title: Pituitary_Smolt-Parr_rep1

city: Kearneysville

first: Laura

last: Robertson

state: WV

address: 11649 Leetown Rd.

department: Leetown Science Center

institute: USGS

description: biological replicate 1 of 6

hyb_protocol: Microarray slides from the same print batch were used for each tissue comparison.  The print batch for the microarrays used in the gill, olfactory rosettes, hypothalamus, and pituitary comparisons had an unusable subarray (column 1, row 8) due to printing errors.  Prior to hybridization, microarray slides were washed ten minutes in 0.1% SDS, and then rinsed five minutes in ultrapure water.  Slides were dried by centrifugation and pre-warmed at 50C for 30 minutes.  For each slide, 15 pmol of the Alexa 555 labeled aRNA or cDNA and 15 pmol of the Alexa 647 labeled aRNA or cDNA were combined and mixed with Ambion SlideHyb no. 2 to a volume of 60 µl for hybridization.  The combined samples and hybridization buffer were heated at 80C for ten minutes and pipetted under a Erie Scientific LifterSlip coverslip on top of the microarray slide.  The slides were incubated at 50C, shaking slowly, for 16-18 hours in a Boekel Scientific Shake ‘N’ Bake hybridization oven.  After hybridization, slides were washed on an orbital shaker for ten minutes in heated 2x SSC + 0.5% SDS; coverslips floated off the slides during this wash.  Slides were then washed for 5 minutes in heated 2x SSC + 0.5% SDS, five minutes in 0.5x SSC, and five minutes in 0.05x SSC.  Slides were dried by centrifugation and immediately scanned.

scan_protocol: Slides were scanned at 10 µm resolution in a Perkin Elmer ScanArray Gx scanner.  Laser power and PMT voltage were adjusted using the Line Scan Protocol such that the signal from the Alexa Fluor 555 dye was approximately equal to the signal from the Alexa Fluor 647 dye for each slide and the signal was saturated for approximately 0.3-0.5% of the features on the slide.

data_processing: Spot-finding was done with ScanArray Express Microarray Analysis System software version 4.0 using the adaptive circle method.  Median spot intensities and median background intensities were imported into the TM4 Microarray Software using the Express Converter version 2.1 utility; median background intensities were subtracted from median spot intensities.  Converted intensity files were imported into TM4 Midas version 2.20 with RMA and spots where the background-corrected intensity was less than zero for either channel (dye) were removed.  The log2 intensity ratios for each array were normalized using a local Lowess normalization (by subarray) and standard deviation regularization for the blocks.

organism: Salmo salar

source_name: male smolt pituitary

label_protocol: Pituitary and hypothalamus RNA were amplified and then labeled using the Ambion Amino Allyl MessageAmpII aRNA amplification kit according to manufacturer’s instructions.  100ng or 200ngRNA was reverse transcribed into complementary DNA (cDNA) using an oligo(dT) primer containing a T7 promoter, then copied to create double-stranded DNA.  In a single round of amplification, this double-stranded DNA was used as a template to synthesize amino-allyl modified RNA (aRNA) with a T7 RNA polymerase in an 8 hour in vitro transcription reaction.  5µg of amino-allyl modified, amplified RNA was labeled with Alexa Fluor 555 or 647 dyes.  Liver, gill, and olfactory rosette RNA samples were not amplified prior to labeling.  For these samples, 10ug total RNA was reverse transcribed and labeled using the Invitrogen Superscript Plus Indirect cDNA Labeling System and Invitrogen Alexa Fluor 555 or 647 dyes according to manufacturer’s instructions, with the following minor modifications:  Qiagen Qiaquick PCR Purification spin columns were used to clean the cDNA following first strand synthesis and following labeling with Alexa Fluor dyes.

growth_protocol: Atlantic salmon of Connecticut River stock obtained as parr from the White River National Fish Hatchery in fall 2005 were reared at the Conte Anadromous Fish Research Center in Turners Falls, MA.  Fish were held in 1.5 m diameter fiberglass tanks receiving flow-through (4 L min-1) Connecticut River water, maintained under natural photoperiod conditions.  Fish were reared under ambient river temperatures through the fall and then at 10 (+ 1)C from February through the remainder of the study.  Fish were fed to satiation twice daily with commercial feed.  In late January, fish were divided into two groups and reared in separate tanks; fish smaller than 11 cm (parr) and greater than 12 cm (smolts).  On April 13, 2006, fish were euthanized in 200 mg/L MS-222 neutralized to pH 7.0 and gill, liver, pituitary, hypothalamus and olfactory rosette tissues were collected in individual tubes and frozen at -80C for microarray analyses.

extract_protocol: Total RNA was extracted using Qiagen RNeasy kits according to manufacturer instructions; all samples were treated with RNase-free DNase.

tag: developmental stage

value: smolt

value: pituitary

tag: gender

value: male

source_name: male parr pituitary

value: parr


title: rectum_1wk_1

status: Public on Aug 20 2012

type: RNA

city: Madison

first: Peter

last: Geiger

state: WI

address: 1400 University Ave

department: Surgery

country: USA

institute: UW-Madison

description: stripping protocol:Stripping protocol came from the following reference: Journal of Biotechnology 128 (2007) 1-13

hyb_protocol: Agilent Two-Color Microarray-Based Gene Expression Analysis 17hrs 65 deg celcius Surehyb chamber

scan_protocol: Agilent Technologies Scanner G2505B US22502567 5um 16bit

data_processing: Agilent Feature extraction versions 9.1 and 9..5 for background subtraction - Local background subtraction and normalization Linear LOWESS.

molecule: total RNA

organism: Mus musculus

source_name: SIRC

label_protocol: Total RNA was amplified and labeled according to manufactures instructions. Agilent Two-Color Microarray-Based Gene Expression Analysis Agilent low RNA input linear amplification kit, PLUS

growth_protocol: Ad lib feeding and drinking.  12hours light:12hours dark. ZT0=time lights turn on the room ~6:00 AM.

extract_protocol: Polytron 10 seconds  and processed with an Qiagen Rneasy Mini kit

treatment_protocol: Mice are sacrificed and large intestines removed, rinsed well and mucosa scraped or whole organ was used.  Mucosa or whole organ is homogenized with a polytron.

tag: strain

tag: stripped array

value: Yes

tag: age

value: 10 weeks

tag: number of pooled samples

tag: tissue

value: Small intestine, colon, rectum

tag: genotype

value: wild type

source_name: 1wk rectum 1

value: 1 week

value: rectum


title: Pituitary_Smolt-Parr_rep2

description: biological replicate 2 of 6


title: Pituitary_Smolt-Parr_rep5

description: biological replicate 5 of 6

source_name: female smolt pituitary

value: female

source_name: female parr pituitary


title: Pituitary_Smolt-Parr_rep4

description: biological replicate 4 of 6


title: colon_1wk_3

source_name: 1wk rt. colon 4,5

value: colon


title: Pituitary_Smolt-Parr_rep3

description: biological replicate 3 of 6


title: Pituitary_Smolt-Parr_rep6

description: biological replicate 6 of 6


title: Rosettes_Smolt-Parr_rep8

description: biological replicate 8 of 8

source_name: female parr rosettes

value: olfactory rosettes

source_name: female smolt rosettes


title: Rosettes_Smolt-Parr_rep6

description: biological replicate 6 of 8


title: Rosettes_Smolt-Parr_rep7

description: biological replicate 7 of 8


title: Rosettes_Smolt-Parr_rep2

description: biological replicate 2 of 8

source_name: male smolt rosettes

source_name: male parr rosettes


title: colon_1wk_2

source_name: 1wk rt. colon 2,3


title: rectum_fet_2

source_name: fet. rectum 2

value: Embryonic Day 18.5


title: Hypothalamus_Smolt-Parr_rep7

description: biological replicate 7 of 8

source_name: male smolt hypothalamus

value: hypothalamus

source_name: male parr hypothalamus


title: Rosettes_Smolt-Parr_rep1

description: biological replicate 1 of 8


title: Rosettes_Smolt-Parr_rep5

description: biological replicate 5 of 8


title: colon_fet_3

value: No

source_name: fet. rt. colon 3


title: Hypothalamus_Smolt-Parr_rep5

description: biological replicate 5 of 8

source_name: female parr hypothalamus

source_name: female smolt hypothalamus


title: colon_1wk_1

source_name: 1wk rt. colon 1


title: Hypothalamus_Smolt-Parr_rep8

description: biological replicate 8 of 8


title: Hypothalamus_Smolt-Parr_rep4

description: biological replicate 4 of 8


title: Hypothalamus_Smolt-Parr_rep6

description: biological replicate 6 of 8


title: Hypothalamus_Smolt-Parr_rep2

description: biological replicate 2 of 8


title: Gill_Smolt-Parr_rep8

description: biological replicate 8 of 8

source_name: female parr gill

value: gill

source_name: female smolt gill


title: rectum_fet_1

source_name: fet. rectum 1

source_name: SIRC


title: colon_fet_2

source_name: fet. rt. colon 2


title: Gill_Smolt-Parr_rep7

description: biological replicate 7 of 8

value: smolt


title: Hypothalamus_Smolt-Parr_rep1

description: biological replicate 1 of 8


title: rectum_fet_3

source_name: fet. rectum 3


title: Gill_Smolt-Parr_rep5

description: biological replicate 5 of 8

source_name: male parr gill

source_name: male smolt gill


title: rectum_1wk_2

source_name: 1wk rectum 2,3


title: colon_fet_1

source_name: fet. rt. colon 1


title: Gill_Smolt-Parr_rep6

description: biological replicate 6 of 8


title: Rosettes_Smolt-Parr_rep3

description: biological replicate 3 of 8

source_name: male parr rosettes

source_name: male smolt rosettes


title: Rosettes_Smolt-Parr_rep4

description: biological replicate 4 of 8


title: rectum_8wk_6

source_name: rectum whole organ

value: 8 weeks


title: Hypothalamus_Smolt-Parr_rep3

description: biological replicate 3 of 8


title: Gill_Smolt-Parr_rep3

description: biological replicate 3 of 8

value: male


title: Gill_Smolt-Parr_rep2

description: biological replicate 2 of 8

value: parr


title: Gill_Smolt-Parr_rep1

description: biological replicate 1 of 8


title: E2F1_skin_rep2

city: Madrid

first: Ramon

last: Garcia-Escudero

state: Madrid

address: Avda Complutense 40, Ed 70A

department: Biomedical Innovation

country: Spain

institute: CIEMAT

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

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

data_processing: The data were analyzed with RMA using RMAExpress.

label: biotin

source_name: skin tissue, tamoxifen tretaed

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

extract_protocol: Extraction of total RNA was performed with RNeasy Qiagen Kit according to the manufacturer's instructions.

treatment_protocol: Tamoxifen treatment was topicallyadministered in the shaved backskin of animals (2x2 cm) at 20 mg/per day dissolved in DMSO/acetone for 5 consecutive days.

tag: genetic background

value: FVB/N

tag: genotype/variation


title: Gill_Smolt-Parr_rep4

description: biological replicate 4 of 8


title: Liver_Smolt-Parr_rep3

description: biological replicate 3 of 8

source_name: female smolt liver

value: liver

source_name: female parr liver


title: 350289

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
miR-147a vs miR-Neg
Date:2009/01/26

hyb_protocol: Agilent : 750.0 ng at 62 degree_C during 16 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : none, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

molecule: polyA RNA

organism: Homo sapiens

label_protocol: Ambion

extract_protocol: Qiagen

tag: label

tag: extract

tag: sample

tag: subject

source_name: miR-Neg

value: miR-Neg


title: 350152

description:
hsa-miR-210 vs miR-Neg
Date:2008/07/25

hyb_protocol: Agilent : 2000.0 ng at 62 degree_C during 17 hours

tag: origin

value: Non Small Cell Lung Carcinoma


title: rectum_8wk_3

value: Yes

value: rectum muc

value: wild type

value: 10 weeks

value: Small intestine, colon, rectum


title: Liver_Smolt-Parr_rep6

description: biological replicate 6 of 8

value: female


title: Liver_Smolt-Parr_rep5

description: biological replicate 5 of 8

source_name: male parr liver

source_name: male smolt liver


title: Liver_Smolt-Parr_rep7

description: biological replicate 7 of 8


title: 350288

description:
miR-Neg vs miR-210
Date:2009/01/26


title: 350074

description:
miR-Neg vs hsa-miR-147b
Date:2008/07/25


title: rectum_8wk_5

source_name: rectum muc


title: 350335

description:
A549 NEG1 vs A549 MIR210
Date:2008/07/30

source_name: A549 NEG1

value: A549 NEG1


title: rectum_8wk_4

source_name: SIRC


title: Liver_Smolt-Parr_rep4

description: biological replicate 4 of 8


title: Liver_Smolt-Parr_rep8

description: biological replicate 8 of 8


title: 350605

description:
A549 MIR147b vs A549 NEG3
Date:2008/07/30

source_name: A549 NEG3

value: A549 NEG3


title: 350601

description:
A549 MIR210 vs A549 NEG1
Date:2008/07/30


title: rectum_8wk_1


title: rectum_8wk_2


title: 350602

description:
A549 NEG2 vs A549 MIR147a
Date:2008/07/30

source_name: A549 NEG2

value: A549 NEG2


title: Liver_Smolt-Parr_rep2

description: biological replicate 2 of 8

value: smolt


title: colon_8wk_6

source_name: colon whole organ

value: No

value: 8 weeks

value: colon


title: Liver_Smolt-Parr_rep1

description: biological replicate 1 of 8

value: male

value: parr


title: 350603

description:
A549 MIR147a vs A549 NEG2
Date:2008/07/30


title: 350604

description:
A549 NEG3 vs A549 MIR147b
Date:2008/07/30


title: colon_8wk_4

value: colon muc


title: Old-3

city: Little Rock

first: Jeanne

last: Wei

address: 4301 West Markham Street

department: Geriatrics

institute: University of Arkansas for Medical Sciences

description: Each array slide hybridized with two samples labeld with either Hy3 or Hy5, with array #1 being hybridized with samples YA-1 (Hy3) and Old-1 (Hy5), array #2 with samples YA-2 (Hy3) and Old-2 (Hy5) and array #3 with samples YA-3 (Hy5) and Old-3 (Hy3). In our publication, we reveal the detail of the experiment and statistical analysis that were provided by Exiqon Inc.

hyb_protocol: The mouse RNA samples were labeled with Hy3 and Hy5 fluorescent dyes respectively and hybridized to a miRCURY LNA™ mouse microRNA Array (version 11.0).

scan_protocol: These procedures were performed at Exiqon Inc.

data_processing: Briefly, each pair of young adult and old mouse samples were labeled with Hy3 and Hy5 fluorescent dyes respectively and hybridized to a miRCURY LNA™ mouse microRNA Array (version 11.0), which held 648 mature microRNA probes, as well as perfectly matched and mismatched probes for quality control. After signal amplification, the background was subtracted and normalized using LOWESS (Locally Weighted Scatter plot Smoothing) regression algorithm. This within-slide normalization was performed to minimize differences between the colors in an intensity-dependent manner. The array output was received in Excel spreadsheets containing the normalized microRNA expression profiles in each heart sample; the expression comparison between old versus YA heart samples and “Expression Matrix” containing normalized Hy3/Hy5 ratios (log2 transformed) from all hybridizations. The list was sorted based on the most variant expressed miRNAs comparing the two sample types. The filtering criteria with an average “log-Median-Ratio” > 0.58 represents at least > 1.5-fold change in microRNA expression. Fast and accurate analysis of microarray data were achieved by using specifically adapted versions of  ImaGene® 9 and Nexus Expression™ 2.

source_name: Mouse heart, 24 month-old

label_protocol: The total RNA samples were shipped to Exqin Inc., which provides microRNA array service.

growth_protocol: Both mice and mouse tissues were obtained from National Institute of Aging (NIA)

extract_protocol: All RNA samples were first isolated from the mouse cardiac ventricles using UltraSpec RNA Isolation Reagent as previously described. To clean mouse DNA contamination and enrich the small RNA fraction, the total RNA samples were purified using miRNeasy Mini kit (Qiagen) and RNase-free DNase I according to the manufacture’s instruction manual.

treatment_protocol: No treatment to mice.

value: Female

value: heart

value: 24 month old


title: 348274

description:
miR-Neg vs hsa-miR-210
Date:2008/07/25

hyb_protocol: Affy-169 : 2000.0 ng at 62 degree_C during 17 hours

value: miR-Neg

value: Non Small Cell Lung Carcinoma


title: IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 4)

city: Diepenbeek

first: Jeroen

middle: Felix Jacobus

last: Bogie

address: Agoralaan Building C

department: Biomedical Research Institute

country: Belgium

institute: Hasselt University

hyb_protocol: Following fragmentation, 11 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000 7G.

data_processing: Bioconductor packages running under the R platform were used to process raw data. Data were processed with RMA method.

label: Biotin

organism: Rattus norvegicus

source_name: Peritoneal macrophages

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Resident peritoneal macrophages were obtained by peritoneal lavage using 10 ml of ice-cold PBS  supplemented with 5 mM EDTA. Peritoneal exudate cells were cultured for 2 hours in RPMI 1640 medium. After a 2 hour incubation at 37°C with 5% CO2, non-adherent cells were washed away. Remaining cells were >95% macrophages. Isolated macrophages were seeded in flat-bottem 12-well plates in RPMI 1640 medium supplemented with 50 U/ml streptomycin, 50 U/ml penicillin and 10% FCS at 37°C with 5% CO2.

extract_protocol: Total RNA was prepared using the RNeasy mini kit (Qiagen), according to the manufacturer’s instructions. The RNA concentration and quality was determined with a NanoDrop spectrophotometer.

treatment_protocol: Macrophages were left untreated or treated with 100 µg/ml of isolated myelin. Following 3 days, both control and myelin-treated macrophages were stimulated with 100 ng/ml IFNү and IL-1β for 9 hours.

tag: weight

tag: cell type

value: peritoneal macrophages

tag: treatment

value: myelin + IFNү/IL1-β


title: colon_8wk_5

source_name: colon muc

value: wild type

value: 10 weeks

value: Small intestine, colon, rectum


title: IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 2)


title: IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 5)

value: control, IFNү/IL1-β


title: IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 5)


title: 347922

description:
miR-Neg vs hsa-miR-147a
Date:2008/07/25


title: IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 3)


title: colon_8wk_3

value: Yes


title: IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 3)


title: 350340

description:
hsa-miR-147b vs miR-Neg
Date:2008/07/25


title: IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 1)


title: colon_8wk_2

value: No

value: 8 weeks


title: IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 4)


title: colon_8wk_1


title: IFNү/IL1-β stimulated myelin-phagocytosing macrophages (repl 1)


title: young adult-3 (YA-3)

source_name: Mouse heart, 4 month-old

tag: gender

value: 4 month old


title: Old-2

tag: strain


title: 350151

description:
hsa-miR-147a vs miR-Neg
Date:2008/07/25


title: 350495

description:
miR-210 vs miR-Neg
Date:2009/01/26


title: 350137

description:
miR-Neg vs miR-147b
Date:2009/01/26


title: 350135

description:
miR-Neg vs miR-147a
Date:2009/01/26


title: IFNү/IL1-β stimulated non-phagocytosing macrophages (repl 2)


title: young adult-2 (YA-2)


title: young adult-1 (YA-1)


title: underPatient10-2

status: Public on Aug 19 2012

city: Kanazawa

first: Masao

last: Honda

address: Takara-Machi 13-1

department: Gastroenterology

country: Japan

institute: Kanazawa University

scan_protocol: Quantitative assessment of the signals on the slides was carried out by scanning on a ScanArray 5000 (General Scanning, Watertown, MA, USA) followed by image analysis using GenePix Pro 4.1(Axon Instruments, Union City, CA, USA)

data_processing:
Because the levels of expression of some housekeeping genes were also changed, especially in advanced stages of liver disease, for the normalization of data we averaged intensities of all spots obtained with Cy3 and Cy5 in each of the 16 rectangles and adjusted intensity of each corrected DNA spot as the average intensity ratio Cy5/Cy3 = 1.0. This global normalization of intensity provided smaller variance of CyS/Cy3 ratio and almost equivalent results to normalization using the housekeeping genes.
Reference papers; Honda M, Yamashita T, Ueda T, Takatori H, Nishino R, Kaneko S. Hepatology. 2006 Nov;44(5):1122-38, Honda M, Kaneko S, Kawai H, Shirota Y, Kobayashi K. Gastroenterology. 2001 Mar;120(4):955-66.

source_name: non tumor lesion of liver biopsy, 8weeks after starting peretinoin administration

label_protocol: As a reference for each microarray analysis, aRNA samples prepared from the normal liver tissue from one of the patients were used. Test RNA samples fluorescently labeled with cyanine (Cy) 5 and reference RNA labeled with Cy3 were used for microarray hybridization

extract_protocol: Total RNA was isolated from liver biopsy samples using an RNA extraction kit (Micro RNA Extraction Kit, Stratagene, La Jolla, CA, USA). Aliquots of total RNA (5 ug) were subjected to amplification with antisense RNA (aRNA) using a Message AmpTM aRNA kit (Ambion, Austin, TX, USA) as recommended by the manufacturer

treatment_protocol: Peretinoin, a member of the acyclic retinoid family, is expected to be an effective chemo preventive drug for HCC.The patients had undergone curative surgical resection or radiofrequency ablation (RFA). They received 300 mg/day or 600 mg/day of peretinoin for 8 weeks and were followed up for 88 weeks with 600 mg/day of peretinoin. Hepatic gene expression profiling obtained from non tumor lesion of these patients prior to administering peretinoin and 8 weeks after starting peretinoin treatment

tag: patient

value: non tumor lesion of liver biopsy

tag: agent

value: peretinoin

tag: time

tag: agent dose

tag: clincal outcome

value: nonRecurrence of HCC

source_name: normal liver sample from a patient [reference]

value: normal liver


title: females imprinted vs. dark reared 03_P1D-F vs P1T-F

city: Sagamihara-shi

first: Shinji

last: Yamaguchi

state: Kanagawa

address: Midori-ku, Suwarashi,

department: Pharmaceutical Sciences

institute: Teikyo University

description: Changes of gene expression associated with filial imprinting

hyb_protocol: The in situ hybridization kit-plus (Agilent Technologies Inc., Palo Alto, CA, USA) was used to hybridize cRNA samples to Agilent Technologies Chicken G2519F - 44 k x 4 DNA oligo microarrays. For each experimental group, two pools of cRNA were hybridized, thus in total twenty arrays were used. Cy3-labelled cRNA (0.75 μg) and Cy5-labelled cRNA (0.75 μg) were hybridised onto the microarray according to the manufacturer's protocol.

scan_protocol: Slides were scanned using a an Agilent Microarray Scanner scanner at a photomultiplier tube (PMT) setting of 450 V. Spot identification and quantification were performed using GenePix 6.0 software (Molecular Devices Corporation, Sunnyvale, CA, USA).

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

organism: Gallus gallus

source_name: female newly-hatched chick brains trained for 1hr

label_protocol: An equimolar pool of total RNA extracts from imprinted chick brains was made in each gender. Total RNA extracts from dark-reared chick brains were pooled in an equimolar proportion and used as the reference sample. The Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies Inc., Palo Alto, CA, USA) was used to synthesize cDNA and fluorescent cRNA. Labelled cRNA was made on the same day for two pools. cDNA was synthesized from 500 ng of purified total RNA from each pool according to the manufacturer's protocol. Cyanine 3-cytidine triphosphate (Cy3, Agilent Technologies) was used to label sample groups, while the reference RNA was labeled with cyanine 5-CTP (Cy5, Agilent Technologies).

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

value: female

value: Cobb

tag: tissue

value: brain

value: imprinted

source_name: female newly-hatched chick brains, dark-reared

value: dark reared


title: underPatient11-1

hyb_protocol: Reference papers; Honda M, Yamashita T, Ueda T, Takatori H, Nishino R, Kaneko S. Hepatology. 2006 Nov;44(5):1122-38, Honda M, Kaneko S, Kawai H, Shirota Y, Kobayashi K. Gastroenterology. 2001 Mar;120(4):955-66.


title: 350290

description:
miR-147b vs miR-Neg
Date:2009/01/26

source_name: miR-Neg

value: miR-Neg


title: underPatient11-2


title: underPatient10-1


title: underPatient12-1


title: underPatient8-1


title: underPatient9-1


title: underPatient9-2


title: underPatient7-2

value: Recurrence of HCC


title: males imprinted vs. dark reared 04_P1D-M vs P1T-M

source_name: male newly-hatchedchick brains trained for 1hr

value: male

source_name: male newly-hatched chick brains, dark-reared


title: underPatient8-2


title: underPatient6-2


title: underPatient7-1


title: Sperm vs. Blood (Pm_A)

type: genomic

city: Lexington

first: Jeramiah

middle: J

last: Smith

state: KY

address: 101 T.H. Morgan Building

department: Biology

institute: University of Kentucky

description: array comparative genomic hybridization sperm (Cy3) vs. blood (Cy5) gDNA.

hyb_protocol: The labeled DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, dried down and rehyrdrated, and 9ug of test and reference DNA combined. Labeled DNA was dissolved in 18ul Nimblegen hybridization reagents, and Nimblegen 385K custom lamprey arrays hybridized in Maui hybridization stations for 40hours at 42C, and then washed in Nimblegen wash buffers using manufacturer's protocols (http://www.nimblegen.com/products/lit/cgh_cnv_userguide_v7p0.pdf).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/cgh_cnv_userguide_v7p0.pdf)

data_processing: Arrays were processed using Nimblegens’s Nimblescan program and standard protocol for CGH analysis (http://www.nimblegen.com/products/lit/cgh_cnv_userguide_v7p0.pdf).

molecule: genomic DNA

organism: Petromyzon marinus

source_name: Sperm DNA from individual Pm_A

label_protocol: Soma-germline and soma-soma array comparative genomic hybridizations experiments using DNA that originated from the same individual. Each experiment was performed in replicate with Cy3 and Cy5 dyes reversed between test and reference genomes. 250 ng test DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers and equivalent amount of reference DNA labeled with cy5-nonamers,  per manufacturer's protocol (http://www.nimblegen.com/products/lit/cgh_cnv_userguide_v7p0.pdf).

growth_protocol: Wild Caught

extract_protocol: DNA isolates were prepared from agarose embedded nuclei (Pm_A) or whole tissues by standard phenol/chloroform extraction (J. Sambrook and D. W. Russell, molecular cloning: a laboratory manual 3rd eds, 3 ed. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 2001).

value: Sperm

tag: sex

value: Male

source_name: Blood DNA from individual Pm_A

value: Blood


title: Liver vs. Blood (Pm_4)

description: array comparative genomic hybridization liver (Cy3) vs. blood (Cy5) gDNA.

source_name: Liver DNA from individual Pm_4

value: Liver

source_name: Blood DNA from individual Pm_4


title: Blood vs. Liver (Pm_4)

description: array comparative genomic hybridization blood (Cy3) vs. liver (Cy5) gDNA.


title: underPatient12-2

value: 8 weeks


title: underPatient6-1

value: non tumor lesion of liver biopsy


title: underPatient5-2

value: peretinoin


title: Blood vs. Sperm (Pm_A)

description: array comparative genomic hybridization blood (Cy3) vs. sperm (Cy5) gDNA.


title: Liver vs. Blood (Pm_21)

source_name: Liver DNA from individual Pm_21

source_name: Blood DNA from individual Pm_21


title: Blood vs. Liver (Pm_21)


title: underPatient5-1

value: nonRecurrence of HCC


title: underPatient4-2

value: normal liver


title: underPatient2-2


title: underPatient4-1


title: underPatient3-1


title: Jurkat + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)

city: Berlin

first: Maria

last: Joosten

address: Hindenburgdamm 30

department: Instiute of Pathology

country: Germany

institute: Charité Berlin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133A Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
Expression arrays were analyzed using the statistical programming environment R (version 2.10.1) and Bioconductor (version 2.5). Microarray data were normalized using Robust Multichip Average (RMA) and fold changes between ALCL and T-cell lines were determined. P-values were calculated using moderated t-test with subsequent Benjamini-Hochberg (BH) correction.We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.
We defined a probe set as significantly regulated if (a) at least a twofold change was observed and (b) the BH-corrected p-value was below 0.05.

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

growth_protocol: Cell lines were cultured with 5% CO2 in RPMI 1640 (PAA, Pasching, Austria) supplemented with 10% fetal bovine serum (PAA) at 37°C.

extract_protocol: RNA was isolated according to standard protocols (Qiagen, Hilden, Germany) and used for Affymetrix GeneChip hybridization (HG-U133A).

treatment_protocol: The four ALCL-derived cell lines and four T-cell lines were treated with 5-aza-2‘-deoxycytidine (5-aza-dC) (Sigma-Aldrich, St Louis, MO, USA) at a concentration of 1 µM for 6 days. 5-aza-dC and medium were replaced at day 2 and 5. On day 5 cells were additionally incubated for 24 h with 625 nM Trichostatin A (TSA) (Sigma-Aldrich). Cells were harvested on day 6.

tag: cell line

value: Jurkat

value: T-cell lymphoma/leukemia cell line


title: underPatient2-1


title: Jurkat untreated

value: untreated


title: CCRF-CEM untreated

value: CCRF-CEM


title: Molt-4 + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)


title: Molt-4 untreated


title: prePatient11-1

source_name: non tumor lesion of liver biopsy, pre peretinoin administration

value: control


title: Karpas 299 untreated

source_name: Karpas 299_untreated

value: Karpas 299

value: ALCL cell line


title: Molt-3 untreated


title: SU-DHL-1 untreated


title: SU-DHL-1 + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)


title: underPatient3-2


title: prePatient12-2


title: Molt-3 + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)


title: Karpas 299 + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)

source_name: Karpas 299_AT


title: JB6 untreated


title: underPatient1-2

value: Recurrence of HCC


title: prePatient10-2


title: CCRF-CEM + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)


title: prePatient12-1


title: JB6 + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)


title: prePatient11-2


title: FE-PD untreated

value: FE-PD


title: underPatient1-1


title: prePatient10-1


title: FE-PD + 1 µM 5-aza-dC (6 days) + 625 nM TSA (24 h)


title: prePatient9-2


title: prePatient8-2


title: prePatient7-2


title: prePatient4-2


title: prePatient7-1


title: prePatient6-2


title: prePatient4-1


title: prePatient9-1


title: prePatient8-1


title: prePatient1-1


title: prePatient1-2


title: prePatient2-1


title: prePatient2-2


title: prePatient5-1


title: prePatient3-1


title: prePatient5-2


title: prePatient6-1


title: prePatient3-2


title: wild-type osteoclasts rep2

status: Public on Aug 18 2012

city: Boston

first: Julia

middle: F.

last: Charles

state: MA

address: 75 Francis Street, Smith Building 6th floor

department: Division of Rheumatology, Immunology and Allergy

institute: Brigham and Women's Hospital

description: gene expression data in osteoclast cultures

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: mouse osteoclast culture, day 3 MCSF/RANKL

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

growth_protocol: Osteoclast precursors were purified from whole bone marrow of n=3 mice (replicate 1) or n=4 mice (replicate 2) by flow cytometric sorting for CD11b- CD3e- B220- ckit+cfms+ cell s and plated at 20,000/24well plate in alpha-meM with mCSF and RANKL.

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

treatment_protocol: Osteoclat precursor cultures were cultured in the presence of MCSF and RANKL for 3 days to generate early osteoclasts.

value: bone marrow macrophage derived osteoclasts

tag: genotype

value: NFATc1 fl/fl MxCre-


title: Cgrsc3-aD (CAGL0D03850g∆)_ingested by THP-1 macrophages for 10 hours_biological replicate 2

city: Hyderabad

first: Rupinder

last: Kaur

state: AP

address: Building 7, Gruhakalpa,Nampally

department: Fungal Pathogenesis

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 1.65 µg of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented. The hybridization cocktail was then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a C. glabrata 4x44K Gene Expression Microarray, (Cat#  G2519F, AMADID 032958) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1

data_processing: Data from replicate probes were averaged and mean expression values were subjected to Quantile normalization.

organism: Nakaseomyces glabratus

source_name: Cgrsc3-aD (CAGL0D03850g∆) ingested by THP-1 macrophages for 10 hours

growth_protocol: YPD-medium grown overnight cultures of wild-type and mutant Candida glabrata cells were inoculated either in RPMI-1640 medium supplemented with 10% heat-inactivated fetal bovine serum or infected to PMA-activated human THP-1 macrophages.

extract_protocol: Total RNA was isolated using acid phenol extraction method and frozen at -80OC. Each of the total RNA preparations was individually assessed for RNA quality based on the 28S/18S ratio and RIN measured on an Agilent 2100 Bioanalyzer system using the RNA 6000 Nano LabChip Kit .

treatment_protocol: After 2 and 10 hr incubation either in RPMI-medium or co-culturing with THP-1 macrophages, yeast cells were collected, washed and lysed with glass beads in trizol.

value: Macrophage-internalized Candida glabrata cells

tag: genotype/variation

value: Cgrsc3-aD (CAGL0D03850g∆)


title: Cgrtt109D (CAGL0D05786g∆)_ingested by THP-1 macrophages for 10 hours_biological replicate 2

source_name: Cgrtt109D (CAGL0D05786g∆) ingested by THP-1 macrophages for 10 hours

label_protocol: 1.65 µg of cyanine 3-labeled linearly amplified cRNA was added to a hybridization cocktail and then fragmented.

value: Cgrtt109D (CAGL0D05786g∆)


title: NFATc1-deficient osteoclasts rep1

value: NFATc1 fl/fl MxCre+


title: wild-type grown_in RPMI medium for 2 hours_biological replicate 2

source_name: wild-type grown in RPMI medium for 2 hours

value: RPMI-grown Candida glabrata cells

value: wild-type


title: wild-type_ingested by THP-1 macrophages for 2 hours_biological replicate 2

source_name: wild-type ingested by THP-1 macrophages for 2 hours


title: Cgrtt109D (CAGL0D05786g∆)_grown in RPMI medium for 10 hours_biological replicate 2

source_name: Cgrtt109D (CAGL0D05786g∆) grown in RPMI medium for 10 hours


title: wild-type_ingested by THP-1 macrophages for 10 hours_biological replicate 2

source_name: wild-type ingested by THP-1 macrophages for 10 hours


title: wild-type_grown in RPMI medium for 10 hours_biological replicate 2

source_name: wild-type grown in RPMI medium for 10 hours


title: Cgrsc3-aD (CAGL0D03850g∆)_grown in RPMI medium for 10 hours_biological replicate 2

source_name: Cgrsc3-aD (CAGL0D03850g∆) grown in RPMI medium for 10 hours


title: wild-type_ingested by THP-1 macrophages for 10 hours_biological replicate 1


title: Cgrsc3-aD (CAGL0D03850g∆)_grown in RPMI medium for 10 hours_biological replicate 1


title: rainbowtrout_restrict_1

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

institute: Tokyo University of Marine Science and Technology

hyb_protocol: After hybridization cocktails preparation, the Agilent 4x44 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol.

scan_protocol: The microarray was processed using the Genepix pro v6.0 and scanned with a Axon Genepix4000B scanner. Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). GeneSpring GX v11.5.1 calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

organism: Oncorhynchus mykiss

source_name: restrict

label_protocol: The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol.

growth_protocol: Fish were fed ad libitum once a week (RF, restricted feed group) or fed ad libitum twice per day (control) for 1 month.

extract_protocol: Total RNA was extracted from fish muscles using the RNeasy Mini Kit.

value: muscle


title: rainbowtrout_restrict_4


title: wild-type_grown in RPMI medium for 10 hours_biological replicate 1


title: Cgrtt109D (CAGL0D05786g∆)_grown in RPMI medium for 10 hours_biological replicate 1


title: wild-type osteoclasts rep1


title: NFATc1-deficient osteoclasts rep2


title: rainbowtrout_feed_4

source_name: feed


title: rainbowtrout_restrict_2


title: rainbowtrout_restrict_3


title: Cgrsc3-aD (CAGL0D03850g∆)_ingested by THP-1 macrophages for 10 hours_biological replicate 1


title: wild-type_grown in RPMI medium for 2 hours_biological replicate 1


title: rainbowtrout_feed_1


title: rainbowtrout_feed_3


title: wild-type_ingested by THP-1 macrophages for 2 hours_biological replicate 1


title: Preeclampsia trophoblasts at 48hr, biological replicate 18

status: Public on Aug 17 2012

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized

scan_protocol: GeneChips were scanned using a GeneArray Scanner

data_processing: RMA normalized

source_name: Primary trophoblasts at 48hr

label_protocol: Double-stranded cDNAs were generated from total RNA samples by using SuperScript II reverse transcriptase (Invitrogen) and a T7-oligo primer (QIAGEN). Biotin-labeled cRNA was synthesized by in vitro transcription using an Enzo Bioassay RNA labeling kit

growth_protocol: Purified primary trophoblasts were cultured on Matrigel coated wells in DME H-21

extract_protocol: Total RNA was extracted using Qiagen RNeasy Plus.

value: placenta

tag: phenotype

value: preeclampsia

tag: culture time (hrs)


title: Cgrtt109D (CAGL0D05786g∆)_ingested by THP-1 macrophages for 10 hours_biological replicate 1


title: Preeclampsia trophoblasts at 24hr, biological replicate 15

source_name: Primary trophoblasts at 24hr


title: Preeclampsia trophoblasts at 12hr, biological replicate 8

source_name: Primary trophoblasts at 12hr


title: Preeclampsia trophoblasts at 48hr, biological replicate 19


title: Preeclampsia trophoblasts at 48hr, biological replicate 16


title: Preeclampsia trophoblasts at 24hr, biological replicate 14


title: Preeclampsia trophoblasts at 12hr, biological replicate 10


title: Preeclampsia trophoblasts at 24hr, biological replicate 13


title: Preeclampsia trophoblasts at 24hr, biological replicate 12


title: Preeclampsia trophoblasts at 24hr, biological replicate 11


title: Preeclampsia trophoblasts at 48hr, biological replicate 17


title: Preeclampsia trophoblasts at 0hr, biological replicate 4

source_name: Primary trophoblasts at 0hr


title: Preeclampsia trophoblasts at 0hr, biological replicate 5


title: Preeclampsia trophoblasts at 48hr, biological replicate 20


title: Preeclampsia trophoblasts at 12hr, biological replicate 7


title: Preeclampsia trophoblasts at 0hr, biological replicate 3


title: Preeclampsia trophoblasts at 12hr, biological replicate 9


title: Preeclampsia trophoblasts at 0hr, biological replicate 2


title: Preeclampsia trophoblasts at 12hr, biological replicate 6


title: Preterm labor trophoblasts at 48hr, biological replicate 2

value: preterm labor


title: Preterm labor trophoblasts at 48hr, biological replicate 3


title: Preterm labor trophoblasts at 48hr, biological replicate 4


title: Preterm labor trophoblasts at 24hr, biological replicate 4


title: Preterm labor trophoblasts at 24hr, biological replicate 5


title: Preterm labor trophoblasts at 24hr, biological replicate 1


title: Preterm labor trophoblasts at 12hr, biological replicate 3


title: Preterm labor trophoblasts at 12hr, biological replicate 4


title: Preterm labor trophoblasts at 24hr, biological replicate 2


title: Preterm labor trophoblasts at 12hr, biological replicate 5


title: Preterm labor trophoblasts at 24hr, biological replicate 3


title: hES_VUB01_1

first: YAU-HUA

last: YU

state: Massachusetts

address: 1 Kneeland Street

institute: Tufts Univ. School of Dental Medicine

description: Gene expression data of human embryonic stem cell

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133_Plus_2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (EukGE-WS2v5_450).

scan_protocol: GeneChips were scanned using the Scanner GSC3000 M10 type.

data_processing: justRMA( ) from and quantile normalization; standardized using 'Mfuzz'

source_name: GSM191030 from GSE7879

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

value: ESC


title: Human embryonic stem cell line T3ES, biological rep3

source_name: GSM239826 from GSE9440


title: hES_VUB01_2

source_name: GSM191031 from GSE7879


title: Preterm labor trophoblasts at 48hr, biological replicate 1


title: Preterm labor trophoblasts at 0hr, biological replicate 5


title: Preterm labor trophoblasts at 12hr, biological replicate 2


title: Preeclampsia trophoblasts at 0hr, biological replicate 1


title: Preterm labor trophoblasts at 0hr, biological replicate 1


title: Preterm labor trophoblasts at 0hr, biological replicate 3


title: Human embryonic stem cell line T3ES, biological rep2

source_name: GSM239825 from GSE9440


title: Preterm labor trophoblasts at 0hr, biological replicate 4


title: Human embryonic stem cell line T3ES, biological rep1

source_name: GSM239824 from GSE9440


title: Preterm labor trophoblasts at 12hr, biological replicate 1


title: Glioblastoma, Tumor Stem-Like Cell, sphere-forming cultivation

description: Gene expression data of Tumor Stem-like cells

source_name: U87mg, sphere

value: TSLC


title: Colon Cancer, Tumor Stem-Like Cell, Snail overexpression, biological replicate 2

source_name: SW480, Snail overexpression


title: Glioblastoma, Parental Tumor Cell, biological replicate 4

description: Gene expression data of Parental Tumor Cells

value: PTC


title: Preterm labor trophoblasts at 0hr, biological replicate 2


title: hES_VUB01_3

source_name: GSM191032 from GSE7879


title: Colon Cancer, Parental Tumor Cell, biological replicate 6


title: Colon Cancer, Parental Tumor Cell, biological replicate 7


title: GSM194309: Sheff 4 hesc replicate 3

source_name: GSM194309: Sheff 4 hesc replicate 3  (GSE7896)


title: GSM194307: Sheff 4 hesc replicate 1

source_name: GSM194307: Sheff 4 hesc replicate 1 (GSE7896)


title: Colon Cancer, Tumor Stem-Like Cell, Snail overexpression, biological replicate 1


title: Oral Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 6

source_name: SAS, sphere


title: Oral Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 4


title: GSM194308: Sheff 4 hesc replicate 2

source_name: GSM194308: Sheff 4 hesc replicate 2  (GSE7896)


title: Oral Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 1


title: Oral Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 3


title: Oral Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 2


title: Oral Cancer, Parental Tumor Cell (SAS), biological replicate 3

source_name: SAS


title: Oral Cancer, Parental Tumor Cell (SAS), biological replicate 1


title: hES_SA01_3

source_name: GSM191035 from GSE7879


title: Oral Cancer, Parental Tumor Cell (SAS), biological replicate 2


title: Oral Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 5


title: hES_SA01_1

source_name: GSM191033 from GSE7879


title: Glioblastoma, Tumor Stem-Like Cell, radio-resistance, biological replicate 1

source_name: Primary culture, radio-resistance


title: Glioblastoma, Parental Tumor Cell, biological replicate 1

source_name: Primary culture, sphere


title: Breast Cancer, Tumor Stem-Like Cell, Snail overexpression, stable clone


title: Breast Cancer, Parental Tumor Cell, biological replicate 3

source_name: MCF7 from GSE 10021 of GEO


title: Glioblastoma, Tumor Stem-Like Cell, radio-resistance, biological replicate 3


title: Glioblastoma, Parental Tumor Cell, biological replicate 3


title: Glioblastoma, Tumor Stem-Like Cell, radio-resistance, biological replicate 4


title: Glioblastoma, Parental Tumor Cell, biological replicate 2


title: Glioblastoma, Tumor Stem-Like Cell, radio-resistance, biological replicate 2


title: Breast Cancer, Tumor Stem-Like Cell, Snail overexpression


title: Breast Cancer, Parental Tumor Cell, biological replicate 1


title: human oocyte, biological rep2

value: ESC (oocyte)


title: human oocyte, biological rep3


title: Colon Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 1

source_name: HT29, sphere


title: Colon Cancer, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 2


title: Breast Cancer, Parental Tumor Cell, biological replicate 2

source_name: MCF7 from E-MTAB-37 of ArrayExpress


title: Colon Cancer, Parental Tumor Cell, biological replicate 5

source_name: HT29 from E-GEOD-11440 of ArrayExpress


title: Atypical Teratoid/Rhabdoid Tumor, Parental Tumor Cell, biological replicate 5


title: Atypical Teratoid/Rhabdoid Tumor, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 2


title: Colon Cancer, Parental Tumor Cell, biological replicate 4


title: Colon Cancer, Parental Tumor Cell, biological replicate 1


title: human oocyte, biological rep1


title: Colon Cancer, Parental Tumor Cell, biological replicate 3


title: Colon Cancer, Parental Tumor Cell, biological replicate 2


title: H1 embryonic stem cells - GFP

source_name: GSM225042 from GSE9196


title: Embryonic Stem Cells, Cell line: Trizol with RNeasy_le1

source_name: GSM251563 from GSE9940


title: H1 hESC_20% O2 rep2

source_name: GSM241166 from GSE9510


title: H9 embryonic stem cells

source_name: GSM225045 from GSE9196


title: H1 hESC_4% O2 rep2

source_name: GSM241165 from GSE9510


title: H1 hESC_20% O2 rep1

source_name: GSM241164 from GSE9510


title: H9 hESC_20% O2 rep1

source_name: GSM241168 from GSE9510


title: H9 hESC_4% O2 rep1

source_name: GSM241167 from GSE9510


title: Embryonic Stem Cells, Cell line: H9 hES cells pool#3_e1_le1

source_name: GSM251576 from GSE9940


title: Atypical Teratoid/Rhabdoid Tumor, Parental Tumor Cell, biological replicate 4

source_name: Glioblastoma cancer cell, BT16


title: Oral Cancer, Parental Tumor Cell (FaDu), biological replicate 2

source_name: FaDu


title: Embryonic Stem Cells, Cell line: H9 hES cell RNA pool#2_e1_le1

source_name: GSM251570 from GSE9940


title: Lung Cancer Parental Tumor Cell, biological replicate 3


title: Oral Cancer, Tumor Stem-Like Cells, Twist over-expression

source_name: FaDu, Twist overexpression


title: Lung Cancer Parental Tumor Cell, biological replicate 1


title: Atypical Teratoid/Rhabdoid Tumor, Parental Tumor Cell, biological replicate 1

source_name: AT/RT cancer cell


title: Lung Cancer Tumor Stem-Like Cells, Snail over-expression

source_name: A549, Snail over-expression


title: hES_SA01_2

source_name: GSM191034 from GSE7879


title: Lung Cancer Tumor Stem-Like Cells, radio-resistant

source_name: A549, radio-resistant strain (3rd passage)


title: Atypical Teratoid/Rhabdoid Tumor, Parental Tumor Cell, biological replicate 3

source_name: Glioblastoma cancer cell, BT12


title: Oral Cancer, Parental Tumor Cell (FaDu), biological replicate 1


title: Old-1

source_name: Mouse heart, 24 month-old

value: Female

value: heart

tag: age

value: 24 month old


title: Oral Cancer, Tumor Stem-Like Cells, Bmi1 over-expression

source_name: FaDu, Bmi1 overexpression

tag: cell type


title: Lung Cancer Tumor Stem-Like Cells, CD133(+), biological replicate 3

source_name: A549, FACS gating, CD133(+)


title: Atypical Teratoid/Rhabdoid Tumor, Parental Tumor Cell, biological replicate 2

source_name: Glioblastoma cancer cell, BT


title: Lung Cancer Parental Tumor Cell, biological replicate 2


title: Atypical Teratoid/Rhabdoid Tumor, Tumor Stem-Like Cell, sphere-forming cultivation, biological replicate 1

source_name: AT/RT cancer cell, sphere


title: breast_unsorted_Bre72

city: Sydney

first: Heidi

last: Hilton

state: NSW

address: Darcy Rd, Westmead

department: Westmead Institute for Cancer Research

country: Australia

institute: University of Sydney

description: Unsorted cell

hyb_protocol: 750ng biotin-labeled sample was hybridized to each HT-12 array using Illumina reagents and standard procedure

scan_protocol: The standard Illumina scanning protocol was used

data_processing: The data were background subtracted and normalized using the cubic spline normalization method using Illumina Genome Studio software

source_name: Normal human breast epithelial cells (sample Bre72) grown in 3D culture, unsorted

label_protocol: Total RNA was amplified and labelled using either Ambion Total Prep reagents (Applied Biosystems, Scoresby, Victoria, Australia) or the TargetAmp Nano-g Biotin-aRNA Labeling kit (Epicentre Biotechnologies, Madison, USA).

growth_protocol: Cells were grown in standard recommended media in matrix-embedded culture at 37C and 5% CO2 for 9-10 days before harvest

extract_protocol: RNA from sorted cells was harvested using the Absolutely RNA Microprep Kit (Stratagene) according to the manufacturer's instructions.

treatment_protocol: Mammospheres were dissociated to single cells and sorted into cell subsets enriched for mature, luminal progenitor or bipotent progenitor-enriched characteristics on the bais of CD49f, MUC1, CD10, CD133 and Thy1 expression

tag: cell sample

value: Unsorted cell


title: breast_bipotent_Bre114

description: Bipotent progenitor-enriched subset

source_name: Normal human breast epithelial cells (sample Bre114) grown in 3D culture and sorted for bipotent progenitor-enriched characteristics

value: Bipotent progenitor-enriched subset


title: breast_mature_Bre72

description: Mature-enriched subset

source_name: Normal human breast epithelial cells (sample Bre72) grown in 3D culture and sorted for mature characteristics

value: Mature-enriched subset


title: breast_bipotent_Bre72

description: Bipotent progenitor-enriched subset

source_name: Normal human breast epithelial cells (sample Bre72) grown in 3D culture and sorted for bipotent progenitor-enriched characteristics


title: Lung Cancer Tumor Stem-Like Cells, CD133(+), biological replicate 2


title: breast_myoepithelial_Bre96

description: Myoepithelial subset

source_name: Normal human breast epithelial cells (sample Bre96) grown in 3D culture and sorted for myoepithelial-enriched characteristics

label_protocol: Total RNA was amplified and labelled using either Ambion Total Prep reagents (Applied Biosystems, Scoresby, Victoria, Australia) or the TargetAmp Nano-g Biotin-aRNA Labeling kit (Epicentre Biotechnologies, Madison, USA) according to the manufacturers' instructions.

treatment_protocol: Mammospheres were dissociated to single cells and sorted into luminal-enriched and myoepithelial-enriched subsets on the bais of EpCAM and CD49f expression

value: Myoepithelial subset


title: breast_lumprog_Bre114

description: Luminal progenitor-enriched subset

source_name: Normal human breast epithelial cells (sample Bre114) grown in 3D culture and sorted for luminal progenitor-enriched characteristics

value: Luminal progenitor-enriched subset


title: breast_lumprog_Bre72

description: Luminal progenitor-enriched subset

source_name: Normal human breast epithelial cells (sample Bre72) grown in 3D culture and sorted for luminal progenitor-enriched characteristics


title: Lung Cancer Tumor Stem-Like Cells, CD133(+), biological replicate 1


title: breast_mature_Bre114

description: Mature-enriched subset

source_name: Normal human breast epithelial cells (sample Bre114) grown in 3D culture and sorted for mature characteristics


title: MSC differentiated donor 4

city: Oslo

first: Sarah

last: Herlofsen

address: Sognsvannveien 9

country: Norway

institute: Norwegian Centre for Stem Cell Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was vst transformed and normalised using quantile normalisation in R

source_name: bone marrow-derived mesenchymal stem cells differentiated 7 days

label_protocol: The assay was performed at the Norwegian Microarray Consortium (NMC), Oslo, Norway, using the manufacturers protocols. Briefly, biotin labeled cRNA was synthesized from 415,8ng ng total RNA using the Illumina®TotalPrep RNA Amplification Kit (Ambion Inc., Austin, TX). 1.5?g of this cRNA was used to hybridize onto Illumina Human-6 v3 Expression Beadchips (Illumina Inc., San Diego, CA) containing 48000 transcripts at 58°C overnight, according to the standard protocol. The hybridized chip was stained with streptavidin-Cy3 using FluoroLinkTMCyTM3 (AmershamTM, PA43001, Buckinghampshire, UK) and scanned with an Illumina beadarray reader.

growth_protocol: Human bone marrow derived MSCs were cultured in DMEM-F12 containing 10%FBS and 1% P/S until reaching 70% confluency. Processed by Trypsination until passage 3 or 4.

extract_protocol: Depolymerisation of the alginate discs to gain single cells for RNA isolation was performed by enzymatic digestion using G-Lyase. The RNA isolation from single cells was performed following the TRIzol protocol (Invitrogen, Carlsbad, CA)

treatment_protocol: Cells were set into 3D self-gelling alginated system and differentiated in chondrogenic medium containing 1mM sodium pyruvate, 0.1mM ascorbic acid-2-phosphate, 0.1 μM dexamethasone, 1% ITS, 1.25 mg/ml human serum albumin, 500 ng/ml bone morphogenic protein-2 and 10 ng/ml recombinant human transforming growth factor-ß1

value: bone marrow-derived mesenchymal

tag: chondrogenic differentiation

value: yes

tag: gender

value: F


title: breast_myoepithelial_Bre88

description: Myoepithelial subset

source_name: Normal human breast epithelial cells (sample Bre88) grown in 3D culture and sorted for myoepithelial-enriched characteristics


title: breast_myoepithelial_Bre72

description: Myoepithelial subset

source_name: Normal human breast epithelial cells (sample Bre72) grown in 3D culture and sorted for myoepithelial-enriched characteristics


title: breast_unsorted_Bre114

description: Unsorted cells

source_name: Normal human breast epithelial cells (sample Bre114) grown in 3D culture, unsorted

value: Unsorted cells


title: breast_luminal_Bre96

description: Luminal subset

source_name: Normal human breast epithelial cells (sample Bre96) grown in 3D culture and sorted for luminal-enriched characteristics

value: Luminal subset


title: MSC differentiated donor 1


title: MSC differentiated donor 2


title: MSC differentiated donor 3


title: breast_luminal_Bre72

description: Luminal subset

source_name: Normal human breast epithelial cells (sample Bre72) grown in 3D culture and sorted for luminal-enriched characteristics


title: breast_luminal_Bre88

description: Luminal subset

source_name: Normal human breast epithelial cells (sample Bre88) grown in 3D culture and sorted for luminal-enriched characteristics


title: MSC undifferentiated donor 1

source_name: bone marrow-derived mesenchymal stem cells undifferentiated

value: no


title: MSC undifferentiated donor 4


title: MSC undifferentiated donor 2


title: breast_luminal_Bre114

description: Luminal subset

source_name: Normal human breast epithelial cells (sample Bre114) grown in 3D culture and sorted for luminal-enriched characteristics


title: Normal vs AGC

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

country: South Korea

institute: Genomictree

description:
methylation profiling in AGC sample
serum DNA from gastric cancer patients(Early and Advanced) and normal healthy individuals

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, microarrays were washed 1 minute at room temperature with CGH/ChIP-on-chip Wash Buffer 1 (Agilent) and 1 minute with 37°C CGH/ChIP-on-chip Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.3.2.1 (Agilent).   VALUEs are the ratios of rMedianSignal/gMedianSignal, and Cy5/cy3 ratios not normalized, only background subtracted and spatially detrended using FES 9.3.2.1.

source_name: pooled DNA of 10 normal serum samples

label_protocol: 4 µg of amplified enriched DNA were labeled using Bioprime kit as following manufacturer's instructions

extract_protocol:
DNA extracted using Qiaquick blood DNA mini kit following manufacturer's instructions
Enrichment protocol: 0.5ug DNA was incubated with MBD2bt protein, and then purification using Magnetic bead.

tag: disease state

value: healthy

value: serum

source_name: pooled DNA of 10 AGC serum samples

value: Advanced gastric cancer


title: MSC undifferentiated donor 3


title: Normal vs EGC

description:
methylation profiling in EGC sample
serum DNA from gastric cancer patients(Early and Advanced) and normal healthy individuals

source_name: pooled DNA of 10 EGC serum samples

value: Early gastric cancer


title: HCC_54

status: Public on Aug 16 2012

city: Shanghai

first: Wei

last: Li

address: 136 Yi Xue Yuan Road

country: China

institute: Liver Cancer Institute, Zhongshan Hospital, Fudan University;

description: The HCC patients had not received adjuvant chemotherapy.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3/Cy5 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: Microarrays were scanned at 5 µm resolution using a GenePix 4000B microarray scanner piloted by GenePix Pro 6.0 software (Axon Instruments, Union City, CA). Scanned images were then imported into NimbleScan software (version 2.5) for grid alignment and raw intensity extraction.

data_processing: The raw microarray data sets were normalized in Agilent GeneSpring GX software (version 11.5) (LOWESS normalization). After normalization, the probes with signal greater than 200 in more than 18 channels among all 118 Cy5/Cy3 channels were chosen for further analysis. Multiple probes representing the same lncRNA or mRNA were merged by getting a median value. The lncRNAs or mRNAs which had absolute value of log2Ratio>=1.59 in at least 4 arrays across the sample sets were selected for further analyses (8,255 lncRNAs and 12,139 mRNAs).

source_name: Frozen hepatocellular carcinoma

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using SuperScript ds-cDNA synthesis kit (Life Technologies, Inc., Carlsbad, CA, USA) in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3/Cy5 labeling of cDNA, the NimbleGen Dual-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

extract_protocol: Total RNA was extracted from the frozen tissues using Trizol (Life Technologies, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol.

value: Male

value: Hepatocellular carcinoma

tag: cancer stage

tag: overall survival (month)

tag: disease free survival (month)

source_name: Frozen normal livers

tag: sample type

value: Reference RNA pool from 20 normal livers


title: HCC_45

value: Female


title: HCC_59


title: HCC_51


title: HCC_49


title: HCC_52


title: HCC_50


title: HCC_53


title: HCC_58


title: HCC_48


title: HCC_56


title: HCC_57


title: HCC_46


title: HCC_44


title: HCC_42


title: HCC_41


title: HCC_47


title: HCC_36


title: HCC_39


title: HCC_37


title: HCC_38


title: HCC_40


title: HCC_43


title: HCC_55


title: HCC_35


title: HCC_34


title: HCC_31


title: HCC_32


title: HCC_24


title: HCC_27


title: HCC_33


title: HCC_16


title: HCC_29


title: HCC_26


title: HCC_23


title: HCC_30


title: HCC_22


title: HCC_28


title: HCC_17


title: HCC_18


title: HCC_20


title: HCC_15


title: HCC_14


title: HCC_21


title: HCC_19


title: HCC_13


title: HCC_25


title: HCC_10


title: HCC_12


title: HCC_8


title: HCC_11


title: HCC_6


title: HCC_9


title: HCC_5


title: HCC_3


title: HCC_7


title: Control 30 min rep 2

city: Golden

first: Shihui

last: YANG

state: CO

address: 1617 Cole Blvd

department: National Bioenergy Center

institute: National Renewable Energy Lab

description: A3_F3 30 min

hyb_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

data_processing: Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).

organism: Acetivibrio thermocellus ATCC 27405

source_name: Control

growth_protocol: Batch fermentations were conducted in approximately 5 L of MTC medium in 7.5-L BioFlo110 bioreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH, and temperature  probes and controls as described previously (Yang et al., 2008).

extract_protocol: RNA was isolated essentially described previously [26]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).

tag: time

value: 30 min

tag: treatment

value: Control


title: HCC_4


title: ETOH 30 min rep 2

description: A4_F4_0.5% 30 min

scan_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.

value: ETOH


title: HCC_1


title: Control 30 min rep 3

description: B6_F1_30 min

label_protocol: The labeling, hybridization, and scanning following NimbleGen company's protocols.


title: ETOH 30 min rep 3


title: Control 30 min rep 4


title: Control 240 min rep 2

value: 240 min


title: ETOH 60 min rep 2

description: F4_Cthe_0.5%_1 h_6

value: 60 min


title: Control 60 min rep 2

description: F3_cthe_1 h


title: ETOH 60 min rep 1

description: F2_Cthe_0.5%_1 h_5


title: Control 30 min rep 1

description: A1_F1-30 min


title: HCC_2


title: Control 60 min rep 1

description: F1_cthe_1 h_5


title: ETOH 30 min rep 1

description: A2_F2-0.5% 30 min


title: Control 120 min rep 2

description: B1_F3 - 2 hr

value: 120 min


title: ETOH 240 min rep 2

description: B4_F2_0.5% 4hr


title: ETOH 120 min rep 2

description: A8_F4_0.5% 2hr


title: Control 120 min rep 3

description: B3_F3 - 2 hr


title: ETOH 240 min rep 3

description: B5_F4_0.5% 4hr


title: ETOH 240 min rep 1

description: A12_F4_0.5% 4hr


title: ETOH 120 min rep 3

description: B9_F4_0.5%_2 hr


title: Control 240 min rep 1

description: A10_F1- 4hr


title: ETOH 120 min rep 1

description: A6_F2-0.5% 2hr


title: Control 120 min rep 1


title: Control 12 min rep 1

description: F1_cthe_12 min_6

value: 12 min


title: Control 2 min rep 2

value: 2 min


title: Control 12 min rep 2

description: F3_cthe_12 min


title: ETOH 12 min rep 2

description: F4_Cthe_0.5%_12 min_6


title: ETOH 2 min rep 1


title: E99 ΔperA 0.05 rep2

city: Norman

first: Scott

middle: M

last: Maddox

state: OK

address: 101 David L. Boren Blvd.

department: Botany and Microbiology

institute: University of Oklahoma

hyb_protocol: Hybridization was at 60 degrees C for 16 h according to Affymetrix protocol ProkGE_WS2v2_450.

scan_protocol: Affymetrix GCOS scanner software and GeneChip Scanner 3000

data_processing: RMA with quartile normalization according to method of Irizarry et al, 2003.  The raw .cel files were processed in RMA using Bioconductor R package: Affy Version: 1.8.1 Date: 2005-09-03, with option Filter.genes corresponding to a subset of probesets from the arrays reflected in the sample files (Enterococcus faecalis).  Replicates were averaged for ratio calculations.

organism: Enterococcus faecalis

source_name: E. faecalis E99 ΔperA mid-log

label_protocol: RNA converted to cDNA by random-hexamer primed first strand synthesis with Superscript II and biotinaylated with Roche Enzo kit according to Affymetrix protocol.

growth_protocol: Cultures were grown in Todd-Hewitt Broth supplemented with 1% glucose at 37C until mid-log, late-log or stationary phase.  RNA extracted from WT cultures was used as a control in comparisions with the ΔperA strain.

extract_protocol: Qiagen RNeasy extraction kit with optional DNase step

treatment_protocol: Cell were allowed to reach mid-log (OD600 0.05), late-log (OD600 0.5) or stationary phase (OD600 1.0)

tag: strain

value: perA mutant

tag: growth phase


title: E99 ΔperA 0.5 rep1

source_name: E. faecalis E99 ΔperA late-log

tag: genotype/variation

value: late log (OD600 0.5)


title: ETOH 12 min rep 1

description: F2_Cthe_0.5%_12 min_6


title: E99 WT 0.5 rep1

source_name: E. faecalis E99 late-log

value: wild-type


title: E99 WT ST rep1

source_name: E. faecalis E99 ST

value: stationary phase (OD600 1.0)


title: E99 ΔperA 0.5 rep2


title: ETOH 2 min rep 2


title: E99 WT ST rep2


title: E99 ΔperA 0.05 rep1


title: E99 WT 0.5 rep2


title: Control 2 min rep 1


title: E99 ΔperA ST rep2

source_name: E. faecalis E99 ΔperA ST


title: E99 ΔperA ST rep1


title: E99 WT 0.05 rep1

source_name: E. faecalis E99 mid-log


title: E99 WT 0.05 rep2


title: Q319 4d

city: Harbin

first: Tao

last: Yu

address: mucai street

institute: Northeast Agricultural University

description: Gene expression data from leaves of Huangzao4,9d post inoculation of Sporisorium reilianum

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

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

organism: Zea mays

source_name: leaves of Q319,4d post inoculation

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

growth_protocol: Teliospores of Sporisorium reilianum were rinsed twice for 10 min in sterile distilled water, treated for 12 min in 2% (w/v) chloramine T(Sigma) and thereafter washed in sterile distilled water.Seeds were sterilized with 2% (w/v) chloramine T for 15 min, washed with sterile distilled water, and then germinated on sterile potato dextrose agar in 3 days at 27℃. Seedlings free of microbial contamination were transferred into Erlenmeyer flasks (27℃,12 h, day/night cycle).

treatment_protocol: Each 5-day-old seedling was inoculated with 1 mL sterile teliospores. After inoculation, the seedings were incubated at 27℃ (12h, day/night cycle). Leaves at 0, 1, 2, 4 and 7 d post-inoculation were collected from each seeding.

tag: infection

value: Sporisorium reilianum f. sp. Zeae (Kühn)

tag: tissue

value: leaves


title: Q319 2d

description: Gene expression data from leaves of Huangzao4,8d post inoculation of Sporisorium reilianum

source_name: leaves of Q319,2d post inoculation


title: Q319 1d

description: Gene expression data from leaves of Huangzao4,7d post inoculation of Sporisorium reilianum

source_name: leaves of Q319,1d post inoculation


title: Huangzao4 1d

description: Gene expression data from leaves of Huangzao4,1d post inoculation of Sporisorium reilianum

source_name: leaves of Huangzao4,1d post inoculation


title: L43 7d

description: Gene expression data from leaves of L43,7d post inoculation of Sporisorium reilianum

source_name: leaves of L43,7d post inoculation


title: Huangzao4 2d

description: Gene expression data from leaves of Huangzao4,2d post inoculation of Sporisorium reilianum

source_name: leaves of Huangzao4,2d post inoculation


title: Q319 7d

description: Gene expression data from leaves of Huangzao4,10d post inoculation of Sporisorium reilianum

source_name: leaves of Q319,7d post inoculation


title: L43 1d

description: Gene expression data from leaves of L43,1d post inoculation of Sporisorium reilianum

source_name: leaves of L43,1d post inoculation


title: L43 0d

description: Gene expression data from leaves of L43,0d post inoculation of Sporisorium reilianum

source_name: leaves of L43,0d post inoculation


title: L43 4d

description: Gene expression data from leaves of L43,4d post inoculation of Sporisorium reilianum

source_name: leaves of L43,4d post inoculation


title: L282 7d

description: Gene expression data from leaves of L282,7d post inoculation of Sporisorium reilianum

source_name: leaves of L282,7d post inoculation


title: Q319 0d

description: Gene expression data from leaves of Huangzao4,6d post inoculation of Sporisorium reilianum

source_name: leaves of Q319,0d post inoculation


title: Huangzao4 7d

description: Gene expression data from leaves of Huangzao4,5d post inoculation of Sporisorium reilianum

source_name: leaves of Huangzao4,7d post inoculation


title: Huangzao4 4d

description: Gene expression data from leaves of Huangzao4,4d post inoculation of Sporisorium reilianum

source_name: leaves of Huangzao4,4d post inoculation


title: Huangzao4 0d

description: Gene expression data from leaves of Huangzao4,0d post inoculation of Sporisorium reilianum

source_name: leaves of Huangzao4,0d post inoculation


title: L43 2d

description: Gene expression data from leaves of L43,2d post inoculation of Sporisorium reilianum

source_name: leaves of L43,2d post inoculation


title: L282 1d

description: Gene expression data from leaves of L282,1d post inoculation of Sporisorium reilianum

source_name: leaves of L282,1d post inoculation


title: L282 0d

description: Gene expression data from leaves of L282,0d post inoculation of Sporisorium reilianum

source_name: leaves of L282,0d post inoculation


title: THOMAS Rapamycin - 12 hours - mAdbID:118712

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: 118712

hyb_protocol: Agilent Hybridization Protocol Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: THOMAS DMSO - 12 hours

label_protocol:
Cy3 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy3.

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted using Trizol reagent (Invitrogen, Carlsbad, CA).

treatment_protocol:
Treatment type: compound
Agent: Dimethyl sulfoxide (DMSO)
Treatment time: 12 hours
In-vitro treatment: Cells were treated with DMSO for 12 hours.

value: Blood

tag: cell line

value: THOMAS

value: B cells

value: Burkitt's Lymphoma

source_name: THOMAS Rapamycin - 12 hours

label_protocol:
Cy5 Labeling Protocol
Other: A 1 ug of total RNA was labeled with Cy5.

treatment_protocol:
Treatment type: compound
Agent: Rapamycin
Treatment dose: 100 pM
Treatment time: 12 hours
In-vitro treatment: Cells were treated with 100 pM of Rapamycin (EMD Chemicals) for 12 hours.


title: L282 2d

description: Gene expression data from leaves of L282,2d post inoculation of Sporisorium reilianum

source_name: leaves of L282,2d post inoculation


title: L282 4d

description: Gene expression data from leaves of L282,4d post inoculation of Sporisorium reilianum

source_name: leaves of L282,4d post inoculation


title: THOMAS Rapamycin - 24 hours - mAdbID:118713

description: mAdb experiment ID: 118713

source_name: THOMAS DMSO - 24 hours

treatment_protocol:
Treatment type: compound
Agent: Dimethyl sulfoxide (DMSO)
Treatment time: 24 hours
In-vitro treatment: Cells were treated with DMSO for 24 hours.

tag: cell type

source_name: THOMAS Rapamycin - 24 hours

treatment_protocol:
Treatment type: compound
Agent: Rapamycin
Treatment dose: 100 pM
Treatment time: 24 hours
In-vitro treatment: Cells were treated with 100 pM of Rapamycin (EMD Chemicals) for 24 hours.


title: Daudi Rapamycin - 24 hours - mAdbID:118709

description: mAdb experiment ID: 118709

source_name: Daudi DMSO - 24 hours

value: Daudi

source_name: Daudi Rapamycin - 24 hours


title: THOMAS Rapamycin - 6 hours - mAdbID:118711

description: mAdb experiment ID: 118711

source_name: THOMAS DMSO - 6 hours

treatment_protocol:
Treatment type: compound
Agent: Dimethyl sulfoxide (DMSO)
Treatment time: 6 hours
In-vitro treatment: Cells were treated with DMSO for 6 hours.

source_name: THOMAS Rapamycin - 6 hours

treatment_protocol:
Treatment type: compound
Agent: Rapamycin
Treatment dose: 100 pM
Treatment time: 3 hours
In-vitro treatment: Cells were treated with 100 pM of Rapamycin (EMD Chemicals) for 3 hours.


title: Daudi Rapamycin - 6 hours - mAdbID:118707

description: mAdb experiment ID: 118707

source_name: Daudi DMSO - 6 hours

source_name: Daudi Rapamycin - 6 hours

treatment_protocol:
Treatment type: compound
Agent: Rapamycin
Treatment dose: 100 pM
Treatment time: 6 hours
In-vitro treatment: Cells were treated with 100 pM of Rapamycin (EMD Chemicals) for 6 hours.


title: Daudi Rapamycin - 12 hours - mAdbID:118708

description: mAdb experiment ID: 118708

source_name: Daudi DMSO - 12 hours

source_name: Daudi Rapamycin - 12 hours


title: THOMAS Rapamycin - 3 hours - mAdbID:118710

description: mAdb experiment ID: 118710

source_name: THOMAS DMSO - 3 hours

treatment_protocol:
Treatment type: compound
Agent: Dimethyl sulfoxide (DMSO)
Treatment time: 3 hours
In-vitro treatment: Cells were treated with DMSO for 3 hours.

source_name: THOMAS Rapamycin - 3 hours


title: Daudi Rapamycin - 3 hours - mAdbID:118706

description: mAdb experiment ID: 118706

source_name: Daudi DMSO - 3 hours

source_name: Daudi Rapamycin - 3 hours


title: Defauw ID3 - 48 hours - mAdbID:117727

description: mAdb experiment ID: 117727

source_name: Defauw ID3 - 48 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing ID3. ID3 expression was induced with doxycycline for 48 hours.

value: Defauw

source_name: Defauw Empty Vector - 48 hours

treatment_protocol:
Treatment type: transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with empty retroviral vectors. Doxycycline induction for 48 hours.


title: RUNX1_shRNA2_Jurkat, biological replicate1

city: Cambridge

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Gene expression data from Jurkat cells transduced with RUNX1 shRNA2 for 72 hrs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix CeneChIP Scanner 3000

data_processing: Individual Arrays were normalized using Robust Multichip Averaging (RMA) within the Affytmetrix package from Bioconductor. Probeset definitions for RefSeq genes were derived from CDF version 13.0.0 downloaded from (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp) based on improved definitions (Sandberg and Larsson, 2007).

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The Jurkat T-ALL cell line was grown in RPMI-1640 medium supplemented with 10% FBS, L-glutamine and penicillin/streptomycin at 37C in a CO2 incubator.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) followed by a column purification using RNeasy Mini Kit (QIAGEN, Valencia, CA) according to the manufacturers instructions.

treatment_protocol: The Jurkat cells were infected with shRNA lentivirus in the presence of polybrene by centrifugation at 2,500 rpm for 1.5 h followed by a incubation for overnight in a CO2 incubator.  Total RNA was harvested after 3 days of infection.

value: Jurkat E6-1


title: RUNX1_shRNA1_Jurkat, biological replicate1

description: Gene expression data from Jurkat cells transduced with RUNX1 shRNA1 for 72 hrs


title: RUNX1_shRNA2_Jurkat, biological replicate2

source_name: Jurkat cells transduced with RUNX1 shRNA2 for 72 hrs


title: Luciferase_shRNA_Jurkat, biological replicate4

description: Gene expression data from Jurkat cells transduced with Luciferase shRNA for 72 hrs


title: RUNX1_shRNA1_Jurkat, biological replicate2

source_name: Jurkat cells transduced with RUNX1 shRNA1 for 72 hrs


title: Defauw shTCF3 - 48 hours - mAdbID:117725

description: mAdb experiment ID: 117725

source_name: Defauw shTCF3 - 48 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 48 hours.

source_name: Defauw shControl - 48 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 48 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 48 hours.


title: Defauw ID3 - 24 hours - mAdbID:117726

description: mAdb experiment ID: 117726

source_name: Defauw ID3 - 24 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing ID3. ID3 expression was induced with doxycycline for 24 hours.

source_name: Defauw Empty Vector - 24 hours

treatment_protocol:
Treatment type: transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with empty retroviral vectors. Doxycycline induction for 24 hours.


title: Defauw shTCF3 - 24 hours - mAdbID:117724

description: mAdb experiment ID: 117724

source_name: Defauw shTCF3 - 24 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 24 hours.

source_name: Defauw shControl - 24 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 24 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 24 hours.


title: AS2neo-alpha-catilin/AS2neo

city: Taipei

first: Tse-Ming

last: Hong

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

hyb_protocol: 0.3 μ g of Cy-labled aRNA was fragmented to an average size of about 60 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled aRNA is then pooled and hybridized to a Human Whole Genome OneArray TM Version 5.1 (PhalanxBiotech Group, Taiwan),  at 50°C for 16 h.

scan_protocol: Scanned on an Agilent microarray scanner (Agilent Technologies, USA)

data_processing: Scanned images are analyzed by Genepix software (Molecular Devices USA). The GPR files were loaded into Rosetta Resolver® System (Rosetta Biosoftware) to process data analysis. Raw intensity was normalized by median scaling. The mean of the technical repeats was shown as 'Normalized Intensity' in alpha-catulin_HOA5.1 data file. The log2(Ratio) are calculated by pair-wise combination and error weighted average.

label_protocol: 0.2 μ g of total RNA was labeled with Cy3 or Cy5 using aminoallyl RNA labeling and then hybridized in duplicate on full human genome arrays (Whole Genome Human OneArray HOA 5.1; Phalanx Biotech)

growth_protocol: A549/AS2neo (control) and A549/AS2neo-alpha-catulin stable cells were cultured in DMEM medium containing 10% FBS,  l-glutamine, and 800ug/ml G418

value: A549 cells


title: GFP_shRNA1_Jurkat, biological replicate4

description: Gene expression data from Jurkat cells transduced with GFP shRNA for 72 hrs


title: Luciferase_shRNA_Jurkat, biological replicate3

source_name: Jurkat cells transduced with Luciferase shRNA for 72 hrs


title: GFP_shRNA1_Jurkat, biological replicate3

source_name: Jurkat cells transduced with GFP shRNA for 72 hrs


title: MYB_shRNA2_Jurkat, biological replicate1

description: Gene expression data from Jurkat cells transduced with MYB shRNA2 for 72 hrs

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


title: BL41 ID3 - 24 hours - mAdbID:117722

description: mAdb experiment ID: 117722

source_name: BL41 ID3 - 24 hours

value: transduced with retroviral vectors expressing ID3

source_name: BL41 Empty Vector - 24 hours

value: transduced with empty retroviral vectors


title: BL41 ID3 - 48 hours - mAdbID:117723

description: mAdb experiment ID: 117723

source_name: BL41 ID3 - 48 hours

source_name: BL41 Empty Vector - 48 hours


title: MYB_shRNA1_Jurkat, biological replicate1

description: Gene expression data from Jurkat cells transduced with MYB shRNA1 for 72 hrs


title: GATA3_shRNA2_Jurkat, biological replicate2

description: Gene expression data from Jurkat cells transduced with GATA3 shRNA2 for 72 hrs


title: BL41 shTCF3 - 48 hours - mAdbID:117721

description: mAdb experiment ID: 117721

source_name: BL41 shTCF3 - 48 hours

value: transduced with retroviral vectors expressing shRNA

source_name: BL41 shControl - 48 hours

value: transduced with retroviral vectors expressing shControl


title: MYB_shRNA2_Jurkat, biological replicate2

source_name: Jurkat cells transduced with MYB shRNA2 for 72 hrs


title: GATA3_shRNA2_Jurkat, biological replicate1

source_name: Jurkat cells transduced with GATA3 shRNA2 for 72 hrs


title: MYB_shRNA1_Jurkat, biological replicate2

source_name: Jurkat cells transduced with MYB shRNA1 for 72 hrs


title: Subject6_HippocampusvsPancreas(dyeswap)

city: Palo Alto

first: Maeve

last: O'Huallachain

address: 1501 S. California Ave. Rm 2204

institute: Stanford University

hyb_protocol: Hybridization and washing was done using NimbleGen hyb and wash buffers per the NImbleGen protocol

scan_protocol: Arrays were scanned using the Roche MS200 scanner per manufacturer's protocol

data_processing: Arrays were processed using NimbleGen's standard protocol for NimbleScan 2.6 aCGH data extraction

source_name: Subject6 Hippocampus

label_protocol: Genomic DNA was labeled using the NimbleGen labeling protocol

extract_protocol:
Tissues were dissected postmortem and flash frozen
DNA was extracted from frozen tissues using the QIAGEN DNeasy Blood & Tissue Kit

value: Hippocampus

source_name: Subject6 Pancreas

value: Pancreas


title: BL41 shTCF3 - 24 hours - mAdbID:117720

description: mAdb experiment ID: 117720

source_name: BL41 shTCF3 - 24 hours

source_name: BL41 shControl - 24 hours


title: Subject6_LMvsPancreas(dyeswap)

source_name: Subject6 LM

value: Leptomeningeal tissue


title: GATA3_shRNA1_Jurkat, biological replicate2

description: Gene expression data from Jurkat cells transduced with GATA3 shRNA1 for 72 hrs


title: Subject6_LivervsPancreas(dyeswap)

source_name: Subject6 Liver

value: Liver


title: Subject6_LivervsPancreas(regular)


title: Subject6_HippocampusvsPancreas(regular)


title: Subject6_MFGvsPancreas(dyeswap)

source_name: Subject6 MFG

value: Middle frontal gyrus


title: Subject6_KidneyvsPancreas(dyeswap)

source_name: Subject6 Kidney

value: Kidney


title: Subject6_LMvsPancreas(regular)


title: GATA3_shRNA1_Jurkat, biological replicate1

source_name: Jurkat cells transduced with GATA3 shRNA1 for 72 hrs


title: E2A_shRNA2_Jurkat, biological replicate1

description: Gene expression data from Jurkat cells transduced with TCF3/E2A shRNA2 for 72 hrs


title: Daudi ID3 - 24 hours - mAdbID:117718

description: mAdb experiment ID: 117718

source_name: Daudi ID3 - 24 hours

value: Blood

source_name: Daudi Empty Vector - 24 hours


title: E2A_shRNA2_Jurkat, biological replicate2

source_name: Jurkat cells transduced with TCF3/E2A shRNA2 for 72 hrs


title: E2A_shRNA1_Jurkat, biological replicate2

description: Gene expression data from Jurkat cells transduced with TCF3/E2A shRNA1 for 72 hrs


title: Subject6_PFGvsPancreas(dyeswap)

source_name: Subject6 PFG

value: Prefrontal gyrus


title: Subject6_OLvsPancreas(dyeswap)

source_name: Subject6 OL

value: Occipital lobe


title: Daudi ID3 - 48 hours - mAdbID:117719

description: mAdb experiment ID: 117719

source_name: Daudi ID3 - 48 hours

value: Daudi

value: B cells

value: Burkitt's Lymphoma

source_name: Daudi Empty Vector - 48 hours


title: Subject6_PFGvsPancreas(regular)


title: Subject6_MFGvsPancreas(regular)


title: Subject6_SIvsPancreas(dyeswap)

source_name: Subject6 SI

value: Small Intestine


title: E2A_shRNA1_Jurkat, biological replicate1

source_name: Jurkat cells transduced with TCF3/E2A shRNA1 for 72 hrs

value: Jurkat E6-1


title: Subject6_STG-MTGvsPancreas(dyeswap)

source_name: Subject6 STG-MTG

value: Superior temporal gyrus-Middle temporal gyrus

source_name: Subject6 Pancreas


title: Subject6_STG-MTGvsPancreas(regular)


title: Daudi shTCF3 - 48 hours - mAdbID:117717

description: mAdb experiment ID: 117717

source_name: Daudi shTCF3 - 48 hours

value: transduced with retroviral vectors expressing shRNA

source_name: Daudi shControl - 48 hours


title: Subject6_KidneyvsPancreas(regular)


title: Subject6_SIvsPancreas(regular)


title: Subject6_IPLvsPancreas(regular)

source_name: Subject6 IPL

value: Inferior parietal lobe


title: Subject6_OLvsPancreas(regular)


title: HEB_shRNA2_Jurkat, biological replicate1

description: Gene expression data from Jurkat cells transduced with TCF12/HEB shRNA2 for 72 hrs


title: Subject6_IPLvsPancreas(dyeswap)


title: Subject5_SIvsLiver(dyeswap)

source_name: Subject5 SI

source_name: Subject5 Liver


title: Daudi shTCF3 - 24 hours - mAdbID:117716

description: mAdb experiment ID: 117716

source_name: Daudi shTCF3 - 24 hours

source_name: Daudi shControl - 24 hours

value: transduced with retroviral vectors expressing shControl


title: HEB_shRNA1_Jurkat, biological replicate2

description: Gene expression data from Jurkat cells transduced with TCF12/HEB shRNA1 for 72 hrs


title: HN5 miR-7 rep 2

city: Nedlands

first: Patrick

middle: Aaron

last: Candy

state: Western Australia

address: 6 Verdun St

department: Cancer Medicine

institute: Perkins Institute

description:
SAMPLE 4
biological replicate 2

data_processing: The data were normalised using quantile normalisation with lumiR (v. 1.14.0) in R (v.2.11.0).

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

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.

value: head and neck cancer cells

tag: transfected with


title: Namalwa shTCF3 - 96 hours - mAdbID:117533

description: mAdb experiment ID: 117533

source_name: Namalwa shTCF3 - 96 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 96 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 96 hours.

value: Namalwa

source_name: Namalwa shControl - 96 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 96 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 96 hours.


title: HEB_shRNA2_Jurkat, biological replicate2

source_name: Jurkat cells transduced with TCF12/HEB shRNA2 for 72 hrs


title: TAL1_shRNA2_Jurkat, biological replicate1

description: Gene expression data from Jurkat cells transduced with TAL1 shRNA2 for 72 hrs


title: Namalwa shTCF3 - 24 hours - mAdbID:117530

description: mAdb experiment ID: 117530

source_name: Namalwa shTCF3 - 24 hours

source_name: Namalwa shControl - 24 hours


title: HEB_shRNA1_Jurkat, biological replicate1

source_name: Jurkat cells transduced with TCF12/HEB shRNA1 for 72 hrs


title: Namalwa ID3 - 96 hours - mAdbID:117529

description: mAdb experiment ID: 117529

source_name: Namalwa ID3 - 96 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 96 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing ID3. ID3 expression was induced with doxycycline for 96 hours.

source_name: Namalwa Empty Vector - 96 hours

treatment_protocol:
Treatment type: transduction
Treatment dose: 20 ng/ml
Treatment time: 96 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with empty retroviral vectors. Doxycycline induction for 96 hours.


title: HN5 miR-7 rep 1

description:
SAMPLE 3
biological replicate 1


title: Namalwa shTCF3 - 72 hours - mAdbID:117532

description: mAdb experiment ID: 117532

source_name: Namalwa shTCF3 - 72 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 72 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shRNA. shTCF3 expression was induced with doxycycline for 72 hours.

source_name: Namalwa shControl - 72 hours

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 20 ng/ml
Treatment time: 72 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing shControl. shRNA expression was induced with doxycycline for 72 hours.


title: TAL1_shRNA2_Jurkat, biological replicate2

source_name: Jurkat cells transduced with TAL1 shRNA2 for 72 hrs


title: HN5 miR-NC rep 2

description:
SAMPLE 2
biological replicate 2

value: miR-NC (negative control)


title: Subject5_SIvsLiver(regular)

value: Liver


title: HN5 miR-NC rep 1

description:
SAMPLE 1
biological replicate 1


title: CaSki-normox

last: Lyng

address: Montebello

department: Department of Radiation Biology

institute: Oslo University Hospital

description: O2 1CH

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0

source_name: Uterine cervical cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: The cells were incubated in Dulbecco's Modified Eagle medium with GlutaMAX supplemented with 10% fetal calf serum (FCS) and 100 U/ml penicillin/streptomycin (Gibco) under a 5% CO2 atmosphere at 37°C, and subcultured twice a week.

extract_protocol: RNA was extracted using RNeasy MiniKit (Quiagen), according to the manufacturers’ instructions.  Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were plated out in plastic dishes (3x105 cells for 6 cm dishes, 9x105 for 10 cm dishes) 24 h prior to exposure to hypoxic (0.2% O2, 5% CO2) or normoxic (95% air, 5% Co2) conditions for 24 h at 37°C. The hypoxia treatment was performed in an Invivo2200 chamber (Ruskinn Technology Ltd, Bridgend, UK) with accurate O2 and CO2 controls.

value: CaSki

value: Uterine cervical cancer

tag: histology

value: Squamous cell carcinoma

value: untreated


title: CaSki-hypox

description: HYP 2CH

value: hypoxia exposed


title: TAL1_shRNA1_Jurkat, biological replicate2

description: Gene expression data from Jurkat cells transduced with TAL1 shRNA1 for 72 hrs


title: TAL1_shRNA1_Jurkat, biological replicate1

source_name: Jurkat cells transduced with TAL1 shRNA1 for 72 hrs


title: Namalwa shTCF3 - 48 hours - mAdbID:117531

description: mAdb experiment ID: 117531

source_name: Namalwa shTCF3 - 48 hours

value: Blood

value: B cells

source_name: Namalwa shControl - 48 hours


title: SiHa-hypox

description: Siha-hyp

value: SiHa


title: Namalwa ID3 - 72 hours - mAdbID:117528

description: mAdb experiment ID: 117528

source_name: Namalwa ID3 - 72 hours

treatment_protocol:
Treatment type: coding sequence transduction
Treatment dose: 20 ng/ml
Treatment time: 72 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with retroviral vectors expressing ID3. ID3 expression was induced with doxycycline for 72 hours.

value: Burkitt's Lymphoma

source_name: Namalwa Empty Vector - 72 hours

treatment_protocol:
Treatment type: transduction
Treatment dose: 20 ng/ml
Treatment time: 72 hours
Treatment temperature: 37 C
In-vitro treatment: Cells were transduced with empty retroviral vectors. Doxycycline induction for 72 hours.


title: Subject5_KidneyvsLiver(dyeswap)

source_name: Subject5 Kidney

value: Kidney

source_name: Subject5 Liver


title: Subject5_KidneyvsLiver(regular)