title: L-428 tGFP/EBF1 rep2

description: sorted tGFP-positive cells


title: L-1236 tGFP rep1

status: Public on Nov 01 2012

type: RNA

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

country: Germany

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description: sorted tGFP-positive cells

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project. Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: L-1236 tGFP

label_protocol: Samples were labelled with WT terminal labelling Kit (Affymetrix, Fremont, USA), washed and stained using the HWS Kit (Affymetrix).

growth_protocol: Cell lines were purchased from DSMZ (Braunschweig, Germany) and cultured in RPMI 1640 supplemented with 10% fetal calf serum (Biochrom; Berlin, Germany), 2 mM glutamine (Invitrogen; Groningen, The Netherlands) and 1% penicillin G/streptomycin sulfate (Invitrogen).

extract_protocol: RNA from tGFP-positive cells was extracted using the RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA was amplified with the WT Expression Kit (Ambion, Austin, USA).

treatment_protocol: L-428 and L-1236 cells were transduced with tGPF-IRES-EBF1 or tGFP-only, cultured for eight days, and sorted according to their tGFP positivity.

tag: cell line

tag: transduction

value: tGFP-only


title: H1 hESC small bio rep4

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Sort based on forward vs side scatter

hyb_protocol: For each array, 15ug of amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Affymetrix Eukaryotic Target Hybridization Controls and protocol.

scan_protocol: Arrays were then scanned with an Affymetrix Scanner 3000.

data_processing: Data was obtained using the Genechip® Operating Software.

source_name: human embryonic stem cell WiCell

label_protocol: Starting with 1ug of total RNA, biotin-labeled cRNA was produced using the Affymetrix 3’ Amplification One-Cycle Target labeling kit according to manufacturer’s protocol.

growth_protocol: H1 hESCs were grown on 6-well gelatinized plates containing a feeder layer of irradiated MEF cells

extract_protocol: RNA from sorted subpopulations was isolated using a midi-Rneasy Qiagen kit and treated with Dnase1 (Invitrogen).

treatment_protocol: H1 hESCs were isolated using forward and side scatter and collected in tubes on a flow cytometer.

tag: sample type

value: FACs sorted small subpopulation of H1 hESC

value: H1 hESC

tag: cell type

value: small subpopulation


title: Anther uninucleate, biological rep3

city: Ottawa

first: Frances

last: Tran

address: 960 Carling Avenue

country: Canada

institute: Agriculture & Agri-Food Canada

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_UNM3

hyb_protocol: Chip hybridization for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

scan_protocol: Wheat GeneChips were scanned by the McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

data_processing: The data was normalized using the Robust Multichip Average (RMA) normalization algorithm which include background correction, quantile normalization, and a median polish summarization.  The data was analyzed using ArrayStar4 (DNAstar) software package.

organism: Secale cereale x Triticum turgidum subsp. durum

source_name: Triticale anthers at uninucleate microspore developmental stage

label_protocol:
Biotinylated  cRNA was synthesized according to standard Affymetrix protocol using the 3'IVT  Express kit from 1ug total RNA
Labelling for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

growth_protocol: Plants maintained in temperature controlled growht chamber at 20°C (day) and 18°C (night) under photoperiod of 16 h light. Plants held at a constant humidity of 70% and fertilized bi-weekly with 20-20-20 NPK.

extract_protocol: CsCl extraction of total RNA for Anther, Ovary, and Stigma @ (TCP) as well as MPG was performed according to Tran et al.  Rneasy plant minikit extraction of total RNA and subsequent DNA clean up using InviTrap® Spin Cell Plant RNA Mini kit was performed according to manufacturer's protocol for Anther, Ovary, and Stigma @ stage UNM, BCP.PicoPureTM RNA Isolation kit including the DNase treatment was performed according to manufacturer's protocol on Anther, Ovary, and Stigma tissues @ TET stage.

tag: tissue

value: Anther

tag: developmental stage

value: uninucleate microspore


title: L-428 tGFP/EBF1 rep1

description: sorted tGFP-positive cells

source_name: L-428 tGFP/EBF1


title: Anther uninucleate, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_UNM1


title: H1 hESC small bio rep2

description: Sort based on forward vs side scatter


title: H1 hESC small bio rep3

description: Sort based on forward vs side scatter


title: H1 hESC small bio rep1

description: Sort based on forward vs side scatter


title: D1 11:10_EMF exposure

city: Cambridge

first: James

last: Metcalfe

address: 80 Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description:
SAMPLE 4
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using the Beadarray reader.

data_processing: Beadstudio v.2.3.47 was used for processing the raw data and the Average method was used for normalization.  Averaged data were filtered for probes with detection pvalue < 0.01 in at least one sample.

source_name: ELF-EMF exposure

label_protocol: Biotinylated cRNA samples were prepared with the Illumina TotalPrep RNA Amplification kit from Ambion.

extract_protocol: The whole blood samples collected in PAXgene blood tubes were stored a 4C overnight and the RNA was extracted the next day with the PAXgene Blood RNA kit from QIAGEN according to the manufacturer's instructions, including the DNase treatment. A pooling strategy was used to detect significant responses that occur in most or all of the volunteers. Equal amounts of RNA (300 ng/sample) were pooled from the 17 RNA samples samples for each of the 40 time points on study days 1 to 4. The 260/280 nm ratio of all pools was > 2.0. The 40 pooled RNA samples were assayed by Agilent Bioanalyser for RNA Integrity Number (RIN) and all RIN values were >8.0 (38/40>9.0).

treatment_protocol: 17 healthy male subjects age 20 -30 each received an extremely low frequency electromagnetic field exposure (ELF-EMF) on study day 1 repeated on study day 3 (7 days later), a  sham exposure ( using counterwound coils in the 1 M cube exposure frames) on study day 2 (the day after study day 1) and a null exposure (no current through coils) on study day 4 (the day after study day 3). All exposures (ELF-EMF, sham or null) were for 2 h at 11.00 - 13.00. 10 ml blood samples were collected at each time point by cannula at 9.00, 11.00, 11.05, 11.10, 11.20,11.40, 12.20, 13.00, 15.00 and 17.00) and transfered directly into PAXgene blood tubes.

tag: tissue source

value: Healthy volunteers

tag: gender

value: male

tag: age

value: 20-30 years

value: Peripheral blood

tag: study day

tag: time-point

tag: treatment

value: ELF-EMF exposure (50 Hz EMF of 62.0 ± 7.1 μT for 2h)


title: Anther uninucleate, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_UNM2


title: L-428 tGFP rep3

description: sorted tGFP-positive cells

source_name: L-428 tGFP


title: D1 11:00 replicate 1a_pre EMF exposure

description:
SAMPLE 2
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: immediately prior to ELF-EMF exposure

value: immediately prior to ELF-EMF exposure


title: Stigma tetrad, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_TET2

source_name: Triticale stigmas at tetrad developmental stage

label_protocol:
Biotinylated  cRNA was synthesized according to standard Affymetrix protocol using the two-cycle  Eukaryotic Target labeling kit from 50-100ng total RNA
Labelling for Affymetrix Wheat GeneChips was performed at McGill University Génome Québec Innovation Centre (www.gqinnovationcenter.com) according to manufacturer's protocol (affymetrix.com)

value: Stigma

value: tetrad


title: HEK-293 control miR-181b Experimental Replicate 2 1895213040_H

city: Callaghan

first: Adam

last: Carroll

state: NSW

address: Ring Road

country: Australia

institute: University of Newcastle

description: Experimental Replicate 2

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Illumina Beadstudio software computed average signal intensities and detection p-values.

label: Biotin

label_protocol: Biotinylated cRNA was prepared using the TotalPrep RNA amplification kit (Ambion) for Illumina arrays.

growth_protocol: Cell models were grown as confluent monolayers in standard tissue culture conditions.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with DNase I treatment and the RNeasy MinElute cleanup kit (Qiagen) in accordance with manufacturer's instructions. Quality control was performed with an Experion (BioRad) bioanalyser.

treatment_protocol: Cells were transfected with either synthetic miRNA or anti-miR inhibitor oligonucleotides. Control refers to untransfected cell models; siEGFP control refers to transfection with an siRNA to EGFP as a transfection control.


title: Ovary tetrad, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_TET3

source_name: Triticale ovaries at tetrad developmental stage

value: Ovary


title: D1 09:00_pre EMF exposure

description:
SAMPLE 1
pooled RNA samples using equal amounts of RNA  from the 17 volunteers

source_name: pre EMF exposure

value: pre EMF exposure


title: H1 hESC large bio rep2

description: Sort based on forward vs side scatter

value: FACs sorted large subpopulation of H1 hESC

value: large subpopulation


title: stable line control replicate 1

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

description: BJAB cells transduced with control retrovirus

hyb_protocol: Samples were prepared with Gene Expression Hybridization Kit (Agilent) and placed in Agilent microarray hybridization chambers and rack. Hybridization occurred for 17 hr. at 65°.

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were processed with Agilent Feature Extraction Software v9.1.1.

data_processing: Background substraction and linear LOWESS normalization was used in Feature Extraction software.

source_name: Stratagene Universal Reference RNA

label_protocol: 500 ng of total RNA was labeled using Low RNA Input Fluor Linear Amp Kit PLUS (Agilent).

growth_protocol: Cells were split to 2x10^5 cells per ml every 48 hr.

extract_protocol: Cells were harvested with RNA-bee (Tel-test). RNA integrity was assayed using a Bioanalyzer 2100 (Agilent) and quantitated with a ND1000 spectrophotometer (Nanodrop).

treatment_protocol: BJAB and BCBL-1 cells were electroporated with siPORT system (Ambion) at 30 nM for mimics and 100 nM for inhibitors (RNA harvested 48 and 72 hr. after transfection, respectively)

tag: reference

value: Pooled cell line RNA

source_name: stable BJAB line

value: BJAB

tag: protocol (transduced)

value: control retrovirus


title: stable line miR-K12-9 replicate 2

description: BJAB cells transduced with retrovirus to express miR-K12-9

value: retrovirus to express miR-K12-9


title: L-428 tGFP rep1

description: sorted tGFP-positive cells

value: tGFP-only


title: H1 hESC large bio rep1

description: Sort based on forward vs side scatter

value: H1 hESC


title: stable line control replicate 2


title: Stigma tetrad, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_TET1


title: H1 hESC large bio rep3

description: Sort based on forward vs side scatter


title: L-428 tGFP rep2

description: sorted tGFP-positive cells


title: Stigma tetrad, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Stigma_TET3


title: stable line miR-K12-9 replicate 1


title: HEK-293 control miR-107 Experimental Replicate 2 1895213040_F

description: Experimental Replicate 2


title: H1 hESC large bio rep4

description: Sort based on forward vs side scatter


title: HEK-293 control miR-107 Experimental Replicate 1 1895213040_E

description: Experimental Replicate 1


title: transfected anti-miR-K12-9 72 hr replicate 1

description: BCBL-1 cells transfected with inhibitor anti-K12-9. Biological replicate 1 of 1.

source_name: transfected BCBL-1 cells

tag: protocol (transfection)

value: inhibitor anti-K12-9

tag: time

value: 72 hr. post transfection


title: transfected anti-neg 72 hr replicate 1

description: BCBL-1 cells transfected with control inhibitor anti-neg. Biological replicate 1 of 1.

value: inhibitor anti-neg


title: CELLS SILENCED FOR SYNDECAN-1,biological  replicate 1

city: Huddinge

first: Tünde

last: Szatmári

state: Stockholm

address: F42 Karolinska Universitetssjukhuset

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institute

hyb_protocol: Standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA) was used.

data_processing: Subsequent data analyses were performed using the Affymetrix Expression Console (version 1.1). The processing methods were: Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median

source_name: human malignant pleural mesothelioma cell-line STAV-AB transfected with  siRNA specific for syndecan-1

label_protocol: Total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

growth_protocol: The STAV-AB malignant mesothelioma cells were cultured in RPMI medium contining 10% human AB serum.

extract_protocol: Total RNA was isolated from sub-confluent cell cultures, using the High Pure RNA isolation Kit (Roche, Mannheim, Germany),  according to the supplied protocol.

treatment_protocol: STAV-AB cells were transfected using LipofectamineTM 2000 (Invitrogen, Carlsbad, CA, USA) one day after seeding. Medium containing the siRNA-lipofectamine complexes was then added to the cells and incubated  for 24 hours before samples were harvested and RNA was extracted.

value: STAV-AB malignant mesothelioma cells

tag: geneotype/variation

value: silenced syndecan-1


title: Anther tetrad, biological rep3

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_TET3

source_name: Triticale anthers at tetrad developmental stage

value: Anther


title: CELLS SILENCED FOR SYNDECAN-1, biological replicate 2

scan_protocol: Standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA) was used.

tag: cell line


title: Anther tetrad, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_TET2

value: tetrad


title: NEGATIVE/SCRAMBLED CONTROL CELLS, biological replicate 3

source_name: human malignant pleural mesothelioma cell-line STAV-AB transfected with scrambled siRNA

value: scrambled control


title: Ovary tetrad, biological rep2

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_TET2

value: Ovary


title: HeLa control miR-181b Experimental Replicate 2 1895213040_D

description: Experimental Replicate 2

source_name: HeLa

value: HeLa


title: transfected miR-K12-9 48 hr replicate 2

description: BJAB cells transfected with miR-K12-9. Biological replicate 2 of 2.

source_name: transfected BJAB cells

value: 48 hr. post transfection


title: Anther tetrad, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Anther_TET1


title: CELLS SILENCED FOR SYNDECAN-1, biological replicate 3


title: Ovary tetrad, biological rep1

description:
Triticale (x Triticosecale Wittmack cv. Alta)
Ovary_TET1


title: HEK-293 control miR-181b Experimental Replicate 1 1895213040_G

description: Experimental Replicate 1


title: HeLa control miR-181b Experimental Replicate 1 1895213040_C

description: Experimental Replicate 1


title: NEGATIVE/SCRAMBLED CONTROL CELLS, biological replicate1


title: HeLa control miR-107 Experimental Replicate 2 1895213040_B

description: Experimental Replicate 2


title: transfected miR-neg 48 hr replicate 2

description: BJAB cells transfected with miR-neg. Biological replicate 2 of 2.

value: Pooled cell line RNA

value: miR-neg


title: transfected miR-neg 48 hr replicate 1

description: BJAB cells transfected with miR-neg. Biological replicate 1 of 2.

value: BJAB


title: EEC22

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

country: Spain

institute: IIB

hyb_protocol: The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.

scan_protocol: After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer´s protocol.

data_processing: The slides were analyzed using Feature Extraction Software 10.0 (Agilent technologies), following manufacturer’s protocol. A hierarchical clustering method was applied to group the genes and samples on the basis of the similarities in expression and the unsupervised analyses were visualized using the SOTA and TreeView software assuming euclidean distances between genes (http://bioinfo.cnio.es/cgi-bin/tools/clustering/sotarray). Genes with potentially significant changes in expression were identified using the POMELO program (http://www.genoma.wi.mit.edu/MPR/software). We tested the null hypothesis of equal means among groups using T-test, computing p-values using a permutation test. To select differentially expressed genes, we adjusted for multiple testing using the False Discovery Rate (FDR) method (Chung et al, 2004)

source_name: Total RNA from breast tumor biopsies

label_protocol: 1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.

extract_protocol: 1mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using   Low RNA Linear Amplification Kit (Agilent technologies),  following manufacturer’s protocol

tag: disease state

value: endometrioid endometrial carcinomas

value: Female

source_name: Pool from the analysed samples


title: NEGATIVE/SCRAMBLED CONTROL CELLS, biological replicate 2


title: EEC23


title: transfected miR-K12-9 48 hr replicate 1

description: BJAB cells transfected with miR-K12-9. Biological replicate 1 of 2.


title: HeLa control miR-107 Experimental Replicate 1 1895213040_A

description: Experimental Replicate 1


title: HUH-YAP-#2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: Hep3B cells transfected with YAP-specific siRNA

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were imported and analyzed with a commercial software called JMP Genomics, version 4, from SAS. The Raw fluorescence intensity values were normalized applying quantile normalization.

source_name: transfected with YAP-specific siRNA

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

growth_protocol: Hep3B cells were grwon under full media conditions for 24 hours. After transfection with siRNAs cells were cultivated for further 24 hours. RNA isolation.

extract_protocol: Nucleospin RNAII II (Macherey-Nagel) was used for total RNA extraction.

treatment_protocol: Transfection of siRNAs was performed according to the Oligofectamine protocol provided by the company (Invitrogen).

value: transfected with YAP-specific siRNA


title: LTCF4KO Fed liver sample 2

city: London

first: Vivian

last: Li

address: 1 Midland Road

institute: The Francis Crick Institute

description:
Sample 21
Sample 20-22 are biological replicates

hyb_protocol: The synthezied cRNA was then purified with RNeasy mini kit (Qiagen). 825ng of the corresponding Cy3 and Cy5 cRNA was fragmentated at 60°C for 30 min in the presence of blocking agent and fragmentation buffer (Agilent), then combined with 55ul 2X hybridization buffer (Agilent) and applied to 4X44k human expression microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially

scan_protocol: Scanned on an Agilent G2505 DNA microarray scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization. Ratios are given in log10.

organism: Mus musculus

source_name: Liver isolated from adult Tcf7l2loxp/loxp;SA-CreERT2 fed ad libitum

label_protocol: 1µg of total RNA were primed with 1.2 µl of T7 promoter primer at 65°C for 10 min together with control spike A/B, then reversed transcribed at 40°C for 2hrs in the presence of MMLV RTase (Agilent), and dNTP mix. It was then followed by the cRNA transcription at 40°C for 2hrs in the presence of T7 RNA polymerase, inorganic pyrophosphatase, NTP mix, DTT, PEG and Cy3/Cy5-labeled-CTP.

growth_protocol: Mice are maintained following stardard protocol.

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Sample 1-8 are newborn pups injected with 50ul of 10% glucose solution subcutaneously for 5 hours.  Sample 9-22: mice were induced with tamoxifen at 3-week-old. After 1-2 months, the mice were either fasted or fed with food for 24hr before tissue isolation.

tag: strain

tag: genotype/variation

value: LTCF4KO (Tcf7l2loxp/loxp;SA-CreERT2)

tag: protocol

value: induced with tamoxifen; fed

source_name: mouse reference RNA (Stratagene)

tag: catalog number

value: mouse reference RNA (Stratagene)


title: HUH-YAP-#3


title: HUH-YAP-#1


title: LTCF4KO Fed liver sample 3

description:
Sample 22
Sample 20-22 are biological replicates


title: SH-SY5Y control Experimental Replicate 2 1897008140_H

description: Experimental Replicate 2

value: control


title: HUH-untreated-#3

description: Hep3B cells, untreated as control

source_name: untreated

value: untreated


title: SH-SY5Y anti-miR-181b Experimental Replicate 2 1897008140_D

description: Experimental Replicate 2


title: LTCF4KO Fed liver sample 1

description:
Sample 20
Sample 20-22 are biological replicates


title: SH-SY5Y anti-miR-181b Experimental Replicate 1 1897008140_C

description: Experimental Replicate 1


title: SH-SY5Y control Experimental Replicate 1 1897008140_G

description: Experimental Replicate 1


title: HUH-untreated-#1

description: Hep3B cells, untreated as control


title: Control Fed liver sample 3

description:
Sample 19
Sample 17-19 are biological replicates

source_name: Liver isolated from adult Tcf7l2loxp/loxp fed ad libitum

value: Control (Tcf7l2loxp/loxp)


title: SH-SY5Y miR-181b Experimental Replicate 2 1897008140_B

description: Experimental Replicate 2

value: miR-181b overexpression


title: LTCF4KO Fasted liver sample 4

description:
Sample 16
Sample 13-16 are biological replicates

source_name: Liver isolated from adult Tcf7l2loxp/loxp;SA-CreERT2 24hours fasted

value: induced with tamoxifen; fasted


title: HUH-nonsense-#3

description: Hep3B cells transfected with nonsense siRNA

source_name: transfection with nonsense siRNA

value: transfection with nonsense siRNA


title: genomic DNA from  PANC-1  cell line (copy number)

type: genomic

city: Vancouver

first: Kelsie

middle: L

last: Thu

state: British Columbia

address: 675 West 10th Avenue

institute: BC Cancer Research Centre

hyb_protocol: Mix the two reactions (reference and sample) and add 100ul Cot-1 DNA (1ug/ul), and purified using a microcon YM-30 column. Resuspend the probe in 45 uL hybridization solution (36 uL DIGeasy+ 4.5 uL (20mg/mL) sheared Herring Sperm DNA + 4.5 uL (10mg/mL) yeast tRNA). Denature the samples at 85°C  for 5min, and incubate at 45°C for 1 hour to allow Cot-1 to anneal to DNA probe. Add 45uL of the probe solution onto the array slide. Gently lower coverslip (22x60mm, Fisher Scientific) onto slide over probe solution. Place the slide into a pre-warmed (45°C) hybridization cassette (Telechem) and add 10uL of H20 in the lower groove (to control humidity). Incubate for 36 - 40hrs at 45°C.  Wash the slide with  0.1X SSC + 0.1% SDS (pH 7.0, pre-warmed to 45°C) for 5 minutes in the dark with agitation, and with 0.1X SCC 5 times. Dry the slides by centrifuging at 500rcf for 1 minute.

scan_protocol: Hybridizations were scanned using the Axon GenePix 4000B scanner. Array images are analyzed with GenePix Pro 6.1.

data_processing: A three-step normalization procedure, including LOWESS fitting, spatial, and median normalization was used.

molecule: genomic DNA

label_protocol: Random-primer labelling reaction  1. For each slide combine: (1 reaction tube for reference & 1 reaction tube for sample)  a) DNA (200ng)  b) 5uL of 5X (PB) random primers buffer (Final concentration: 5X Promega Klenow buffer and 7ug/ul random octomers)  c) Dilute to 16.5uL total volume with ddH2O    2. Boil for 10 min at 100°C in PCR machine. Transfer immediately to ice for 2 min  3. Add 4ul of 10X dNTP mix (2mM each dATP, dGTP, dTTP, 1.2mM dCTP) - Vortex very well  4. Add CyeDyes: Vortex and spin prior to adding  • Add 2uL (2nmoles) of Cy3 labelled dCTP to Reference DNA (Novagen Male Genomic)  • Add 2uL (2nmoles) of Cy5 labelled dCTP to sample DNA   5. Add 2.5uL of Klenow (9U/uL) and mix by pipetting   6. Incubate 37oC overnight (~18hours).

extract_protocol: Genomic DNA was extracted by the standard phenol-chloroform extraction followed by ethanol precipitation

value: male

value: pancreatic ductal epithelioid carcinoma

source_name: Normal male

tag: sample type

value: anonymous male diploid reference DNA

value: normal


title: genomic DNA from  SW1990 cell line (copy number)

tag: gender

value: pancreatic adenocarcinoma


title: LTCF4KO Fasted liver sample 3

description:
Sample 15
Sample 13-16 are biological replicates


title: genomic DNA from  SU8686  cell line (copy number)

value: female

value: pancreatic ductal adenocarcinoma


title: genomic DNA from  PL45  cell line (copy number)


title: SH-SY5Y control Experimental Replicate 2 1897008128_F

description: Experimental Replicate 2


title: HUH-nonsense-#2


title: Control Fed liver sample 2

description:
Sample 18
Sample 17-19 are biological replicates


title: Control Fed liver sample 1

description:
Sample 17
Sample 17-19 are biological replicates


title: HUH-untreated-#2

description: Hep3B cells, untreated as control


title: SH-SY5Y siEGFP-Control Experimental Replicate 1 1897008128_G

description: Experimental Replicate 1

value: siEGFP-Control


title: LTCF4KO Fasted liver sample 1

description:
Sample 13
Sample 13-16 are biological replicates

value: LTCF4KO (Tcf7l2loxp/loxp;SA-CreERT2)


title: HUH-nonsense-#1


title: SH-SY5Y siEGFP-Control Experimental Replicate 2 1897008128_H

description: Experimental Replicate 2


title: LTCF4KO Fasted liver sample 2

description:
Sample 14
Sample 13-16 are biological replicates


title: genomic DNA from  Panc08.13 cell line (copy number)


title: Control Fasted liver sample 4

description:
Sample 12
Sample 9-12 are biological replicates

source_name: Liver isolated from adult Tcf7l2loxp/loxp 24hours fasted


title: E11.5 total heart cells

city: Dallas

first: Guo

middle: N

last: Huang

state: TX

address: 6000 Harry Hines Blvd, NA8.510

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

description: SAMPLE 1

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with GenomeStudio, Gene Expression Module (v.1.9.0).

source_name: E11.5 total heart cells

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

extract_protocol: RNA was extracted with QIAGEN miRNeasy Mini Kit in accordance with the prescribed protocol provided with the manufacture. Quality control was performed with Agilent Bioanalyser.

tag: strain background

value: mixed; C57BL/6, 129 and CD-1

tag: developmental stage

tag: tissue

value: heart

tag: cell type

value: total dissociated heart cells


title: genomic DNA from  Panc10.05 cell line (copy number)


title: Control Fasted liver sample 3

description:
Sample 11
Sample 9-12 are biological replicates

tag: reference

value: mouse reference RNA (Stratagene)


title: genomic DNA from  Panc05.04  cell line (copy number)


title: E11.5 lacZ-positive epicardial cells

description: SAMPLE 2

source_name: E11.5 lacZ-positive epicardial cells

value: lacZ-positive epicardial cells


title: BM macrophages Dex treated and LPS stimulated, technical replicate 1 (3hr expt)

city: Berlin

first: N. Henriette

last: Uhlenhaut

address: Robert-Roessle-Str 10

institute: Max Delbrueck Center

description: technical replicate 1

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using the VAMPIRE Bayesian model with a 2-sided Bonferroni-corrected threshold of 0.05. The normalized data set contains only those probe sets with a P or M Flag in at least 1 out of 8 samples.

source_name: BM macrophages Dex treated and LPS stimulated - 3 hr

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

tag: background strain

value: wildtype

tag: age

value: 10 weeks

value: primary bone marrow derived macrophages

tag: treatment

value: o/n Dex, LPS 3 hr


title: genomic DNA from  Panc04.03 cell line (copy number)

value: male


title: SH-SY5Y miR-181b Experimental Replicate 1 1897008140_A

description: Experimental Replicate 1

value: miR-181b overexpression


title: Control Fasted liver sample 2

description:
Sample 10
Sample 9-12 are biological replicates

value: Control (Tcf7l2loxp/loxp)

value: induced with tamoxifen; fasted


title: SH-SY5Y control Experimental Replicate 1 1897008128_E

description: Experimental Replicate 1

value: control


title: HEK-293 anti-miR-181b Experimental Replicate 2 1895213044_D

description: Experimental Replicate 2


title: HEK-293 anti-miR-107 Experimental Replicate 2 1895213044_C

description: Experimental Replicate 2


title: HeLa anti-miR-107 Experimental Replicate 2 1895213044_A

description: Experimental Replicate 2

value: HeLa


title: BM macrophages LPS stimulated, technical replicate 2 (3hr expt)

description: technicall replicate 2

source_name: BM macrophages LPS stimulated - 3 hr

value: LPS 3 hr


title: HEK-293 anti-miR-107 Experimental Replicate 1 1897008128_D

description: Experimental Replicate 1


title: genomic DNA from  Panc03.27 cell line (copy number)

value: female

value: pancreatic adenocarcinoma

value: anonymous male diploid reference DNA

value: normal


title: BM macrophages LPS stimulated, technical replicate 1 (3hr expt)

description: technical replicate 1


title: Tcf7l2-/- newborn liver sample 4

description:
Sample 8
Sample 5-8 are biological replicates

source_name: Liver isolated from 5hours postnatal TCF4ko newborns

value: Tcf7l2-/- (TCF4KO)

value: 50ul of 10% glucose solution subcutaneously for 5 hours

value: mouse reference RNA (Stratagene)


title: BM macrophages Dex treated and LPS stimulated, technical replicate 2 (3hr expt)

description: technicall replicate 2

value: wildtype

value: 10 weeks


title: BM macrophages Dex treated, technical replicate 2 (3hr expt)

description: technicall replicate 2

source_name: BM macrophages Dex treated

value: primary bone marrow derived macrophages

value: o/n Dex


title: BM macrophages Dex treated, technical replicate 1 (3hr expt)

description: technical replicate 1

value: male


title: genomic DNA from  MIAPaCa-2  cell line (copy number)


title: Control Fasted liver sample 1

description:
Sample 9
Sample 9-12 are biological replicates

value: Control (Tcf7l2loxp/loxp)


title: Tcf7l2-/- newborn liver sample 3

description:
Sample 7
Sample 5-8 are biological replicates


title: genomic DNA from  Panc02.13 cell line (copy number)


title: genomic DNA from  Panc02.03 cell line (copy number)


title: HeLa anti-miR-107 Experimental Replicate 1 1897008128_B

description: Experimental Replicate 1

source_name: HeLa


title: Tcf7l2-/- newborn liver sample 2

description:
Sample 6
Sample 5-8 are biological replicates


title: Tcf7l2-/- newborn liver sample 1

description:
Sample 5
Sample 5-8 are biological replicates


title: BM macrophages unstimulated, technical replicate 2 (3hr expt)

description: technicall replicate 2

source_name: BM macrophages unstimulated

value: unstimulated


title: genomic DNA from  Hs766T  cell line (copy number)


title: HEK-293 anti-miR-181b Experimental Replicate 1 1897008128_C

description: Experimental Replicate 1


title: genomic DNA from  HPAF-II  cell line (copy number)

source_name: HPAF-II

value: HPAF-II


title: BM macrophages unstimulated, technical replicate 1 (3hr expt)

description: technical replicate 1


title: Tcf7l2+/+ newborn liver sample 4

description:
Sample 4
Sample 1-4 are biological replicates

source_name: Liver isolated from 5hours postnatal wt newborns

value: Tcf7l2+/+ (wildtype)


title: genomic DNA from  HPAC  cell line (copy number)

source_name: HPAC

value: HPAC

value: pancreatic ductal adenocarcinoma


title: HeLa anti-miR-181b Experimental Replicate 2 1895213044_B

description: Experimental Replicate 2

value: HeLa


title: BM macrophages Dex treated and LPS stimulated, technical replicate 2 (6hr expt)

description: technical replicate 2

data_processing: The data were normalized using cubic spline in Illumina GenomeStudio and also using GeneSpring GX (Agilent) default parameters, with quantile normalization and log transformation. The normalized data set contains only those probe sets with a P or M Flag in at least 1 out of 8 samples.

source_name: BM macrophages Dex treated and LPS stimulated - 6 hr

extract_protocol: Total RNA was isolated using the QIAGEN RNeasy mini kit including the on-column DNase I treatment, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Dexamethasone + LPS 6 hr


title: genomic DNA from  BxPC-3  cell line (copy number)

value: female

value: pancreatic adenocarcinoma

value: anonymous male diploid reference DNA

value: normal


title: genomic DNA from  Capan-2  cell line (copy number)


title: BM macrophages LPS stimulated, technical replicate 1 (6hr expt)

description: technical replicate 1

source_name: BM macrophages LPS stimulated - 6 hr

value: wildtype

value: LPS 6 hr


title: BM macrophages Dex treated and LPS stimulated, technical replicate 1 (6hr expt)

description: technical replicate 1

value: 10 weeks

value: primary bone marrow derived macrophages


title: Tcf7l2+/+ newborn liver sample 2

description:
Sample 2
Sample 1-4 are biological replicates

value: 50ul of 10% glucose solution subcutaneously for 5 hours

source_name: mouse reference RNA (Stratagene)

value: mouse reference RNA (Stratagene)


title: genomic DNA from  Capan-1  cell line (copy number)

value: male


title: Tcf7l2+/+ newborn liver sample 1

description:
Sample 1
Sample 1-4 are biological replicates


title: BM macrophages LPS stimulated, technical replicate 2 (6hr expt)

description: technical replicate 2


title: HeLa anti-miR-181b Experimental Replicate 1 1897008128_A

description: Experimental Replicate 1


title: BM macrophages Dex treated, technical replicate 2 (6hr expt)

description: technical replicate 2

value: Dexamethasone


title: Tcf7l2+/+ newborn liver sample 3

description:
Sample 3
Sample 1-4 are biological replicates

value: Tcf7l2+/+ (wildtype)


title: genomic DNA from  AsPC-1 cell line (copy number)


title: BM macrophages unstimulated, technical replicate 2 (6hr expt)

description: technical replicate 2

value: EtOH


title: RCC-MF

city: Groningen

first: Klaas

last: Kok

department: Genetics

country: Netherlands

institute: UMCG

description: Raw data file: RCCMF_014693.txt

hyb_protocol: According to protocols recommendated by AGILENT

scan_protocol: Agilent scanner at 2 um resolution

data_processing: AGILENT feature extraction software

source_name: RCC-MF

growth_protocol: See publication by Duns et al, Cancer Research 2010

treatment_protocol: untreated

tag: name

value: RCC-MF

value: ccRCC derived cell line

value: Male

value: clear cell renal cell carcinoma (lung metastasis)

tag: tumor stage

value: pT2,N1,Mx/GII-III (lung-metastasis)

tag: age of diagnosis

source_name: Reference pool

value: This pool consists of healthy individuals, either  50 males or 50 females. The persons were selected randomly, and blind from a large pool of anonymous "in house" control DNA samples. The reference pool was home-made.


title: RCC-JF

description: Raw data file: RCCJF_014693.txt

source_name: RCC-JF

label_protocol: According to protocols recommendated by AGILENT

extract_protocol: See publication by Duns et al, Cancer Research 2010

value: RCC-JF

tag: cell line

value: Female

value: clear cell renal cell carcinoma primary tumour


title: BM macrophages Dex treated, technical replicate 1 (6hr expt)

description: technical replicate 1

tag: genotype/variation

value: wildtype

value: 10 weeks


title: genomic DNA from  CFPAC-1  cell line (copy number)

tag: disease state

value: pancreatic ductal adenocarcinoma

source_name: Normal male

value: anonymous male diploid reference DNA

value: normal


title: RCC-1

description: Raw data file: RCC1_014693.txt


title: Diabetic 48h rep 3

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

description: Gene expression data from regenerating caudal fin of Danio rerio

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

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Partek GS 6.5 software (St. Louis, MO) using GCRMA normalization algorithm

organism: Danio rerio

source_name: Caudal fin of Danio rerio

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: Wild-type zebrafish were maintained under standard laboratory conditions  using a light schedule of 14 h on and 10 h off at a temperature of 28.5°C. Fish were fed  twice daily using a combination of dry food and brine shrimp.

extract_protocol: For each time point, triplicate samples from 15 caudal fins were collected and immediately placed into Triazol. The samples were homogenizedand then centrifuged. The RNA was extracted from the supernatant using the purelink RNA mini-kit (Life Technologies Corporation, Carlsbad, CA) according to the manufacturer's protocol.

treatment_protocol: Fish were anesthetized by placing them in 1:1000 2-phenoxyethanol for 1-2 minutes.  0.3% streptozocin solution in 5mM citrate buffer, pH 5.0 to a dose of 350 mg/kg was injected in the dorsal half of the fin with a PLI-90 injector (Harvard Biosciences, Inc., MA). The drug was injected on days 1,3,5, 12 and 19 of the experiment Control fish were injected with a like volume of citrate buffer.

value: Diabetic

tag: time (post amputation)

value: caudal fin


title: BM macrophages unstimulated, technical replicate 1 (6hr expt)

description: technical replicate 1

value: male

value: primary bone marrow derived macrophages

value: EtOH


title: genomic DNA from  HPDE cell line (DNA methylation)

description: pancreatic cancer cell line

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

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

data_processing: background normalization in BeadStudio software as per Illumina protocol

label: Cy5 and Cy3

source_name: HPDE

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from all cell lines using standard phenol chloroform extraction followed by ethanol precipitation

value: HPDE

tag: sample type

value: immortalized non-malignant human pancreatic duct cells


title: Diabetic 48h rep 1


title: RCC-ER

description: Raw data file: RCCER_014693.txt

source_name: RCC-ER

value: RCC-ER

value: ccRCC derived cell line

tag: gender

value: Male

value: pT3a, N1,Mx/GIII


title: genomic DNA from  PL45  cell line (DNA methylation)

description: pancreatic cancer cell line

value: cancer


title: Diabetic 48h rep 2


title: RCC-FG2

description: Raw data file: RCCFG2_014693.txt

value: clear cell renal cell carcinoma primary tumour

value: This pool consists of healthy individuals, either  50 males or 50 females. The persons were selected randomly, and blind from a large pool of anonymous "in house" control DNA samples. The reference pool was home-made.


title: Diabetic 24h rep 2


title: genomic DNA from  SU8686  cell line (DNA methylation)

description: pancreatic cancer cell line

value: female

value: pancreatic ductal adenocarcinoma


title: Diabetic 24h rep 3


title: genomic DNA from  SW1990 cell line (DNA methylation)

description: pancreatic cancer cell line

value: pancreatic adenocarcinoma


title: HepG2_BR, rep3

city: Ilmenau

first: Uta

last: Fernekorn

department: Nano-Biosystem Technology

institute: Ilmenau Technical University

description:
5701375050_C
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).

hyb_protocol: RNA extracts were hybridized on a Sentrix® BeadChip (Illumina: human HT12v4) using the standard Illumina hybridization protocol and detected via Cy3-Streptavidin.

scan_protocol: Illumina BeadArray Reader with BeadScan 3.6.17 Scanning software.

data_processing: The data were normalized using log2 variance stabilization, a method described by W. Huber et al. in Bioinformatics 18 Suppl.1:96-S104 (2002) (PMID 12169536). Distribution of p-values of the bead signals and false discovery rates were calculated using the R-package fdr-tool (R Foundation for Statistical Computing, Vienna, Austria). A linear model was applied with the cell type and culture conditions regarded as co-variants. Altogether, probes giving a false positive rate of 0.1% were selected and further processed via hierarchical clustering.

source_name: HepG2, BR

label_protocol: RNA extracts were labeled with biotin.

growth_protocol: HepG2 cells were cultivated for five days under 2D and 3D statical and perfused conditions. 3D cultivation was performed in a structured, microporous scaffold. Cultivation was started with 0.25x10^6 cells in 2D and with 1x10^6 vital cells for the 3D experiments. The day of seeding was defined as d0.

extract_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion, Applied Biosystems).

value: hepatocarcinoma cell line

tag: growth type

value: perfused 3D culture


title: genomic DNA from  Panc10.05 cell line (DNA methylation)

description: pancreatic cancer cell line

value: male


title: HepG2_BR, rep1

description:
5701375050_F
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).


title: RCC-AB

description: Raw data file: RCCAB_014693.txt

source_name: RCC-AB

value: RCC-AB

value: pT2, N0, MX/GII


title: Diabetic 12h rep 3

value: Diabetic

value: caudal fin


title: genomic DNA from  PANC-1  cell line (DNA methylation)

description: pancreatic cancer cell line

value: pancreatic ductal epithelioid carcinoma


title: HepG2_3D, rep3

description:
5701375049_F
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).

source_name: HepG2, 3D

value: statical 3D culture


title: HepG2_3D, rep2

description:
5701375050_L
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).


title: HepG2_BR, rep2

description:
5701375049_B
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).


title: genomic DNA from  Panc05.04  cell line (DNA methylation)

description: pancreatic cancer cell line


title: HepG2_3D, rep1

description:
5701375050_B
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).


title: genomic DNA from  Panc08.13 cell line (DNA methylation)

description: pancreatic cancer cell line


title: Diabetic 24h rep 1


title: Diabetic 12h rep 2


title: P9(S34L_O)

city: Stanford

first: Bo

last: Wu

state: Ca

address: 300 Pasteur Dr. Grant/S259

department: Urology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86412.gif

hyb_protocol: not provided

scan_protocol: scanner model: G2505C

data_processing: VALUE is log(REDsignal/GREENsignal)

source_name: Mouse universal reference RNA

label_protocol: 5 ug of total RNA were primed with T7 Promoter Primer at 65 oC for 10 min, then reversed transcribed at 40 oC for 2 h in the presence of MMLV-RT, and 10 mM dNTP, Cy3- or Cy5-label

extract_protocol: not provided

value: Mouse universal reference RNA

source_name: Kidney RNA P9

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

treatment_protocol: operation_protocol: >Mice were anesthetized and subjected to unilateral obstruction for 1 day, 2 days, 5 days or 9 days. The left ureter was ligated to generate an obstructed kidney. For each time point additional mice underwent dissection of the left ureter without ligation to serve as sham controls

tag: strain

value: obstruction

value: Kidney

tag: day samples were collected post operation

value: 9 d

tag: somatic modification

value: L


title: genomic DNA from  Panc03.27 cell line (DNA methylation)

description: pancreatic cancer cell line

value: female

value: cancer


title: Control (D) 48h rep 3

value: Control

tag: tissue


title: genomic DNA from  Panc02.03 cell line (DNA methylation)

description: pancreatic cancer cell line

value: pancreatic adenocarcinoma


title: Diabetic 0h rep 2


title: P9(S35L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86414.gif

tag: reference


title: P5(S19L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86383.gif

source_name: Kidney RNA P5

value: 5 d


title: genomic DNA from  Panc04.03 cell line (DNA methylation)

description: pancreatic cancer cell line

value: male


title: Diabetic 0h rep 1


title: HepG2_2D, rep1

description:
5701375050_A
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).

source_name: HepG2, 2D

tag: cell type

value: hepatocarcinoma cell line

value: 2D culture


title: HepG2_2D, rep3

description:
5701375049_A
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).


title: SMG7 siRNA_treated rep 2

city: Seoul

first: Hana

last: Cho

address: Anam 5ga, Sungbukku

department: School of Life Sciences and Biotechnology

country: South Korea

institute: Korea University

description:
replicate 2
SAMPLE 10

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4).

data_processing: Array data export processing and analysis was performed usingIllumina GenomeStudio v2009.2 (Gene Expression Module v1.5.4). Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal value was transformed by logarithm and normalized by quantile method.  The comparative analysis between Control and Test samples was further carried out using fold-change.

source_name: SMG7 siRNA_treated HeLa cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (Hyclone) containing 10% fetal bovine serum (Hyclone).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Cells were transiently transfected with the indicated in vitro-synthesized siRNA (Invitrogen)

value: HeLa

tag: transfected with

value: SMG7 siRNA

tag: transfection reagent

value: Oligofectamine (Invitrogen)


title: Diabetic 0h rep 3

value: Diabetic

value: caudal fin


title: PNRC2 siRNA_treated rep 2

description:
replicate 2
SAMPLE 9

source_name: PNRC2 siRNA_treated HeLa cells

value: PNRC2 siRNA


title: P1(S03L_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86392.gif

value: Mouse universal reference RNA

source_name: Kidney RNA P1

tag: treatment

value: control

value: Kidney

value: 1 d


title: SMG5 siRNA_treated rep 2

description:
replicate 2
SAMPLE 8

source_name: SMG5 siRNA_treated HeLa cells

value: SMG5 siRNA


title: Diabetic 12h rep 1


title: HepG2_2D, rep2

description:
5701375050_G
Total RNA was electrophoretically detected by RNA Integrity Number (RIN method).


title: P2(S39R_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86419.gif

source_name: Kidney RNA P2

value: 2 d

value: R


title: P5(S31L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86408.gif

value: obstruction

value: 5 d

value: L


title: genomic DNA from  Hs766T  cell line (DNA methylation)

description: pancreatic cancer cell line

value: male

value: pancreatic adenocarcinoma

value: cancer


title: Control (D) 48h rep 2

value: Control


title: genomic DNA from  MIAPaCa-2  cell line (DNA methylation)

description: pancreatic cancer cell line


title: Upf1 siRNA_treated rep 2

description:
replicate 2
SAMPLE 7

source_name: Upf1 siRNA_treated HeLa cells

value: HeLa

value: Upf1 siRNA

value: Oligofectamine (Invitrogen)


title: P5(S22L_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86375.gif

value: Mouse universal reference RNA


title: Control (D) 48h rep 1

description: Gene expression data from regenerating caudal fin of Danio rerio

value: caudal fin


title: genomic DNA from  Panc02.13 cell line (DNA methylation)

description: pancreatic cancer cell line

value: female


title: P5(S21L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86374.gif

value: Kidney


title: genomic DNA from  HPAC  cell line (DNA methylation)

description: pancreatic cancer cell line

source_name: HPAC

value: HPAC

value: pancreatic ductal adenocarcinoma


title: Control (D) 24h rep 3

source_name: Caudal fin of Danio rerio


title: Control (D) 24h rep 1


title: Control (D) 12h rep 3


title: P2(S04L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86393.gif

value: 2 d


title: Ptf1a-injected embryos NF36, biological rep 4

city: Woods Hole

first: Cassandra

middle: Kathryn

last: Bilogan

state: MA

address: 7 MBL St

department: Eugene Bell Center for Regenerative Biology and Tissue Engineering

institute: Marine Biology Laboratory

description: Gene expression data from 15 Ptf1a-injected embryo, anterior endoderm dissected at NF36

hyb_protocol: 10 μg of fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip Xenopus Genome array. The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: The arrays were scanned on a GeneChip® Scanner 3000 7G. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: The data were analyzed with Affymetrix expression control using PLIER algorithm and quantile normalization, no scaling was used during the primary analysis.

organism: Xenopus laevis

source_name: Anterior endoderm of 15 Ptf1a-injected embryos NF36

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (typically 10 μg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit. 15 μg of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual).

growth_protocol: Embryos were grown in 0.1XMMR.

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

treatment_protocol: Emrbyos were injected at the 8-cell stage into the two dorsal vegetal blastomeres with either 400 pg of GFP mRNA or 400 pg GFP mRNA and 800 pg Ptf1a mRNA, for dissection tadpoles were anaesthetized in MS-222

tag: developmental stage

tag: over-expression

value: GFP+Ptf1a mRNA

value: Anterior endoderm


title: Control (D) 12h rep 2


title: Ptf1a-injected embryos NF36, biological rep 2


title: Ptf1a-injected embryos NF36, biological rep 1


title: GFP-injected embryos NF36, biological rep 4

description: Gene expression data from 15 GFP-injected embryo, anterior endoderm dissected at NF36

source_name: Anterior endoderm of 15 GFP-injected embryos NF36

value: GFP mRNA


title: Control (D) 24h rep 2


title: genomic DNA from  Capan-2  cell line (DNA methylation)

description: pancreatic cancer cell line

tag: cell line

value: male


title: P9(S09L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86398.gif

value: obstruction

value: 9 d

value: L


title: genomic DNA from  Capan-1  cell line (DNA methylation)

description: pancreatic cancer cell line

value: pancreatic adenocarcinoma

tag: disease state

value: cancer


title: Ptf1a-injected embryos NF36, biological rep 3


title: P9(S33L_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86410.gif

value: control


title: genomic DNA from  CFPAC-1  cell line (DNA methylation)

description: pancreatic cancer cell line


title: genomic DNA from  HPAF-II  cell line (DNA methylation)

description: pancreatic cancer cell line

source_name: HPAF-II

value: HPAF-II


title: P1(S06R_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86371.gif

value: Mouse universal reference RNA

value: 1 d

value: R


title: Control (D) 0h rep 3

value: Control

tag: time (post amputation)

value: caudal fin


title: genomic DNA from  BxPC-3  cell line (DNA methylation)

description: pancreatic cancer cell line

value: female

tag: sample type


title: P1(S05L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86395.gif

value: Kidney


title: P5(S32L_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86409.gif

value: 5 d


title: Blood_3healthydonors_4

city: Taiyuan City

first: Cuiping

last: CHI

state: Shan Xi Province

address: Xue Fu Street No. 102

department: Radiation Medicine

country: China

institute: China Institute for Radiation Protection

description: Gene expression in peripheral blood of 3 healthy donors

hyb_protocol: Labeled cRNA (825ng) of the respective sample was fragmented and hybridized onto Agilent whole human genome microarrys (4×44K G4112F,slide number,66634) using Gene expression hybridization kit (5188-5242,Agilent Technologies). hybridization was performed for 17h,rotating at a speed of 10rpm at 65℃ in an Agilent hybridization oven(G2545A).After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute with 37℃GE Wash buffer 2 (5188-5327,Agilent Technologies).

scan_protocol: The slides were scanned with Agilent microarray scanner (G2505C) using one color setting for 4×44K array slides(scan resolution 5μm, dye channel was set to green and green PMT was set to 100%)

data_processing: Images were processed with Agilent Feature Extraction Version 10.7.1.1 to obtain raw data files. The raw data files which contain “Processed Signal” were processed using the Limma package developed within the Bioconductor project in the R statistical programming environment. After log transformation, the data were normalized using “quantile” method. Whole expressional data results were filtered according to the values of AFE quantification flags of gIsFound，IsWellAboveBG, gIsSaturated and the computing results of WellAboveNeg. After combinations of the replicated probes, the processed data was used to analyze the differentially expressed genes using a threshold of absolute log2 fold change value cut off at 1.

source_name: Peripheral blood,3 health donors,ABC, Mixture(1:1:1)

label_protocol: Labeling was done using Agilent Low RNA Input linear Amplification kit (5184-3523) according to the manufacture`s instructions, followed by RNAeasy Column Purification(74106, QIAGEN) . Briefly, using T7 promoter element coupled oligodT primer, cDNA was genenated. From cDNA, labeled cRNA was generated via an in vitro transcription reaction using T7 RNA polymerase and aa-UTP(AM8436,Ambion),and consequently aa-UTP incorporated cRNA was dyed with Cy3 NHS ester(PA13105,GE). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using QIAGEN QIAamp RNA blood mini kit (52304) following the manufacture`s instructions. The RNase-Free DNase Set (79254,QIAGEN) was used to digest DNA efficiently during RNA purification. RNA quality was assessed by spectrophotometry(NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have a 260/280 ratio higher than 1.7 and an 18S/28S rRNA ratio ~2.

treatment_protocol: The biological doses of the three exposed persons were 2.3, 1.7 and 1.3 Gy respectively, estimated using chromosome aberration method.

value: whole blood

tag: gender

tag: age

tag: stress

tag: dose


title: Control (D) 0h rep 2


title: Control (D) 12h rep 1


title: GFP-injected embryos NF36, biological rep 3

value: GFP mRNA

value: Anterior endoderm


title: GFP-injected embryos NF36, biological rep 2


title: Control (D) 0h rep 1


title: Blood_accidentlyexposed_1.3Gy_3

description: Gene expression 3yr post accidental exposure in peripheral blood

source_name: Peripheral blood,3yr post irradiation, 3

value: male

value: irradiation


title: genomic DNA from  AsPC-1 cell line (DNA methylation)

description: pancreatic cancer cell line

value: pancreatic adenocarcinoma


title: P1(S03R_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86406.gif

source_name: Mouse universal reference RNA

tag: strain

tag: day samples were collected post operation

tag: somatic modification


title: Ptf1a-injected embryos NF32, biological rep 3

description: Gene expression data from 15 Ptf1a-injected embryo, anterior endoderm dissected at NF32

source_name: Anterior endoderm of 15 Ptf1a-injected embryos NF32

value: GFP+Ptf1a mRNA

tag: tissue


title: P2(S30L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86404.gif

tag: reference

value: obstruction

value: 2 d

value: L


title: Blood_accidentlyexposed_1.7Gy_2

source_name: Peripheral blood,3yr post irradiation, 2


title: Blood_accidentlyexposed_2.3Gy_1

source_name: Peripheral blood,3yr post irradiation, 1


title: Metabolic memory 48h rep 2

treatment_protocol: Fish were anesthetized by placing them in 1:1000 2-phenoxyethanol for 1-2 minutes.  0.3% streptozocin solution in 5mM citrate buffer, pH 5.0 to a dose of 350 mg/kg was injected in the dorsal half of the fin with a PLI-90 injector (Harvard Biosciences, Inc., MA). The drug was injected on days 1,3,5, 12 and 19 of the experiment. This was followed by 60 days of keeping the fish without the drug. Control fish were injected with a like volume of citrate buffer.

value: Metabolic memory


title: P2(S18L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86402.gif

value: Mouse universal reference RNA


title: P2(S08L_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86396.gif

value: control


title: EEC21

source_name: Total RNA from breast tumor biopsies

value: endometrioid endometrial carcinomas

value: Female

source_name: Pool from the analysed samples


title: Metabolic memory 48h rep 3

description: Gene expression data from regenerating caudal fin of Danio rerio

value: caudal fin


title: Metabolic memory 48h rep 1


title: Time point 1 replica 4

city: Moncada

last: Ancillo

state: Valencia

address: Ctr. Moncada-Naquera Km 4.5

department: Protección Vegetal y Biotecnología

institute: Instituto Valenciano de Investigaciones Agrarias (IVIA)

description: Leaves of Etrog citron (Citrus medica L.) infected but still symptomless (30 dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 4

hyb_protocol: Microarray hybridisation and washing were performed as described by Martinez-Godoy et al. (2008).

scan_protocol: Hybridized microarray slides were scanned at 532-nm for the Cy3 and 635-nm for the Cy5 dyes, with a GenePix 4000B scanner (Axon Molecular Devices, Sunnyvale CA), at 10-nm resolution and 100% laser power.

data_processing: Median global intensity and LOWESS correction were applied. Genes were grouped into clusters using the Self-Organising Tree Algorithm (SOTA)(Herrero et al., 2001). Significant expression profile differences between the experimental groups were obtained using the MaSigPro analysis (Conesa et al., 2006).

organism: Citrus medica

label_protocol: RNA was labelled following an indirect method (Randolph and Waggoner, 1997). Reverse transcription, cDNA purification, dye coupling and fluorescent cDNA purification was accomplished as described by Forment et al. (2005), except that total RNA (40 ug) was used instead of poly(A)+ RNA.

growth_protocol: Plants were maintained in a temperature-controlled greenhouse (28/32°C night/day) and symptom expression was recorded at weekly intervals

extract_protocol: Total RNA was extracted from leaves according to the protocol described by Ancillo et al. (2007).

treatment_protocol: Eight plants of the sensitive selection 861-S1 of Etrog citron (Citrus medica L.) grafted on Rough lemon (C. jambhiri Lush.) rootstock were graft-inoculated on the rootstock, each one with two bark pieces from a CEVd-infected Etrog citron plant, and eight additional plants were left as non-inoculated controls. The severe CEVd isolate (CEVd-117) was used

tag: variety

value: Etrog citron (Citrus medica L.)

tag: infection status

value: infected but still symptomless (30 dpi)

source_name: Common reference obtained by mixing equimolar amounts of all samples

value: Mix of equimolar amounts of all samples


title: Control (MM) 48h rep 3

value: Control


title: Time point 2 replica 1

description: Leaves of Etrog citron (Citrus medica L.) infected but symptomatic (90dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 1

value: infected but symptomatic (90dpi)


title: Ptf1a-injected embryos NF32, biological rep 1

tag: developmental stage

value: Anterior endoderm


title: P1(S38L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86418.gif

source_name: Kidney RNA P1

tag: treatment

value: Kidney

value: 1 d


title: EEC20

extract_protocol: 1mg of total RNA from each independent tumours were labelled with Cy5-dUTP and as control a pooled RNA obtained from equal concentration of each RNA tumor sample labelled with Cy3-dUTP was used. The amplification and labelling of mRNA were performed using   Low RNA Linear Amplification Kit (Agilent technologies),  following manufacturer’s protocol


title: Time point 2 replica 4

description: Leaves of Etrog citron (Citrus medica L.) infected but symptomatic (90dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 4


title: GFP-injected embryos NF32, biological rep 3

description: Gene expression data from 15 GFP-injected embryo, anterior endoderm dissected at NF32

source_name: Anterior endoderm of 15 GFP-injected embryos NF32

tag: over-expression

value: GFP mRNA


title: Time point 2 replica 3

description: Leaves of Etrog citron (Citrus medica L.) infected but symptomatic (90dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 3


title: P1(S02L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86391.gif

value: obstruction


title: Time point 2 replica 2

description: Leaves of Etrog citron (Citrus medica L.) infected but symptomatic (90dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 2


title: Control (MM) 48h rep 2

tag: disease state


title: Ptf1a-injected embryos NF32, biological rep 2

value: GFP+Ptf1a mRNA


title: P9(S10L_C)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86399.gif

source_name: Kidney RNA P9

value: 9 d

value: L


title: GFP-injected embryos NF32, biological rep 1


title: EEC19


title: P9(S36L_O)

description: Image: http://smd.stanford.edu/MicroArray/gifs/2010-02/86416.gif

value: Mouse universal reference RNA


title: GFP-injected embryos NF32, biological rep 2


title: EEC16

value: endometrioid endometrial carcinomas


title: Time point 1 replica 2

description: Leaves of Etrog citron (Citrus medica L.) infected but still symptomless (30 dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 2


title: Control (MM) 48h rep 1

tag: time (post amputation)


title: EEC18

value: Female


title: Time point 1 replica 3

description: Leaves of Etrog citron (Citrus medica L.) infected but still symptomless (30 dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 3


title: EEC15


title: Control siRNA_treated rep 2

description:
replicate 2
SAMPLE 6

source_name: Control siRNA_treated HeLa cells

tag: cell line

value: HeLa

tag: transfected with

value: Control siRNA

tag: transfection reagent

value: Oligofectamine (Invitrogen)


title: GFP-injected embryos NF36, biological rep 1

description: Gene expression data from 15 GFP-injected embryo, anterior endoderm dissected at NF36


title: Time point 0 replica 4

description: Leaves of Etrog citron (Citrus medica L.) before inoculation, labeled with Cy3, compared to a common reference, labeled with Cy5; replica 4

value: Etrog citron (Citrus medica L.)

value: before inoculation

value: Mix of equimolar amounts of all samples


title: SMG5 siRNA_treated rep 1

description:
replicate 1
SAMPLE 3

source_name: SMG5 siRNA_treated HeLa cells

value: SMG5 siRNA


title: EEC17

tag: gender


title: Metabolic memory 24h rep 3

source_name: Caudal fin of Danio rerio

value: Metabolic memory

value: caudal fin


title: Metabolic memory 24h rep 2


title: Control (MM) 24h rep 3

value: Control


title: Time point 0 replica 3

description: Leaves of Etrog citron (Citrus medica L.) before inoculation, labeled with Cy3, compared to a common reference, labeled with Cy5; replica 3


title: EEC14


title: Upf1 siRNA_treated rep 1

description:
replicate 1
SAMPLE 2

source_name: Upf1 siRNA_treated HeLa cells

value: Upf1 siRNA


title: EEC13


title: SMG7 siRNA_treated rep 1

description:
replicate 1
SAMPLE 5

source_name: SMG7 siRNA_treated HeLa cells

value: SMG7 siRNA


title: EEC12


title: Time point 0 replica 1

description: Leaves of Etrog citron (Citrus medica L.) before inoculation, labeled with Cy3, compared to a common reference, labeled with Cy5; replica 1


title: Control (MM) 24h rep 2

description: Gene expression data from regenerating caudal fin of Danio rerio


title: Time point 0 replica 2

description: Leaves of Etrog citron (Citrus medica L.) before inoculation, labeled with Cy3, compared to a common reference, labeled with Cy5; replica 2


title: Control (MM) 24h rep 1


title: EEC10


title: Time point 1 replica 1

description: Leaves of Etrog citron (Citrus medica L.) infected but still symptomless (30 dpi), labeled with Cy3, compared to a common reference, labeled with Cy5; replica 1

value: infected but still symptomless (30 dpi)


title: Metabolic memory 12h rep 2


title: Metabolic memory 24h rep 1


title: Metabolic memory 12h rep 3


title: IL-17A 2

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

description:
replicate 2
101069-05

hyb_protocol: HumanHT12 v.4 Expression BeadChip, 750ng of bitinylated cRNA used

scan_protocol: Illumina iScan array scanner

data_processing: Illumina' Genomestudio v.2010.1 with default settings

source_name: HaCaT

label_protocol: biotinylation of cRNA

growth_protocol: HaCaT cells were grown in DMEM medium (1.5mM Ca), supplemented with 10% FCS, p/s and glu

extract_protocol: Qiagen RNeasy Plus Mini Ki

treatment_protocol: samples were exposed to cytokines at 200ng/ml for 12h

value: HaCaT

tag: cell type

value: keratinocytes


title: Control siRNA_treated rep 1

description:
replicate 1
SAMPLE 1


title: IL-17A 1

description:
replicate 1
101069-04


title: EEC8

data_processing: The slides were analyzed using Feature Extraction Software 10.0 (Agilent technologies), following manufacturer’s protocol. A hierarchical clustering method was applied to group the genes and samples on the basis of the similarities in expression and the unsupervised analyses were visualized using the SOTA and TreeView software assuming euclidean distances between genes (http://bioinfo.cnio.es/cgi-bin/tools/clustering/sotarray). Genes with potentially significant changes in expression were identified using the POMELO program (http://www.genoma.wi.mit.edu/MPR/software). We tested the null hypothesis of equal means among groups using T-test, computing p-values using a permutation test. To select differentially expressed genes, we adjusted for multiple testing using the False Discovery Rate (FDR) method (Chung et al, 2004)

value: endometrioid endometrial carcinomas


title: IL-17A 3

description:
replicate 3
101069-06


title: EEC11

value: Female


title: EEC7


title: Control 3

description:
replicate 3
101069-03


title: Metabolic memory 12h rep 1


title: MDS42 ΔnusA* 2

city: Madison

first: Jason

middle: Matthew

last: Peters

state: WI

address: 1550 Linden Drive

institute: UW-Madison

description: tiling expression microarray MDS42 ΔnusA* cells

hyb_protocol: Samples were hybridized to arrays by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/chip/index.html).

scan_protocol: Arrays were scanned by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/chip/index.html).

data_processing: Raw probe intensities were normalized across samples using RMA analysis implemented in the NimbleScan software package (v.2.4).

organism: Escherichia coli K-12

source_name: MDS42 ΔnusA*

label_protocol: Labeling was performed with an amino-allyl indirect labeling protocol followed by a Dnase I fragmentation step.

growth_protocol: Cells were grown in MOPS minimal medium with 0.2% glucose at 37 oC  in gas-sparged Roux bottles or shaking flasks to mid-log phase (OD600 ~ 0.3-0.4).

extract_protocol: Total RNA was extracted from cell pellets by hot phenol extraction. The integrity of total RNA was determined from agarose gel or microchannel electrophoretograms.

treatment_protocol: Cultures were transferred directly into an ice-cold ethanol/phenol stop solution, which immediately inactivated cellular RNases. Cells were collected by centrifugation and stored at -80 oC until RNA extraction.

tag: strain

tag: genotype/variation

value: 43 deletions, ΔnusA*


title: EEC6


title: EEC9


title: Control (MM) 12h rep 1


title: Metabolic memory 0h rep 3


title: EEC4


title: Metabolic memory 0h rep 2


title: PNRC2 siRNA_treated rep 1

description:
replicate 1
SAMPLE 4

source_name: PNRC2 siRNA_treated HeLa cells

value: HeLa

value: PNRC2 siRNA


title: Control 2

description:
replicate 2
101069-02


title: EEC3


title: EEC5


title: Control (MM) 12h rep 3


title: Metabolic memory 0h rep 1


title: MDS42 ΔnusG 1

description: tiling expression microarray MDS42 ΔnusG cells

source_name: MDS42 ΔnusG

value: 42 deletions, ΔnusG


title: MDS42 + 20 ug/ml bicyclomycin 1

description: tiling expression microarray MDS42 cells treated with bicyclomycin

source_name: MDS42 + 20 ug/ml bicyclomycin

value: 42 deletions

tag: treated with

value: 20 ug/ml bicyclomycin


title: ECS214

value: endometrial carcinosarcomas


title: ECS213


title: MDS42 ΔnusA* 1

value: 42 deletions, ΔnusA*


title: ECS211


title: Control 1

description:
replicate 1
101069-01


title: ECS212


title: EEC1


title: Control (MM) 0h rep 3

tag: tissue

value: caudal fin


title: MDS42 ΔnusG 2

value: 43 deletions, ΔnusG


title: EEC2


title: MDS42 + 20 ug/ml bicyclomycin 2


title: Control (MM) 0h rep 2

value: Control


title: Mouse 5

city: Zurich

first: Markus

last: Stoffel

state: ZH

address: Schafmattstr. 22

department: Molecular Health Science

country: Switzerland

institute: ETH Zurich

description: Total RNA was extracted from brown adipose tissue using the Trizol extraction method.

hyb_protocol: 100 ng reference RNA was dephosphorylated by incubation with calf intestinal phosphatase at 37°C for 30 min and denatured using 100% DMSO at 100°C for 5 min. Samples were labelled with pCp-Cy3 using T4 ligase by incubation at 16°C for 1 hour. Each labelled RNA sample was hybridised to an individual array on 8_x_15K format Agilent mouse miRNA array slides, with each array containing probes for 567 mouse miRNAs

scan_protocol: Arrays were scanned on an Agilent scanner according to recommendations provided by Agilent (see CXR Biosciences website)

data_processing: Data were acquired using Agilent Feature Extraction software version 9.5.3.1. US22502575_251911911060_S01_miRNA_107_Sep09_1_3.txt array yielded a very poor hybridization signal and did not pass the Agilent quality control metrics in the Feature Extraction software. The signature lists were produced using the resolver error weighted mean.

source_name: Brown adipose tissue

label_protocol: Cy3 labeling of RNA was performed according to recommendations provided by Agilent (see CXR Biosciences website)

growth_protocol: Primary tissue was taken from 8 week old mive

extract_protocol: Total RNA was extracted using the Trizol method

treatment_protocol: Groups of mice were either kept at room temperature  (RT) or cold exposure (8C for 24 hours)

tag: Sex

value: Male

tag: temperature

tag: age

value: 8 weeks


title: Mouse 4_technical replicate


title: MDS42 2

description: tiling expression microarray MDS42 cells


title: ECS210

city: Madrid

last: Moreno-Bueno

institute: IIB

scan_protocol: After hybridization and washing, the slides were scanned in an Axon GenePix Scanner (Axon Instruments), according to manufacturer´s protocol.

source_name: Total RNA from breast tumor biopsies

label_protocol: 1mg from tRNA was labelled and array hybridized using the Low RNA Linear Amplification Kit (Agilent) following manufacturer’s protocol.


title: Control (MM) 0h rep 1


title: Mouse 4


title: Δrac ΔnusG 2

description: tiling expression microarray Δrac ΔnusG cells

source_name: Δrac ΔnusG

value: Δrac ΔnusG


title: Δrac + 20 ug/ml bicyclomycin 2

description: tiling expression microarray Δrac cells treated with bicyclomycin

source_name: Δrac + 20 ug/ml bicyclomycin

value: Δrac


title: ECS204

source_name: Pool from the analysed samples


title: ECS207


title: Mouse 1_technical replicate


title: ECS205


title: MDS42 1


title: ECS208


title: Δrac ΔnusG 1


title: Mouse 2


title: Δrac 2

description: tiling expression microarray Δrac cells

source_name: Δrac


title: Δrac 1

description: tiling expression microarray Δrac cells


title: ECS203


title: ECS202


title: Mouse 3


title: ECS209


title: Mouse 1


title: MG1655 H-NS 2

description: ChIP-chip MG1655 cells H-NS

data_processing: Datasets were normalized using locally weighted linear regression (LOWESS) normalization on raw Cy3 and Cy5 signals to correct for intensity-dependent dye effects within each array using the “normalizeWithinArrays” function in the limma package for the statistical program R (v.2.14.2).

source_name: H-NS ChIP DNA from MG1655 cells

label_protocol: Samples were labeled by Nimblegen according to established protocols (http://www.nimblegen.com/products/lit/chip/index.html).

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 µM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 µM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 µl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

treatment_protocol: Cells were cross-linked by the addition of formaldehyde at 1% final concentration with continued shaking at 37 °C for 5 min before quenching with glycine (100 mM final).

value: wild-type

value: bacterial cells

tag: chip antibody

value: anti-H-NS

source_name: Input DNA from MG1655 cells

tag: sample type

value: input DNA


title: MG1655 Δhns RNAP 2

description: ChIP-chip MG1655 Δhns cells RNAP

source_name: RNAP ChIP DNA from MG1655 Δhns cells

value: Δhns

value: anti-b(RNAP) NT63

tag: chip antibody vendor

value: Neoclone

tag: chip antibody cat. #

source_name: Input DNA from MG1655 Δhns cells


title: CT, replicate 9, conventional

status: Public on Oct 31 2012

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

institute: CIPF

description: CT, replicate 9, conventional

hyb_protocol: A 2000ng cRNA product was hybridized with Whole Human Genome Oligo Microarray Kit (Agilent p/n G2519F-014850) containing 41,000+ unique human genes and transcripts.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) according to the manufacturer’s protocol

data_processing: Data extracted using Agilent Feature Extraction Software 10.7.1 following the Agilent grid template 014850_D_F_20100430 protocol GE1_107_Sep09 and the QC Metric Set GE1_QCMT_Sep09

source_name: CT, replicate 9

label_protocol: Total RNA was quantified by spectrometry (NanoDrop ND1000, NanoDrop Technologies, Wilminton, Delaware USA) and fragment size distribution was analysed by RNA 6000 Pico Bioanalyzer assay (Agilent Technologies, Palo Alto, California USA). RNA 150ng was concentrated in a SpeedVac to a working dilution and used to produce Cyanine 3-CTP-labeled cRNA using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305) according to the ‘One-Color Microarray-Based Gene Expression Analysis’ protocol Version 6.0 (Agilent p/n G4140-90040). This method uses T7 RNA polymerase which simultaneously amplifies target material and incorporates cyanine 3- labelled CTP

extract_protocol: A volume of approximately 10mm3 was extracted from each frozen tissue using the disposable sterile biopsy punch Acupunch 2mm (Acuderm Inc, Lauderdale, FL, USA). RNA was extracted following the manufacturer´s instructions (Qiagen, Hilden, Germany). Briefly, tissue was disrupted and homogenized in 700µl of Qiazol (Qiagen ref:1023537) using a Tissueruptor by Qiagen for 20 seconds. The homogenate was incubated at room temperature for 5 minutes. After adding 140µl of chloroform and centrifuging at 12,000xg for 15 minutes at 4ºC, 350µl of the aqueous phase was subjected to automatic total RNA extraction using the Qiacube equipment and the miRNeasy Mini Kit (ref:217004), both provided by Qiagen.

treatment_protocol: Serrated adenocarcinomas (SACs) were diagnosed on the basis of criteria proposed by Mäkinen et al. and conventional carcinomas (CC) according to prior established criteria. Frozen samples of 11 SACs were retrieved from the biobank of our institution for gene expression profiling. In addition to serrated morphology, one of 11 SACs displayed poorly-differentiated areas and seven showed a mucinous component. Frozen samples of 15 CC were selected as a control group from the same tumor bank. Paraffin blocks of 70 SAC, 70 CC and 20 hMSI-H cases, included in previous reports, were available for immunohistochemical validation of microarray results.

tag: carcinoma type

value: conventional

tag: carcinoma subtype

value: CT


title: ECS198

first: Gema

hyb_protocol: The arrays hybridization was performed using In Situ Hybridization Kit Plus (Agilent technologies) according to Peinado et al, Cancer Research 2008.

tag: disease state

value: endometrial carcinosarcomas

value: Female


title: ST, replicate 3, serrated

description: ST, replicate 3, serrated

source_name: ST, replicate 3

value: serrated

value: ST


title: ST, replicate 4, serrated

description: ST, replicate 4, serrated

source_name: ST, replicate 4


title: ST, replicate 2, serrated

description: ST, replicate 2, serrated

source_name: ST, replicate 2


title: CMT, replicate 3, conventional

description: CMT, replicate 3, conventional

source_name: CMT, replicate 3

value: CMT


title: SPT, replicate 1, serrated

description: SPT, replicate 1, serrated

source_name: SPT, replicate 1

value: SPT


title: MG1655 RNAP 1

description: ChIP-chip MG1655 cells RNAP

source_name: RNAP ChIP DNA from MG1655 cells


title: MDS42 ΔnusA* RNAP 2

description: ChIP-chip MDS42 ΔnusA* cells RNAP

source_name: RNAP ChIP DNA from MDS42 ΔnusA* cells

value: 43 deletions, ΔnusA*

source_name: Input DNA from MDS42 ΔnusA* cells


title: CT, replicate 8, conventional

description: CT, replicate 8, conventional

source_name: CT, replicate 8


title: Mouse 6

source_name: Brown adipose tissue

value: Male

value: 8 weeks


title: Control (MM) 12h rep 2

source_name: Caudal fin of Danio rerio

value: Control

tag: time (post amputation)

value: caudal fin


title: Δrac + 20 ug/ml bicyclomycin 1

source_name: Δrac + 20 ug/ml bicyclomycin

value: Δrac

value: 20 ug/ml bicyclomycin


title: ST, replicate 5, serrated

description: ST, replicate 5, serrated

source_name: ST, replicate 5


title: SMT, replicate 4, serrated

description: SMT, replicate 4, serrated

source_name: SMT, replicate 4

value: SMT


title: CT, replicate 4, conventional

description: CT, replicate 4, conventional

source_name: CT, replicate 4


title: MDS42 ΔnusA* RNAP 1

description: ChIP-chip MDS42 ΔnusA* cells RNAP

value: 42 deletions, ΔnusA*

value: bacterial cells

value: anti-b(RNAP) NT63

value: Neoclone

value: input DNA


title: ST, replicate 6, serrated

description: ST, replicate 6, serrated

source_name: ST, replicate 6

value: serrated


title: SMT, replicate 2, serrated

description: SMT, replicate 2, serrated

source_name: SMT, replicate 2


title: SMT, replicate 1, serrated

description: SMT, replicate 1, serrated

source_name: SMT, replicate 1


title: CT, replicate 7, conventional

description: CT, replicate 7, conventional

source_name: CT, replicate 7

value: conventional

value: CT


title: SMT, replicate 3, serrated

description: SMT, replicate 3, serrated

source_name: SMT, replicate 3


title: CT, replicate 3, conventional

description: CT, replicate 3, conventional

source_name: CT, replicate 3


title: CT, replicate 6, conventional

description: CT, replicate 6, conventional

source_name: CT, replicate 6


title: CT, replicate 11, conventional

description: CT, replicate 11, conventional

source_name: CT, replicate 11


title: CT, replicate 5, conventional

description: CT, replicate 5, conventional

source_name: CT, replicate 5


title: CT, replicate 2, conventional

description: CT, replicate 2, conventional

source_name: CT, replicate 2


title: MG1655 RNAP 2

description: ChIP-chip MG1655 cells RNAP

source_name: RNAP ChIP DNA from MG1655 cells

value: wild-type

source_name: Input DNA from MG1655 cells


title: ECS201

source_name: Total RNA from breast tumor biopsies

value: endometrial carcinosarcomas

tag: gender

value: Female

source_name: Pool from the analysed samples


title: CMT, replicate 1, conventional

description: CMT, replicate 1, conventional

source_name: CMT, replicate 1

value: CMT


title: MDS42 ΔnusG RNAP 2

description: ChIP-chip MDS42 ΔnusG cells RNAP

source_name: RNAP ChIP DNA from MDS42 ΔnusG cells

value: 43 deletions, ΔnusG

tag: cell type

source_name: Input DNA from MDS42 ΔnusG cells


title: CT, replicate 10, conventional

description: CT, replicate 10, conventional

source_name: CT, replicate 10


title: CPT, replicate 1, conventional

description: CPT, replicate 1, conventional

source_name: CPT, replicate 1

value: CPT


title: CMT, replicate 2, conventional

description: CMT, replicate 2, conventional

source_name: CMT, replicate 2


title: ST, replicate 1, serrated

description: ST, replicate 1, serrated

source_name: ST, replicate 1

value: ST


title: MDS42 RNAP 1

description: ChIP-chip MDS42 cells RNAP

source_name: RNAP ChIP DNA from MDS42 cells

tag: strain

value: 42 deletions

source_name: Input DNA from MDS42 cells


title: MDS42 RNAP 2

description: ChIP-chip MDS42 cells RNAP

tag: genotype/variation


title: MDS42 ΔnusG RNAP 1

description: ChIP-chip MDS42 ΔnusG cells RNAP

value: 42 deletions, ΔnusG


title: MG1655 Δhns RNAP 1

description: ChIP-chip MG1655 Δhns cells RNAP

source_name: RNAP ChIP DNA from MG1655 Δhns cells

value: Δhns

source_name: Input DNA from MG1655 Δhns cells


title: UniRef Processing Control [SAMPLE 47]

city: Bethesda

first: Kory

middle: R

last: Johnson

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: UniRef Processing Control

hyb_protocol: The entire purified labeled miRNA sample was dried using a speed-vac on medium setting and resuspended in 18ul of DNase/RNase-free water. To each sample, 4.5ul of 10x GE Blocking Agent and 22.5ul of 2x Hybridization Buffer (Agilent) were added. Samples were gently vortexed, incubated at 100oC for 5 minutes and chilled in an ice water bath for 5 minutes. The entire volume of each sample was hybridized to Agilent Human miRNA microarray kit (G4470A) for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, 5uM scanning mode ‘Single Pass’, eXtended Dynamic range selected, Dye channel set to Green and Green PMT set to XDR high 100%, XDR low 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol miRNA-v1_95_May07 and Grid: 016436_D_20070426) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: UniRef Processing Control

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 0.1 ug RNA using the miRNA Labeling Reagent and Hybridization kit (Agilent) according to the manufacturer's instructions, followed by purification using Micro Bio-spin 6 columns (Bio-Rad).

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.

extract_protocol: Total RNA was extracted using the mirVana RNA Isolation kit (Ambion) as recommended by the vendor for array-based assays. Concentration was determined using a NanoDrop ND-1000 UV-VIS Spectrophotometer.

tag: class

value: UniRef

tag: condition

tag: line

tag: passage

tag: processing control


title: ECS200

address: Arturo Duperier


title: UniRef Processing Control [SAMPLE 45]

description: UniRef Processing Control


title: UniRef Processing Control [SAMPLE 46]

description: UniRef Processing Control


title: ESC UNDIFF LINE WA07 PASSAGE 43

description: ESC UNDIFF LINE WA07 PASSAGE 43

hyb_protocol: see Agilent CGH 244k standard protocols.

data_processing: Agilent Feature Extraction ver9.5.1.1, protocol name: CGH-v4_95_Feb07.

source_name: ESC UNDIFF LINE WA07 PASSAGE 43

label_protocol: Cy5 and Cy3 (see Agilent CGH 244k standard protocols).

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells. Human pluripotent stem cells were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM beta-mercaptoethanol (beta-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. Pluripotent stem cells were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.

extract_protocol: Genomic DNA was extracted using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer’s instructions. Control male and female genomic DNA was purchased from Promega.

value: embryonic stem cells

value: undifferentiated

tag: cell line

value: FEMALE

source_name: Promega Human Female

tag: catalog number

tag: lot number


title: UniRef Processing Control [SAMPLE 48]

description: UniRef Processing Control


title: ESC UNDIFF LINE WA01 PASSAGE 52

description: ESC UNDIFF LINE WA01 PASSAGE 52

scan_protocol: see Agilent CGH 244k standard protocols.

source_name: ESC UNDIFF LINE WA01 PASSAGE 52

value: MALE

source_name: Promega Human Male


title: ESC UNDIFF LINE WA13 PASSAGE 76

description: ESC UNDIFF LINE WA13 PASSAGE 76

source_name: ESC UNDIFF LINE WA13 PASSAGE 76


title: ESC UNDIFF LINE WA14 PASSAGE 35

description: ESC UNDIFF LINE WA14 PASSAGE 35

source_name: ESC UNDIFF LINE WA14 PASSAGE 35


title: CT, replicate 1, conventional

description: CT, replicate 1, conventional

source_name: CT, replicate 1

value: conventional


title: UniRef Processing Control [SAMPLE 49]

description: UniRef Processing Control


title: ESC UNDIFF LINE ES05 PASSAGE 59

description: ESC UNDIFF LINE ES05 PASSAGE 59

source_name: ESC UNDIFF LINE ES05 PASSAGE 59


title: UniRef Processing Control [SAMPLE 44]

description: UniRef Processing Control


title: ESC UNDIFF LINE WA09 PASSAGE 41

description: ESC UNDIFF LINE WA09 PASSAGE 41

source_name: ESC UNDIFF LINE WA09 PASSAGE 41


title: ESC UNDIFF LINE SA02 PASSAGE 35

description: ESC UNDIFF LINE SA02 PASSAGE 35

source_name: ESC UNDIFF LINE SA02 PASSAGE 35


title: UniRef Processing Control [SAMPLE 43]

description: UniRef Processing Control


title: Somatic Tissue Brain

description: Somatic Tissue Brain

source_name: Somatic Tissue Brain

value: Somatic Tissue


title: Somatic Tissue Liver

description: Somatic Tissue Liver

source_name: Somatic Tissue Liver


title: ESC UNDIFF LINE WA14 PASSAGE 39

description: ESC UNDIFF LINE WA14 PASSAGE 39

source_name: ESC UNDIFF LINE WA14 PASSAGE 39

value: ESC

value: UNDIFF


title: ESC UNDIFF LINE SA01 PASSAGE 28

description: ESC UNDIFF LINE SA01 PASSAGE 28

source_name: ESC UNDIFF LINE SA01 PASSAGE 28


title: ESC UNDIFF LINE WA14 PASSAGE 35

description: ESC UNDIFF LINE WA14 PASSAGE 35


title: Somatic Tissue Heart

description: Somatic Tissue Heart

source_name: Somatic Tissue Heart


title: ESC UNDIFF LINE WA13 PASSAGE 76

description: ESC UNDIFF LINE WA13 PASSAGE 76


title: ESC UNDIFF LINE TE03 PASSAGE 66

description: ESC UNDIFF LINE TE03 PASSAGE 66

source_name: ESC UNDIFF LINE TE03 PASSAGE 66


title: ESC UNDIFF LINE BG02 PASSAGE 50

description: ESC UNDIFF LINE BG02 PASSAGE 50

source_name: ESC UNDIFF LINE BG02 PASSAGE 50


title: ESC UNDIFF LINE UC01 PASSAGE 60

description: ESC UNDIFF LINE UC01 PASSAGE 60

source_name: ESC UNDIFF LINE UC01 PASSAGE 60


title: ESC UNDIFF LINE ES01 PASSAGE 71

description: ESC UNDIFF LINE ES01 PASSAGE 71

source_name: ESC UNDIFF LINE ES01 PASSAGE 71

source_name: Promega Human Female


title: ESC UNDIFF LINE ES06 PASSAGE 58

description: ESC UNDIFF LINE ES06 PASSAGE 58

source_name: ESC UNDIFF LINE ES06 PASSAGE 58


title: ESC UNDIFF LINE BG01 PASSAGE 63

description: ESC UNDIFF LINE BG01 PASSAGE 63

source_name: ESC UNDIFF LINE BG01 PASSAGE 63

source_name: Promega Human Male


title: ESC UNDIFF LINE ES03 PASSAGE 84

description: ESC UNDIFF LINE ES03 PASSAGE 84

source_name: ESC UNDIFF LINE ES03 PASSAGE 84


title: ESC UNDIFF LINE UC06 PASSAGE 110

description: ESC UNDIFF LINE UC06 PASSAGE 110

source_name: ESC UNDIFF LINE UC06 PASSAGE 110


title: ESC UNDIFF LINE BG03 PASSAGE 50

description: ESC UNDIFF LINE BG03 PASSAGE 50

source_name: ESC UNDIFF LINE BG03 PASSAGE 50


title: ESC UNDIFF LINE UC06 PASSAGE 59

description: ESC UNDIFF LINE UC06 PASSAGE 59

source_name: ESC UNDIFF LINE UC06 PASSAGE 59


title: ESC UNDIFF LINE TE04 PASSAGE 32

description: ESC UNDIFF LINE TE04 PASSAGE 32

source_name: ESC UNDIFF LINE TE04 PASSAGE 32


title: ESC UNDIFF LINE ES04 PASSAGE 72

description: ESC UNDIFF LINE ES04 PASSAGE 72

source_name: ESC UNDIFF LINE ES04 PASSAGE 72


title: ESC UNDIFF LINE WA09 PASSAGE 41

description: ESC UNDIFF LINE WA09 PASSAGE 41

source_name: ESC UNDIFF LINE WA09 PASSAGE 41