs, biological rep1


title: Colo205 CTRL2

description: Gene expression data from cell line

source_name: Colo205 cell line untreated 24 hrs, biological rep2


title: Cy3-SkMuscle, Labeling #2

description: Cy3-SkMuscle, Labeling #2

source_name: Human Skeletal Muscle tissue

value: Skeletal Muscle


title: Bingchenggensis_72hr

description: gene expression after 72hr in mycelium

source_name: mycelium, 72hr, replicate 1


title: Bingchenggensis_69hr

description: gene expression after 69hr in mycelium

source_name: mycelium, 69hr, replicate 1


title: 08_WT_TX

tag: treatment


title: Bingchenggensis_60hr

description: gene expression after 60hr in mycelium

source_name: mycelium, 60hr, replicate 1


title: HCT-116 TRT2

description: Gene expression data from cell line

source_name: HCT-116 cell line treated with the compound for 24 hrs, biological rep2

value: Danusertib


title: Cy3-Liver, Labeling #2

description: Cy3-Liver, Labeling #2

source_name: Human Liver tissue

value: Liver


title: 05_p53-RB-_NT


title: Bingchenggensis_57hr

description: gene expression after 57hr in mycelium

source_name: mycelium, 57hr, replicate 1


title: Cy3-Heart-Labeling #2

description: Cy3-Heart-Labeling #2

source_name: Human Heart tissue

value: Heart


title: Cy3-Breast, Labeling #2

description: Cy3-Breast, Labeling #2

source_name: Human Breast tissue

value: Breast

value: Ambion (ABI) (Life Technologies)


title: 04_p53-RB-_NT

source_name: frozen liver tissue


title: Bingchenggensis_45hr

description: gene expression after 45hr in mycelium

source_name: mycelium, 45hr, replicate 1


title: 03_WT_NT


title: 06_p53-RB-_NT


title: Cy3-Testes, Labeling #1

description: Cy3-Testes, Labeling #1

source_name: Human Testes tissue


title: HCT-116 TRT1

description: Gene expression data from cell line

source_name: HCT-116 cell line treated with the compound for 24 hrs, biological rep1


title: Cy3-Brain, Labeling #2

description: Cy3-Brain, Labeling #2

source_name: Human Brain tissue

value: Brain


title: MDA-MB-468 TRT2

description: Gene expression data from cell line

source_name: MDA-MB-468 cell line treated with the compound for 24 hrs, biological rep2


title: HCT-116 CTRL1

description: Gene expression data from cell line

source_name: HCT-116 cell line untreated 24 hrs, biological rep1


title: HCT-116 CTRL2

description: Gene expression data from cell line

source_name: HCT-116 cell line untreated 24 hrs, biological rep2


title: 07_WT_TX


title: Cy3-Thymus, Lableing #1

description: Cy3-Thymus, Lableing #1

source_name: Human Thymus tissue

value: male


title: MDA-MB-468 TRT1

description: Gene expression data from cell line

source_name: MDA-MB-468 cell line treated with the compound for 24 hrs, biological rep1


title: Bingchenggensis_51hr

description: gene expression after 51hr in mycelium

source_name: mycelium, 51hr, replicate 1

value: mycelium


title: Bingchenggensis_42hr

description: gene expression after 42hr in mycelium

source_name: mycelium, 42hr, replicate 1


title: Bingchenggensis_39hr

description: gene expression after 39hr in mycelium

source_name: mycelium, 39hr, replicate 1


title: 02_WT_NT


title: MDA-MB-468 CTRL2

description: Gene expression data from cell line

source_name: MDA-MB-468 cell line untreated 24 hrs, biological rep2


title: Cy3-SkMuscle, Labeling #1

description: Cy3-SkMuscle, Labeling #1

source_name: Human Skeletal Muscle tissue


title: Cy3-Placenta, Labeling #1

description: Cy3-Placenta, Labeling #1

source_name: Human Placenta tissue

value: female


title: GFP2

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: Brain cells with GFP staining purified by FACS

hyb_protocol: The hybridization cocktails containing 2.5 ug of the fragmented, end-labeled cDNA were applied to the GeneChip® Mouse Gene 1.0 ST arrays. Hybridization was performed for 16 hours, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script.

scan_protocol: Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to produce CEL intensity files.

data_processing: Data were background corrected with GC bin, quantile normalized and summarized by interPLIER algorithm with Affymetrix Expression Console.

label: Biotin

source_name: GFP+ cortical cells

label_protocol: One µg of each sample was processed using the Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf)

growth_protocol: In vivo mouse brain cells

extract_protocol: Qiagen RNA extraction kit was used according to manufacturer's guide

treatment_protocol: RFP or GFP staining pattern

value: brain

tag: cell type

value: cortical neural progenitor

tag: developmental stage

value: progenitor

tag: reporter

value: GFP


title: GFP3


title: Cy3-Ovary, Labeling #1

description: Cy3-Ovary, Labeling #1

source_name: Human Ovary tissue

value: Ovary


title: Bingchenggensis_24hr

description: gene expression after 24hr in mycelium

source_name: mycelium, 24hr, replicate 1


title: MDA-MB-468 CTRL1

description: Gene expression data from cell line

source_name: MDA-MB-468 cell line untreated 24 hrs, biological rep1

tag: agent

value: mut


title: GFP1


title: Bingchenggensis_30hr

description: gene expression after 30hr in mycelium

source_name: mycelium, 30hr, replicate 1


title: MCF7 TRT2

description: Gene expression data from cell line

source_name: MCF7 cell line treated with the compound for 24 hrs, biological rep2

tag: tissue origin

value: WT


title: Bingchenggensis_33hr

description: gene expression after 33hr in mycelium

source_name: mycelium, 33hr, replicate 1


title: Bingchenggensis_18hr

description: gene expression after 18hr in mycelium

source_name: mycelium, 18hr, replicate 1


title: RFP2

description: Brain cells with RFP staining purified by FACS

source_name: RFP+ cells

value: neuronal progeny

value: Differentiated

value: RFP


title: RFP1


title: Cy3-Liver, Labeling #1

description: Cy3-Liver, Labeling #1

source_name: Human Liver tissue

value: Liver


title: RFP3


title: Bingchenggensis_12hr

description: gene expression after 12hr in mycelium

source_name: mycelium, 12hr, replicate 1


title: Cy3-Breast, Labeling #1

description: Cy3-Breast, Labeling #1

source_name: Human Breast tissue

value: Breast


title: Cy3-Heart-Labeling #1

description: Cy3-Heart-Labeling #1

source_name: Human Heart tissue

value: Heart

value: Ambion (ABI) (Life Technologies)


title: MCF7 TRT1

description: Gene expression data from cell line

source_name: MCF7 cell line treated with the compound for 24 hrs, biological rep1

value: Danusertib

tag: tp53 status


title: Cy3-Brain, Labeling #1

description: Cy3-Brain, Labeling #1

source_name: Human Brain tissue

tag: tissue

value: Brain

value: male


title: MCF7 CTRL1

description: Gene expression data from cell line

source_name: MCF7 cell line untreated 24 hrs, biological rep1


title: IOTA24C

status: Public on Sep 19 2011

city: Burlington

first: Jeffrey

middle: P

last: Bond

state: VT

address: 95 Carrigan Dri e

department: Microbiology and Molecular Genetics

institute: University of Vermont

hyb_protocol: Standard Affymetrix protocols were used at 45°C, for 16h, at 60 pm

scan_protocol: Standard Affmetrix protocols were followed using GS3000.

data_processing: Robust Multi-array Average (RMA) using GeneSifter software.

source_name: Human ovarian epithelial cells (IOSE 398), 24h

label_protocol: RNA samples were converted to double stranded cDNA using a standard Eberwine synthesis reaction using reverse transcriptase and T7-oligo d[T] according to the manufacturers instructions (Affymetrix, Santa Clara, CA). Following a column-based clean up of the double strand cDNA, an in-vitro transcription amplification reaction was performed to generate biotinylated-cRNA. cRNA was fragmented and prepared as an Affymetrix  hybridization solution.

growth_protocol: IOSE cells were maintained in 50:50 199/MCB105 medium containing 10% FBS and 50 μg/ml gentamicin. Cells at near confluency were switched to maintenance medium containing 0.5% FBS for 24 h prior to particulate exposure.

extract_protocol: Total RNA was extracted from treated and control cells using an RNeasy Plus Mini kit according to the manufacturers protocol (Qiagen, Valencia, CA).

treatment_protocol: The surface area of asbestos fibers and particles was measured using nitrogen gas sorption analysis. Fiber and particle size dimensions were determined by scanning electron microscopy. Following sterilization under ultraviolet light overnight to avoid endotoxin and microbial contamination, particulates were suspended in HBSS at 1 mg/ml, sonicated for 15 min in a water bath sonicator, and triturated 5 X through a 22-gauge needle. This suspension was added to cell medium at 75 micrometer^2 / centimeter^2 for 24h.

value: IOSE 398

value: ovarian epithelial

tag: treatment time


title: IOCR24C


title: IOTA24A


title: IOTA24B


title: IOTI24B


title: MCF7 CTRL2

description: Gene expression data from cell line

source_name: MCF7 cell line untreated 24 hrs, biological rep2


title: IOCO24C

treatment_protocol: The surface area of asbestos fibers and particles was measured using nitrogen gas sorption analysis. Fiber and particle size dimensions were determined by scanning electron microscopy. Following sterilization under ultraviolet light overnight to avoid endotoxin and microbial contamination, particulates were suspended in HBSS at 1 mg/ml, sonicated for 15 min in a water bath sonicator, and triturated 5 X through a 22-gauge needle. This suspension was added to cell medium at 0 micrometer^2 / centimeter^2 for 24h.


title: IOTI24C


title: IOCR24A


title: IOTI24A


title: IOCO24B


title: IOCR24B


title: IOCR8A

source_name: Human ovarian epithelial cells (IOSE 398), 8h

treatment_protocol: The surface area of asbestos fibers and particles was measured using nitrogen gas sorption analysis. Fiber and particle size dimensions were determined by scanning electron microscopy. Following sterilization under ultraviolet light overnight to avoid endotoxin and microbial contamination, particulates were suspended in HBSS at 1 mg/ml, sonicated for 15 min in a water bath sonicator, and triturated 5 X through a 22-gauge needle. This suspension was added to cell medium at 75 micrometer^2 / centimeter^2 for 8h.


title: IOCR8C


title: IOTA8C


title: IOCR8B


title: IOTI8C


title: IOC024A


title: IOCO8A

treatment_protocol: The surface area of asbestos fibers and particles was measured using nitrogen gas sorption analysis. Fiber and particle size dimensions were determined by scanning electron microscopy. Following sterilization under ultraviolet light overnight to avoid endotoxin and microbial contamination, particulates were suspended in HBSS at 1 mg/ml, sonicated for 15 min in a water bath sonicator, and triturated 5 X through a 22-gauge needle. This suspension was added to cell medium at 0 micrometer^2 / centimeter^2 for 8h.


title: IOTA8A


title: IOC08C


title: IOCO8B


title: LPCR124B

source_name: Human mesothelial (LP9/TERT-1), 24h

growth_protocol: LP9/TERT-1 cells were maintained in 50:50 DMEM/F-12 medium containing 10% fetal bovine serum (FBS), and supplemented with penicillin (50 units/ml) streptomycin (100 μg/ml), hydrocortisone (100 μg/ml), insulin (2.5 μg/ml), transferrin (2.5 μg/ml) and selenium (2.5 μg/ml).

treatment_protocol: The surface area of asbestos fibers and particles was measured using nitrogen gas sorption analysis. Fiber and particle size dimensions were determined by scanning electron microscopy. Following sterilization under ultraviolet light overnight to avoid endotoxin and microbial contamination, particulates were suspended in HBSS at 1 mg/ml, sonicated for 15 min in a water bath sonicator, and triturated 5 X through a 22-gauge needle. This suspension was added to cell medium at 15 micrometer^2 / centimeter^2 for 24h.

value: mesothelial


title: IOTI8B


title: IOTI8A


title: LPCR124A


title: IOTA8B


title: LPTA124A


title: LPTA124B


title: LPTI124C


title: LPCR58A

source_name: Human mesothelial (LP9/TERT-1), 8h


title: LPTA124C


title: LPCO24B


title: LPCR58B


title: LPGB524B


title: LPCO24C


title: LPCR124C


title: LPTI124B


title: LPGB524A


title: LPCR58C


title: LPTI124A


title: LPCO24A


title: LPGB524C


title: LPCR18C

treatment_protocol: The surface area of asbestos fibers and particles was measured using nitrogen gas sorption analysis. Fiber and particle size dimensions were determined by scanning electron microscopy. Following sterilization under ultraviolet light overnight to avoid endotoxin and microbial contamination, particulates were suspended in HBSS at 1 mg/ml, sonicated for 15 min in a water bath sonicator, and triturated 5 X through a 22-gauge needle. This suspension was added to cell medium at 15 micrometer^2 / centimeter^2 for 8h.


title: LPCR18A


title: LPTA58B


title: LPTA18A


title: LPTA58C


title: LPTA18C


title: LPTA58A


title: LPTI18C


title: LPTI18B


title: LPTI18A


title: LPCO8B


title: LPCO8C


title: LPCO8A


title: LPCR18B


title: LPTA18B


title: H1ESC ELAVL1 RIP RNA Rep2

city: Albany

first: Frank

last: Doyle

address: 257 Fuller Rd

department: Nanobiology

institute: UAlbany CNSE

description: Immunoprecipitated RNA as part of ribonucleoprotein complexes

hyb_protocol: Affymetrix Standard

scan_protocol: Affymetrix GeneChipScanner 30007G using Affymetrix Gene Chip Command Console v3.1

data_processing: Agilent GeneSpringGX software (version 11.0) Iterative PLIER 16 with quantile normalization applied across replicates within replicate groups

source_name: H1ESC ELAVL1 RIP RNA

label_protocol: Nugen pico

growth_protocol: Obtained from Cellular Dynamics International (http://www.cellulardynamics.com/)

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeSunyAlbanyGeneSt#TRACK_HTML
RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols. Antibodies specific to the RNA Binding Protein (RBP) in question were first coated onto protein A/G containing magnetic beads and then used to immunoprecipitate the targeted, endogenously-formed mRNP complexes. Antibody-coated beads were incubated/tumbled with cell lysate overnight in the cold followed by extensive rinsing and subsequent purification of associated RNA using Phenol/Chloroform extraction and ethanol precipitation.

tag: rip antibody


title: HepG2 PABPC1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_09_HepG2_PABP_0002_6_2_03302010_(HuGene-1_0-st-v1).CEL

source_name: HepG2 PABPC1 RIP RNA

label_protocol: Affymetrix WT standard


title: H1ESC Negative Control Rep2

source_name: H1ESC T7 control RIP RNA

value: anti-bacteriophage coat protein T7


title: HepG2 Negative Control Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_HepG2_G10_pool_06032010_(HuGene-1_0-st-v1).CEL

source_name: HepG2 T7 control RIP RNA


title: HepG2 ELAVL1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_12_HepG2_HUR_0003_5_3_03302010_(HuGene-1_0-st-v1).CEL

source_name: HepG2 ELAVL1 RIP RNA


title: H1ESC Negative Control Rep3


title: HepG2 Negative Control Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_HEPG2_G10_0018_06162010_(HuGene-1_0-st-v1).CEL


title: HeLaS3 PABPC1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_04_HeLa_PABP_0008_4_8_03302010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 PABPC1 RIP RNA


title: H1ESC Total RNA Rep2

description: total cellular RNA as input into the accompanying RIP samples

source_name: H1ESC RIP input RNA (total)


title: HeLaS3 ELAVL1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_06_HeLa_HUR_0002_3_2_03302010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 ELAVL1 RIP RNA


title: HepG2 Total RNA Rep2

description:
total cellular RNA as input into the accompanying RIP samples
ST_13_HepG2_total002_5_4_03172010_(HuGene-1_0-st-v1).CEL

source_name: HepG2 RIP input RNA (total)


title: HeLaS3 PABPC1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_03_HeLa_PABP_0006_4_6_03302010_(HuGene-1_0-st-v1).CEL


title: H1ESC Total RNA Rep3


title: P493 anti Myc (Epi)

city: Baltimore

first: Hongkai

last: Ji

state: MD

address: 615 North Wolfe Street, Rm E3638

department: Department of Biostatistics

institute: Johns Hopkins Bloomberg School of Public Health

description:
control CEL files KZel-MycChIP-P493aHGF-1a-HuProm1.CEL and KZel-MycChIP-P493aHGF-3a-HuProm1.CEL were also used and are provided on the Series record as supplementary files.
Myc ChIP with Epitomics antibody in P493-6 B cells, Rep 1-2, promoter

hyb_protocol: The labeled DNA was hybridized to the Affymetrix GeneChip human promoter arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA. The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 2.0 (AGCC v2.0) software from Affymetrix, using the standard default settings

data_processing:
Data was quantile normalized and analyzed with TileMapv2 implemented in CisGenome software. Log2(IP/Input) fold changes (fc) and TileMap moving average (ma) statistics were reported in BAR files.
fc.bar and ma.bar are generated by CisGenome software. fc.bar contains log2(IP/Control) fold changes for each probe. ma.bar contains a moving average statistic (i.e. the MA statistic in TileMap) for each probe. bed files contain all high quality binding sites reported in the paper.

source_name: ChIP-DNA P493 anti Myc Epitomics

label_protocol: 7.5 ug of amplified ChIP DNA was fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes.

growth_protocol: All cells were grown in defined growth media and were in log phase collected for ChIP

extract_protocol: Cells were treated with 1% formaldehyde to crosslink DNA and proteins. Cells were washed and nuclei were isolated, lysed and chromatin was sheared. Chromatin was immunoprecipitated with either anti MYC or anti rabbit IgG. Purified DNA was amplified and labeled following Affymetrix Chromatin Immunoprecipitatin Assay protocol.

value: Human B cell line

tag: antibody

value: Anti Myc Epitomics (1472-1  Lot# YE122601-2)

source_name: ChIP-DNA P493 anti rabbit IgG

value: Human P493-6 B cell line

value: Anti rabbit IgG


title: P493 anti Myc (SC)

description:
control CEL file KZel-MycChIP-P493aHGF-1a-HuProm1.CEL was also used and is provided on the Series record as supplementary files.
Myc ChIP with Santa Cruz antibody in P493-6 B cells, Rep 1-3, promoter

source_name: ChIP-DNA P493 anti Myc santa cruz

value: Anti Myc Santa Cruz (Cat # SC-764)

value: Anti rabbit IgG (Cat#SC-2027)


title: H9 anti Myc

description:
control CEL file KZel-MycChIP-H9aHGF-3a-HuProm1.CEL was also used and is provided on the Series record as supplementary files.
Myc ChIP with Santa Cruz antibody in H9 human ES cells, Rep 1-3, promoter

source_name: ChIP DNA H9 anti Myc Santa Cruz

value: human embryonic cell line

source_name: ChIP DNA H9 anti rabbit IgG

value: Human H9 embryonic cell line


title: H1ESC ELAVL1 RIP RNA Rep3


title: HepG2 Total RNA Rep3

description:
total cellular RNA as input into the accompanying RIP samples
ST_14_HepG2_total003_5_5_03172010_(HuGene-1_0-st-v1).CEL


title: HepG2 PABPC1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_10_HepG2_PABP_0003_6_3_03302010_(HuGene-1_0-st-v1).CEL


title: HepG2 ELAVL1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_13_HepG2_HUR_0008_5_8_03302010_(HuGene-1_0-st-v1).CEL


title: HeLaS3 ELAVL1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_07_HeLa_HUR_0004_3_4_03302010_(HuGene-1_0-st-v1).CEL


title: HeLaS3 Total RNA Rep2

description:
total cellular RNA as input into the accompanying RIP samples
ST_09_HeLa_total001_5_1_03172010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 RIP input RNA (total)


title: HeLaS3 Negative Control Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_HeLa_G10_pool_06032010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 T7 control RIP RNA


title: HeLaS3 Total RNA Rep3

description:
total cellular RNA as input into the accompanying RIP samples
ST_10_HeLa_total002_5_2_03182010_(HuGene-1_0-st-v1).CEL


title: HeLaS3 Negative Control Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_15_HeLa_G10_pool1_03172010_(HuGene-1_0-st-v1).CEL


title: K562 SLBP RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST K562_SLBP3_0007and0009_04282010_(HuGene-1_0-st-v1).CEL

source_name: K562 SLBP RIP RNA

value: anti-SLBP


title: P493-6 tet 48hr biological rep1

description: Human P493-6 cell line tet treated 48hr

hyb_protocol: The labeled sense strand DNA was hybridized to the Affymetrix GeneChip human Exon 1.0 ST arrays for 17hr at 45 C with constant rotation (60 rpm).  Affymetrix Fluidics Station 450 was used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cDNA.  The staining was further amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.

scan_protocol: Fluorescence was detected using the Affymetrix G3000 GeneArray Scanner and image analysis of each GeneChip was perfomed through the Affymetrix GeneChip Command Console version 2.0 (AGCC v2.0) software from Affymetrix, using the standard default settings.

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.comprehensive.mps

source_name: human cell line tet treated 48 hrs

label_protocol: RNA samples were labeled using the Whole Transcript Sense Target Labeling protocol described by Affymetrix and reagent from Affymetrix. Briefly, ribosomal RNA was reduced from the samples using Ribominus Human/Mouse Transcriptome isolation kit (Invitrogen, Carlsbad, California) from 1 micrograms of total RNA.  The isolated RNA was then used to synthesize first strand cDNA using random oligonucleotides with T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California).  Following the double stranded cDNA synthesis, the product was purified using cDNA clean-up column, and cRNA was generated through in vitro transcription.  10 ug of cRNA was then used to generate sense strand cDNA using random primer, dNTP-dUTP mix, and Superscript II reverse transcriptase (Invitrogen, Carlsbad, California).  Sense strand cDNA was then purified using cDNA clean-up column, fragmented using UDG and APE at 37C for 60 minutes, and terminal labeled with biotinylated nucleotide and terminal DNA transferase at 37C for 60 minutes

growth_protocol: P493-6 cells were grown in RPMI medium

extract_protocol: Total RNA from both untreated and tet treated cells were extracted using a Qiagen RNeasy kit.

treatment_protocol: Treated cells were incubated with 0.1 ug/ml of tetracycline for 48 hrs

value: P493-6 cells

value: 48hrs with tet


title: K562 PABPC1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_K562_PABP_IP7_10_03042010_(HuGene-1_0-st-v1).CEL

source_name: K562 PABPC1 RIP RNA


title: K562 CELF1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_K562_CUGBP_3_0020_06032010_(HuGene-1_0-st-v1).CEL

source_name: K562 CUGBP1 RIP RNA


title: K562 CELF1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_K562_CUGBP_2_0019_06032010_(HuGene-1_0-st-v1).CEL


title: P493-6 tet 48hr biological rep3

description: Human P493-6 cell line tet treated 48hr


title: P493-6 untreated biological rep3

description: Human P493-6 cell line untreated

source_name: human cell line untreated

value: untreated


title: K562 PABPC1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_K562_PABP_IP3_07_03112010_(HuGene-1_0-st-v1).CEL


title: K562 SLBP RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
SLBP_IP_2_07152009_(HuGene-1_0-st-v1).CEL


title: P493-6 tet 48hr biological rep2

description: Human P493-6 cell line tet treated 48hr


title: K562 ELAVL1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
15_HuR_IP_K562_10222009_(HuGene-1_0-st-v1).CEL

source_name: K562 ELAVL1 RIP RNA


title: LP1_BETi_4hr_rep2

city: Cambridge

first: Barbara

middle: M

last: Bryant

state: MA

address: 215 First Street

institute: Constellation Pharmaceuticals

hyb_protocol: The fragmented and labelled ST-cDNA was added to the hybridization cocktail in accordance with the NuGEN™ guidelines for hybridization onto Affymetrix GeneChip® arrays. Following the hybridization for 18 hours at 45°C in an Affymetrix GeneChip® Hybridization Oven 640, the array was washed and stained on the GeneChip® Fluidics Station 450 using the appropriate fluidics script.

scan_protocol: The arrays were inserted into the Affymetrix autoloader carousel and scanned using the GeneChip Scanner 3000.  Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: CEL files were processed by the Affymetrix Expression Console software package using the gene-level RMA algorithm on the core set of probesets and the annotation file Huex-1_0-st-v2_na31_hg19 provided by Affmyetrix.

source_name: LP1 cell line, 4hr after treatment with BET inhibitor

label_protocol: Total RNA was amplified using the NuGEN Applause™ WT Amp Plus ST Amplification System. First-strand synthesis of cDNA was performed using a unique first-strand DNA/RNA chimeric primer mix, resulting in cDNA/mRNA hybrid molecules. Following fragmentation of the mRNA component of the cDNA/mRNA molecules, second-strand synthesis was performed and double-stranded cDNA was formed with a unique DNA/RNA heteroduplex at one end. In the final amplification step, RNA within the heteroduplex was degraded using RNaseH, and replication of the resultant single-stranded cDNA was achieved through DNA/RNA chimeric primer binding and DNA polymerase enzymatic activity.  A modification step targeting the amplified single-stranded cDNA resulted in the generation of sense target (ST) cDNA product compatible with the Affymetrix  GeneChip® Exon arrays.  The ST-cDNA was purified for accurate quantitation and to ensure optimal performance during the fragmentation and labeling process. The ST- cDNA was assessed using spectrophotometric methods in combination with the Agilent Bioanalyzer.  The appropriate amount of amplified ST-cDNA was fragmented and labeled using the Encore™ Biotin Module. The enzymatically and chemically fragmented product (50-100 nt) was labeled via the attachment of biotinylated nucleotides onto the 3'-end of the fragmented ST-cDNA.

growth_protocol: LP1 cells were cultured in IMDM/10% Fetal Bovine Serum/1% penicillin/streptomycin.  Raji cells were cultured in RPMI/10% Fetal Bovine Serum/1% penicillin/streptomycin.

extract_protocol: Total RNA was prepared using a Qiagen RNEasy Mini Kit with on column DNAse digestion according to the manufacturer's instructions.

treatment_protocol: LP1 or Raji cells were treated with the active or inactive BET inhibitor at 500 nM for 4 or 8 h.

value: BET inhibitor

tag: treatment time (hours)


title: P493-6 untreated biological rep1

description: Human P493-6 cell line untreated

tag: cell line


title: Raji_inactive_8hr_rep2

source_name: Raji cell line, 8hr after treatment with inactive enantiomer

value: Raji

value: Inactive enantiomer


title: P493-6 untreated biological rep2

description: Human P493-6 cell line untreated


title: LP1_none_0hr_rep2

source_name: LP1 cell line, 0hr after treatment with no compound


title: Raji_BETi_8hr_rep2

source_name: Raji cell line, 8hr after treatment with BET inhibitor


title: K562 ELAVL1 RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
14_HuR_IP_K562_10222009_(HuGene-1_0-st-v1).CEL


title: LP1_inactive_8hr_rep1

source_name: LP1 cell line, 8hr after treatment with inactive enantiomer


title: GM12878 IGF2BP1  RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
IMP_IP_6_GM12878_08102009.CEL

source_name: GM12878 IGF2BP1 RIP RNA


title: LP1_BETi_8hr_rep1

source_name: LP1 cell line, 8hr after treatment with BET inhibitor


title: K562 Total RNA Rep2

description:
total cellular RNA as input into the accompanying RIP samples
G10_Input_K562_07152009_(HuGene-1_0-st-v1).CEL

source_name: K562 RIP input RNA (total)


title: K562 Total RNA Rep3

description:
total cellular RNA as input into the accompanying RIP samples
SLBP_Input_07152009_(HuGene-1_0-st-v1).CEL


title: LP1_inactive_4hr_rep1

source_name: LP1 cell line, 4hr after treatment with inactive enantiomer


title: LP1_none_0hr_rep1


title: K562 Negative Control Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_01_T7_IP_K562_12072009_(HuGene-1_0-st-v1).CEL

source_name: K562 T7 control RIP RNA


title: K562 Negative Control Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
G10_IP_K562_07152009_(HuGene-1_0-st-v1).CEL


title: GM12878 IGF2BP1  RIP RNA Rep2

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
IMP_IP_5_GM12878_08102009.CEL


title: Raji_inactive_4hr_rep2

source_name: Raji cell line, 4hr after treatment with inactive enantiomer


title: Raji_inactive_8hr_rep1


title: GM12878 CELF1 RIP RNA Rep3

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
CUGBP1_IP_28_GM12878_08052009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 CUGBP1 RIP RNA