title: HCC xenograft mice treated with sorafenib (BRI1010D)

description: HCC xenograft mice brivanib treated after resistance (BRI1010D)


title: HCC xenograft mice treated with sorafenib (RES54D)

status: Public on Jun 16 2016

type: RNA

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: HCC xenograft mice with acquired sorafenib resistance (RES54D)

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) in R.3.0.1

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Standard Affymetrix protocol

extract_protocol: At least three subcutaneous Huh7-derived tumors corresponding to each experimental group; sorafenib-resistant, sorafenib-sensitive and non-treated control group, were excised and subjected to isolation and spheroid assays after being mechanically dissociated by gentle pipetting in Ca/Mg-free PBS on ice, and filtered through a 40 µm cell strainer (BD Falcon) to obtain single cell suspension. Cells were exposed to red cell lysis buffer (Sigma-Aldrich) to remove red blood cells. No enzymatic digestion was used to isolate cells. Cell viability was quantified in a Neubauer cytometer using the trypan blue (1%; Sigma Aldrich) exclusion method. After tumor harvest and generation of single cell suspensions tumor cells where directly cultured into non-adherent conditions to allow the formation of spheroids. Briefly, cells were grown in serum free epithelial growth medium (MEGM, BioWhittaker) supplemented with B27 (Invitrogen), 20 ng/mL EGF and 20 ng/mL bFGF (BD Biosciences), and 4 μg/mL insulin (Sigma). Live cells were then plated in 96-well ultra-low attachment plates (Corning) at limiting dilution (10, 102, 103 and 104 cells) and sphere formation was assessed microscopically after 10 days of growth.

tag: phenotype

value: sorafenib-acquired resistant


title: HCC xenograft mice treated with sorafenib (SEN84D)

description: HCC xenograft mice sorafenib sensitive (SEN84D)

value: sorafenib sensitive


title: HCC xenograft mice treated with sorafenib (RES48D)

description: HCC xenograft mice with acquired sorafenib resistance (RES48D)


title: Young MEP, biological rep2

status: Public on Jun 17 2016

city: Lund

first: Alexandra

last: Rundberg Nilsson

address: Klinikgatan 26

department: Experimental Hematology

country: Sweden

institute: Lund University

hyb_protocol: 3.0 µg of fragmented and labeled SPIA cDNA were hybridized to Affymetrix Human Gene 1.1 ST Array Plates. For hybridization, washing and staining an Affymetrix GeneTitan system was used.

scan_protocol: GeneChips were scanned using an Affymetrix GeneTitan system controlled by the Affymetrix GeneChip Command Console software v3.3 (AGCC).

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using the RMA algorithm (Irizarry et al., 2003) in the Affymetrix GeneChip Expression Console v1.3 software.

source_name: Young MEP, 20-26 years

label_protocol: SPIA cDNA was generated from 0.6 to 20 ng of total RNA, followed by fragmentation and biotin labeling according to the NuGEN Ovation PicoSL WTA System V2 and NUGEN Encore Biotin Module manuals.

growth_protocol: Freshly isolated human bone marrow.

extract_protocol: Total RNA was extracted from cells stabilized in RLT buffer according to the Purification of total RNA from animal and human cells protocol of the QIAGEN RNeasy Micro Kit.

treatment_protocol: Human hemaotpoietic stem and progenitor populations (HSPCs) were isolated be means of FACS and sorted into RLT buffer, after which they were immediatly frozen on dry ice. Samples were shipped on dry ice to KFB Center of Excellence for Fluorescent Bioanalytics, Regensburg, Germany, prepared and subjected to the Affymetrix Human Gene 1.1 ST array (www.kfb-regensburg.de)

tag: tissue

value: Bone marrow

tag: genotype

value: Healthy donors

tag: age

value: 20-26 years


title: CL1-0 shKSRP-1

city: Taipei

first: Kuo-Tai

last: Hua

address: No. 1, Sec. 1, Jen-Ai Rd.

country: Taiwan

institute: National Taiwan University

description: Gene expression data from CL1-0 cells with KSRP shRNA

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

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

source_name: lung cancer

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: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were selected with G418 or puromycin for two weeks.  Stably transduced cells were use for this experiment.

value: CL1-0 cells expressing KSRP shRNA


title: CL1-5 pEGFP-KSRP

description: Gene expression data from CL1-5 cells with KSRP overexpression

value: CL1-5 cells expressing EGFP-tagged KSRP


title: CL1-0 shscramble

description: Gene expression data from CL1-0 cells with scramble shRNA

value: CL1-0 cells expressing scramble shRNA


title: CHIR+

city: Osaka

first: Katsumi

last: Fumoto

state: State...

country: Japan

institute: Osaka university

description: Gene expression data from fetal mouse lung cultured in the presence of CHIR

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Mus musculus

source_name: Cultured epithelium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA. (Using GeneChip 3' IVT Express Kit)

growth_protocol: The epithelium isolated from fetal mouse lung (embryonic day 11) were embedded in matrigel and cultured in FGF10 containing medium with CHIR99021 for 4 days. Then, the epithelium were fragmented into several pieces and re-embedded in matrigel and cultured in FGF10-containing medium in the presence or absence of CHIR for 2days.

extract_protocol: Total RNAs were extracted by using RNA extraction kit (macherey nagel) and cDNAs were generated by using SuperScript VILO.

tag: strain

value: ICR

value: embryonic day 11

value: Cultured fetal lung epithelium

tag: culture condition

value: in the presence of CHIR


title: CL1-0 shKSRP-2


title: Cy5 7 Yp Vs Cy3 110 Op

city: SASKATOON

first: Muhammad

middle: Irfan-ur-Rehman

last: Khan

state: SASKATCHEWAN

address: 52 Campus drive

department: Veterinary Biomedical Sciences

country: Canada

institute: University of Saskatchewan

hyb_protocol: This document applies to the hybridization of microarray slides 4x44K printed  with oligonucleotides by Agilent for all EmbryoGENE related projects.

scan_protocol: Images were scanned using Tecan scanning protocol..

data_processing: Arraypro software was used to extract target intensities. Background of a target was subtracted from the median signal intensity of the foreground of the target. If the difference was a negative value due to higher intensity of background vs. foreground signals, the negative value was replaced with a default value of 0.5. Flexarry software (1.6.1.1) was used to obtain the list of differentially expressed gene. The median pixel value for each target was transformed to the log2 and normalized “within array” for dye bias using nonparametric regression (locally weighted scatter plot smoothing; “lowess”), and subjected to “between-array” normalization to unify intensities across the arrays using quantile method. Finally, a list of differentially expressed genes was obtained by running a simple linear model for microarray data; i.e., “simple limma algorithm”. A gene was considered to be differentially expressed when a ≥ 2-fold change in its expression at P-value of ≤ 0.05.

organism: Bos taurus

label_protocol: This document describes the procedure used for labelling aRNA using the Universal Linkage System (ULS) by Kreatech for Gene Expression studies using microarray slides from Agilent. ULS is a non-enzymatic protocol that allows direct labeling of unmodified, amplified RNA. ULS will react with unmodified, amplified RNA and label it by formation of a coordinative bond on the N7 position of guanine. Fluorophore Cy3 and Cy5 are linked via a spacer to the ULS molecule.

growth_protocol: Three mother-daughter pairs (n=6 in total) of Hereford cows were synchronized with single intramuscular injection of PGF2 alpha (Lutalyse® @ 25mg, i.m., Pfizer). Ovulations (Day 0) and subsequent follicular dynamics were tracked using 7.5 MHz trans-rectal ultrasound probe (Aloka® SSD 900; B mode). Two intramuscular injections of PGF2 alpha (Lutalyse® @ 25mg, i.m., Pfizer) were administered 12 h apart (on Day 4.5 and 5), respectively. Luteinizing hormone (Lutropin® 25 mg, i.m., Bionich) was administered, intramuscularly; 24 h after (Day 6) last injection of PGF2 alpha (Lutalyse® @ 25mg, i.m., Pfizer).On Day 7, preovulatory dominant follicle was collected either by ultrasound guided follicle aspiration or after ovariectomy. Follicular fluid was aliquoted into two RNase free 1.5 ml tubes after searching and removing the oocyte. Granulosa cells were obtained by centrifuging follicular fluid at 700g for 5 minutes. Follicular fluid was removed from both aliquots and granulosa cells were either snap frozen in liquid nitrogen or suspended in 300-700 µl of RNAlater® (Ambion Inc.) for 12 hours at 4°C. All samples were kept at -80°C until mRNA extraction.

extract_protocol:
This document applies to the total RNA extraction using the PicoPure RNA Isolation Kit from Molecular Devices. The PicoPure RNA Isolation Kit enables to recover total cellular RNA from pico-scale samples. Researchers can obtain high recoveries of total cellular RNA from as little as a single cell to samples with up to 100 ug of RNA. RNA extraction from larger samples should be done using another kit or technique.
amplication: This procedure describes the amplification of RNA using the RiboAmpb HSPlus RNA Amplification kit (Molecular devices). This procedure may be required for microarray experiments with extremely limited amounts of starting material. The RiboAmpb HSPlus RNA Amplification Kit enables the production of microgram quantities of antisense RNA (aRNA) from picogram quantities of total cellular RNA. The RiboAmpb HSPlus Kit achieves high yields of aRNA with a proprietary linear amplification process using double-stranded cDNA as template in a two round T7 RNA polymerase catalyzed amplification.

tag: sample type

tag: breed (cattle)

value: Hereford

tag: follicular size

value: Pre-ovulatory

tag: cell collection method

value: aspiration

tag: follicular status

value: dominant

tag: reproductive status (cattle)

value: Heifer/nulliparous

value: Multiparous


title: Cy5 126 Op Vs Cy3 184 Yp


title: Cy5 184 Yp Vs Cy3 126 Op


title: U937_inf_T3_1

type: genomic

city: London

first: Deniz

last: Cizmeci

address: Imperial College London

country: United Kingdom

institute: Imperial College London

hyb_protocol: Briefly, 500 ng of genomic DNA was sodium bisulfite converted using the EZ-96 DNA Methylation kit (Zymo research, CA, USA) using the manufacturer’s instructions.

scan_protocol: Post-hybridization allelic-specific single-base extension of the probes incorporates a fluorescent label enabling detection.

data_processing: For each CpG site a beta value was generated by the relative intensity of the green fluorescent signal (methylated (M)) to the red and green signal combined (M/M+U+100). Quality control checks and quantile normalization were implemented using WateRmelon (dasen method). Samples with more than 1% of sites with a detection p-value greater than 0.05 were removed as were probes with 1% of samples with a detection p-value greater than 0.05. Probes were removed if they had a bead count less than 3 in 1% of samples. Cross-hybridizing probes were removed, leaving 425496 probes for analysis.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Experiment 2 U937 macrophages infected with Burkholderia pseudomallei K96243 3 hours (T3)

label_protocol: The DNA methylation profile was determined using the Infinium HumanMethylation450 BeadChip (450K) (Illumina Inc.) following the manufacturer’s instructions.

growth_protocol: The human leukemic monocyte lymphoma cell line (U937, ATCC CRL-1593.2) was maintained in RPMI 1640 supplemented with 10% foetal bovine serum (FBS) at 37°C. U937 cells were differentiated to macrophage-like cells following exposure to 20 ng/ml (final concentration) of phorbol 12-myristate 13-acetate (PMA) for 48 hours at 37°C and differentiation evidenced by increased adherence to tissue culture flasks.

extract_protocol: DNA was isolated using an AllPrep kit (Qiagen) and stored at -80ºC until required.

treatment_protocol: Overnight cultures of B. pseudomallei K96243 were diluted in L-15 medium and added to differentiated U937 cells at a multiplicity of infection (MOI) of 10. Uninfected controls were overlaid with L15 medium only. The cells were then incubated at 37°C to allow infection. The cells were washed 3 times with PBS and incubated with fresh L15 medium containing 1mg/ml kanamycin to kill extracellular bacteria. At appropriate time points the cells were washed 3 times in warm PBS and lysed with 0.1% (vol/vol) Triton X-100.

tag: cell line

value: macrophage-like U937 cells

tag: infection

value: infected with B.pseudomallei

tag: time

value: 3 hours post infection


title: Cy5 13 Op Vs Cy3 11 Yp


title: CL1-5 pEGFP

description: Gene expression data from CL1-5 cells with vector control

value: CL1-5 cells expressing vector control


title: U937_un_T3_1

source_name: Experiment 2 uninfected U937 macrophages 3 hours (T3)

value: control


title: U937_un_T1_1

source_name: Experiment 2 uninfected U937 macrophages 1 hour (T1)

value: 1 hour post infection


title: U937_inf_T4_5

source_name: Experiment 2 U937 macrophages infected with Burkholderia pseudomallei K96243 4 hours (T4)

value: 4 hours post infection


title: CHIR-

description: Gene expression data from fetal mouse lung cultured in the absence of CHIR

value: ICR

value: in the absence of CHIR


title: U937_inf_T4_4

source_name: Experiment 1 U937 macrophages infected with Burkholderia pseudomallei K96243 4 hours (T4)


title: Disease Differentiated muscle cell, biological rep3

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway

department: School of Medicine

country: USA

institute: The Johns Hopkins University

description:
Gene Expression Data
ICho-MUS-GM-4a-PrimeView_(PrimeView).CEL

hyb_protocol: Following fragmentation cRNAs were hybridized 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer.

data_processing: Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  RMA normalization was used to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.

source_name: induced Pluripotent stem cell

label_protocol: Biotinylated cRNAs were prepared with the GeneChip HT 3' IVT Express Kit per manufacturer's instructions.

growth_protocol: hESC lines and hiPSC lines were cultured with mouse embryonic fibroblasts (MEFs, Globalstem) pre-plated at 12-15,000 cells/cm2. Medium containing DMEM/F12, 20% knockout serum replacement, 1mM L-glutamine, 100 uM MEM non-essential amino acids, and 0.1 mM beta-mercaptoethanol was used. Ten ng/ml of FGF-2 was added after sterile filtration and cells were fed daily and passaged weekly using 6U/mL dispase or mechanically.

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

treatment_protocol: For myogenic differentiation, cells were rendered to single cells using Accutase and plated on gelatin for 10 minutes to remove MEFs. Non-adherent cells were collected and plated on Geltrex treated dishes at a density of 150k cells for one well of a 24-well plate in the presence of MEF-conditioned N2 media containing 10 ng/ml of FGF-2 and 10 uM of Y-27632. And Inhibitor of GSK-3β and/or Notch signaling pathway were treated for the skeletal muscle differentiation.

tag: cell source

value: induced Pluripotent stem cell

tag: protocol

value: differentiated

tag: cell type

value: Disease Differentiated muscle cell


title: U937_inf_T2_3

source_name: Experiment 2 U937 macrophages infected with Burkholderia pseudomallei K96243 2 hours (T2)

value: 2 hours post infection


title: U937_inf_T1_1

source_name: Experiment 2 U937 macrophages infected with Burkholderia pseudomallei K96243 1 hour (T1)


title: Cy5 110 Op Vs Cy3 7 Yp

value: Hereford

value: Pre-ovulatory

value: aspiration


title: U937_un_T2_3

source_name: Experiment 2 uninfected U937 macrophages 2 hours (T2)


title: U937_inf_T4_3


title: U937_un_T4_1

source_name: Experiment 1 uninfected U937 macrophages 4 hours (T4)


title: U937_un_T4_3

source_name: Experiment 2 uninfected U937 macrophages 4 hours (T4)


title: Differentiated muscle cell, biological rep3

description:
Gene Expression Data
ICho-MYO-S4-1a-PrimeView_(PrimeView).CEL

source_name: embryonic stem cell (H9)

value: embryonic stem cell (H9)

value: Differentiated muscle cell


title: U937_inf_T2_2

source_name: Experiment 1 U937 macrophages infected with Burkholderia pseudomallei K96243 2 hours (T2)

value: macrophage-like U937 cells

value: infected with B.pseudomallei


title: Control Differentiated muscle cell, biological rep3

description:
Gene Expression Data
ICho-MUS-C-4a-PrimeView_(PrimeView).CEL

value: Control Differentiated muscle cell


title: Control Differentiated muscle cell, biological rep2

description:
Gene Expression Data
ICho-MUS-C-3a-PrimeView_(PrimeView).CEL


title: Cy5 11 Yp Vs Cy3 13 Op

value: dominant

value: Heifer/nulliparous

value: Multiparous


title: Control Differentiated muscle cell, biological rep1

description:
Gene Expression Data
ICho-MUS-C-1a-PrimeView_(PrimeView).CEL


title: Disease Differentiated muscle cell, biological rep2

description:
Gene Expression Data
ICho-MUS-GM-3a-PrimeView_(PrimeView).CEL


title: Differentiated muscle cell, biological rep2

description:
Gene Expression Data
ICho-MYO-S3-1a-PrimeView_(PrimeView).CEL


title: Fetal Skeletal muscle, biological rep3

description:
Gene Expression Data
ICho-MYO-M3-1a-PrimeView_(PrimeView).CEL

source_name: Fetal Skeletal muscle (Agilent)

value: Fetal Skeletal muscle (Agilent)


title: U937_un_T4_2

value: control

value: 4 hours post infection


title: U937_inf_T4_1


title: U937_inf_T4_2


title: Differentiated muscle cell, biological rep1

description:
Gene Expression Data
ICho-MYO-S2-1a-PrimeView_(PrimeView).CEL

value: differentiated


title: Fetal Skeletal muscle, biological rep2

description:
Gene Expression Data
ICho-MYO-M2-1a-PrimeView_(PrimeView).CEL


title: U937_un_T2_2

source_name: Experiment 1 uninfected U937 macrophages 2 hours (T2)


title: U937_un_T2_1


title: H9_shARNT_HYPOX_D3+2_87_2522_3_1

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

institute: University of California San Diego

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered for detection pValue < 0.01 and normalised using Robust Spline Normalisation with lumi in R v3.2.1

label: Biotin

source_name: shARNT_Hypoxia (2% O2)

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

growth_protocol: Human embryonic stem cells (WA09/H9) were maintained on Geltrex-coated plates (BD Biosciences ) in StemPro (Thermo Fisher) + bFGF (12 ng/ml)

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 v4 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

treatment_protocol: Human embryonic stem cells (WA09/H9) maintained in StemPro (D-2) were switched to minimal media (EMIM (Erb et al., 2011) containing KO DMEM/F12 (Gibco), 1% Insulin-Transferrin-Selenium Mix (Sigma-Aldrich), 1% NEAA (Gibco), 2mM L-Glutamine (Corning), 0.1mM 2-mercaptoethanol (Gibo), and 2% BSA (Gemini Bio Products) ) for 2 days then treated with BMP4 (StemRD, 10ng/ml) for 3 days in minimal media+BMP4 (D3), after which cells were replated onto Geltrex in Feeder Conditioned Media +BMP4 and cultured in normoxia (20% O2) or hypoxia (2% O2) for 2 days (D3+2). Cells were infected with lentiviral shRNA for shScramble (control) or shARNT, the beta subunit of the Hypoxia Inducible Factor (HIF) complex.

tag: origin

value: Embryonic

tag: treatment

value: shARNT

tag: oxygen status

value: Hypoxia (2% O2)


title: Embryonic stem cell, biological rep1

description:
Gene Expression Data
ICho-MYO-H1-1a-PrimeView_(PrimeView).CEL

value: non-differentiated


title: U937_inf_T2_1

value: 2 hours post infection


title: Embryonic stem cell, biological rep3

description:
Gene Expression Data
ICho-MYO-H3-1a-PrimeView_(PrimeView).CEL

value: embryonic stem cell (H9)


title: Fetal Skeletal muscle, biological rep1

description:
Gene Expression Data
ICho-MYO-M1-1a-PrimeView_(PrimeView).CEL

source_name: Fetal Skeletal muscle (BioChain)

value: Fetal Skeletal muscle (BioChain)


title: H9_shARNT_NORMOX_D3+2_87_2523_3_1

source_name: shARNT_Normoxia (20% O2)

value: Normoxia (20% O2)


title: H9_shARNT_HYPOX_D3+2_87_2522_2_1


title: H9_shARNT_NORMOX_D3+2_87_2523_1_1


title: Embryonic stem cell, biological rep2

description:
Gene Expression Data
ICho-MYO-H2-1a-PrimeView_(PrimeView).CEL


title: H9_shARNT_D3_87_2524_2_1


title: H9_shARNT_NORMOX_D3+2_87_2523_2_1


title: H9_shARNT_D3_87_2524_3_1


title: H9_shARNT_D-2_87_2521_2_1


title: H9_shARNT_HYPOX_D3+2_87_2522_1_1


title: H9_shARNT_D-2_87_2521_1_1


title: H9_shARNT_D-2_87_2521_3_1


title: H9_shARNT_D3_87_2524_1_1


title: H9_Scramble_NORMOX_D3+2_87_2520_3_1

source_name: shScramble_Normoxia (20% O2)

value: shScramble


title: Disease Differentiated muscle cell, biological rep1

description:
Gene Expression Data
ICho-MUS-GM-1a-PrimeView_(PrimeView).CEL

value: induced Pluripotent stem cell

value: Disease Differentiated muscle cell


title: H9_Scramble_HYPOX_D3+2_87_2519_2_1

source_name: shScramble_Hypoxia (2% O2)


title: H9_Scramble_NORMOX_D3+2_87_2520_2_1


title: H9_Scramble_NORMOX_D3+2_87_2520_1_1


title: H9_Scramble_HYPOX_D3+2_87_2519_3_1


title: H9_Scramble_HYPOX_D3+2_87_2519_1_1


title: miR-206 Mimic, biological rep4

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: An Affymetrix Gene Chip Scanner 3000 was used to scan the probe arrays.

data_processing: Partek Genomics 6 (Partek Inc., Saint Louis, MO, USA) was used for data processing and analysis.

source_name: RD cells_miR-206 Mimic

label_protocol: Samples were prepared according to Affymetrix protocols (Affymetrix, Inc). 200 nanograms of total RNA was used in conjunction with the Affymetrix recommended protocol for the GeneChip 2.0 ST chips

growth_protocol: RD cells grown in 10% FBS, DMEM at 37°C

extract_protocol: miRNeasy extraction of total RNA according to manufacturer's instructions

treatment_protocol: Cells transfected with 30nM miR-206 or NC Mimic with Lipofectamine RNAiMax

value: RD

value: rhabdomyosarcoma cells

tag: transfected with

value: miR-206 miRNA Mimic

tag: time point

value: 48 hrs post transfection


title: miR-206 Mimic, biological rep2


title: miR-206 Mimic, biological rep3


title: miR-206 Mimic, biological rep1


title: H9_Scramble_D3_87_2518_2_1


title: H9_Scramble_D3_87_2518_3_1


title: Fig5Rpb3-TAP-cmk

city: Madison

first: Aseem

last: Ansari

state: WI

address: 440 Henry Mall

department: Biochemistry and The Genome Center

institute: University of Wisconsin-Madison

hyb_protocol: 24 pmol of ChIP DNA and an equivalent mass of input DNA were mixed in a speedvac on medium heat for 30 min. The samples were resuspended in 18 uL of hybrdization buffer and loaded using NimbleGen X1 mixers and hybridzed on a MAUI instrument.

scan_protocol: Arrays were scanned on a GenePix 4000B instrument as previously described (Chinchilla et al., 2012).

data_processing: Probe intensities were extracted with NimbleScan using the .ndf file (attached). Global and local normalization was performed using in-house R code available upon request, log2-transformed and averaged with a five-probe moving average to smooth the data.

organism: Saccharomyces cerevisiae BY4741

source_name: Rpb3-TAP ChIP from kin28is budding yeast treated with CMK

label_protocol: ChIP DNA was end-repaired, linkers were ligated and ligation-mediated PCR was performed as previously described (Chinchilla et al., 2012).

growth_protocol: Yeast were grown in His-dropout media + 2% dextrose at 30 °C in a shaking incubator from an OD600 of 0.1 to mid-log phase OD600 of 0.5 to 1.

extract_protocol: For every immunoprecipitation, 50 ul of protein G conjugated Dynabeads (Life Technologies), pre-washed with lysis buffer (50mM HEPES-KOH [pH 7.5], 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate, 1mM, Aprotinin, 1mM Leupeptin, 1mM PMSF, 1mM Benzamidine, 1.45mM Pepstatin, 1mM NaN3, 1mM Na3VO4, 1mM NaF), were mixed with the whole cell extract-antibody mixture to pulldown Pol II complexes. Washes and elution were performed as previously described (Tietjen et al., 2010).

treatment_protocol: Cells were treated with 2 or 5 uM of inhibitor (1-NAPP-1 or CMK) or equivalent solvent control (DMSO) at mid-log phase (50 mL, OD600 0.4 to 1) for 1 hr before crosslinking with 1% formaldehyde for 5 min.

tag: chip antibody

value: TAP (Thermo)

value: CMK

source_name: Input DNA from kin28is budding yeast treated with CMK

tag: sample type

value: input


title: Fig5Ser5p-cmk

source_name: Ser5p ChIP from kin28is budding yeast treated with CMK

value: Ser5p (Eick, 3E8)


title: Fig5Ser2p-cmk

source_name: Ser2p ChIP from kin28is budding yeast treated with CMK

value: Ser2p (Bethyl)


title: Fig5Ser2p-dmso

source_name: Ser2p ChIP from kin28is budding yeast treated with DMSO

value: DMSO

source_name: Input DNA from kin28is budding yeast treated with DMSO


title: H9_Scramble_D3_87_2518_1_1

value: Embryonic


title: NC Mimic, biological rep4

source_name: RD cells_NC Mimic

value: Negative Control (NC) miRNA Mimic


title: Med8-FLAG-dmso

organism: Saccharomyces cerevisiae

source_name: Med8-FLAG ChIP from kin28is budding yeast treated with DMSO

value: FLAG


title: Med8-FLAG-cmk

source_name: Med8-FLAG ChIP from kin28is budding yeast treated with CMK


title: NC Mimic, biological rep3


title: Fig5Rpb3-TAP-dmso

source_name: Rpb3-TAP ChIP from kin28is budding yeast treated with DMSO


title: Fig3Ser7p-1napp1

source_name: Ser7p ChIP from kin28is budding yeast treated with 1-NAPP-1

value: Ser7p (Eick, 4D12)

source_name: Input DNA from kin28is budding yeast treated with 1-NAPP-1


title: Fig3Ser5p-1napp1

source_name: Ser5p ChIP from kin28is budding yeast treated with 1-NAPP-1


title: Fig3Ser5p-cmk


title: Fig3/5Ser7p-dmso

source_name: Ser7p ChIP from kin28is budding yeast treated with DMSO


title: H9_Scramble_D-2_87_2517_1_1

source_name: shScramble_Normoxia (20% O2)

value: shScramble

value: Normoxia (20% O2)


title: H9_Scramble_D-2_87_2517_2_1


title: Fig3/5Ser7p-cmk

source_name: Ser7p ChIP from kin28is budding yeast treated with CMK


title: HT29_siGATA6

status: Public on Jun 15 2016

city: Tokyo

first: Testu

last: Akiyama

address: 1-1-1, Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

institute: Tokyo University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: Data sets were imported into Gene Spring for normalization and statistical analysis.

source_name: HT29, GATA6 siRNA

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was prepared using TRIsure (BIO LINE)

value: siRNA targeting GATA6


title: HT29_siREG4

source_name: HT29, REG4 siRNA


title: Intestinal mucosal mast cells, rep1

first: Nobuhiro

last: Nakano

address: 2-1-1 Hongo, Bunkyo-ku

department: Graduate School of Medicine

institute: Juntendo University

description: Sorted as FcεRI and c-Kit/CD117 positive cells by flow cytometry

hyb_protocol: Hybridization and fluidics were performed according to standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G according to standard Affymetrix protocols.

data_processing: Row data (CEL files) were obtained by analyzing image data with GeneChip Command Console software. The data were processed and analyzed using GeneSpring GX ver.13.1 software (Agilent Technologies, Santa Clara,CA).

source_name: Mucosal mast cells isolated from the small intestine of naïve mice

label_protocol: Biotinylated cDNA were prepared by amplification of 2 ng RNA using a GeneChip WT Pico Reagent Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Bone marrow-derived mast cells (BMMCs) were generated by culturing BALB/c bone marrow cells with murine interleukin-3 (10 ng/ml) and stem cell factor (10 ng/ml) for 3-4 weeks. Intestinal mucosal mast cells were isolated from the small intestine lamina propria of naive BALB/c mice by flow cytometry.

extract_protocol: Total RNA was purified using an RNeasy Mini kit or RNeasy Micro kit (Qiagen, Valencia, CA).

tag: strain

value: BALB/c

value: intestinal mast cell

value: isolated from the small intestine lamina propria of naïve BALB/c mice by flow cytometry


title: H9_Scramble_D-2_87_2517_3_1


title: BMMCs cultured with Notch ligand Dll1, rep1

description: Sorted as c-Kit/CD117 positive cells by magnetic bead separation

source_name: Bone marrow derived mast cells cultured in the presence of Notch ligand Dll1 for 6 days

value: bone marrow derived mast cell

value: cocultured with mouse Notch ligand Dll1-expressing CHO cells for 6 days


title: NC Mimic, biological rep1

value: RD

value: rhabdomyosarcoma cells

value: 48 hrs post transfection


title: HT29_siControl reanalyzed 2

source_name: HT29, Control siRNA

value: control


title: HT29_siControl reanalyzed 1


title: HT29_siLGR5

source_name: HT29, LGR5 siRNA

value: siRNA targeting LGR5


title: Fig5Ser5p-dmso

source_name: Ser5p ChIP from kin28is budding yeast treated with DMSO

value: Ser5p (Eick, 3E8)

value: DMSO

source_name: Input DNA from kin28is budding yeast treated with DMSO

value: input


title: BMMCs cultured with TGF-β, rep1

source_name: Bone marrow derived mast cells cultured in the presence of TGF-β for 6 days

value: cultured with TGF-β1 (5 ng/ml) for 6 days


title: human malignant mesothelioma MS1 cell line; sorted SP subpopulations, rep1

city: Seoul

first: Myung-Chul

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: deparment of clinical pathology

country: South Korea

institute: College of Veterinary Medicine, Seoul National University

description: The cell line was cultured in RPMI 1640 medium with 10% fetal bovine serum and supplements at 37◦C in a humidified atmosphere containing 5% CO2

hyb_protocol: End-labeled miRNA was hybridized to the GeneChip® miRNA arrays for 16 hours at 48 ℃ and 60 rpm as described in the protocol. After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450 (Affymetrix).

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

data_processing: The intensity values of CEL files were normalized to remove bias between the arrays, using the Robust Multi-array Average (RMA) + Detected Above Background (DABG) algorithm implemented in the Affymetrix Expression Console software (version 1.3.1.). Highly expressed genes that showed over 1.5-fold difference between the signal values of control and test samples were selected for further study.

source_name: malignant mesothelioma, MS1 cell line

label_protocol: Per RNA sample, 1.6 ug was used as input into the Affymetrix procedure as recommended by protocol (Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kits for Affymetrix GeneChip® miRNA Arrays). Briefly, 1.6 ng of total RNA was tailed by poly(A) and end-labeled by FlashTag™ sequence that has biotin using PAP enzyme and T4 DNA Ligase, respectively.

extract_protocol: Total RNAs including miRNAs were isolated from the sorted SP and NSP cells by using miRNeasy extraction kit (Qiagen, Valencia, CA, USA) according to instructions provided by the manufacturer. RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Palo Alto, CA, USA), and quantity was determined by Nanodrop-1000 Spectrophotometer (Thermo scientific, Wilmington, DE, USA).

treatment_protocol: 106 cells/mL in pre-warmed RPMI containing 2% FBS and 10mM HEPES were incubated with Hoechst 33342 dye (5μg/mL; Sigma–Aldrich, St. Louis, MO, USA) for 90 min at 37◦C with intermittent mixing. After centrifugation at 480 × g for 5 minute and subsequent PBS washing containing 2% FBS at 4◦C, the incubated cells were subjected to SP analysis. Becton-Dickinson FACS Aria III flow cytometer sorter (SNU FACSCenter, Seoul, South Korea) equipped with Hoechst Blue with a 450/50 broad pass (BP) filter and Hoechst Red with a 675/30 BP filter was used to detect Hoechst 33342 staining. Verapamil hydrochloride (50μM, Sigma–Aldrich, St. Louis, MO, USA) which blocks Hoechst 33342 dye efflux was used to identify SP fractions. SP and NSP cells were collected by flow cytometry assisted cell sorter (FACS) based on the intensities of fluorescence, and subjected to further analyses.

value: malignant mesothelioma

tag: fraction

value: SP


title: NC Mimic, biological rep2

source_name: RD cells_NC Mimic

value: Negative Control (NC) miRNA Mimic


title: HT29_siControl


title: Fig3Ser2p-1napp1

source_name: Ser2p ChIP from kin28is budding yeast treated with 1-NAPP-1

value: Ser2p (Bethyl)


title: BMMCs, rep1

source_name: Bone marrow derived mast cells cultured in normal medium for 6 days

value: BALB/c

value: cultured in normal medium for 6 days


title: Fig3Ser5p-dmso


title: Fig3Ser2p-dmso

source_name: Ser2p ChIP from kin28is budding yeast treated with DMSO


title: human malignant mesothelioma MS1 cell line; sorted NSP subpopulations, rep1

growth_protocol: The cell line was cultured in RPMI 1640 medium with 10% fetal bovine serum and supplements at 37◦C in a humidified atmosphere containing 5% CO2

value: NON-SP


title: pancreatic cancer, KO, replicate 3

first: Roman

last: Sasik

state: CA

address: 9500 Gilman Dr.

department: Center for Computational Biology and Bioinformatics

institute: UCSD

description:
Mouse_KO6
Gene expression data from pancreatic tumor cells KeasG12D/+;p53f/f;ptf1a-Cre

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

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

data_processing: CEL files analyzed with gcrma (Bioconductor), normalized with multiple loess normalization

source_name: pancreatic tumor cells

extract_protocol: Total RNA extracted using Rneasy Qiagen kit

value: pancreatic tumor cell

tag: genotype

tag: age

value: 11 weeks


title: pancreatic cancer, KO, replicate 1

description:
Mouse_KO3
Gene expression data from pancreatic tumor cells KeasG12D/+;p53f/f;ptf1a-Cre


title: Fig3Rpb3-TAP-dmso

source_name: Rpb3-TAP ChIP from kin28is budding yeast treated with DMSO

value: TAP (Thermo)


title: Fig3Rpb3-TAP-1napp1

source_name: Rpb3-TAP ChIP from kin28is budding yeast treated with 1-NAPP-1

source_name: Input DNA from kin28is budding yeast treated with 1-NAPP-1


title: pancreatic cancer, wt, replicate 3

description:
Mouse_WT6
Gene expression data from pancreatic tumor cells KeasG12D/+;p53f/f;ptf1a-Cre

value: wt


title: pancreatic cancer, wt, replicate 1

description:
Mouse_WT3
Gene expression data from pancreatic tumor cells KeasG12D/+;p53f/f;ptf1a-Cre


title: pancreatic cancer, KO, replicate 2

description:
Mouse_KO4
Gene expression data from pancreatic tumor cells KeasG12D/+;p53f/f;ptf1a-Cre


title: sorted non-TPCs from mouse 920

city: Stanford

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

department: Pediatrics

institute: Stanford University

description: Gene expression data from SCLC mouse non-TPCs

hyb_protocol: The fragmented and labeled targets were hybridized to the arrays per standard Affymetrix protocol, which includes 16 hour (overnight) hybridization at 45°C at 60rpm in an Affymetrix GeneChip Hybridization Oven 645. The arrays were then washed and stained in an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were analyzed using Robust Multichip Average (RMA) using Affymetrix default analysis settings and quantile as normalization method.

source_name: Mouse SCLC cells sorted with the non-TPCs markers

label_protocol: Affymetrix WT Plus kit was used to generate ssDNA targets. Fragmentation and biotin-labeling were performed using Affymetrix WT Terminal Labeling and Hybridization kit.

growth_protocol: Tumors were harvested from Rb/p53/p130 mutant mice 6-7 months after Adeno-Cre infection

extract_protocol: Cells were sorted in Trizol and then total RNA was extracted using the PureLink RNA Micro Kit (Invitrogen).

treatment_protocol: No treatment was done. Single cell supsension was obtained from the tumors and then stained with cell surface markers

value: SCLC primary cells

tag: tumor genotype

value: Rb/p53/p130 triple knockout mouse model

tag: background strain

value: mixed C57BL/6;129Sv/J


title: sorted TPCs from mouse 0107

description: Gene expression data from SCLC mouse TPCs

source_name: Mouse SCLC cells sorted with the TPCs markers


title: postnatal 1MO, biological rep2

city: Paris

first: Sonia

last: Alonso-Martin

address: 105 bd de l'Hôpital

department: Development and stem cells

country: France

institute: Myology Research Center U974-INSERM - UPMC-Paris VI - Institut de Myologie

description:
C57BL/6J mouse
P-1.B.2012

hyb_protocol: High-density oligonucleotide arrays containing 45,000 sets of oligonucleotide probes (25 mers) that cover all 30,000 genes encoded by the murine genome (Affymetrix Mouse Genome 430 2.0 Arrays, Ref 900495) were used for gene expression detection. Hybridization during 16 hours at 45°C in a rotary oven (Affymetrix), washing and staining (GeneChip® Fluidics Station 450) and scanning (GeneChip Scanner 3000) were carried out according to NuGEN and Affymetrix protocols.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing:
Expression Console software (Affymetrix) was used for image analysis and to determine probe signal levels. The quality and statistical analysis of the data were made using the GeneSpring GX11 analysis software (Agilent Technologies).
Data needed to be pre-treated before final analysis to normalize two different sets of arrays (2006 or 2012 as indicated in description field). Expression profiles were normalized in batch using RMA algorithm (affy R package) yielding a (probe sets, samples) matrix. As the 36 samples were obtained by merging two series including respectively 15 and 21 samples, Combat algorithm (Johnson WE – Biostatistics – 2007) was used to normalize the corresponding batch effect. Expression profiles were aggregated by Gene Symbol (mean across probe sets) using Affymetrix csv annotation file (na32 version).

source_name: mouse abdominal, pectoral and intercostal muscle including skeletal muscle satellite cells

label_protocol: Biotinylated cRNA were prepared according to the Encore Biotin Module (NuGEN) protocol from 100ng total RNA (http://www.nugen.com/nugen/index.cfm/support/product-resources/tech/encore-biotin-module-performance/). Single-stranded cDNA is fragmented and characterized by chemical and enzymatic methods leading to molecules of about 50 to 100 bases. Next, a biotin labeled nucleotide is attached to the 3' end of each fragment.

growth_protocol: Pax3GFP/+ mice were bred with C56BL/6J and the day where plugs were detected was consider as E0.5.

extract_protocol: RNasy® Micro Kit (QIAGEN) RNA extraction protocol was used according to the manufacturer's instructions.

treatment_protocol: Pax3GFP/+ embryos of the appropriate stage were selected  for GFP under fluorescent scope. Adult mice were detected by PCR and splotch white tag in the belly. Muscle samples were isolated from the trunk and digested in DMEM high glucose but no phenol red, 0.1% Trypsin, 0.1% Collagenase D and 0.01mg/mL DNaseI, and purified by filtration using 100µm and 40µm cell strainers. GFP cells were stained using propidium iodide to exclude dead cells and purified via FACS Aria II based on gating of GFP signal.

value: 1 month


title: Fig3Rpb3-TAP-cmk

source_name: Rpb3-TAP ChIP from kin28is budding yeast treated with CMK

value: CMK

source_name: Input DNA from kin28is budding yeast treated with CMK

value: input


title: postnatal 1MO, biological rep1

description:
C57BL/6J mouse
P-1.A.2012

value: abdominal, pectoral and intercostal muscle including skeletal muscle satellite cells


title: sorted TPCs from mouse 1127


title: postnatal 2MO, biological rep1

description:
C57BL/6J mouse
P-2.A.2012

source_name: mouse abdominal, pectoral and intercostal muscle including skeletal muscle quiescent satellite cells

value: 2 months


title: postnatal 2MO, biological rep2

description:
C57BL/6J mouse
P-2.B.2012

value: abdominal, pectoral and intercostal muscle including skeletal muscle quiescent satellite cells


title: postnatal 2MO, biological rep3

description:
C57BL/6J mouse
P-2.C.2012


title: postnatal 18MO, biological rep1

description:
C57BL/6J mouse
P-18.A.2012

source_name: mouse abdominal, pectoral and intercostal muscle including skeletal muscle quiescent aged satellite cells

value: 18 months


title: sorted non-TPCs from mouse 0107


title: postnatal P12, biological rep4

description:
C57BL/6J mouse
P-12.D.2006

source_name: mouse trunk muscles including skeletal muscle proliferant satellite cells


title: sorted non-TPCs from mouse 1127


title: postnatal 1MO, biological rep3

description:
C57BL/6J mouse
P-1.C.2012


title: postnatal 18MO, biological rep3

description:
C57BL/6J mouse
P-18.C.2012

value: abdominal, pectoral and intercostal muscle including skeletal muscle quiescent aged satellite cells


title: postnatal 18MO, biological rep2

description:
C57BL/6J mouse
P-18.B.2012


title: Fig3Ser2p-cmk

source_name: Ser2p ChIP from kin28is budding yeast treated with CMK

value: Ser2p (Bethyl)


title: postnatal P12, biological rep2

description:
C57BL/6J mouse
P-12.B.2006

value: trunk muscles including skeletal muscle proliferant satellite cells


title: postnatal P12, biological rep1

description:
C57BL/6J mouse
P-12.A.2006


title: embryo at E15.5, biological rep2

description:
C57BL/6J mouse fetus
E-15.5.C.2006

source_name: mouse trunk muscles including skeletal muscle fetal progenitors


title: pancreatic cancer, wt, replicate 2

description:
Mouse_WT4
Gene expression data from pancreatic tumor cells KeasG12D/+;p53f/f;ptf1a-Cre

value: pancreatic tumor cell


title: postnatal P1, biological rep4

description:
C57BL/6J mouse
P-1.D.2006


title: postnatal P12, biological rep3

description:
C57BL/6J mouse
P-12.C.2006


title: embryo at E17.5, biological rep4

description:
C57BL/6J mouse fetus
E-17.5.A.2006

value: trunk muscles including skeletal muscle fetal progenitors


title: embryo at E15.5, biological rep3

description:
C57BL/6J mouse fetus
E-15.5.A.2006


title: postnatal P1, biological rep2

description:
C57BL/6J mouse
P-1.B.2006


title: embryo at E17.5, biological rep5

description:
C57BL/6J mouse fetus
E-17.5.B.2006


title: embryo at E14.5, biological rep2

description:
C57BL/6J mouse embryo
E-14.5.B.2012

source_name: mouse interlimb somites including skeletal muscle embryonic progenitors


title: postnatal P1, biological rep3

description:
C57BL/6J mouse
P-1.C.2006


title: embryo at E12.5, biological rep3

description:
C57BL/6J mouse embryo
E-12.5.C.2012

value: interlimb somites including skeletal muscle embryonic progenitors


title: embryo at E11.5, biological rep3

description:
C57BL/6J mouse embryo
E-11.C.2012


title: embryo at E17.5, biological rep2

description:
C57BL/6J mouse fetus
E-17.5.D.2012


title: embryo at E17.5, biological rep3

description:
C57BL/6J mouse fetus
E-17.5.E.2012


title: embryo at E17.5, biological rep1

description:
C57BL/6J mouse fetus
E-17.5.C.2012


title: postnatal P1, biological rep1

description:
C57BL/6J mouse
P-1.A.2006


title: embryo at E14.5, biological rep1

description:
C57BL/6J mouse embryo
E-14.5.A.2012


title: embryo at E12.5, biological rep1

description:
C57BL/6J mouse embryo
E-12.5.A.2012


title: embryo at E15.5, biological rep1

description:
C57BL/6J mouse fetus
E-15.5.B.2006


title: embryo at E12.5, biological rep2

description:
C57BL/6J mouse embryo
E-12.5.B.2012


title: embryo at E14.5, biological rep3

description:
C57BL/6J mouse embryo
E-14.5.C.2012


title: Gene expression comparison of shRNA-mediated NUPR1 knockdown Hep3B clone vs control (mock-transfected) Hep3B clone, 2

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

institute: CHU-Q, Centre de recherche-HDQ

description: Cy5 label sample being the reference

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: shRNA-NUPR1 knockdown Hep3B clone

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: Hep3B cells were maintained in RPMI medium supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: The human HCC cell lineHep3B was stably transfected with NUPR1 shRNA cloned into the pSilencer 4.1 puro vector (Ambion). Viral supernatants were generated by transfecting 293T cells with the shRNA construct and the packaging vectors psPAX2 and pMD2.G (Addgene, Cambridge, MA). Hep3B cells were stably transfected with the shRNA-NUPR1 plasmid using the ExGen 500 transfection reagent (Fermentas Canada Inc., Burlington ON), according to the manufacturer’s instructions. Cells were consecutively grown for 2 weeks in selection medium containing  0,5 μg/mL puromycin (Wisent, Canada) to isolate stable clones. Cells were also mock-transfected with the pSilencer 4.1 puro vector, and stably transfected clones were isolated as controls.

value: hepatocellular carcinoma (HCC)

source_name: control (mock-transfected) Hep3B clone


title: embryo at E13.5, biological rep2

description:
C57BL/6J mouse embryo
E-13.5.B.2006


title: embryo at E11.5, biological rep1

description:
C57BL/6J mouse embryo
E-11.A.2012


title: Gene expression comparison of shRNA-mediated NUPR1 knockdown Hep3B clone vs control (mock-transfected) Hep3B clone, 1

description: Cy3 label sample being the reference


title: ERH1 deletion H3K9 dimethyl ChIP rep1

city: Bethesda

first: Shiv

last: Grewal

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: H3K9me2 immunoprecipitated DNA

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures are grown at 32˚C to OD600=~0.5.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220), CFP antibody (Abcam, ab290) or with GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at room temperature. For tagged strains, cells were further crosslinked with DMA for 45 min at 30  C

value: ERH1 deletion

source_name: Whole-cell extract DNA


title: MMI1-CFP ChIP rep2

source_name: CFP-MMI1 immunoprecipitated DNA

value: Wild type


title: WP3-heat shock 90 min-rep6

city: Shanghai

first: Huahua

last: Jian

address: No.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

description:
raw data file: Heat90min-cy3+Heat0min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy5 and WP3 cDNA-heat shock 90 min was labeled with Cy3

hyb_protocol: Klenow enzyme labeling strategy was adopted after reverse transcription. Briefly, 20 μg amplified RNA was mixed with 4 μl random hexamers, denatured at 70°C for 5 min, and cooled on ice. Then, 4 μl of first-strand buffer, 2 μl of 0.1M DTT, 1 μl 10mM dNTP, and 1.5 μl SuperScipt Ⅱ (Invitrogen) were added. The mixtures were incubated for 10 min at 25°C, then for 90 min at 42°C. The cDNA products were purified using the PCR purification kit and vacuum evaporated to 10 μl, and then it was mixed with 4 μg random nanomer, heated to 95°C for 3 min, and snap cooled on ice. After that, 10 μl buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (Amersham Biosciences) were added to final concentrations of 120 mM dATP, dGTP, dTTP and 60 mM dCTP, and 40mM Cy-dye. Klenow enzyme (Takara, Japan) was then added, and the reaction was performed for 90 min at 37°C. Labeled cDNA was purified with the PCR purification kit and resuspended in elution buffer.

scan_protocol: All microarrays were scanned with a LuxScan 10K canner using microarray scanner 2.3 software (CapitalBio, Beijing, China). We quantified signal intensites of individual spot from the 24-bit TIFF images using SpotData Pro 2.2 (CapitalBio, Beijing, China).

data_processing:
For every microarray slide, there are 16416 spots, which were divided into 48 blocks. For every block, there are 18 columns and 19 rows. 16416=48*18*19.  There are 3 spots for a single gene on a single microarray slide, thus we get 3 ratios of the expression level of this gene in 2 samples (rep1, rep2 and rep3).  As dye-swaps were performed (label cDNA with different fluorecent dye), we can get another 3 ratios of the expression level of this gene in 2 samples (rep4, rep5 and rep6).
The replicate spots on the array were printed in the same row in adjacent columns.  Replicate number was assigned to the spots in ascending column order. For example, WP00027 is printed  in block 1, row 2, columns 13, 14 and 15. Replicate 1/4 is column 13, 2/5 is column 14 and replicate 3/6 is column 15.
S-plus software was used for the normalization of microarray data. A spatial and intensity-dependent normalization based on a LOWESS program were used. Normalized data was log transformed and loaded into MAANOVA under R environment for multiple testing, by fitting a mixed effects ANOVA model.  Microarray spots with P values <0.01 in the T-test and log2 ratio>1 or <-1 were regarded as differentially expressed genes.

organism: Shewanella piezotolerans WP3

source_name: WP3 cells at mid-exponential phase

label_protocol: The retro-transcription of the 20 μg total RNA was accorded with the Invitrogen manufacturer’s instruction. cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 40°C for 90 min.

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

tag: culture protocol

value: WP3 cells were cultured at 20°C in 2216E medium

source_name: WP3 cells at mid-exponential phase and were incubated at 40°C for 90 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 40℃ for 90 min


title: embryo at E11.5, biological rep2

description:
C57BL/6J mouse embryo
E-11.B.2012


title: JY742 H3K9me2 ChIP rep1

value: Wild type:H+


title: WP3-heat shock 90 min-rep5


title: MMI1 deletion H3K9 dimethyl ChIP rep1

value: MMI1 deletion cells


title: CCR4 deletion H3K9 dimethyl ChIP rep1

value: CCR4 deletion


title: MMI1 deletion H3K9 dimethyl ChIP rep2


title: MMI1 deletion ERH1-GFP ChIP rep1

source_name: ERH1-GFP immunoprecipitated DNA


title: embryo at E13.5, biological rep1

description:
C57BL/6J mouse embryo
E-13.5.A.2006


title: ERH1 deletion H3K9 dimethyl ChIP rep2


title: Mouse 1 PRH

city: Birmingham

first: Joseph

middle: William

last: Wragg

state: West Midlands

address: Edgbaston

department: Institute of Biomedical Research

institute: University of Birmingham

description: Gene expression in adenoviral PRH infected 4T1 tumours

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to an Agilent SurePrint G3 Mouse Gene Expression v2 8x60K microarray chip (G4852B) for 17 hours at 65 °C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x80k array slides (Scan Area 61x21.6 mm, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Mouse 1 PRH

label_protocol: Cy3 labeled cRNA was prepared from 50ng RNA, using the Agilient low input, quick amp, one colour labelling kit according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 4T1 cells were infected with Adenoviral-PRH or empty Adenovirus at MOI 50 for 24 hrs. Cells were washed 4x with PBS, trypsinised, washed and resuspended in Opti-mem (Invitrogen) at 1.25x106 cells/ml and kept on ice for 20-30 min before injection. Aliquots 200 μl / 2.5x105 of the cells were injected into the no. 3 fat pad of 6-8 week old female BALB/C mice. Tumours were harvested 22 days after innoculation.

extract_protocol: Total RNA was isolated from the endothelial isolates using the Qiagen miRNA easy kit according to the manufacturer's protocol.

tag: agent

value: Adenoviral-PRH

tag: cell line


title: MMI1-CFP ChIP rep1


title: MMI1 deletion ERH1-GFP ChIP rep2


title: CCR4 deletion H3K9 dimethyl ChIP rep2


title: ERH1-GFP ChIP rep2


title: ERH1-GFP ChIP rep1


title: Mouse 5 PRH

source_name: Mouse 5 PRH


title: Mouse 5 Control

description: Gene expression in empty adenovirus infected 4T1 tumours

source_name: Mouse 5 Control

value: Empty adenovirus


title: Mouse 1 Control

source_name: Mouse 1 Control


title: sorted TPCs from mouse 920

source_name: Mouse SCLC cells sorted with the TPCs markers

tag: cell type

value: SCLC primary cells

value: Rb/p53/p130 triple knockout mouse model

value: mixed C57BL/6;129Sv/J


title: Mouse 3 PRH

source_name: Mouse 3 PRH


title: Wildtype H3K9 dimethyl ChIP rep1

value: Wild type:smt0


title: Wildtype H3K9 dimethyl ChIP rep2


title: Mouse 3 Control

source_name: Mouse 3 Control


title: Mouse 2 Control

source_name: Mouse 2 Control


title: Mouse 2 PRH

source_name: Mouse 2 PRH


title: WP3-heat shock 90 min-rep4


title: WP3-heat shock 90 min-rep2

description:
raw data file: Heat0min-cy3+Heat90min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy3 and WP3 cDNA-heat shock 90 min was labeled with Cy5


title: WP3-heat shock 90 min-rep3


title: WP3-heat shock 60 min-rep2

description:
raw data file:Heat0min-cy3+Heat60min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy3 and WP3 cDNA-heat shock 60 min was labeled with Cy5

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 40°C for 60 min.

source_name: WP3 cells at mid-exponential phase and were incubated at 40°C for 60 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 40℃ for 60 min


title: WP3-heat shock 30 min-rep6

description:
raw data file: Heat30min-cy3+Heat0min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy5 and WP3 cDNA-heat shock 30 min was labeled with Cy3

growth_protocol: Shewanella strains were cultured in modified marine medium 2216E (5 g/l tryptone, 1 g/l yeast extract, 0.1 g/l FePO4, 34 g/l NaCl)  at 20°C, and then were incubated at 40°C for 30 min.

source_name: WP3 cells at mid-exponential phase and were incubated at 40°C for 30 min

value: WP3 cells were cultured at 20℃ in 2216E medium and were incubated at 40℃ for 30 min


title: WP3-heat shock 60 min-rep3


title: WP3-heat shock 60 min-rep5

description:
raw data file:Heat60min-cy3+Heat0min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy5 and WP3 cDNA-heat shock 60 min was labeled with Cy3


title: WP3-heat shock 60 min-rep4


title: WP3-heat shock 60 min-rep1


title: WP3-heat shock 30 min-rep5


title: WP3-heat shock 90 min-rep1


title: WP3-heat shock 30 min-rep3

description:
raw data file: Heat0min-cy3+Heat30min-Cy5.gpr
WP3 cDNA-untreated was labeled with Cy3 and WP3 cDNA-heat shock 30 min was labeled with Cy5


title: WP3-heat shock 30 min-rep4


title: WP3-heat shock 60 min-rep6


title: LRSKBr3 cells transfected with siERRaphal Replicate 1

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

institute: McGill University

description:
replicate 1 siERRalphal condition Lap-resistant cells
GD_GE_28

hyb_protocol: Standard Illumina hybridization protocol using  Illumina HumanHT-12 V4.0 expression beadchip (gene symbol) array and direct hybridizaion whole-genome expression assay

scan_protocol: Standard Illumina scanning protocol using iScan system

data_processing: The data was normalised using Lumi-normalization and ttest differential gene expression detection in Flexarray

label_protocol: biotin labelled cRNA, standard labeling protocol according to Illumina BeadChIp technology

growth_protocol: Cells (SKBr3 and LRSKBr3) were cultured in DMEM supplemented with 10% FBS. LRSKBr3 cells are maintained in Lapatinib (2uM) For Growth factor treatments, cells were deprived of FBS (to starve) for 48 hours and treated with EGF, HRG or veh for 24 hours prior to harvesting prior to RNA extraction.

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

treatment_protocol: All cells were transfected with siRNA against ERRalpha or with siControl for 60 hours prior to harvesting and RNA extraction. For growth factor treatments, cells were maintained in DMEM depleted of FBS for 24 hours prior to treatment with 100uM EGF or HRG or veh for 24 hours prior to harvesting. Lapatinib-resistant cells are maintainted in 2uM Lapatinib.

tag: tissue source and disease

value: breast cancer

value: Lapatinib-resistant breast cancer cells (LRSKBr3)

tag: sample group

value: 1uM Lapatinib siERR


title: LRSKBr3 cells transfected with siControl Replicate 2

description:
replicate 2 control condition Lap-resistant cells
GD_GE_N

value: 1uM Lapatinib siC


title: pSKBr3 cells transfected with siERRaphal Replicate 1

description:
replicate 1 siERRalphal condition parental cells
GD_GE_19

value: parental breast cancer cells (pSKBr3)

value: DMSO siERR


title: pSKBr3 cells transfected with siERRalphal Replicate 2

description:
replicate 2 siERRalpha condition parental cells
GD_GE_G


title: HRG-treated SKBr3 cells transfected with siControl Replicate 1

description:
replicate 1 control condition in HRG-treatment
GD_GE_9

value: breast cancer cells

value: HRG, siC


title: EGF-treated SKBr3 starved cells transfected with siERRalpha Replicate 2

description:
replicate 2 siERRal condition in EGF-treatment
GD_GE_AA

value: EGF, siERRalpha


title: EGF-treated SKBr3 cells transfected with siControl Replicate 2

description:
replicate 2 control condition in EGF-treatment
GD_GE_X

value: EGF, siC


title: EGF-treated SKBr3 starved cells transfected with siERRalpha Replicate 1

description:
replicate 1 siERRal condition in EGF-treatment
GD_GE_11


title: pSKBr3 cells transfected with siControl Replicate 2

description:
replicate 2 control condition parental cells
GD_GE_E

source_name: pSKBr3 cells transfected with siControl

value: DMSO siC


title: HRG-treated SKBr3 cells transfected with siControl Replicate 2

description:
replicate 2 control condition in HRG-treatment
GD_GE_Y


title: HRG-treated SKBr3 starved cells transfected with siERRalpha Replicate 2

description:
replicate 2 siERRal condition in HRG-treatment
GD_GE_BB

value: HRG siERRalpha


title: pSKBr3 cells transfected with siControl Replicate 1

description:
replicate 1 control condition parental cells
GD_GE_17


title: LRSKBr3 cells transfected with siControl Replicate 1

description:
replicate 1 control condition Lap-resistant cells
GD_GE_26


title: HRG-treated SKBr3 starved cells transfected with siERRalpha Replicate 1

description:
replicate 1 siERRal condition in HRG-treatment
GD_GE_12


title: WP3-heat shock 30 min-rep1

value: WP3 cells were cultured at 20°C in 2216E medium


title: WP3-heat shock 30 min-rep2


title: D96_Obese

city: Vancouver

first: Alexander

middle: G

last: Beristain

state: BC

address: 950 West 28th Ave

department: Obstetrics & Gynecology

institute: The University of British Columbia

data_processing: Raw expression data were log transformed and quantile normalized using he limma library beadarray packages of the Bioconductor open-source project in the R statistical environment

source_name: uterine NK cell

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

extract_protocol: RNA was extracted using Ambion RNAqueous Total RNA Isolation columns, followed by Dnase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with an Agilent Bioanalyzer; only samples with RIN values >7 were used.

treatment_protocol: Uterine decidual mucoa was collected after elective terminations of pregnancy from consenting women at BC Women's Hospital. Tissue natural killer cells were isolated via enzymatic digestion in collagenase and purified by density gradient centrifugation and immuno-magnetic bead purification using a NK cell enrichment cocktail (Stem Cell Technology).

tag: gestational age in weeks

value: uterine NK cell

tag: bmi

tag: crp (ug/ml)

value: hsCRP = 10.0


title: D210_Obese

value: hsCRP = 5.7


title: D92_Obese

value: hsCRP = 3.5


title: D285_Control

value: hsCRP = 0.6


title: D180_Obese

value: hsCRP = 6.6


title: D273_Control

value: hsCRP = 1.64


title: D87_Obese

value: hsCRP = 9.5


title: D207_Control

value: hsCRP = 0.3


title: D274_Control

value: hsCRP = 4.6


title: SKBr3 starved cells transfected with siControl Replicate 2

description:
replicate 2 control condition starved
GD_GE_W

value: breast cancer

value: breast cancer cells

value: starved siC


title: SKBr3 starved cells transfected with siERRalpha Replicate 2

description:
replicate 2 siERRal condition starved
GD_GE_Z

value: starved siERRalpha


title: RNA U87 MG  Rep2

city: washington

first: haijie

last: xiao

state: DC

address: 2300 eye street

department: Biochemistry

institute: george washington University

hyb_protocol: Samples were hybridized with GeneChip Human Affymetrix Human Transcriptome Array 2.0 [transcript (gene) version]

scan_protocol: according to the manufacturer's instruction (Affymetrix)

data_processing:
Generate TAC-ready files and perform quality control (QC) in Expression Console
RMA expression value derived from Expression Console software

source_name: U87 MG cells

label_protocol: Single-stranded cDNA was generated from the amplified cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: cells grown in DMEM medium (Gibco 11965) with 10% FBS

extract_protocol: total RNA were extracted by using puelink RNA mini kit from Ambion

treatment_protocol: no treatment

value: glioblastoma cancer cell line U87

tag: genotype/variation

value: control


title: RNA GUCY1B3 overexpression stable U87 MG  Rep3

description: RMA expression value derived from Expression Console software

source_name: GUCY1B3 overexpression stable U87 MG cells

value: GUCY1B3 overexpression


title: D169_Obese

value: uterine NK cell

value: hsCRP = 4.2


title: RNA U87 MG  Rep1


title: EGF-treated SKBr3 cells transfected with siControl Replicate 1

description:
replicate 1 control condition in EGF-treatment
GD_GE_8

value: EGF, siC


title: D288_Obese

value: hsCRP = 5.6


title: SKBr3 starved cells transfected with siControl Replicate 1

description:
replicate 1 control condition starved
GD_GE_7


title: D202_Control

value: hsCRP = 8.43


title: RNA U87 MG  Rep3


title: SKBr3 starved cells transfected with siERRalpha Replicate 1

description:
replicate 1 siERRal condition starved
GD_GE_10


title: D199_Control

value: hsCRP = 0.2


title: D77_Control

value: hsCRP = 1.4


title: LRSKBr3 cells transfected with siERRalphal Replicate 2

description:
replicate 2 siERRalpha condition Lap-resistant cells
GD_GE_P

value: Lapatinib-resistant breast cancer cells (LRSKBr3)

value: 1uM Lapatinib siERR


title: JY742 H3K9me2 ChIP rep2

source_name: H3K9me2 immunoprecipitated DNA

value: Wild type:H+

source_name: Whole-cell extract DNA


title: D194_Obese

value: hsCRP = 1.6


title: D74_Control

value: hsCRP = 0.0


title: D196_Obese

value: hsCRP = 11.1


title: D182_Control

value: hsCRP = 0.8


title: RNA GUCY1B3 overexpression stable U87 MG  Rep2

value: glioblastoma cancer cell line U87


title: RNA GUCY1B3 overexpression stable U87 MG  Rep1


title: PCC6803_WT_48h_N-recovery_1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 0.6 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505C US90900275, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensities were normexp background substracted (offset=50) and quantile normalized.

organism: Synechocystis sp. PCC 6803

label_protocol: DNAse treated RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Synechocystis strains used in this study were propagated in BG11 medium supplemented with 5 mM NaHCO3, as described previously (Rippka et al., 1979). In liquid culture all strains were grown under continuous illumination with white light in a range of 40 to 50 μmol photons m−2 s−1 at 27°C. The growth of the culture was monitored via the optical density at 750 nm wavelength (OD750). Nitrogen starvation was induced by washing exponentially growing cells once with BG11 medium lacking sodium nitrate (BG110) and transferring them into BG110 at an OD750 of 0.4 as described previously (Schlebusch and Forchhammer, 2010). The recovery was triggered by pelleting the cells and transferring the starved cells into BG11 at an OD750 of 0.4.

extract_protocol: RNA for tailing arrays was extracted via the PGTX method adapted from Pinto et al (Pinto et al., 2009). Therefore, 15 ml cyanobacterial culture (OD750 ~1.0) was rapidly harvested on Supor®-800 membranes (Pall; Life Sciences; 0.8µm, 47mm) with a vacuum pump assembly. The folded membrane was then transferred in 2 ml screw lid vial containing ~250 µl sterile glass beads and 1 ml PGTX, vortexed shortly, snap frozen in liquid nitrogen and stored at -80°C until continuing with the extraction. The samples were homogenized in a “FastPrep®-24” (MP Biomedicals) 4 times for 15 s at 4°C and incubated at 65°C for at least 15 min while shaking. For 1 ml of PGTX mixture 0,.6 ml of a Chloroformchloroform:Isoamyl isoamyl alcohol mixture (24:1) was added and mixed for 10 min before centrifugation at 4000 x g for 15 min. The supernatant was transferred into sterile RNase-free 2 ml cups and mixed with an equal amount ofand the c Chloroform:Isoamyl isoamyl alcohol mixture (24:1) before another centrifugation step for 15 min at 4000 xgextraction repeated. 0.3 µl of RNA grade glycogen as well as anthe equal amount volume of isopropanol was added to the supernatant before incubation at -80°C overnight. Finally, the samples were centrifugated for 30 min at 25000 x g and 4°C before washing the resulting pellet with 1 ml of 70 % (v/v) cold ethanol. After removing the supernatant, the pellet was air dried on ice. The resulting RNA was then diluted in the desired amount of RNase-free water for further use

value: WT


title: PCC6803_WT_24h_N-recovery_2

treatment_protocol: Nitrogen starvation was induced by washing exponentially growing cells once with BG11 medium lacking sodium nitrate (BG110) and transferring them into BG110 at an OD750 of 0.4 as described previously (Schlebusch and Forchhammer, 2010). The recovery was triggered by pelleting the cells and transferring the starved cells into BG11 at an OD750 of 0.4.


title: PCC6803_WT_24h_N-recovery_1


title: PCC6803_WT_4h_N-recovery_2


title: D68_Obese

value: hsCRP = 10.2


title: Jurkat_TRAIL_resistant_clone1_1microM_SAHA_rep2

city: Basel

first: Robert

last: Ivanek

address: Hebelstrasse 20

department: Department of Biomedicine

country: Switzerland

institute: University of Basel

description: replicate 2

data_processing: Data analysis was performed in R-software, in beadarray and limma packages from BioConductor project.

label_protocol: Standard Illumina labeling protocol

growth_protocol: Cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% (FBS) and 1% penicillin/streptomycin. TRAIL-resistant Jurkat clone TR1 was established by selective pressure of TRAIL 1000 ng/mL over the period of 12 weeks.

extract_protocol: Total cellular RNA was isolated from biologic duplicates of untreated Jurkat cells (WT) and TRAIL resistant Jurkat cell line subclone (TR1), and 1 µM and 0.5 µM suberoylanilide-hydroxamic acid (SAHA, vorinostat) treated TR1 cell clones for 12 hours using RNAblue (Top-Bio, Czech Republic). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technology). Extracted RNA was amplified using the Illumina RNA Amplification Kit (Ambion) and hybridized to the Illumina HumanRef-8 BeadChip (Illumina).

treatment_protocol: Cells wer either untreated or treated for 12 hours with 1 µM or 0.5 µM suberoylanilide-hydroxamic acid (SAHA, vorinostat).

value: TRAIL resistant

tag: tissue

value: T cell leukemia / lymphoma line

tag: treatment

value: 1 µM SAHA for 12 hours


title: Jurkat_TRAIL_resistant_clone1_0.5microM_SAHA_rep2

description: replicate 2

value: 0.5 µM SAHA for 12 hours


title: Jurkat_TRAIL_resistant_clone1_0.5microM_SAHA_rep1

description: replicate 1


title: Jurkat_TRAIL_sensitive_rep1

description: replicate 1

value: Jurkat-WT

value: TRAIL sensitive


title: PCC6803_WT_14d_N-depletion_1


title: PCC6803_WT_14d_N-depletion_2


title: D181_Obese

value: uterine NK cell

value: hsCRP = 12.7


title: PCC6803_WT_12h_N-recovery_2


title: Jurkat_TRAIL_resistant_clone1_1microM_SAHA_rep1

description: replicate 1


title: Jurkat_TRAIL_sensitive_rep2

description: replicate 2


title: Jurkat_TRAIL_resistant_clone1_untreated_rep1

description: replicate 1


title: D190_Control

value: hsCRP = 1.8


title: Jurkat_TRAIL_resistant_clone1_untreated_rep2

description: replicate 2


title: D82_Control

value: hsCRP = 0.6


title: D184_Control


title: PCC6803_WT_12h_N-recovery_1


title: PCC6803_WT_4h_N-recovery_1


title: 86441_M430-2_16_D.COLON_MGI_GENE-4

city: Cincinnati

first: Jing

last: Chen

state: OH

address: 3333 Burnet Ave

institute: CCHMC

hyb_protocol: The biotinylated cRNA was prepared and hybridized to the Mouse 430A_2.0 GeneChip in accordance with Affymetrix protocols.

scan_protocol: GeneChips were scanned by the Affymetrix GeneChip Scanner.

data_processing: Microarray data was preprocessed using RMA implemented in R with BrainArray custom CDF.

source_name: High-fat Diet_D.COLON

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

growth_protocol: Nine-week-old male, ob/ob (B6.V-Lepob/J), and ob lean control (Lepob, heterozygote from the colony) mice were purchased from Jackson Lab (Bar Harbor, Main) and acclimatized to a constant temperature and humidity (72°F and 50% relative humidity with a 12 h light and dark cycle from 05:00 h to 17:00 h) and had free access to food (LabDiet 5K20, LabDiet, St. Louis, MO) and water.  At the age of twelve weeks, all animals were fasted for four hours in the morning and euthanized at 1pm under isoflurane anathesia. Nine-week-old male, C57BL/6J mice were purchased from Jackson Lab (Bar Harbor, Main) and acclimatized to a constant temperature and humidity (72°F and 50% relative humidity with a 12 h light and dark cycle from 05:00 h to 17:00 h) for one week with free access to food (LabDiet 5001, LabDiet, St. Louis, MO) and water.  After acclimation, half of the mice (n=6) were kept on the regular chow diet (LabDiet 5001) and half of them (n=6) were switched to TD93075 (Harlan Teklad, Madison, Wisconsin), a high-fat diet with 54.8%Kcal from fat for four weeks. At the end of the study, all animals were fasted for four hours in the morning and euthanized at 1pm under isoflurane anesthesia.

extract_protocol: Gastrointestinal tissues (whole stomach and about 1cm of intestinal samples from the middle of each part of the intestine) were collected.  Finally a 1cm3 segment of the inferior right lobe of the liver was taken. Segments were immediately snap frozen in liquid nitrogen and stored at -80°C for subsequent RNA extraction.  RNA extraction was performed using the RNeasy Mini kit (Qiagen Inc, Valencia, Calif). Total RNA yield and purity was estimated by UV spectroscopy (Nanodrop ND-1000 Spectrophotometer; Nanodrop Technologies, Wilmington, DE, USA) and RNA quality was assessed on an Agilent 2100 Bioanalyzer.  Subsequently mRNA expression analysis was carried out.

tag: group

value: High-fat Diet

tag: animal


title: 86431_M430-2_15_DUODENUM_MGI_GENE-4

source_name: High-fat Diet_DUODENUM

tag: genotype

value: DUODENUM


title: Jurkat_TRAIL_sensitive_rep2

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

source_name: TRAIL sensitive

growth_protocol: Cells were cultured in Iscove's modified Dulbecco's medium (IMDM) supplemented with 10% (FBS) and 1% penicillin/streptomycin. TRAIL-resistant Jurkat clones (TR1, TR2, TR3) were established by selective pressure of TRAIL 1000 ng/mL over the period of 12 weeks.

extract_protocol: Total cellular RNA was isolated from biologic duplicates of untreated Jurkat cells (WT) and TRAIL resistant Jurkat cell line subclones (TR1, TR2, TR3) using RNAblue (Top-Bio, Czech Republic) according to the manufaccturer’s instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technology). Extracted RNA was amplified using the Illumina RNA Amplification Kit (Ambion) and hybridized to the Illumina HumanRef-8 BeadChip (Illumina).

value: T cell leukemia / lymphoma


title: Jurkat_TRAIL_resistant_clone2_rep2

description: replicate 2

source_name: TRAIL resistant


title: Jurkat_TRAIL_sensitive_rep1

description: replicate 1


title: PCC6803_WT_0h_N-depletion_2


title: 86432_M430-2_15_JEJUNUM_MGI_GENE-4

source_name: High-fat Diet_JEJUNUM

value: JEJUNUM


title: PCC6803_WT_0h_N-depletion_1


title: 86440_M430-2_16_A.COLON_MGI_GENE-4

source_name: High-fat Diet_A.COLON


title: Jurkat_TRAIL_resistant_clone3_rep1

description: replicate 1


title: Jurkat_TRAIL_resistant_clone2_rep1

description: replicate 1


title: 86433_M430-2_15_ILEUM_MGI_GENE-4

source_name: High-fat Diet_ILEUM

value: ILEUM


title: 86434_M430-2_15_A.COLON_MGI_GENE-4


title: Jurkat_TRAIL_resistant_clone3_rep2

description: replicate 2


title: 86436_M430-2_16_STOMACH_MGI_GENE-4

source_name: High-fat Diet_STOMACH

value: STOMACH


title: 86439_M430-2_16_ILEUM_MGI_GENE-4


title: 86430_M430-2_15_STOMACH_MGI_GENE-4


title: Jurkat_TRAIL_resistant_clone1_rep1

description: replicate 1


title: Jurkat_TRAIL_resistant_clone1_rep2

description: replicate 2


title: 86428_M430-2_13_A.COLON_MGI_GENE-4


title: 86437_M430-2_16_DUODENUM_MGI_GENE-4


title: 86429_M430-2_13_D.COLON_MGI_GENE-4


title: 86426_M430-2_13_JEJUNUM_MGI_GENE-4


title: 86427_M430-2_13_ILEUM_MGI_GENE-4


title: 86423_M430-2_11_D.COLON_MGI_GENE-4


title: 86422_M430-2_11_A.COLON_MGI_GENE-4


title: 86438_M430-2_16_JEJUNUM_MGI_GENE-4


title: TS1 cells_Rep1

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Copy number variation data

hyb_protocol: Samples were hybridized to the arrays at 50oC for 16-18 hours

scan_protocol: Washing and staining of the hydridized array was performed using the Affymetrix 450 fluidics station, and arrays were scanned using the Affymetrix GeneChip 3000 7G Plus scanner

data_processing:
Array images and intensity data were collected using the Affymetrix GEneChip Command Console (AGCC) Software.  Array data were analyzed using the R package MouseDivGeno.  Data from normal tissue of matched mouse strains were used as references to identify regions of copy number gain or loss.
The 27 mouse tumor cell lines were assayed by the Mouse Diversity Genotyping array, a Affymetrix mouse genotyping array similar to human SNP 6.0. The array were analyzed by using the R package MouseDivGeno.  Copy number analysis was performed using data from normal DNA of matched mouse strains as references for copy number inference. Reference set can be downloaded from http://cgd.jax.org/datasets/diversityarray/CELfiles.shtml.

source_name: Mouse mammary tumor-derived cell line TS1

label_protocol: The Affymetrix SNP 6.0 protocol was used.  gDNA was subjected to spearate restriction enzyme digestions using Sty1 and Nsp.  For each digest reaction (2/sample) restriction products were ligated to a common adaptor and amplifed by PCR.  The amplified reaction products for each sample were pooled, purified and then fragmented.  Fragmented PCR amplicons were end-labeled using terminal deoxynucleotidyl transferase with the Biotin-labled GeneChip DNA Labeling Reagent.

growth_protocol: Cells were cultured in their recommended growth media using standard procedures

extract_protocol: RNA-free DNA was prepared from the cell lines using the Gentra Puregene Cell Kit (Qiagen) according to manufacturer's protocol and resuspended in low EDTA TE buffer.  DNA quantity was assessed using PicoGreen fluorometry and integrity was assessed by agarose gel electrophoresis.  Qualified gDNA samples were normalized to 50ng/ul.

tag: mouse strain

value: FVB/N

tag: cell line origin

value: Genetically engineered mouse mammary tumor

tag: malignancy status

value: Malignant

tag: metastatic ability

value: High


title: TS/A-E1 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line TS/A-E1

tag: cell line

value: BALB/c

value: Spontaneous mammary tumor


title: 86425_M430-2_13_DUODENUM_MGI_GENE-4


title: 86419_M430-2_11_DUODENUM_MGI_GENE-4


title: 86416_M430-2_10_A.COLON_MGI_GENE-4


title: 86418_M430-2_11_STOMACH_MGI_GENE-4


title: 86421_M430-2_11_ILEUM_MGI_GENE-4


title: 86417_M430-2_10_D.COLON_MGI_GENE-4


title: 86420_M430-2_11_JEJUNUM_MGI_GENE-4


title: r3T cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line r3T


title: 86415_M430-2_10_ILEUM_MGI_GENE-4


title: TM15 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line TM15


title: 86413_M430-2_10_DUODENUM_MGI_GENE-4


title: NIC WT cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line NIC WT

value: NIC WT

value: Not tested


title: Myc83 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line Myc83


title: 86414_M430-2_10_JEJUNUM_MGI_GENE-4


title: 86411_M430-2_9_D.COLON_MGI_GENE-4


title: MVT2 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line MVT2


title: NK cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line NK

value: NK


title: D183_Control

source_name: uterine NK cell

tag: cell type

value: uterine NK cell

value: hsCRP = 1.0


title: 86410_M430-2_9_A.COLON_MGI_GENE-4

value: High-fat Diet


title: M6 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line M6


title: 86409_M430-2_9_ILEUM_MGI_GENE-4


title: 86408_M430-2_9_JEJUNUM_MGI_GENE-4


title: F3II cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line F3II


title: 86406_M430-2_9_STOMACH_MGI_GENE-4


title: LCL9_fluoxetine_21days

city: Bonn

first: Julia

middle: Carolin

last: Stingl

address: Kurt-Georg-Kiesinger Allee 3

department: Research

institute: Federal Institute for Drugs and Medical Devices

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 0.025ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 0.025ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner using one color scan setting .

data_processing: The scanned images were analyzed with Feature Extraction Software 10 (Agilent) using default parameters (protocol GE1_1100 and Grid: 039494_D_F_20120411) to obtain background subtracted and spatially detrended Processed Signal intensities.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: LCLs were grown in RPMI medium supplemented with 15% heat-inactivated fetal bovine serum, antibiotics (100 µg/ml penicillin, 100 µg/ml streptomycin) and a final concentration of 4 mM L-glutamine. Medium exchanging was done every second day.

extract_protocol: RNA was extracted using the NucleoSpin® RNA Kit (Macherey-Nagel, Germany) according to the manufacturer instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: LCLs were treated with 0.5µg/ml fluoxetine (dissolved in DMSO) for 21 days. MOCK treated control cultures were grown in parallel.

tag: disease state

value: depressive disorder

value: fluoxetine

tag: clinical treatment outcome

value: non-responder


title: LCL10_control_21days

value: control


title: E0771 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line E0771


title: Met-1 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line Met-1


title: 86407_M430-2_9_DUODENUM_MGI_GENE-4

source_name: High-fat Diet_DUODENUM

value: DUODENUM


title: 86412_M430-2_10_STOMACH_MGI_GENE-4

value: STOMACH


title: MVT1 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line MVT1

value: FVB/N

value: Genetically engineered mouse mammary tumor


title: 86404_M430-2_8_A.COLON_MGI_GENE-4

source_name: Normal Diet_A.COLON

value: Normal Diet


title: EpH4 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line EpH4

value: BALB/c

value: Spontaneously immortalized mammary epithelium

value: Non-malignant


title: EMT6 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line EMT6

value: Spontaneous mammary tumor

value: Malignant

value: High


title: 86403_M430-2_8_ILEUM_MGI_GENE-4

source_name: Normal Diet_ILEUM

value: ILEUM


title: 86405_M430-2_8_D.COLON_MGI_GENE-4

source_name: Normal Diet_D.COLON


title: 67NR cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line 67NR


title: HRM-1 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line HRM-1


title: 780 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line 780

value: Not tested


title: P35 Hp 205 2

city: Farmington

first: Jeffrey

last: Chuang

state: CT

address: 263 Farmington Avenue

department: Computational Biology

institute: The Jackson Laboratory for Genomic Medicine

hyb_protocol: 2.3µg of biotin-labeled and fragmented cDNA was then hybridized onto GeneChip® Mouse Gene 1.0 ST Arrays (Affymetrix) for 16 hours at 45°C.  Post-hybridization staining and washing were performed according to manufacturer’s protocols using the Fludics Station 450 instrument (Affymetrix)

scan_protocol: The arrays were scanned with a GeneChipTM Scanner 3000 laser confocal slide scanner.

data_processing: Average signal intensities for each probe set were calculated using Expression Console software (Version 1.1, Affymetrix) using the average (RMA) method  Fs, a modified F-statistic incorporating shrinkage estimates of variance components from within the R/maanova package was used to determine differentially expressed genes by one pairwise comparisons   Permutations analysis was used to calculate the levels of statistical significance of pairwise comparisons and these were adjusted for multiple testing using the false discovery rate, q-value method   Differentially expressed genes are declared at an FDR q-value threshold of 0.05

source_name: hippocampus

label_protocol: Following reverse transcription with random primers-T7 primers (Affymetrix, Santa Clara, Ca), double stranded cDNA was synthesized with the GeneChip® WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara, Ca).  In an in vitro trancription (IVT) reaction with T7 RNA polymerase, the cDNA was linearly amplified to generate cRNA.  In the second cycle of cDNA synthesis, random primers are used to generate single stranded DNA in the sense orientation.  Incorporation of dUTP in the cDNA synthesis step allows for the fragmentation of the cDNA strand utilizing uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) that specifically recognizes the dUTP and allows for breakage at these residues. Labeling occurs by terminal deoxynucleotidyl transferase (TdT) where biotin is added by a Affymetrix Labeling Reagent.

extract_protocol: The cerebellum and hippocampus were collected from B6J and B6J-nmf205-/- mice at 3 weeks and 5 weeks of age. Total RNA was isolated by TRIzolPlus(TM) methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA).

tag: strain

tag: age


title: P35 Hp 205 3


title: Db-7 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line Db-7

value: Low


title: Plasma cfRNA from colorectal cancer patient3

city: Jerusalem

first: Vardit

last: Moshayoff

address: Hadassaah Medical Center, Ein Kerem

country: Israel

institute: BioMarCare technology

hyb_protocol: the use of the GeneChip® Hybridization, Wash and Stain Kit (catalog no. 900720, Affymetrix) and the GeneChip human 1.0 ST Arrays (catalog no. 901085, Affymetrix). Hybridization cocktail was prepared by mixing the following materials: 25 microliter of fragmented, biotin-labeled and amplified cDNA, 1.9 microliter control oligonucleotide B2 (3 nM), 5.5 microliter of 20X Eukaryotic hybridization controls (bioB, bioC, bioD, cre), 55 microliter 2X Hybridization Buffer, 11 microliter 100% DMSO, 11.6 microliter water. The procedure was performed according to manufacturer instructions.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw CEL files were imported into Partek Genomics Suite and preprocessed using RMA background correction, quantile normalization and log2 transformation. No probe summarization to probeset was performed.

label_protocol: For gene expression profiling using Affymetrix expression microarray, cDNA was synthesized using the Ovation PicoSL WTA System (catalog no. 3312, Nugen), according to kit's protocol. Subsequently, the cDNA was purified with MiniElute Reaction Cleanup kit (catalog no. 28204, Qiagen), according to kit protocol. Next, fragmentation and biotin labeling of the cDNA was done by Encore biotin module (catalog no. 4200, Nugen). The extent of fragmentation was monitored using Bioanalyzer 2100 Pico chip (Agilnet) using 1 µl of the reaction volume.

growth_protocol: not applicable

extract_protocol: Plasma total RNA was purified from 3.2ml of plasma mixed with 11.2 TRIzol reagent, with addition of 15 microgram of linear acrylamide. 200 μl of chloroform were added per each 1 ml of Trizol and mixed vigorously. After incubated for 10 minutes at room temperature, the mixture was centrifuged for 15 minutes at 14000 rpm at 4°C. The aqueous phase was transferred to a new tube and mixed vigorously with equal volume of chloroform, incubated for 3 minutes at room temperature and centrifuged for 15 minutes at 14,000 rpm at 4°C. Following the centrifugation, the upper phase was transferred to a new tube and mix thoroughly with a total of 2.8 ml of RLT plus buffer RNeasy mini kit (catalog no. 74104, Qiagen). This mixture was passed through the kit's gDNA eliminator mini spin column as described by the manufacture protocol. The flow-through was collected in a new tube, and 1.5 times volume of 100% EtOH was added. The solution was well mixed and incubated at -20°C for over-night. Next, 700 ml of the mixture was loaded on an RNeasy spin column and micro-centrifuged at 23°C, 14,000 RPM, for 30 seconds and flow-through was saved. The rest of the thawed solution was passed through the same RNeasy spin column, as described above.RNA purification process was completed by following the RNeasy mini kit protocol. The RNA-loaded RNeasy spin column were washed with 700 ml of RW1 buffer, centrifuged at 23°C 14,000 RPM for 30 seconds and flow through discarded. Additional two washes of spin column were done with 500 ml of RPE buffer. Finally, RNA was eluted in 35 ml of RNase-free water.

treatment_protocol: Subject were classified as being either healthy, having adavnaced adenoma or cancer according to colonoscopy result or biopsy results.

tag: subject status/id

value: colorectal cancer patient3

tag: gender

value: Male

tag: age (yrs)

tag: colonoscopy result

value: adenocarcinoma at descending colon 2.5 cm

tag: molecule subtype

value: human plasma circulating free RNA


title: P35 Hp 205 1


title: CMYC cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line c-Myc

value: c-Myc


title: 6DT1 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line 6DT1

value: FVB/N


title: LCL10_fluoxetine_21days

value: depressive disorder

tag: treatment

value: fluoxetine

value: non-responder


title: Plasma cfRNA from colorectal cancer patient2

description:
no operation to determine tumor stage
BC17_CA

value: colorectal cancer patient2

value: Female

value: rectum mass


title: LCL9_control_21days

value: control


title: D2.0R cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line D2.0R

value: BALB/c

value: Spontaneous mammary tumor

value: Malignant


title: 86402_M430-2_8_JEJUNUM_MGI_GENE-4

source_name: Normal Diet_JEJUNUM

tag: group

value: Normal Diet

tag: genotype

tag: tissue

value: JEJUNUM

tag: animal


title: LCL8_fluoxetine_21days

value: responder


title: LCL8_control_21days


title: LCL7_fluoxetine_21days


title: P35 Hp WT 3

value: wild type


title: 86401_M430-2_8_DUODENUM_MGI_GENE-4

source_name: Normal Diet_DUODENUM

value: DUODENUM


title: P35 Hp WT 2


title: 86400_M430-2_8_STOMACH_MGI_GENE-4

source_name: Normal Diet_STOMACH

value: STOMACH


title: Plasma cfRNA from colorectal cancer patient1

description:
no operation to determine tumor stage
BC16_CA

value: colorectal cancer patient1

value: hepatic flexure mass

value: human plasma circulating free RNA


title: LCL7_control_21days

value: depressive disorder

value: non-responder


source_name: Plasma cfRNA from adanced adenoma subject4.

value: adanced adenoma subject4

value: Male

value: 6mm mass- villo tubular


title: P35 Hp WT 1


title: Plasma cfRNA from adanced adenoma subject3

value: adanced adenoma subject3

value: 14mm mass- villo tubular


title: Plasma cfRNA from adanced adenoma subject2

value: adanced adenoma subject2

value: Female

value: 10mm mass- villotubular adenoma high grade dysplasia


title: 4T07 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line 4TO7

tag: mouse strain

value: BALB/c

tag: cell line origin

value: Spontaneous mammary tumor

tag: malignancy status

value: Malignant

tag: metastatic ability

value: Low


title: 86399_M430-2_7_D.COLON_MGI_GENE-4

value: Normal Diet


title: Plasma cfRNA from adanced adenoma subject1

value: adanced adenoma subject1

value: 30mm mass- villo tubular HGD


title: D2A1 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line D2A1

tag: cell line

value: High


title: Plasma cfRNA from healthy subject3

source_name: Plasma cfRNA from healthy subject

value: healthy subject3

value: normal

value: human plasma circulating free RNA


title: 2855 cells_Rep1

description: Copy number variation data

source_name: Mouse mammary tumor-derived cell line 2855

value: FVB/N

value: Genetically engineered mouse mammary tumor

value: Not tested


title: LCL6_fluoxetine_21days

tag: disease state

value: depressive disorder

value: fluoxetine

tag: clinical treatment outcome

value: responder


title: 86396_M430-2_7_JEJUNUM_MGI_GENE-4

value: JEJUNUM


title: P35 Cm 205 2

source_name: cerebellum

tag: strain

tag: age


title: LCL5_fluoxetine_21days