title: glmY

city: Dallas

first: Charley

last: Gruber

state: TX

address: 6000 Harry Hines

department: Microbiology

institute: UTSW

description: ΔglmY

hyb_protocol: standard Affymetric protocols

scan_protocol: standard Affymetric protocols

data_processing:
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.3.1.187

organism: Escherichia coli

source_name: glmY mutant bacteria

label_protocol: standard Affymetric protocols

growth_protocol: Bacteria were grown for 6 hours statically at 37C under 5% CO2 in low glucose DMEM

extract_protocol: Ambion RiboPure RNA isolation protocol

treatment_protocol: No treatment

value: EHEC strain 86-24

value: ΔglmY; glmY deletion

tag: culture media

value: low glucose DMEM

tag: culture age

value: 6 hrs (grown statically at 37C)


title: glmZ

status: Public on Feb 01 2015

type: RNA

country: USA

description: ΔglmZ

label: biotin

molecule: total RNA

source_name: glmZ mutant bacteria

tag: strain

tag: genotype/variation

value: ΔglmZ; glmZ deletion


title: SH-199

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was normalized by neqc (Shi et al., Nucleic Acids Res. 2010), and its batch effect (day of experiment) was adjusted by ComBat (Johnson et al., Biostatistics. 2007)

organism: Homo sapiens

source_name: PBMC

label_protocol: Standard Illumina label protocol

extract_protocol: PBMCs were prepared from 20 mL of peripheral blood by density gradient centrifugation using Ficoll-Paque (GEHealthcare Life Sciences, Uppsala, Sweden). All samples were cryopreserved until RNA extraction. Total RNA was isolated using TRIzol LS reagent (Invitrogen, Carlsbad, Calif) and purified using RNeasy Mini Kit (Qiagen, Valencia, Calif), according to the manufacturer’s instructions. Quality and integrity of the purified total RNA were confirmed using an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, Calif) and Nanodrop ND-1000 (Thermo Fisher Scientific, Wilmington, Del).

treatment_protocol: This is a retrospective analysis with peripheral blood samples from a subset of 112 patients with metastatic CRPC, who were positive for human leukocyte antigen (HLA)-A2, A24, A3 super type (-A3, -A11, -A30, -A31 and -A33) or -A26 and enrolled in phase 1, 1-2, and 2 clinical trials for PPV between February 2001 and April 2008. These studies were approved by the ethics review committee at the participating hospitals in Japan (Kurume University Hospital, Kinki University Hospital, Okayama University Hospital, and Nara Medical University Hospital). The detailed method of clinical trials was described in our previous reports.

tag: os

tag: event

tag: age


title: SH-291


title: wt

description: wt

source_name: wt bacteria

value: wild type


title: SH-198


title: SH-191


title: SH-193


title: SH-189


title: SH-195


title: SH-187


title: TC-1 tumor: WT vs fat-1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0(Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

organism: Mus musculus

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

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

tag: cell line


title: SH-194


title: SH-196


title: Em-Myc; shEzh2.556#2

city: Cold Spring Harbor

first: Claudio

last: Scuoppo

address: 1 Bungtown Rd

institute: Cold Spring Harbor

description: Gene expression data from Em-lymphomas generated by Ezh2.556 shRNAs

hyb_protocol: standard affymetrix protocol

scan_protocol: standard affymetrix protocol

data_processing: standard affymetrix protocol

source_name: Sorted B cell lymphoma cells

label_protocol: Total RNA was extracted from the cells using Trizol (Invitrogen) and the RNeasy mini kit (Qiagen, Hilden, Germany).

extract_protocol: Lymphomas were purified by using Dynabeads Mouse CD43 kit (Untouched™ B Cells, Life Technologies) and confirmed to be at least 95% B220-positive GFP-positive by flow cytometry.

tag: cell type

value: B-cell lymphoma

tag: treatment


title: 6647_30min_repl1

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

country: Italy

institute: Rizzoli Orthopaedic Institute

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. After hybridization, slides were washed sequential

scan_protocol: Hybridized slides were scanned using GenePix 4000B microarray scanner (Axon Instruments) that acquires data at two wavelenghts simultaneously [532nm (green) and 635nm (red)]. Signal and background intensities for both channels were calculated with GenePix 3.0 (Axon Instruments).

data_processing: Lowess normalized, background subtracted value data obtained from log2 of processed Red signal/processed Green signal. (BRB-ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools.html).

source_name: Ewing's Sarcoma cell line 6647, treated 30 min.

label_protocol: Total RNA was used to obtain labeled cRNA, according to the manufacturer's instructions (Low RNA Input Fluorescent Linear Amplification Kit-Agilent Technologies).

growth_protocol: Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM), supplemented with 100 units/ml penicillin, 100 µg/ml streptomycin and 10% inactivated fetal bovine serum (FBS).

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

treatment_protocol: Cells were treated 5x106 cells/ml in suspension with 10µg/ml 0662 MAb at indicated time points.

value: Ewing's Sarcoma cell line

value: anti-CD99 0662 Mab

tag: time

value: 30 minutes.

source_name: Ewing's Sarcoma cell line 6647, control

value: control, no treatment


title: 6647_30min_repl2


title: 6647_60min_repl1

source_name: Ewing's Sarcoma cell line 6647, treated 60 min

value: 60 minutes.


title: SH-188


title: SH-190


title: SH-192


title: 6647_60min_repl2


title: SH-185


title: Em-Myc; shEzh2.556#1


title: 6647_120min_repl1

source_name: Ewing's Sarcoma cell line 6647, treated 120 min.

value: 120 minutes.


title: Family64 rep4 slide2

city: Kearneysville

first: Beth

middle: M

last: Cleveland

state: WV

address: 11861 Leetown Rd

institute: NCCCWA/ARS/USDA

description: dye swap for sample 15

hyb_protocol: Microarray slides were prepared for hybridization by washing twice in 0.2% SDS for 5 minutes each, then rinsing in nanopure water for 5 minutes, followed by a final wash in warmed nanopure water for 3 minutes.  Slides were dried by centrifugation and placed in a humidified InSlide Out hybridization oven at 60 C.  For hybridization, 25 pmol of each labeled cDNA sample were used.  A saline treated and an IGF-I sample, coupled with either Alexa Fluor 555 or 647 dyes, were combined and concentated with a Microcon YM-30 concentrator and mixed with 75 uL of SlideHyb no. 2.  The samples were heated to 95 degrees for 10 min, and then pipetted under a LeftSlip coverslip which was placed on top of the slide.  The arrays were hydribized overnight at 50 degrees in the InSlide Out hybridization oven.  After incubation, the slides were subsuquently washed in a shaker at room temperature for 5 min, once in 2X SSC/0.5% SDS, then twice in 0.5X SSC.  Slides were dried by centrifugation and immediately scanned.

scan_protocol: All slides were scanned using a ScanArray Microarry Scanner (PerkinElmer, Inc).  Scans were performed with a 5 um resolution and the Line Scan tool was used to optimize laser and PMT intensities.

data_processing: The acquired images were processed using the gene annotation file (gal) procided by the manufacturer and spots were quantified with ScanArray Express Software using the default adaptive circle method.  The raw data intensities collcted from two-channel arrays were pre-processed with scripts written in R language.  These scripts included functions from the statistical packages MURRAY, ARRAYQUALITY, and LIMMA from the Bioconductor project.  The array data pre-processing included arrays diagnostics, data quality assessment, data filtering, data background correction, and data normalization.  The R scripts for data pre-processing are available on request (roger.vallejo@ars.usda.gov).

organism: Oncorhynchus mykiss

source_name: fish 175

label_protocol: Complementary DNA containing amino-modified bases was synthesized from 15 micrograms of total RNA using Invitrogen's Superscript Indirect cDNA labeling system and oligo dT primers, and then labeled with the Alexa Fluor 555 or 647 dues following the manufacturer's protocol with minor modifications.

growth_protocol: Fish were pit-tagged to allow for individual and family identification.  After implanting the osmotic pump, families were combined according to treatment.  Feed was withheld for the remainder of the 2-week study period.

extract_protocol: Total RNA was isolated using TRI-Reagent (Sigma-Aldrich) per manufacturer's protocol.  The RNA pellet was washed twice with 70% ethanol prior to resuspension in nuclease-free water.

treatment_protocol: Osmotic pumps were filled with either IGF-I or saline and implanted into the peritoneal cavity of each fish.  Osmotic pumps were inserted through a 1-cm incision made 2-cm anterior of the pelvic fin.  The incisions were closed using surgical staples and treated with triple antibiotic ointment.  Osmotic pumps released either 25 ug IGF-I/kg/day or saline, the latter of which served as a control.  Feed was withheld for the remainder of the study, which lasted for 2 wks.

value: saline

tag: family

tag: tissue

value: muscle

source_name: fish 193

value: IGF-I


title: Primary Melanoma_100

city: New York

first: Eva

last: Hernando-Monge

state: NY

address: 550 1st Ave. Smilow 305

institute: NYU Langone Medical Center

description: 1_Exiqon is Cy3

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 14.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes.

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.  Spots were flagged as follows: 0 - no flag, spot OK; 1 - manual flagging; 2 - empty spot; 3 - poor spot; 4 - negative spot; 5 - empty spot (manual); poor spot (manual); negative spot (manual).  Spots flagged 1 or higher were removed from consideration.  Capture probes for which both Hy3 and Hy5 values were less than 1.5x the median signal intensity for a given slide were excluded from further analysis.  Excluded capture probes are indicated byt the acronym' NA' in the expression matrix.  For each spot, a log base 2 ratio (Hy3/Hy5) was calculated, and the median log-ratio of four replicate spots per array was selected as representative of relative miRNA expression for a given sample.  Median log-ratios were used for all subsequent analyses.

label: Cy3 (Hy3)

source_name: Cutaneous primary melanoma

label_protocol: 300 ng total RNA from sample and reference was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: RNA was extracted using Qiagen miRNeasy FFPE kits following the manufacturer's recommended protocol.  RNA quantity and quality was assessed by Nanodrop and Agilent 2100 Bioanalyzer.

treatment_protocol: After surgical excision, primary melanomas were fixed in formalin and embedded in parrafin by NYU Langone's clinical pathology lab.  5uM  FFPE sections were affixed to Leica PEN membrane slides.  3 tp 10 sections were used for RNA extraction from each patient case.  A consecutive section was stained by H&E and tumor area was marked by an attending pathologist.  Tumor was macro-dissected from sections under a dissecting microscope and transferred to microfuge tubes prior to RNA extraction.  RNA extraction was performed within 4 days of tissue section to reduce air-related RNA degradation

tag: identifier

tag: gender

value: F

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

tag: ulceration status

value: Present

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: IIB

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma

tag: Cause of death

label: Cy5 (Hy5)

source_name: Common Reference

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_101

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

value: Axial

value: IIC


title: Family64 rep3 slide1

description: dye swap for sample 14

source_name: fish 179

tag: treatment

tag: family

tag: tissue

source_name: fish 167


title: SH-182

tag: os

tag: event


title: SH-186


title: Primary Melanoma_098

description: 1_Exiqon is Cy3

value: Few

tag: ulceration status

value: Absent

tag: histotype

value: Superficial Spreading

tag: anatomical site of primary tumor

tag: Stage

value: IIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met


title: Primary Melanoma_099

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

tag: primary tumor thickness (mm)

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Died, No Melanoma

tag: Cause of death

value: Other

tag: material


title: SH-184

tag: os

tag: event


title: Primary Melanoma_097

description: 1_Exiqon is Cy3

tag: mitotic index

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

value: IB

tag: recurrence

tag: time to 1st recurrence (days)


title: Primary Melanoma_096

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Moderate

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met


title: Em-Myc; shEzh2.781#1

description: Gene expression data from Em-lymphomas generated by Ezh2.781 shRNAs

tag: cell type

value: B-cell lymphoma

tag: treatment


title: Em-Myc; shEzh2.781#2


title: Em-Myc B cells #2

description: Gene expression data from Em-myc sorted premalignant B-cell

source_name: Splenic B cells form premalignaant Em-myc mouse

value: normal B cells

value: control


title: Em-Myc B cells #1


title: Family64 rep3 slide2

description: dye swap for sample 13

value: saline

tag: family

tag: tissue

value: muscle

value: IGF-I


title: SH-180

tag: os

tag: event


title: Family64 rep2 slide2

description: dye awap for sample 11

source_name: fish 215

source_name: fish 495


title: SH-178


title: Family64 rep4 slide1

description: dye swap for sample 16


title: Primary Melanoma_095

description: 1_Exiqon is Cy3

value: M

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

value: Present

tag: histotype

value: Acral Lentiginous

tag: anatomical site of primary tumor

value: Extremity

value: IIIC

value: Y

value: RLN

value: N

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_094

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: age

value: Nodular

value: Axial

tag: Stage

value: IIIB

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: DLN,DS,DV

tag: brain as isolated 1st site of recurrence

tag: b-met


title: 6647_120min_repl2

tag: cell line

value: Ewing's Sarcoma cell line

tag: treatment

value: anti-CD99 0662 Mab

tag: time

value: 120 minutes.

value: control, no treatment


title: SH-179

tag: os

tag: event


title: SH-181


title: Primary Melanoma_093

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

tag: ulceration status

value: Absent

tag: histotype

tag: anatomical site of primary tumor

value: IIIA

value: DV

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma

tag: Cause of death


title: Primary Melanoma_092

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Few

value: Present

value: Extremity

tag: Stage

value: IIB

tag: recurrence

value: Y

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: RS

tag: brain as isolated 1st site of recurrence

value: N

value: Died, With Melanoma

tag: material


title: Primary Melanoma_091

description: 1_Exiqon is Cy3

value: F

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

tag: histotype

value: Superficial Spreading

value: Axial

value: RLN

tag: b-met

value: Melanoma

value: Equal mixture of all samples


title: Family64 rep1 slide1

description: dye swap for sample 10

source_name: fish 247

tag: treatment

value: IGF-I

tag: family

tag: tissue

value: muscle

source_name: fish 163

value: saline


title: #483 4EGI-1 3

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

country: Germany

institute: Hannover Medical School

description: Polysome fraction from 4EGI-1 TREATED #483 T-ALL CELLS

hyb_protocol: amplified, fragmented, biotin labeled cDNA was hybridized for 18 hr at 45C on Mouse GeneChip1.0 ST Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0007

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: # 483 T-ALL clone + 4EGI-1

label_protocol: RNA was amplified by the Applause WT-Amp ST System (NuGEN Technologies, Bemmel, The Netherlands), amplified cDNA was fragmented and biotin labeled using the Encore Biotin Module (NuGEN Technologies)

growth_protocol: #483 were treated with  4EGI-1 or DMSO. Polysomal fractions were prepared via sucrose density gradients and subjected to Microarray analysis

extract_protocol: polysome fractions were collected and supplied with 0.1 volume of 3 M sodium acetate (pH 5.2) and 1 volume of isopropanol for overnight precipitation at -20 °C. RNA was purified using Nucleospin RNAII tubes (Macherey & Nagel). Cytoplasmic RNA was extracted using standard TRIZOL Protocols. For polysomal RNA polysome fractions were pooled, precipitated by adding LiCl to a final concentration of 2 M and resolubilized in 15 µl of RNase-free water.

treatment_protocol: #483 were treated with 100 uM 4EGI-1 or DMSO for 2h.

tag: strain

tag: fraction

value: polysome


title: Family64 rep1 slide2

description: dye swap for sample 9


title: Family64 rep2 slide1

description: dye swap for sample 12


title: Primary Melanoma_090

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

value: Absent

value: Nodular

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: IIA

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma

tag: Cause of death


title: Family107 rep4 slide1

description: dye swap for sample 8

source_name: fish 137

source_name: fish 127


title: SH-173

source_name: PBMC

tag: os

tag: event


title: #483 4EGI-1 2

tag: treatment


title: #483 4EGI-1 1


title: SH-175


title: #483 untreated 3

description: Polysome fraction from untreated #483 T-ALL CELLS

source_name: # 483 T-ALL clone

value: untreated


title: SH-174


title: Family107 rep4 slide2

description: dye swap for sample 7

tag: family


title: Family107 rep3 slide1

description: dye swap for sample 6

source_name: fish 111

tag: tissue

source_name: fish 109


title: Primary Melanoma_089

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

tag: ulceration status

tag: histotype

tag: recurrence

value: Y

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

value: DV,RS

tag: brain as isolated 1st site of recurrence

value: N

tag: b-met

value: Died, With Melanoma

tag: material


title: SH-170

tag: age


title: SH-171

tag: os


title: SH-172

tag: event


title: #483 4EGI-1 Total 3

description: Cytoplasmic fraction from 4EGI-1 TREATED #483 T-ALL CELLS

tag: strain

tag: treatment

tag: fraction

value: cytoplasmic


title: Primary Melanoma_088

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: primary tumor thickness (mm)

value: Few

value: Present

tag: anatomical site of primary tumor

tag: Stage

value: RS

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

tag: Cause of death

value: Melanoma

value: Equal mixture of all samples


title: #483 untreated 1

value: polysome


title: Family107 rep1 slide1

description: dye swap for sample 2

source_name: fish 125

value: IGF-I

tag: family

tag: tissue

value: muscle

source_name: fish 121

value: saline


title: Family107 rep2 slide2

description: dye swap for sample 3

source_name: fish 161

source_name: fish 157


title: #483 untreated 2


title: Family107 rep3 slide2

description: dye swap for sample 5


title: #483 untreated Total 3

description: Cytoplasmic fraction from untreated #483 T-ALL CELLS


title: Family107 rep2 slide1

description: dye swap for sample 4


title: #483 untreated Total 2


title: #483 4EGI-1 Total 1


title: Primary Melanoma_087

description: 1_Exiqon is Cy3

source_name: Cutaneous primary melanoma

value: F

tag: age

tag: mitotic index

value: Many

tag: ulceration status

value: Absent

tag: histotype

value: Nodular

value: Extremity

value: IIIC

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

source_name: Common Reference

tag: material


title: Primary Melanoma_086

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: primary tumor thickness (mm)

value: Superficial Spreading

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IB

value: Y

value: RLN

value: N

tag: time to b-met (days)

tag: follow-up time (days)

value: Died, With Melanoma


title: Primary Melanoma_084

description: 1_Exiqon is Cy3

value: M

tag: age

tag: mitotic index

value: Moderate

value: DLN,DS

tag: follow-up time (months)

tag: last status

tag: Cause of death

value: Melanoma

value: Equal mixture of all samples


title: Primary Melanoma_085

description: 1_Exiqon is Cy3

value: F

tag: ulceration status

tag: histotype

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

value: Alive, No Melanoma


title: SH-169

tag: os

tag: event


title: SH-168


title: SH-166


title: Trt.4

city: Philadelphia

first: Denise

middle: C

last: Connolly

state: PA

address: 333 Cottman Avenue

institute: Fox Chase Cancer Center

description: Gene expression of AZD1480 treated, replicate 4

hyb_protocol: 1.65 ug of Cy-3 labeled cRNA targets is hybridized onto Agilent 4x44k whole genome arrays for 17 hours at 65º C and washed according to Agilent procedure.

scan_protocol: The hybridized slides are scanned at 5µm resolution on Agilent scanner (Agilent)  G2505B.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: AZD1480 treated, replicate 4

label_protocol: 500 ng total RNA was amplified and labeled using Agilent QuickAmp labeling kit following the manufacturer protocol.

growth_protocol: mice (n=4/group) with ~500 mm3 tumors were treated with vehicle or 30 mg/kg AZD1480 and euthanized 6 hours later for tumor tissue collection

extract_protocol: Mouse tissue RNA samples were prepared using the RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions

treatment_protocol: vehicle treated or AZD1480(30 mg/kg) treated

tag: tissue

value: ovarian tumor

tag: treatment

tag: genotype


title: #483 4EGI-1 Total 2

tag: strain

tag: fraction

value: cytoplasmic


title: SH-163

tag: age


title: SH-167


title: Primary Melanoma_082

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: primary tumor thickness (mm)

tag: mitotic index

value: Absent

value: Nodular

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: IIIB

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Alive, With Melanoma

tag: material


title: Primary Melanoma_083

description: 1_Exiqon is Cy3

tag: ulceration status

value: Present

tag: histotype

value: Axial

value: IIIC

tag: recurrence

value: Y

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

value: DS

value: N

tag: follow-up time (months)

tag: last status

tag: Cause of death


title: Family107 rep1 slide2

description: dye swap for sample 1

tag: treatment

value: saline

tag: family

tag: tissue

value: muscle

value: IGF-I


title: Primary Melanoma_081

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

value: Superficial Spreading

tag: anatomical site of primary tumor

tag: Stage

value: IIIA

tag: site of 1st recurrence

value: Alive, No Melanoma

value: Equal mixture of all samples


title: SH-162

tag: os

tag: event


title: SH-161


title: Primary Melanoma_080

description: 1_Exiqon is Cy3

value: Few

tag: ulceration status

tag: histotype

value: Nodular

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

value: DV

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Died, With Melanoma

value: Melanoma

tag: material


title: Trt.2

description: Gene expression of AZD1480 treated, replicate 2

source_name: AZD1480 treated, replicate 2

tag: tissue

value: ovarian tumor

tag: treatment

tag: genotype


title: Ctrl.3

description: Gene expression of vehicle treated, replicate 3

source_name: Vehicle treated, replicate 3

value: vehicle


title: SH-159

tag: age


title: Ctrl.4

description: Gene expression of vehicle treated, replicate 4

source_name: Vehicle treated, replicate 4


title: Control, rep5

city: OSLO

first: Ingvild

last: Moe

address: Sognsvannsvn 20

country: Norway

institute: Oslo University hospital

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was quantile normalized using Bioconductor in R.

label: Biotin

source_name: Cardiac myocytes, control

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

growth_protocol: Ca2+-tolerant cardiac myocytes were isolated from mouse hearts by coronary perfusion with collagenase type 2. The cells were plated in laminin-coated tissue culture wells in MEM with HBSS, supplemented with 0.1% BSA, 100 U/mL penicillin-G and 10 mmol/L BDM.

extract_protocol: Total RNA was isolated using the RNeasy system (Qiagen).

treatment_protocol: The cardiac myocytes were cultured in the absence or presence of 200 nmol/L CTGF for 48 hours.

tag: strain

value: 12-16 weeks

value: heart

tag: cell type

value: cardiac myocytes


title: #483 untreated Total 1

value: untreated

tag: fraction

value: cytoplasmic


title: Control, rep6


title: Primary Melanoma_079

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

tag: ulceration status

value: Present

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIC

value: N

tag: site of 1st recurrence

tag: follow-up time (months)

tag: last status

tag: Cause of death


title: Trt.1

description: Gene expression of AZD1480 treated, replicate 1

source_name: AZD1480 treated, replicate 1

tag: tissue

tag: treatment


title: Primary Melanoma_078

description: 1_Exiqon is Cy3

value: M

tag: age

value: Many

tag: histotype

value: Nodular

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Alive, No Melanoma

tag: material

value: Equal mixture of all samples


title: Trt.3

description: Gene expression of AZD1480 treated, replicate 3

source_name: AZD1480 treated, replicate 3

value: ovarian tumor

tag: genotype


title: Control, rep1

tag: strain

value: 12-16 weeks

tag: cell type


title: Primary Melanoma_077

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

value: Superficial Spreading

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: IIB

tag: site of 1st recurrence

tag: follow-up time (months)

tag: last status

value: Died, No Melanoma

value: Other


title: Control, rep3

tag: age

tag: tissue

value: heart

value: cardiac myocytes

tag: treatment


title: Stimulated with CTGF, rep6

source_name: Cardiac myocytes, CTGF

value: connective tissue growth factor (CTGF)


title: Ctrl.2

description: Gene expression of vehicle treated, replicate 2

source_name: Vehicle treated, replicate 2

value: vehicle


title: SH-158

source_name: PBMC

tag: os

tag: event


title: Control, rep4

tag: strain


title: Ctrl.1

description: Gene expression of vehicle treated, replicate 1

source_name: Vehicle treated, replicate 1

tag: genotype


title: Control, rep2

tag: cell type


title: SH-160


title: Primary Melanoma_076

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

value: Present

tag: histotype

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: Cause of death

tag: material


title: Primary Melanoma_075

description: 1_Exiqon is Cy3

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

value: Nodular

tag: anatomical site of primary tumor

tag: Stage

tag: site of 1st recurrence

tag: follow-up time (months)

tag: last status

value: Unknown


title: Primary Melanoma_074

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: Moderate

value: Absent

tag: histotype

tag: recurrence

tag: time to 1st recurrence (days)

value: Alive, No Melanoma

value: Equal mixture of all samples


title: Primary Melanoma_073

description: 1_Exiqon is Cy3

value: Few

value: Axial

value: IIB

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)


title: Stimulated with CTGF, rep2

tag: strain

tag: age

value: 12-16 weeks

tag: tissue

value: heart

tag: cell type

value: cardiac myocytes

tag: treatment


title: Primary Melanoma_072

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

tag: anatomical site of primary tumor

tag: Stage

value: Y

tag: site of 1st recurrence

value: DV

tag: follow-up time (months)

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material


title: SH-154

tag: os

tag: event


title: M5_GFP-RFP+

city: Paris

first: Antonio

middle: Angelo

last: Freitas

address: 25 Rue du Dr. Roux

department: Lymphocyte Population Biology Unit

country: France

institute: Institut Pasteur

description: SAMPLE 19

hyb_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA).

scan_protocol: The Agilent Feature Extraction Software (FES 10.7.3.1 ) was used to read out and process the microarray image files.

data_processing: Quantile normalized signal intensity data in log2 space using Agilent Feature Extraction Software (v.10.7.3.1).

source_name: T CD4(+) Regulatory T cells.

label_protocol: Cy3 labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Mouse Genome Oligo Microarrays (8x60K) using Agilent’s recommended hybridization chamber and oven. Finally, microarrays were washed once with wash buffer 1 for 1 min at RT followed by a second wash with wash buffer 2 for 1 min at 37°C and a final wash step with acetonitrile for 30 sec at RT.

extract_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

treatment_protocol: RNA was isolated using the RNeasy Mini®  (Qiagen). For the subseqent amplification of the RNA the SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

tag: strain background

tag: genotype/variation

value: Tg IL-2-GFP x FOXP3mRFP

tag: developmental stage

value: adult

tag: gender

value: female

value: Spleen/Lymph nodes

value: Conventional CD4+ T lymphocytes

tag: cell subtype

value: GFP-RFP+; T CD4(+) Regulatory T cells.


title: SH-150

tag: age


title: SH-148


title: M4_GFP-RFP+

description: SAMPLE 18

tag: tissue

tag: cell type


title: SH-152


title: M2_GFP-RFP+

description: SAMPLE 16


title: SH-145


title: Stimulated with CTGF, rep3

tag: strain

tag: treatment

value: connective tissue growth factor (CTGF)


title: Primary Melanoma_071

description: 1_Exiqon is Cy3

tag: identifier

value: M

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

tag: ulceration status

value: Present

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status

value: Died, No Melanoma

value: Heart Attack/Old Age

value: Equal mixture of all samples


title: Stimulated with CTGF, rep5

tag: strain

tag: age

value: 12-16 weeks

tag: tissue

value: heart

tag: cell type

value: cardiac myocytes


title: M3_GFP-RFP+

description: SAMPLE 17

tag: strain background

tag: genotype/variation

value: Tg IL-2-GFP x FOXP3mRFP

tag: developmental stage

value: adult

tag: gender

value: female

tag: cell subtype


title: SH-147

tag: os

tag: event


title: M1_GFP-RFP+

description: SAMPLE 15

value: Spleen/Lymph nodes

value: Conventional CD4+ T lymphocytes

value: GFP-RFP+; T CD4(+) Regulatory T cells.


title: Primary Melanoma_070

description: 1_Exiqon is Cy3

tag: identifier

value: F

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIB

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: follow-up time (months)

value: Alive, No Melanoma

tag: Cause of death

tag: material


title: M5_GFP-RFP-

description: SAMPLE 14

source_name: T CD4(+) cells

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: gender

tag: tissue

tag: cell type

tag: cell subtype

value: GFP-RFP-; T CD4(+) cells


title: M3_GFP-RFP-

description: SAMPLE 12


title: M4_GFP-RFP-

description: SAMPLE 13


title: Stimulated with CTGF, rep4

tag: strain

tag: age

tag: treatment

value: connective tissue growth factor (CTGF)


title: SH-142

tag: os

tag: event


title: SH-143


title: Primary Melanoma_068

description: 1_Exiqon is Cy3

tag: identifier

value: M

tag: primary tumor thickness (mm)

tag: mitotic index

value: Few

tag: ulceration status

value: Absent

tag: histotype

value: Desmoplastic

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status

value: Died, No Melanoma

value: Other

value: Equal mixture of all samples


title: Primary Melanoma_069

description: 1_Exiqon is Cy3

tag: gender

tag: age

value: Many

value: Present

tag: site of 1st recurrence

tag: follow-up time (months)

tag: Cause of death

tag: material


title: SH-144

tag: os

tag: event


title: M2_GFP-RFP-

description: SAMPLE 11

tag: strain background

tag: genotype/variation

value: Tg IL-2-GFP x FOXP3mRFP

tag: developmental stage

value: adult

value: female

tag: tissue

value: Spleen/Lymph nodes

tag: cell type

value: Conventional CD4+ T lymphocytes

tag: cell subtype


title: Stimulated with CTGF, rep1

tag: strain

value: 12-16 weeks

value: heart

value: cardiac myocytes

tag: treatment


title: Primary Melanoma_066

description: 1_Exiqon is Cy3

tag: identifier

value: F

tag: primary tumor thickness (mm)

tag: mitotic index

value: Moderate

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: IIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status

value: Alive, No Melanoma


title: SH-141

tag: os

tag: event

tag: age


title: M5_GFP+RFP+

description: SAMPLE 9

source_name: IL-2p Regulatory T CD4(+)cells

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: gender

tag: tissue

tag: cell type

tag: cell subtype

value: GFP+RFP+; IL-2p Regulatory T CD4(+)cells


title: Undifferentiated hES biological rep 2 of 3

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina iScanner

data_processing: The data were analyzed with GenomeStudio using Illumina default analysis settings. No normalization and background correction are performed first, then quantile normalization and background correction are done.

source_name: H9 hESCs

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

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

value: undifferentiated hES


title: Primary Melanoma_067

description: 1_Exiqon is Cy3

source_name: Cutaneous primary melanoma

tag: identifier

value: M

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIB

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

tag: follow-up time (months)

tag: Cause of death

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_065

description: 1_Exiqon is Cy3

tag: gender

tag: age

value: Absent

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status

source_name: Common Reference


title: SH-139

tag: os

tag: event


title: M5_GFP+RFP-

description: SAMPLE 5

source_name: IL-2p T CD4(+) cells

tag: strain background

tag: genotype/variation

value: Tg IL-2-GFP x FOXP3mRFP

tag: developmental stage

value: adult

value: female

tag: tissue

value: Spleen/Lymph nodes

tag: cell type

value: Conventional CD4+ T lymphocytes

tag: cell subtype

value: GFP+RFP-; IL-2p T CD4(+) cells


title: Primary Melanoma_063

description: 1_Exiqon is Cy3

tag: identifier

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

tag: histotype

value: Superficial Spreading

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: IIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

tag: follow-up time (months)

value: Alive, No Melanoma

tag: Cause of death

tag: material


title: Undifferentiated hES biological rep 3 of 3

value: undifferentiated hES


title: M3_GFP+RFP+

description: SAMPLE 7

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: gender

value: GFP+RFP+; IL-2p Regulatory T CD4(+)cells


title: SH-138

tag: os

tag: event

tag: age


title: M1_GFP+RFP+

description: SAMPLE 6

tag: tissue

tag: cell type

tag: cell subtype


title: M1_GFP-RFP-

description: SAMPLE 10

value: GFP-RFP-; T CD4(+) cells


title: M3_GFP+RFP-

description: SAMPLE 3


title: Primary Melanoma_064

description: 1_Exiqon is Cy3

tag: identifier

value: F

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

value: Present

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

tag: Stage

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status


title: SH-136

tag: os

tag: event

tag: age


title: SH-137


title: SH-140


title: Primary Melanoma_062

description: 1_Exiqon is Cy3

tag: gender

value: M

value: Axial

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

tag: follow-up time (months)

tag: Cause of death

tag: material

value: Equal mixture of all samples


title: Undifferentiated hES  biological rep 1 of 3

tag: cell type


title: O4 sorted cells biological rep 2 of 3

value: O4 FACSsorted hES derived oligodendrocytes, 70 days old


title: O4 sorted cells biological rep 3 of 3


title: SH-106


title: M4_GFP+RFP+

description: SAMPLE 8

tag: strain background

tag: genotype/variation

value: Tg IL-2-GFP x FOXP3mRFP

tag: developmental stage

value: adult

value: female

tag: tissue

value: Spleen/Lymph nodes

value: Conventional CD4+ T lymphocytes

tag: cell subtype


title: O4 sorted cells  biological rep 1 of 3


title: M4_GFP+RFP-

description: SAMPLE 4

value: GFP+RFP-; IL-2p T CD4(+) cells


title: Primary Melanoma_059

description: 1_Exiqon is Cy3

tag: identifier

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

value: Absent

tag: histotype

value: Superficial Spreading

tag: anatomical site of primary tumor

tag: Stage

value: IIA

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status

value: Alive, No Melanoma


title: Primary Melanoma_061

description: 1_Exiqon is Cy3

tag: gender

tag: age

value: Moderate

value: Present

tag: recurrence

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

tag: follow-up time (months)

tag: Cause of death

tag: material


title: Primary Melanoma_060

description: 1_Exiqon is Cy3

tag: identifier

value: M

tag: primary tumor thickness (mm)

tag: mitotic index

value: Few

tag: ulceration status

tag: histotype

value: Nodular


title: Primary Melanoma_058

description: 1_Exiqon is Cy3

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: N

tag: time to 1st recurrence (months)

tag: brain as isolated 1st site of recurrence

tag: b-met

value: Equal mixture of all samples


title: MSC_A549_13

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

country: United Kingdom

institute: University College London

description: replicate 4

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the ‘normalize quantiles’ function in the BeadStudio Software.

source_name: Mesenchymal Stem Cells

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

growth_protocol: MSCs were grown in alpha-MEM supplemented with 20%FBS, 1%SP. Medium was changed twice a week. Passages 2-6 were used for experiments.

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

treatment_protocol: Cells were treated with conditioned medium from MDAMB231 cells or A549 cells (from a confluent T175)

tag: treatment

value: conditioned medium from A549

tag: cell type

value: mesenchymal stem cells


title: Primary Melanoma_057

description: 1_Exiqon is Cy3

tag: gender

tag: age

value: Extremity

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status


title: MSC_A549_12

description: replicate 4


title: SH-091

tag: os

tag: event


title: MSC_A549_11

description: replicate 4


title: M2_GFP+RFP-

description: SAMPLE 2

tag: strain background

tag: genotype/variation

value: Tg IL-2-GFP x FOXP3mRFP

tag: developmental stage

value: adult

value: female

tag: tissue

value: Spleen/Lymph nodes

value: Conventional CD4+ T lymphocytes

tag: cell subtype


title: Primary Melanoma_056

description: 1_Exiqon is Cy3

tag: identifier

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

tag: ulceration status

value: Absent

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

value: IIA

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: follow-up time (months)

value: Alive, No Melanoma

tag: Cause of death

tag: material


title: SH-090

tag: os

tag: event

tag: age


title: MSC_A549_10

description: replicate 4

tag: treatment

tag: cell type


title: SH-057


title: M1_GFP+RFP-

description: SAMPLE 1

tag: strain background

tag: genotype/variation

tag: developmental stage

tag: gender

tag: tissue

tag: cell subtype

value: GFP+RFP-; IL-2p T CD4(+) cells


title: SH-060


title: MSC_MDCM9

description: replicate 3

value: conditioned medium from MDAMB231


title: MSC_MDCM8

description: replicate 3


title: MSC_MDCM6

description: replicate 3


title: atria MRV2, rep2

city: Taipei

first: Tzu-Hao

last: Chang

address: 250 Wu-Xin Street

department: Graduate Institute of Biomedical Informatics

country: Taiwan

institute: Taipei Medical University

description: Expression data from Sus scrofa atria aged 18 months

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45℃ on GeneChip Procine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The CEL files were generated using Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Signal intensities were derived from CEL files and Signal intensity derived from the CEL files, using RMA method

organism: Sus scrofa

source_name: Sus scrofa atria, mitral regurgitation pigs treated with valsartan, sacrificed 12 months after surgery

label_protocol: see standard Affymetrix protocol

growth_protocol: Pigs in the MR, MRV and NC groups received usual diet and were raised in the cages under the temperature of 20-24 ℃ and humidity of 50-70%.

treatment_protocol: Mitral regurgitation was created in Lanyu miniature pigs by a 2.8 mm hole on the middle scallop of the posterior mitral leaflet in the MR and MRV groups. Pigs in the MRV groups additionally received valsartan (3.43 mg/kg/day), a type I angiotensin II receptor blocker, from one week before surgery and then daily after surgery.

value: left atria


title: SH-103


title: MSC_MDCM7

description: replicate 3


title: Primary Melanoma_054

description: 1_Exiqon is Cy3

tag: identifier

value: M

tag: primary tumor thickness (mm)

tag: mitotic index

value: Few

tag: ulceration status

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Axial

tag: Stage

tag: recurrence

value: N

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: time to b-met (days)

tag: follow-up time (days)

tag: last status


title: SH-059

tag: os

tag: event

tag: age


title: atria MRV1, rep1

tag: tissue


title: SH-056


title: Primary Melanoma_055

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: primary tumor thickness (mm)

value: Extremity

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: follow-up time (months)

tag: Cause of death

tag: material

value: Equal mixture of all samples


title: SH-055


title: MSC_NEG5

description: replicate 2

tag: treatment

tag: cell type

value: mesenchymal stem cells


title: Primary Melanoma_053

description: 1_Exiqon is Cy3

tag: mitotic index

tag: ulceration status

tag: histotype

value: Superficial Spreading

tag: anatomical site of primary tumor

tag: Stage

value: IB

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: time to b-met (days)


title: Primary Melanoma_052

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

value: Absent

tag: brain as isolated 1st site of recurrence

tag: follow-up time (days)

tag: last status


title: SH-054

tag: os

tag: event


title: MSC_NEG4

description: replicate 2

tag: treatment

tag: cell type


title: atria NC1, rep1

source_name: Sus scrofa atria, normal control, age-matched to MR pigs

tag: tissue


title: atria MR1, rep1

source_name: Sus scrofa atria, mitral regurgitation pigs untreated with valsartan, sacrificed 12 months after surgery


title: SH-053


title: Primary Melanoma_051

description: 1_Exiqon is Cy3

tag: mitotic index

value: Many

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: b-met

tag: follow-up time (months)

tag: Cause of death

tag: material


title: MSC_NEG3

description: replicate 2


title: MSC_NEG2

description: replicate 2


title: Primary Melanoma_050

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: time to b-met (days)

tag: follow-up time (days)

value: Alive, No Melanoma


title: atria MR2, rep2

tag: tissue


title: SH-052

tag: os

tag: event


title: Primary Melanoma_048

description: 1_Exiqon is Cy3

tag: mitotic index

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: b-met

tag: last status


title: Primary Melanoma_049

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

tag: time to 1st recurrence (days)

tag: follow-up time (months)

tag: Cause of death

tag: material


title: atria NC2, rep2

tag: tissue


title: Pool 3 liver samples of male offspring from ON mice 15

city: Barcelona

first: Susana

last: Kalko

state: BARCELONA

address: c/Rosello 153

department: Bioinformatics Platform

country: Spain

institute: IDIBAPS

hyb_protocol: Biotin-labeled cRNA was cleaned-up, quantified and subsequently fragmented by metal-induced hydrolysis (GeneChip Sample Cleanup Module, Affymetrix Inc). Hybridization was performed with GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc) according to manufacture's instructions.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G (Affymetrix Inc).

data_processing: Raw expression measures were summarized after background correction and normalization steps using the RMA methodology in the Affymetrix package from the Bioconductor project.

source_name: Mus musculus whole liver tissue

label_protocol: cRNA amplification and biotin labeling was synthesized from 2ug total RNA by means of cDNA synthesis (One-Cycle cDNA Synthesis Kit, Affymetrix Inc, Santa Clara, CA) followed by an in vitro transcription reaction in the presence of T7 RNA Polymerase and of biotinylated nucleotide analog/ribonucleotide mix (GeneChip IVT Labeling Kit, Affymetrix Inc, Santa Clara, CA)

extract_protocol: 10 ug RNA was extracted from liver tissue with Trizol reagent, following manufacture's instructions.

treatment_protocol: Animals were sacrificed, liver tissue was excised and rapidly frozen in liquid nitrogen for RNA isolation.

value: liver

tag: treatment group

value: adult male offspring from ON mice


title: MSC_NEG1

description: replicate 2

tag: treatment

tag: cell type


title: Pool 3 liver samples of male offspring from ON mice14


title: Pool 3 liver samples of male offspring from IUGR mice 12

value: adult male offspring from IUGR mice


title: REFERENCE CONTROL2

description: replicate 1

source_name: Universal Human Reference RNA (Stratagene)

tag: sample type

value: reference


title: Pool 3 liver samples of male offspring from ON mice13


title: Pool 3 liver samples of male offspring from IUGR mice 10


title: Pool 3 liver samples of male offspring from IUGR mice 11


title: Pool 3 liver samples from mice overfed during lactation, ON 9

value: adult male mice overfed during lactation (ON)


title: SH-051

tag: os

tag: event


title: Pool 3 liver samples from mice overfed during lactation, ON 7


title: Primary Melanoma_047

description: 1_Exiqon is Cy3

value: M

tag: mitotic index

value: Few

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: time to 1st recurrence (months)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)


title: Pool 3 liver samples from mice overfed during lactation, ON 8

tag: tissue

tag: treatment group


title: Primary Melanoma_046

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: primary tumor thickness (mm)

value: Moderate

value: N

tag: time to 1st recurrence (days)

tag: follow-up time (months)

tag: last status

tag: Cause of death

tag: material


title: Primary Melanoma_045

description: 1_Exiqon is Cy3

value: F

tag: mitotic index

tag: ulceration status

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Axial

tag: Stage

tag: recurrence

tag: time to 1st recurrence (months)


title: SH-050

tag: os

tag: event


title: SH-046


title: REFERENCE CONTROL1

description: replicate 1

tag: sample type


title: Primary Melanoma_044

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Superficial Spreading

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Died, No Melanoma

value: Diabetes

value: Equal mixture of all samples


title: SH-045


title: SH-047


title: Primary Melanoma_042

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

value: Absent

value: IB

tag: time to 1st recurrence (days)

tag: follow-up time (months)

tag: last status

tag: Cause of death

value: Unknown

tag: material


title: Primary Melanoma_043

description: 1_Exiqon is Cy3

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: time to 1st recurrence (months)

value: Alive, No Melanoma


title: Primary Melanoma_041

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

value: Many

value: Present

value: Extremity

value: IIIC

value: Y

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

value: Died, With Melanoma

value: Melanoma


title: Pool 3 liver samples from mice underfed (50%) in utero, IUGR 5

tag: tissue

value: liver

tag: treatment group

value: adult male mice previously exposed to 50% caloric restriction in utero (IUGR)


title: SH-043

tag: os

tag: event


title: SH-044


title: Primary Melanoma_040

description: 1_Exiqon is Cy3

value: F

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

value: Nodular

value: Axial

tag: time to 1st recurrence (days)

value: DS,DV

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status


title: SH-042


title: Primary Melanoma_039

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: time to 1st recurrence (months)

value: RLN

tag: Cause of death

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_038

description: 1_Exiqon is Cy3

value: M

tag: age

tag: primary tumor thickness (mm)

tag: mitotic index

value: Many

value: Acral Lentiginous

value: IIIB

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence


title: SH-039

tag: os

tag: event


title: Pool 3 liver samples from mice underfed (50%) in utero, IUGR 6

tag: tissue

tag: treatment group


title: Pool 3 control liver samples from first and second generation offspring 1

value: control male mice


title: Pool 3 liver samples from mice underfed (50%) in utero, IUGR 4


title: Primary Melanoma_036

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: Moderate

tag: ulceration status

value: Present

value: Y

tag: time to 1st recurrence (days)

value: DS

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status


title: Primary Melanoma_037

description: 1_Exiqon is Cy3

tag: age

tag: primary tumor thickness (mm)

value: Absent

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: time to 1st recurrence (months)

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material


title: Pool 3 control liver samples from first and second generation offspring 3

tag: tissue

value: liver

tag: treatment group


title: Pool 3 control liver samples from first and second generation offspring 2


title: SH-034

tag: os

tag: event


title: SH-032


title: Primary Melanoma_035

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: F

tag: mitotic index

tag: ulceration status

value: Nodular

value: Axial

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)


title: SH-037

tag: age


title: Primary Melanoma_034

description: 1_Exiqon is Cy3

value: M

tag: primary tumor thickness (mm)

tag: histotype

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

tag: recurrence

tag: time to 1st recurrence (months)

value: RS

value: N

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Equal mixture of all samples


title: SH-038

tag: os

tag: event


title: BL patient material_p13

city: Groningen

first: Melanie

last: Winkle

state: Groningen

address: Hanzeplein 1

department: Pathology & Medical Biology

country: Netherlands

institute: UMC Groningen

description: mRNA and lncRNA expression analysis_BL tumor tissue

hyb_protocol: According to the manufacturers instructions

scan_protocol: Agilent DNA Microarray Scanner, Agilent Feature Extraction software version 10.7.3.1.

data_processing: GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: BL tumor tissue with MYC translocation

label_protocol: Cy3 labelled using 50-100ng total RNA in combination with the LowInput QuickAmp Labelling Kit, Cyanine 3 CTP Dye Pack and RNA Spike-In kit (all Agilent Technologies).

extract_protocol: Standard Trizol RNA isolation (Life Technologies)

tag: diagnosis

value: Burkitt lymphoma (BL)

tag: markers


title: SH-035


title: SH-030


title: SH-031


title: BL patient material_p12


title: SH-029


title: Primary Melanoma_032

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: mitotic index

value: Many

tag: ulceration status

value: IIIA

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: Cause of death

tag: material


title: Primary Melanoma_033

description: 1_Exiqon is Cy3

tag: age

tag: primary tumor thickness (mm)

value: Few

value: Present

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

value: IIIB

tag: recurrence

value: Y

tag: time to 1st recurrence (months)

value: RLN

tag: b-met

tag: time to b-met (days)


title: Primary Melanoma_030

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: Moderate

value: Absent

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma


title: Primary Melanoma_031

description: 1_Exiqon is Cy3

tag: mitotic index

tag: ulceration status

value: Superficial Spreading

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

value: DV

tag: brain as isolated 1st site of recurrence

value: Died, With Melanoma

value: Melanoma


title: BL patient material_p11

tag: diagnosis

tag: markers


title: SH-033

tag: os

tag: event

tag: age


title: BL patient material_p10


title: MUP-EGFP-AAV8, Biological Rep 1

city: Kansas City

first: Udayan

last: Apte

state: KS

address: 3901 Rainbow Blvd, MS1018

department: Pharmacology

institute: University of Kansas Medical Center

description:
Ctrl-1
Gene expression data from 3 month livers.

hyb_protocol: 200ul hybridization solution per GeneChip using the GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Single Scan; Affymetrix GeneChip Scanner 3000 7G with Autoloader; Affymetrix GeneChip Command Console (AGCC) ver. 1.1.

data_processing: The data were analyzed with Partek Genomics Suite version 6.5 (RMA) using RMA default analysis settings: RMA Background Correction; Quantile Normalization; Median Polish probeset summarization.

source_name: wild type liver

label_protocol: Biotinylated In-vitro transcription using the GeneChip 3` IVT Express .

growth_protocol: Three-month-old HNF4alpha mice were treated with Control Virus or Cre-carrying virus. Livers were harvested 1 week after single injection of 400 microL/mouse, ip.

extract_protocol: Trizol / Phase lock gel protocol.

treatment_protocol: Contro Virus (MUP-EGFP-AAV8) or Cre-carrying Virus (MUP-iCre-AAV8).

tag: strain

value: mixed

tag: genotype

value: wild type

tag: tissue

value: liver

value: 3 months


title: SH-049

source_name: PBMC


title: Primary Melanoma_028

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: primary tumor thickness (mm)

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: IIC

tag: recurrence

tag: time to 1st recurrence (months)

value: DS,DV,RS

value: N

tag: b-met

tag: time to b-met (days)

tag: Cause of death

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_029

description: 1_Exiqon is Cy3

value: F

tag: mitotic index

tag: ulceration status

value: Absent

value: IIIA

value: Y

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

value: RLN

tag: brain as isolated 1st site of recurrence

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status


title: SH-027

tag: os

tag: event

tag: age


title: MUP-iCre-AAV8

description:
KO-1
Gene expression data from 3 month livers.

source_name: HNF4alpha-knockout liver

tag: strain

tag: genotype

value: HNF4alpha knockout

tag: tissue


title: SH-011


title: BL patient material_p7

tag: diagnosis

value: Burkitt lymphoma (BL)

tag: markers


title: Primary Melanoma_027

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: primary tumor thickness (mm)

value: Moderate

value: Present

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: time to 1st recurrence (months)

value: RS

tag: b-met

tag: time to b-met (days)

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material


title: MUP-EGFP-AAV8, Biological Rep 2

description:
Ctrl-2
Gene expression data from 3 month livers.

tag: strain

value: mixed

value: wild type

value: liver

tag: age

value: 3 months


title: BL patient material_p9


title: BL patient material_p8


title: SH-028

tag: os

tag: event


title: SH-005


title: SH-010


title: Primary Melanoma_026

description: 1_Exiqon is Cy3

tag: mitotic index

value: Many

tag: ulceration status

value: Nodular

value: Extremity

value: IIC

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

value: LR

tag: brain as isolated 1st site of recurrence

value: N

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma

value: Equal mixture of all samples


title: SH-012


title: SH-007


title: BL patient material_p5

tag: diagnosis

value: Burkitt lymphoma (BL)

tag: markers


title: BL patient material_p3


title: Primary Melanoma_025

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

value: M

tag: primary tumor thickness (mm)

value: Present

tag: histotype

tag: anatomical site of primary tumor

value: Axial

tag: Stage

tag: recurrence

value: Y

tag: time to 1st recurrence (months)

value: DV

tag: b-met

tag: time to b-met (days)


title: Primary Melanoma_024

description: 1_Exiqon is Cy3

tag: age

tag: mitotic index

value: Moderate

tag: ulceration status

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

value: RS

value: Died, With Melanoma

tag: Cause of death

value: Melanoma

tag: material


title: Primary Melanoma_023

description: 1_Exiqon is Cy3

tag: identifier

value: Many

value: Nodular

tag: brain as isolated 1st site of recurrence

tag: follow-up time (days)

tag: follow-up time (months)

tag: last status


title: Primary Melanoma_022

description: 1_Exiqon is Cy3

tag: gender

tag: primary tumor thickness (mm)

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

value: IIC


title: BL patient material_p6

tag: diagnosis

tag: markers


title: BL patient material_p4


title: Primary Melanoma_021

description: 1_Exiqon is Cy3

value: F

tag: age

tag: mitotic index

tag: ulceration status

value: Unknown

value: Extremity

value: IIB

tag: recurrence

tag: time to 1st recurrence (months)

tag: b-met

tag: time to b-met (days)


title: Primary Melanoma_019

description: 1_Exiqon is Cy3

tag: identifier

value: Acral Lentiginous

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

value: RLN

tag: brain as isolated 1st site of recurrence

value: N

tag: follow-up time (days)

tag: Cause of death

tag: material

value: Equal mixture of all samples


title: Primary Melanoma_020

description: 1_Exiqon is Cy3

tag: gender

tag: primary tumor thickness (mm)

value: Few

value: Present

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

value: Y

tag: follow-up time (months)

tag: last status

value: Alive, No Melanoma


title: Primary Melanoma_018

description: 1_Exiqon is Cy3

value: M

tag: age

tag: mitotic index

tag: ulceration status

value: Axial

tag: recurrence

tag: time to 1st recurrence (months)

value: LR


title: SH-003

tag: os

tag: event


title: SH-001


title: SH-002


title: Primary Melanoma_016

description: 1_Exiqon is Cy3

tag: identifier

value: Many

value: Nodular

tag: time to 1st recurrence (days)

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Died, With Melanoma

value: Melanoma


title: Primary Melanoma_017

description: 1_Exiqon is Cy3

tag: gender

tag: primary tumor thickness (mm)

tag: histotype

tag: anatomical site of primary tumor

value: Extremity

tag: Stage

value: DV

tag: Cause of death

tag: material


title: BJAB BCL11A-XL - repeat 2 - mAdbID:26597

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: mAdb experiment ID: 26597

hyb_protocol: NCI cDNA Microarray Hybridization Other: For pre-hybrization, apply 40 ul of pre-hybridization buffer (5X SSC, 0.1% SDS, 1% BSA) to the array and incubate at 42°C for at least 30 minutes and up to an hour. Wash off the pre-hybridization solution by rapidly plunging the slide in distilled water for 2 minutes, then transfer slide to 100% isopropanol for 2 minutes. Allow slide to air dry completely prior to use. (Can spin dry if in a rush.) (NOTE: Do not exceed 1 hour after pre-hybridization/drying before setting up hybridization.) For hybridization, combine Cy3 and Cy5 labeled targets together (~9 ul recovered for each). Add 1 µl COT-1 DNA (8-10 ug/ul) and 1 ul poly A (8-10 ug/ul). Denature target at 100°C for 1 minute, then snap cool on ice. (Final volume should be about 20 ul.) Make fresh 2X Formamide hybridization buffer (50% formamide, 10X SSC, 0.2% SDS) and warm to 42°C just before adding to samples. Add 20 ul of 2X F-hyb buffer to samples. Load 40 ul sample onto microarray. Add 20 ul of 3X SSC to wells in hyb chamber to maintain humidity. Incubate overnight (12-16 hours) at 42°C in water bath or hybridization oven. After hybridization of slides, wash slides for 2 minute in 2X SSC with 0.1% SDS (with occasional plunging), for 2 minute in 1X SSC (with occasional plunging), for 2 minutes in 0.2X SSC (with occasional plunging), for 1 minute in 0.05X SSC, and spin for 3 minutes at 650 rpm to dry. (Refer to "NCI Microarray Manual")

scan_protocol: Creator: GenePix Pro 3.0.6.66 Scanner: GenePix 4000B [82703] PMTVolts: 660;; 670 ScanPower: 100;; 100 LaserPower: 4.37;; 4.74 Temperature: 33.99

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

source_name: BJAB pXY-PURO Negative Control

label_protocol:
Cy3 Sample Labeling Protocol
Other: Labeled using amino allyl conjugation method.

extract_protocol:
TRIzol Extraction
Other: Total RNA was extracted using TRIzol reagent according to manufacturer's instructions.

tag: cell line

value: BJAB

tag: cell type

value: B cell

tag: disease state

value: Human Burkitt's Lymphoma

tag: protocol

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-PURO (negative control vector) using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.

source_name: BJAB pXY-BCL11A-XL

label_protocol:
Cy5 Sample Labeling Protocol
Other: Labeled using amino allyl conjugation method.

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-BCL11A-XL using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.


title: Primary Melanoma_015

description: 1_Exiqon is Cy3

tag: identifier

value: F

tag: age

tag: mitotic index

value: Moderate

tag: ulceration status

value: Present

value: Superficial Spreading

value: IIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

value: RS

value: N

tag: follow-up time (months)

tag: last status

value: Died, No Melanoma

value: Other

value: Equal mixture of all samples


title: CLL patient material_p7

description: mRNA and lncRNA expression analysis_CLL tumor tissue

source_name: lymph node derived CLL tumor tissue

tag: diagnosis

value: chronic lymphocytic leukemia (CLL)

tag: markers

value: CD20+, CD5+, Cyclin D1-, variable ZAP70 expression


title: BL patient material_p1

value: Burkitt lymphoma (BL)


title: SH-004

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was normalized by neqc (Shi et al., Nucleic Acids Res. 2010), and its batch effect (day of experiment) was adjusted by ComBat (Johnson et al., Biostatistics. 2007)

label_protocol: Standard Illumina label protocol

tag: os

tag: event


title: CLL patient material_p9


title: CLL patient material_p5


title: CLL patient material_p6


title: BL patient material_p2


title: Cutaneous lesion 10

city: Marseille

first: Pablo

last: Oliveira

state: PACA

address: 27, bd Jean Moulin

institute: INSERM

description: Transcription profilling

hyb_protocol: 1.5 µg of cRNACy3 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 manufacturer’s instructions. On completion of the fragmentation reaction, 250 mL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized hybridized (65° C for 17 hours) to the SurePrint G3 Human Gene Expression v2 microarray (G4851B; Agilent Technologies), which comprises 50,599 biological features. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 and 1 minute with 37° C GE Wash buffer 2, and then dried immediately by brief centrifugation.

scan_protocol: The slides were scanned immediately after washing on the SureScan Microarray Scanner (Agilent Technologies). Subsequently, the images were converted into expression values using the Feature Extraction software (version 9.5.3; Agilent Technologies).

data_processing: The scanned images were converted into expression values using the Feature Extraction software (version 9.5.3; Agilent Technologies). Data were quantile-normalized with GeneSpring GX software (Agilent Technologies).

source_name: Cutaneous lesion (L. braziliensis) 10

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using Quick Amp Labeling Kit (Agilent Technologies), according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).

extract_protocol: Eight lesion biopsies from patients infected with L. braziliensis (from the border of the ulcers, before treatment) and 8 normal skin samples from uninfected donors were collected and immediately stored in RNAlater solution (Life Technologies). Tissue (20 mg) was placed in microtubes containing 1.4 mm-diameter ceramic beads (CK14; Bertin Technologies) and 350 µL of RTL lysis buffer (Qiagen) supplemented with 3.5 µL of b-mercaptoethanol (Sigma-Aldrich). Complete disruption of the tissue was achieved with a Precellys 24 homogenizer (Bertin Technologies). We added 400 µL of Trizol reagent (Life Technologies) and 150 µL of chloroform (Sigma-Aldrich) and the tubes were then vigorously vortexed and incubated for 5 minutes at room temperature. The aqueous phase was recovered, mixed with 500 µL of 70% ethanol, and the RNA was purified using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. The recovered RNA was quantified by spectrophotometric analysis (NanoVue Plus Spectrophotometer; GE Life Sciences) and its integrity was assessed with a 2100 Bioanalyzer (Agilent Technologies). All 16 samples included in the gene expression profiling experiment were suitable for microarray analysis, in terms of RNA quality [RNA Integrity Number (RIN) ≥ 8.0].

tag: tissue

value: skin


title: Cutaneous lesion 6

description: Transcription profilling

source_name: Cutaneous lesion (L. braziliensis) 6


title: Primary Melanoma_014

description: 1_Exiqon is Cy3

source_name: Cutaneous primary melanoma

tag: gender

value: M

tag: primary tumor thickness (mm)

value: Many

value: Absent

tag: histotype

value: Nodular

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: Y

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Alive, Status Unknown

tag: Cause of death

source_name: Common Reference

tag: material


title: CLL patient material_p4

tag: diagnosis


title: BJAB BCL11A-XL - repeat 1 - mAdbID:25389

description: mAdb experiment ID: 25389

scan_protocol: Creator: GenePix Pro 3.0.6.81 Scanner: GenePix 4000B [82703] PMTVolts: 730;; 650 ScanPower: 100;; 100 LaserPower: 5.78;; 4.56 Temperature: 39.42

tag: cell line

value: BJAB

tag: cell type

value: B cell

tag: disease state

value: Human Burkitt's Lymphoma

tag: protocol

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-PURO (negative control vector) using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.

value: Phoenix-A (phiNX-A) amphotropic 293 cells were used to package retroviruses containing pXY-BCL11A-XL using Fugene-6 reagent (Roche). Retroviral supernatant was used to infect target cells. Following puromycin selection, cells were pelleted by centrifugation and media-aspirated.


title: Primary Melanoma_012

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: mitotic index

tag: ulceration status

value: Present

value: Extremity

value: IIA

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

value: RLN

value: N

tag: follow-up time (months)

tag: last status

value: Died, With Melanoma

value: Melanoma

value: Equal mixture of all samples


title: CLL patient material_p8

value: chronic lymphocytic leukemia (CLL)

tag: markers

value: CD20+, CD5+, Cyclin D1-, variable ZAP70 expression


title: Cutaneous lesion 4

description: Transcription profilling

source_name: Cutaneous lesion (L. braziliensis) 4

tag: tissue

value: skin


title: CLL patient material_p3

tag: diagnosis


title: CLL patient material_p1


title: Primary Melanoma_013

description: 1_Exiqon is Cy3

value: M

tag: primary tumor thickness (mm)

value: Few

value: Absent

tag: histotype

value: Desmoplastic

tag: anatomical site of primary tumor

value: Axial

tag: Stage

value: Y

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Died, No Melanoma

tag: Cause of death

value: Unknown

tag: material


title: Cutaneous lesion 11

description: Transcription profilling

source_name: Cutaneous lesion (L. braziliensis) 11


title: Primary Melanoma_011

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: mitotic index

value: Moderate

tag: ulceration status

value: Nodular

value: Extremity

value: IB

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)


title: Cutaneous lesion 5

description: Transcription profilling

source_name: Cutaneous lesion (L. braziliensis) 5

tag: tissue


title: Congenital Nevi_009

description: 1_Exiqon is Cy3

source_name: Congenital Nevi

tag: primary tumor thickness (mm)

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: follow-up time (months)

tag: last status


title: P493-6_nuclear fraction_cy5_array 2

description: mRNA and lncRNA expression analysis_P493-6 B cells_nuclear fraction

data_processing: Data imported as single color array from two channel file US45102948_253973110006_S01_GE2_107_Sep09_2_1.txt; GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: P493-6_nuclear fraction_cy5_array 2

growth_protocol: RPMI-1640 medium supplemented with 100U/ml penicillin, 0.1mg/ml  streptomycin, 2mM ultraglutamine and 10% Fetal Calf Serum (all Cambrex Biosciences, Walkersville, MD, USA), 37⁰C, 5% CO2

extract_protocol: 1ml of Qiazol (Qiagen, Carlsbad, USA) was added to the ~200µl of cytoplasmic fraction, to the nuclear pellet and to the total cell pellet. RNA was isolated using Phase Lock Gel Heavy (5 Prime Inc., Hilden, Germany) and  the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: The conditional c-myc allele was repressed by addition of 0,1µg/mL of Tetracycline Hydrochloride (UMCG Pharmacy, Groningen, NL) for 72h.

tag: cell line

tag: treatment

value: 0.1ug/mL Tetracycline, 72h


title: Normal skin T1

description: Transcription profilling

source_name: Normal skin  (non-infected) T1


title: CLL patient material_p2

tag: diagnosis

tag: markers


title: P493-6_cytoplasmic fraction_cy5_array 1

description: mRNA and lncRNA expression analysis_P493-6 B cells_cytoplasmic fraction

data_processing: Data imported as single color array from two channel file US45102948_253973110006_S01_GE2_107_Sep09_1_1.txt; GeneSpring GX 12.5 software (Agilent Technologies); quantile normalization without base line transformation.

source_name: P493-6_cytoplasmic fraction_cy5_array 1


title: P493-6_total fraction_cy3_array 2

description: mRNA and lncRNA expression analysis_P493-6 B cells_total fraction

source_name: P493-6_total fraction_cy3_array 2


title: Congenital Nevi_008

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: Cause of death

tag: material

value: Equal mixture of all samples


title: P493-6_c-myc on t=4h_rep1

description: mRNA and lncRNA expression analysis_P493-6 B cells_4h after tetracycline treatment

hyb_protocol: According to Manufacturers instructions

source_name: P496-6 cells, Tetracycline-, t=4h

treatment_protocol: For repression of Myc in P493-6, 0,1µg/mL of Tetracycline Hydrochloride (UMCG Pharmacy, Groningen, NL) was added to the culture medium for 72h. For Myc re-induction the cells were spun down (200rcf, 5min) and re-suspended in fresh, tetracycline-free, complete medium for the indicated time.


title: Congenital Nevi_007

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)


title: Congenital Nevi_006

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: follow-up time (months)

tag: last status


title: Cutaneous lesion 2

description: Transcription profilling

source_name: Cutaneous lesion (L. braziliensis) 2

tag: tissue


title: Congenital Nevi_005

description: 1_Exiqon is Cy3

tag: site of 1st recurrence

tag: brain as isolated 1st site of recurrence

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

tag: Cause of death


title: Normal skin 25

description: Transcription profilling

source_name: Normal skin  (non-infected) 25


title: P493-6_total fraction_cy3_array 1

source_name: P493-6_total fraction_cy3_array 1

tag: cell line

tag: treatment


title: Congenital Nevi_003

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

tag: material


title: Congenital Nevi_004

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: follow-up time (months)

tag: last status


title: Primary Melanoma_010

description: 1_Exiqon is Cy3

value: F

value: Superficial Spreading

tag: site of 1st recurrence

value: RS

tag: brain as isolated 1st site of recurrence

value: N

tag: b-met

tag: time to b-met (days)

tag: follow-up time (days)

value: Alive, No Melanoma

tag: Cause of death


title: Cutaneous lesion 1

description: Transcription profilling

source_name: Cutaneous lesion (L. braziliensis) 1

tag: tissue

value: skin


title: Normal skin L1

description: Transcription profilling

source_name: Normal skin  (non-infected) L1


title: Normal skin 11

description: Transcription profilling

source_name: Normal skin  (non-infected) 11


title: Normal skin F3

description: Transcription profilling

source_name: Normal skin  (non-infected) F3


title: Normal skin O2

description: Transcription profilling

source_name: Normal skin  (non-infected) O2


title: P493-6_c-myc on t=24h_rep2

description: mRNA and lncRNA expression analysis_P493-6 B cells_24h after tetracycline treatment

source_name: P496-6 cells, Tetracycline-, t=24h

tag: cell line


title: Congenital Nevi_002

description: 1_Exiqon is Cy3

tag: primary tumor thickness (mm)

tag: mitotic index

tag: ulceration status

tag: histotype

tag: anatomical site of primary tumor

tag: Stage

tag: recurrence

source_name: Common Reference


title: Congenital Nevi_001

description: 1_Exiqon is Cy3

tag: identifier

tag: gender

tag: age

tag: time to 1st recurrence (days)

tag: time to 1st recurrence (months)

tag: follow-up time (months)

tag: material


title: P493-6_c-myc on t=24h_rep1


title: Normal skin S8

description: Transcription profilling

source_name: Normal skin  (non-infected) S8


title: P493-6_c-myc off_rep2

description: mRNA and lncRNA expression analysis_P493-6 B cells_Tetracycline treated 72h

source_name: P496-6 cells, Tetracycline+, t=72h


title: P493-6_c-myc off_rep1


title: P493-6_c-myc on_rep2

description: mRNA and lncRNA expression analysis_P493-6 B cells_untreated

source_name: P496-6 cells, Tetracycline-


title: P493-6_c-myc on t=4h_rep2


title: HFO_gasphase_rep3

city: Munich

first: Sebastian

last: Oeder

address: Biedersteinerstr. 29

department: Center for Allergy and Environment (ZAUM)

institute: Technische Universität München

description: Gene expression in BEAS-2B cells after 4h on-line exposure to filtered HFO combustion aerosol

hyb_protocol: Hybridisation to Sure Print G3 Human Gene Expression Microarrays (8x60k) was erformed according to the manufacturers protocol  (Agilent, Waldbronn, Germany).

scan_protocol: Scanning was performed according to the manufacturers protocol  (Agilent, Waldbronn, Germany).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

source_name: BEAS-2B, 4h, HFO, gas phase, replicate 3

label_protocol: Total RNA was Cy3-labeled according to the manufacturers protocol  (Agilent, Waldbronn, Germany).

growth_protocol: Human immortalized bronchial epithelial cells BEAS-2B (ATCC® CRL-9609™; http://www.lgcstandards-atcc.org/Products/All/CRL-9609.aspx) were cultured in Bronchial Epithelial Growth Medium (BEGM, Lonza Inc., Walkersville, MD) supplemented with 100 units/ml penicillin/streptomycin and on plates that were pre-coated with 0.01 mg/ml fibronectin, 0.03 mg/ml bovine collagen Type 1 and 0.01 mg/ml BSA.

extract_protocol: Total RNA was extracted using the AllPrep RNA/Protein Kit (Qiagen, Hilden, Germany).

treatment_protocol: In a fully automatic Air-liquid-interface exposure chamber cell cultures grown on porous membrane inserts, which supply the nutrient medium, are exposed directly to diluted aerosol from combustion sources (Fig. S2). The aerosol is humidified by steam injection to 85 % relative humidity and temperature is controlled to 37°C. The flow rate is 100 ml/min.

tag: cell type

tag: fuel type

value: Heavy Fuel Oil

tag: aerosol

value: filtered aerosol


title: DF_gasphase_rep3

description: Gene expression in BEAS-2B cells after 4h on-line exposure to filtered DF combustion aerosol

source_name: BEAS-2B, 4h, DF, gas phase, replicate 3

value: Human immortalized bronchial epithelial cells BEAS-2B

value: Diesel Fuel


title: DF_aerosol_rep3

description: Gene expression in BEAS-2B cells after 4h on-line exposure to complete DF combustion aerosol

source_name: BEAS-2B, 4h, DF, aerosol, replicate 3

value: complete aerosol


title: HFO_aerosol_rep2

description: Gene expression in BEAS-2B cells after 4h on-line exposure to complete HFO combustion aerosol

source_name: BEAS-2B, 4h, HFO, aerosol, replicate 2


title: P493-6_c-myc on_rep1

tag: cell line


title: HFO_gasphase_rep1

source_name: BEAS-2B, 4h, HFO, gas phase, replicate 1


title: DeltaBcVEL1_r5

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

institute: INRAE

description: This sample is of Botrytis cinerea B0510 mutant deltaBcVEL1, cultured onto solid grape juice medium with cellophane overlays. It is the fourth of four deltaBcVEL1 biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization on microarrays were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche)  and the reagents from Invitrogen (Life technologies, France).

scan_protocol: Scanning was performed by PartnerChip (http://www.partnerchip.fr/) using NimbleScan.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the ANAIS website (http://anais.versailles.inra.fr/).

organism: Botrytis cinerea

source_name: Botrytis cinerea B0510_deltaBcVEL1

label_protocol: Synthesis of double-stranded cDNA and Cy3-labeling were done by PartnerChip (http://www.partnerchip.fr/) using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)

growth_protocol: Conidial suspensions of wild type B05.10 and mutant strains deltaBcVEL1 and deltaBcLAE1 were spread onto solid grape juice medium with cellophane overlays, and incubated for 48 h.

extract_protocol: Total RNA was extracted according to the total RNA isolation protocol described by Reid et al. (2006), but with 10M rather than 8M LiCl, and resuspended in RNAse/DNAse-free water. The total RNA was then treated with a DNA-freeTM kit to remove any trace of DNA (Ambion – Applied Biosystems).

tag: genotype

value: Mutant deltaBcVEL1


title: HFO_aerosol_rep3

source_name: BEAS-2B, 4h, HFO, aerosol, replicate 3


title: DeltaBcVEL1_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcVEL1, cultured onto solid grape juice medium with cellophane overlays. It is the first of four deltaBcVEL1 biological replicates used in this experiment, each from separate cultures.


title: WT_r6

description: This sample is of wild-type Botrytis cinerea B0510, cultured onto solid grape juice medium with cellophane overlays. It is the fourth of four wild-type_dark (WT) biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea B0510_wild-type

value: Wild-type


title: DeltaBcVEL1_r3

description: This sample is of Botrytis cinerea B0510 mutant deltaBcVEL1, cultured onto solid grape juice medium with cellophane overlays. It is the third of four deltaBcVEL1 biological replicates used in this experiment, each from separate cultures.


title: DeltaBcLAE1_r3

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays. It is the third of four deltaBcLAE1 biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea B0510_deltaBcLAE1

value: Mutant deltaBcLAE1


title: Normal skin O1

description: Transcription profilling

source_name: Normal skin (non-infected) O1

tag: tissue


title: WT_r3

description: This sample is of wild-type Botrytis cinerea B0510, cultured onto solid grape juice medium with cellophane overlays. It is the third of four wild-type_dark (WT) biological replicates used in this experiment, each from separate cultures.


title: DeltaBcLAE1_r5

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays. It is the fourth of four deltaBcLAE1 biological replicates used in this experiment, each from separate cultures.


title: WT_r1

description: This sample is of wild-type Botrytis cinerea B0510, cultured onto solid grape juice medium with cellophane overlays. It is the first of four wild-type_dark (WT) biological replicates used in this experiment, each from separate cultures.


title: DF_gasphase_rep2

source_name: BEAS-2B, 4h, DF, gas phase, replicate 2


title: HFO_aerosol_rep1

source_name: BEAS-2B, 4h, HFO, aerosol, replicate 1


title: DeltaBcLAE1_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLAE1, cultured onto solid grape juice medium with cellophane overlays. It is the first of four deltaBcLAE1 biological replicates used in this experiment, each from separate cultures.


title: DeltaBcVEL1_r2

description: This sample is of Botrytis cinerea B0510 mutant deltaBcVEL1, cultured onto solid grape juice medium with cellophane overlays. It is the second of four deltaBcVEL1 biological replicates used in this experiment, each from separate cultures.


title: HFO_gasphase_rep2

source_name: BEAS-2B, 4h, HFO, gas phase, replicate 2


title: DF_gasphase_rep1

source_name: BEAS-2B, 4h, DF, gas phase, replicate 1


title: P25 postnatal, biological rep. 1

status: Public on Jan 27 2015

city: Louisville

first: Douglas

last: Darling

state: KY

address: 501 S. Preston St.

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

description:
microRNA expression during parotid acini terminal differentiation
P25 1

data_processing:
raw CT values were normalized to the median value on the plate
Fold/Change work sheet lists LogFoldChanges in expression between time points measured

label: SYBR green

organism: Rattus norvegicus

source_name: Rat embryo day P25 (parotid acini total RNA)

label_protocol: Exiqon’s Universal cDNA Synthesis Kit was used per the manufacturer instructions and combined with exicon's SYBR green master mix

extract_protocol: RNAqueous micro kit from Ambion was used per the manufacturer instructions

tag: strain background

value: Sprague Dawley

tag: genotype/variation

value: albino

value: acinar cells from the parotid


title: P25 postnatal, biological rep. 3

description:
microRNA expression during parotid acini terminal differentiation
P25 6


title: P25 postnatal, biological rep. 2

description:
microRNA expression during parotid acini terminal differentiation
P25 4


title: P15 postnatal, biological rep. 3

description:
microRNA expression during parotid acini terminal differentiation
P15 5

source_name: Rat embryo day P15 (parotid acini total RNA)


title: P15 postnatal, biological rep. 2

description:
microRNA expression during parotid acini terminal differentiation
P15 3


title: P15 postnatal, biological rep. 1

description:
microRNA expression during parotid acini terminal differentiation
P15 6a


title: LSD2-KD2

status: Public on Jan 31 2015

city: Kumamoto

first: Shinjiro

last: Hino

address: 2-2-1 Honjo

institute: Kumamoto University

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: GCS3000 Scanner.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling, and baseline transformed to the median of all 5 samples. GeneSpring GX12 software was used for summarization by MAS5.0 algorithm and baseline transformation (median shift).

source_name: HepG2 cells introduced with siRNA-2 against LSD2

label_protocol: GeneChip 3' IVT Express Kit.

growth_protocol: HepG2 cells were cultured in high glucose (25mM D-glucose) Dulbecco-modified Eagle's Medium (DMEM) (Sigma) supplemented with 10% (v/v) heat-inactivated fetal bovine serum and penicillin/streptomycin.

extract_protocol: After cultured for 3 to 4 days, semiconfluent cells were harvested for RNA extraction using RNeasy kit.

treatment_protocol: For the knockdown experiments, specific siRNAs were introduced to the cells using RNAiMAX reagent (Invitrogen) when the cells were approximately 50% confluent.

value: hepatic cells line

tag: sirna


title: WT_r2

description: This sample is of wild-type Botrytis cinerea B0510, cultured onto solid grape juice medium with cellophane overlays. It is the second of four wild-type_dark (WT) biological replicates used in this experiment, each from separate cultures.


title: DF_aerosol_rep1

description: Gene expression in BEAS-2B cells after 4h on-line exposure to complete DF combustion aerosol

source_name: BEAS-2B, 4h, DF, aerosol, replicate 1


title: P5 postnatal, biological rep. 3

description:
microRNA expression during parotid acini terminal differentiation
P5 12a

source_name: Rat embryo day P5 (parotid acini total RNA)