title: SJTALL021913

description: processed signal intensity


title: SJTALL021912

status: Public on Jan 20 2016

type: RNA

city: Memphis

first: William

last: Evans

state: TN

address: 262 Danny Thomas Place

department: Pharmaceutical Sciences

country: USA

institute: St Jude Children's Research Hospital

description: processed signal intensity

hyb_protocol: hybridization was done at 56 degrees Celsius for 16 hours followed by washing on an HS Pro instrument from Tecan.

scan_protocol: Scanning was performed using an Agilent G2505B scanning system

data_processing: raw counts were processed using the limma package(version 3.6.9) from Bioconductor

molecule: total RNA

organism: Homo sapiens

source_name: Leukemia cells

label_protocol: miRCURY Power labeling kit used according to manufacturer's (Exiqon) instructions

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

tag: source

value: bone marrow


title: SJBALL227

description: processed signal intensity


title: SJBALL230

description: processed signal intensity


title: SJETV022010

description: processed signal intensity


title: SJHYPER022013

description: processed signal intensity


title: SJPHALL026

description: processed signal intensity


title: SJTALL021910

description: processed signal intensity


title: SJETV021937

description: processed signal intensity


title: SJHYPER021934

description: processed signal intensity


title: SJTALL021911

description: processed signal intensity


title: SJE2A063

description: processed signal intensity


title: SJHYPER022008

description: processed signal intensity


title: SJBALL022047

description: processed signal intensity


title: SJHYPER022001

description: processed signal intensity


title: SJHYPER021928

description: processed signal intensity


title: SJTALL021909

description: processed signal intensity


title: SJMLL006

description: processed signal intensity


title: SJHYPER022003

description: processed signal intensity


title: SJETV022004

description: processed signal intensity


title: SJBALL022002

description: processed signal intensity


title: SJE2A062

description: processed signal intensity


title: SJETV021927

description: processed signal intensity


title: SJTALL021906

description: processed signal intensity


title: SJHYPER021999

description: processed signal intensity


title: SJBALL021992

description: processed signal intensity


title: SJBALL218

description: processed signal intensity


title: SJETV021997

description: processed signal intensity


title: SJHYPER021996

description: processed signal intensity


title: SJHYPER21925

description: processed signal intensity


title: SJTALL21904

description: processed signal intensity


title: SJETV021986

description: processed signal intensity


title: SJETV021990

description: processed signal intensity


title: SJBALL021987

description: processed signal intensity


title: SJHYPO021991

description: processed signal intensity


title: SJMLL005

description: processed signal intensity


title: SJHYPER022044

description: processed signal intensity


title: SJHYPER021984

description: processed signal intensity


title: SJBALL215

description: processed signal intensity


title: SJINF022

description: processed signal intensity


title: SJHYPO147

description: processed signal intensity


title: SJTALL021903

description: processed signal intensity


title: SJBALL224

description: processed signal intensity


title: intentionally hemolyzed sample

city: Kyoto

first: Katsutoshi

last: Shoda

address: 465 Kajii-cho, Kamigyo-ku

department: Division of Digestive Surgery, Department of Surgery

country: Japan

institute: Kyoto Prefectural University of Medicine

hyb_protocol: Add 0.6µL of Hybridization buffer A, 2.9µL of nuclease-free water and 105µL of miRNA Hybridization buffer plus to reaction product. Degasification by a degasifier for 20 minutes. Incubate at 65℃ for 3 minutes. Centrifuge at max speed for 1 minute at room temperature. Incubate at 32℃ by application to “3D-Gene” Human/Mouse miRNA. Apply 110µL (2-array type) or 50µL (4-array type) of hybridization solution to “3D-Gene”. Seal application holes of “3D-gene” by cover seal and set in hybridization chamber on shaker in 32℃ incubator. Place 15µL of nuclease-free water (total 30µL). Close chamber and start shaking at 250rpm. Incubate at 32℃ for 16 hours

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan)3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing:
The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid.
A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: plasma, replicate1

label_protocol: Dissolve Hy5 fluorescent label pellet by addition of 29µL of nuclease-free water. Prepare spike control (TRT-X304) if necessary. Transfer RNA sample to 1.5µL tube, and adjust to 250ng/µL by addition of nuclease-free water. Add CIP buffer, Calf Intestine Phosphatase and miRNA spike control to total RNA 500ng. Prepare master mix. Add 2µL of total RNA (250ng/µL), 0.5µL of CIP buffer, 0.5µL of Calf Intestine Phosphatase and 1.0µL of miRNA spike control into a PCR tube to the total amount of 4 µL. Incubate the thus obtained PCR tube at 37℃ for 30 minutes. Heat denature at 95℃ for 5 minutes. Place on ice for 2 minutes. Adjust to 12.5µl by addition of 3µL of Labeling buffer, 1.5µL of Fluorescent label (Hy5), 2µL of DMSO and 2µL of Labeling enzyme to CIP reaction product. Incubate at 16℃ for 1 hour. Incubate at 65℃ for 15 minutes. Preserve at 4℃ until hybridization.

extract_protocol: Total RNA was extracted from 400 µl of plasma samples using a miRVana PARIS kit (Ambion, Austin, TX, USA) and eluted into 100 µl of pre-heated (95 °C) elution solution according to the manufacturer’s instructions. After plasma samples were thawed on ice and treated with Qiazol, synthetic Caenorhabditis elegans miRNA oligonucleotides, cel-miR-39 (a mixture of 25 fmol of each oligonucleotide in a total volume of 5 µl) were added to each plasma sample in order to normalize the efficacy of RNA extraction. RNA samples were stored at -80 °C until further processing.

tag: subject status

value: healthy volunteer

tag: gender

value: male

tag: age

value: 35 yrs

tag: tissue

value: plasma

tag: sample type

value: intentionally hemolyzed sample


title: fresh sample

value: fresh sample


title: control group-1

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

country: China

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

organism: Mus musculus

source_name: normal control mouse

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: Kunming mouse, male, 4~6 weeks old, 18~22 g, fed in the condition of 18~22℃ and the humidity keeping between 50~60%. Animals could eat and drink freely.

extract_protocol: RNA extraction by Trizol Reagent ( Invitrogen #15596-026 ). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: 50 male Kunming mice were randomly divided into 5 groups, namely, normal control group, model group, Daji/Gancao-synergy group, Daji/Gancao-antagonism group, Daji group. Normal control group was intragastrically administrated with normal saline; model group constructed HCC ascites model; Daji/Gancao-synergy group, Daji/Gancao-antagonism group and Daji group constructed HCC ascites model, and were intragastrically administrated with Euphorbia Pekinensis and Radix Glycytthizae at the dose of 0.02ml/g.

tag: strain background

value: Kunming

tag: genotype/variation

value: Healthy mouse

tag: Sex

value: 4~6 weeks old

tag: weight

tag: intragastric administration

value: normal saline

value: Peritoneal tissue

tag: model

tag: treatment outcome

value: normal to growth, the fur bright, good spirit


title: DJ/GC-synergy group-3

source_name: HCC acites_DJ/GC-synergy group

value: hepatocellular carcinoma (HCC) acites

value: hepatocellular carcinoma acites

value: compare with normal control, the spirit drooping, abnormal increase of abdomen circumference and body weight, belly tympanites, belly has ascites; the abdomen circumference and body weight less than the mouse of Euphorbia Pekinensis group.


title: control group-2


title: control group-3


title: DJ/GC-synergy group-1


title: DJ group-3

source_name: HCC acites_DJ group

value: Euphorbia Pekinensis

value: compare with normal control, the spirit drooping, abnormal increase of abdomen circumference and body weight, belly tympanites, belly has ascites; the abdomen circumference and body weight less than the mouse of model group.


title: DJ/GC-antogonism group-1

source_name: HCC acites_DJ/GC-antogonism group

value: compare with normal control, the spirit drooping, abnormal increase of abdomen circumference and body weight, belly tympanites, belly has ascites; as same as model.


title: DJ/GC-synergy group-2

value: male


title: DJ group-1


title: DJ group-2


title: model group-3

source_name: HCC acites_model group

value: compare with normal control, the spirit drooping, abnormal increase of abdomen circumference and body weighr, belly tympanites, belly has ascites


title: model group-1


title: DJ/GC-antogonism group-3


title: model group-2


title: DJ/GC-antogonism group-2


title: APCMin/+, ATB-346, rep3

city: London

first: Mark

middle: John

last: Paul-Clark

state: London

address: Dovehouse Street

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

description:
replicate 3
SAMPLE 21

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background corrected using Illumina GenomeStudio

label: biotin

source_name: Mouse colon

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

extract_protocol: RNA was extracted using Life Technologies MagMAX-96 Total RNA isolation kit and treated with TURBO DNase in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: 6 week old APCMin/+ or C57B/l6 control mice were treated with vehicle (0.05% DMSO, 0.95% carboxymethylcellulose), ATB-346 (14.5mg/kg) or naproxen (10mg/kg) by once-daily oral gavage for 7 days. Mice were sacrificed and colon collecteda at 14 weeks of age.

tag: strain

value: APCMin/+

value: 14 weeks

value: colon


title: APCMin/+, Naproxen, rep3

description:
replicate 3
SAMPLE 15

value: naproxen


title: APCMin/+, ATB-346, rep6

description:
replicate 6
SAMPLE 24


title: APCMin/+, ATB-346, rep2

description:
replicate 2
SAMPLE 20


title: APCMin/+, Vehicle, rep1

description:
replicate 1
SAMPLE 5

value: vehicle


title: APCMin/+, Vehicle, rep7

description:
replicate 7
SAMPLE 11


title: APCMin/+, Naproxen, rep6

description:
replicate 6
SAMPLE 18


title: APCMin/+, Vehicle, rep2

description:
replicate 2
SAMPLE 6


title: T30_6768

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

data_processing: The data were log2 transformed and normalized using RSN normalization from lumi package in R.

source_name: Prostate tissue

label_protocol: Biotinylated cRNA were prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

growth_protocol: Mice were maintained under pathogen-free conditions at the animal facility of Fondazione IRCCS Istituto Nazionale dei Tumori. Animal experiments were authorized by the Institute Ethical Committee and performed in accordance to institutional guidelines and national law (DL116/92).

extract_protocol: RNA was isolated from prostates samples using the guanidinium thiocyanate/cesium chloride gradient method described in Chirgwin et al. Biochemistry 1979, 18(24):5294-5299.

treatment_protocol: Prostates were collected at different ages and samples were freezed quickly after necropsy until following extraction.

value: C57BL/6-tgN (TRAMP)8247Ng

value: Male

tag: age (weeks)

tag: genotype

value: TRAMP

tag: palpable tumor

value: Yes

tag: tumor type

value: Adenocarcinoma

tag: early classification


title: APCMin/+, Naproxen, rep5

description:
replicate 5
SAMPLE 17


title: APCMin/+, Vehicle, rep8

description:
replicate 8
SAMPLE 12


title: Wild-type, Vehicle, rep2

description:
replicate 2
SAMPLE 2

value: Wild-type


title: Wild-type, Vehicle, rep4

description:
replicate 4
SAMPLE 4


title: APCMin/+, Vehicle, rep3

description:
replicate 3
SAMPLE 7


title: APCMin/+, Naproxen, rep4

description:
replicate 4
SAMPLE 16


title: APCMin/+, ATB-346, rep4

description:
replicate 4
SAMPLE 22


title: APCMin/+, ATB-346, rep5

description:
replicate 5
SAMPLE 23


title: APCMin/+, Vehicle, rep4

description:
replicate 4
SAMPLE 8


title: Wild-type, Vehicle, rep1

description:
replicate 1
SAMPLE 1


title: OPT18_450

value: B6.tgN (TRAMP)8247Ng Spp1<tm1Blh>/J

tag: gender

value: No

value: Reliquia


title: APCMin/+, Naproxen, rep2

description:
replicate 2
SAMPLE 14

tag: age


title: OPT18_1339

value: Ineuntes


title: APCMin/+, Vehicle, rep5

description:
replicate 5
SAMPLE 9

tag: tissue


title: OPT15_2957


title: APCMin/+, ATB-346, rep1

description:
replicate 1
SAMPLE 19


title: OPT18_1322


title: Wild-type, Vehicle, rep3

description:
replicate 3
SAMPLE 3


title: T18_421


title: APCMin/+, Naproxen, rep1

description:
replicate 1
SAMPLE 13


title: APCMin/+, Vehicle, rep6

description:
replicate 6
SAMPLE 10


title: OPT15_3020


title: OPT18_1323


title: OPT18_1335

value: Neuroendocrine


title: OPT15_3022


title: T30_6769


title: OPT15_2962


title: T18_1578


title: OPT18_1340


title: OPT18_1330


title: T18_408


title: OPT18_2967


title: OPT18_443


title: OPT18_1327


title: OPT18_444


title: OPT18_1328


title: HPDE-IndKRASWT -DOX Data.irs_KC_9798_AEG3H8v2_26064_38500

status: Public on Jan 19 2016

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
HPDE cells, with KRAS-wildtype, and without Dox treatment
HPDE-IndKRASWT -DOX

hyb_protocol: Hybridizations were performed using One-colour hybridization on SurePrint G3 Human GE Microarray (Agilent)

scan_protocol: Slide were scanned in an Agilent Microarray Scanner and the data were analyzed using Agilent Feature Extraction Software (v.9.1).

data_processing: quantile normalized, background subtracted data. Agilent and Bioconductor software was used.

source_name: Immortalized Human Pancreatic Duct Epithelial (HPDE) Cells

label_protocol: standard Agilent protocol

growth_protocol: All cell lines were propagated at 37°C and 5% CO2 in humidified atmosphere. HPDE cells were cultured in keratinocyte SFM medium (KSFM; Life Technologies) supplied with prequalified human recombinant Epidermal Growth Factor 1-53 and Bovine Pituitary Extract.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and quantified using a NanoDrop (ThermoScientific).

treatment_protocol: HPDE cells were transduced with either control, wild-type KRAS or KRASG12D(pInducer) with or without DOX (100ng/ml) for 72 h.

tag: cell type

value: human pancreatic ductal epithelial (HPDE) cell

tag: treatment

value: without Dox treatment

tag: transfection

value: KRAS-wildtype


title: OPT18_1329


title: OPT18_1336


title: HPDE-IndKRASWT -DOX Data.irs_KC_9796_AEG3H8v2_26062_38501


title: OPT15_2956


title: T18_1545


title: T30_6771


title: T30_6775


title: HPDE-IndKRASWT +DOX Data.irs_KC_9798_AEG3H8v2_26064_38503

description:
HPDE cells, with KRAS-wildtype, and with Dox treatment
HPDE-IndKRASWT +DOX

value: Dox treatment


title: HPDE-IndKRASWT +DOX Data.irs_KC_9797_AEG3H8v2_26063_38502


title: HPDE-IndKRASG12D -DOX Data.irs_KC_9796_AEG3H8v2_26062_38505

description:
HPDE cells, with KRAS-G12D, and without Dox treatment
HPDE-IndKRASG12D -DOX


title: HPDE-IndKRASG12D -DOX Data.irs_KC_9797_AEG3H8v2_26063_38506


title: HPDE-IndKRASG12D -DOX Data.irs_KC_9798_AEG3H8v2_26064_38504


title: OPT18_1325


title: OPT18_1333


title: WS2-iPSC-rep3

city: New York

first: Matthew

middle: A

last: Lalli

state: NY

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

description: iPSCs grown on Matrigel in mTesr

hyb_protocol: Standard Illumina hybridization protocol performed at Sanford Burnham Microarray Facility

scan_protocol: Standard Illumina scanning protocol performed at Sanford Burnham Microarray Facility

data_processing: Data were log2 transformed and quantile normalized. Batch effects were corrected using SVA in R

label: Biotin

source_name: Induced pluripotent stem cells

label_protocol: Biotinylated cRNA were prepared at Sanford Burnham Microarray Facility

extract_protocol: mirVana

value: Induced pluripotent stem cells

tag: individual or treatment

value: Williams syndrome 2


title: HPDE-IndKRASG12D +DOX Data.irs_KC_9798_AEG3H8v2_26064_38509

description:
HPDE cells, with KRAS-G12D, and with Dox treatment
HPDE-IndKRASG12D +DOX


title: WS2-iPSC-rep2

description: iPSCs grown on Matrigel in mTesr


title: HPDE-IndKRASG12D +DOX Data.irs_KC_9797_AEG3H8v2_26063_38508


title: HPDE-IndGFP -DOX Data.irs_KC_9798_AEG3H8v2_26064_38496

description:
HPDE cells, with GFP control, and without Dox treatment
HPDE-IndGFP -DOX

value: GFP control


title: B98_1022329.094 [Sample 123]

city: Rotterdam

first: Pim

last: French

address: Dr Molewaterplein 50

department: Neurology

country: Netherlands

institute: Erasmus MC

description: raw data file: Belob2_for_GEO_102329_French.txt

scan_protocol: Standard Illumina scan protocol

data_processing: Raw and normalized data are uploaded, the normalised data was done using quantile normalisation and batch effect removal in R

label_protocol: Standard Illumina labelling protocol

extract_protocol: Qiagen allprep DNA/RNA FFPE kit

treatment_protocol: randomized phase II clinical trial, patients treated with bevacizumab, CCNU or the combination

tag: subject status

value: Glioblastoma (GBM) patient

tag: patient id

tag: tumor subtype

tag: tcga subtype

value: Classical

tag: survival (months)

tag: sensor

value: dead

value: Beva (bevacizumab monotherapy)

tag: sample type

value: FFPE


title: B40_102380.33 [Sample 134]

description: raw data file: Belob3_for_GEO_102380_French.txt


title: B96_1022329.093 [Sample 122]

source_name: Glioblastoma_BC 90/110

value: BC 90/110 (combination treatment of beva and CCNU)


title: HPDE-IndKRASG12D +DOX Data.irs_KC_9796_AEG3H8v2_26062_38507


title: B124_102380.32 [Sample 133]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 32, scraped to enrich for tumor content

value: Mesenchymal

value: CCNU (Lomustine) monotherapy


title: B93_1022329.091 [Sample 119]


title: B74_102380.29 [Sample 130]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 101, scraped to enrich for tumor content

value: Neural


title: HPDE-IndGFP +DOX Data.irs_KC_9796_AEG3H8v2_26062_38499

description:
HPDE cells, with GFP control, and with Dox treatment
HPDE-IndGFP +DOX


title: B15_102380.24 [Sample 125]


title: B99_102380.30 [Sample 131]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 124, scraped to enrich for tumor content

value: Proneural


title: B54_102380.27 [Sample 128]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 6 and 86, screaped to enrich for tumor content


title: B92_1022329.090 [Sample 118]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 8


title: B43_102380.26 [Sample 127]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 76, scraped to enrich for tumor content


title: B9_1022329.031 [Sample 115]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 1


title: B109_102380.31 [Sample 132]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 20, scraped to enrich for tumor content


title: B94_1022329.092 [Sample 120]


title: HPDE-IndGFP +DOX Data.irs_KC_9798_AEG3H8v2_26064_38498

value: human pancreatic ductal epithelial (HPDE) cell


title: B90_1022329.089 [Sample 116]


title: HPDE-IndGFP -DOX Data.irs_KC_9797_AEG3H8v2_26063_38495

value: without Dox treatment


title: B95_1022329.141 [Sample 121]


title: HPDE-IndGFP +DOX Data.irs_KC_9797_AEG3H8v2_26063_38497


title: B111_102380.35 [Sample 135]


title: B41_102380.25 [Sample 126]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 74, scraped to enrich for tumor content


title: WS2-iPSC-rep1

description: iPSCs grown on Matrigel in mTesr


title: HPDE-IndGFP -DOX Data.irs_KC_9796_AEG3H8v2_26062_38494


title: B68_102380.28 [Sample 129]

description:
raw data file: Belob3_for_GEO_102380_French.txt
replicate of Sample 97, scraped to enrich for tumor content


title: BAZKD-NPC-rep3

description: ReNcell NSC media - FGF - EGF + BAZ1B shRNA

source_name: ReNcell BAZ1B shRNA

value: ReNcell

value: BAZ1B shRNA


title: BAZKD-NPC-rep1


title: BAZKD-NPC-rep2


title: Diff-NPC-rep3

description: ReNcell NSC media - FGF - EGF

source_name: ReNcell differentiated

value: Differentiated


title: Diff-NPC-rep2

description: ReNcell NSC media - FGF - EGF


title: Undiff-NPC-rep3

description: ReNcell NSC media + FGF + EGF

source_name: ReNcell self-renewal

value: Undifferentiated


title: B88_1022329.088 [Sample 113]


title: CTRL2-iPSC-rep1

description: iPSCs grown on Matrigel in mTesr

value: Induced pluripotent stem cells

value: Control 2


title: Undiff-NPC-rep2

description: ReNcell NSC media + FGF + EGF


title: Undiff-NPC-rep1

description: ReNcell NSC media + FGF + EGF


title: CTRL2-iPSC-rep2

description: iPSCs grown on Matrigel in mTesr


title: B86_1022329.140 [Sample 112]

value: Glioblastoma (GBM) patient

value: Classical

value: alive


title: B83_1022329.086 [Sample 110]

value: dead

value: Beva (bevacizumab monotherapy)

value: FFPE


title: CTRL2-iPSC-rep3

description: iPSCs grown on Matrigel in mTesr


title: WS1-iPSC-rep2

description: iPSCs grown on Matrigel in mTesr

value: Williams syndrome 1


title: WS1-iPSC-rep1

description: iPSCs grown on Matrigel in mTesr


title: WS1-iPSC-rep3

description: iPSCs grown on Matrigel in mTesr


title: B84_1022329.087 [Sample 111]

value: Mesenchymal

value: BC 90/110 (combination treatment of beva and CCNU)


title: B89_1022329.148 [Sample 114]


title: CTRL1-iPSC-rep3

description: iPSCs grown on Matrigel in mTesr

value: Control 1


title: Diff-NPC-rep1

description: ReNcell NSC media - FGF - EGF


title: CTRL1-iPSC-rep2

description: iPSCs grown on Matrigel in mTesr


title: B80_1022329.084 [Sample 108]

value: CCNU (Lomustine) monotherapy


title: B75_1022329.079 [Sample 102]


title: B79_1022329.083 [Sample 106]

value: Proneural


title: B77_1022329.081 [Sample 104]


title: B82_1022329.085 [Sample 109]


title: B78_1022329.082 [Sample 105]


title: B8_1022329.131 [Sample 107]


title: B66_1022329.073 [Sample 95]


title: B67_1022329.074 [Sample 96]


title: B76_1022329.080 [Sample 103]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 7


title: B70_1022329.076 [Sample 99]


title: CTRL1-iPSC-rep1

description: iPSCs grown on Matrigel in mTesr


title: CTRL2-neuron-rep3

description: iPSCs directly induced into neuron via NeuroD1 infection. Grown for 2 weeks

source_name: Directly induced neurons from iPSC

value: Induced neuron


title: CTRL1-neuron-rep2


title: CTRL1-neuron-rep3


title: CTRL2-neuron-rep1


title: CTRL2-neuron-rep2


title: CTRL1-neuron-rep1


title: B7_1022329.030 [Sample 98]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 10


title: B60_1022329.070 [Sample 92]

description: raw data file: Belob2_for_GEO_102329_French.txt


title: B63_1022329.139 [Sample 93]


title: B58_1022329.138 [Sample 90]


title: WS2-neuron-rep3

value: Williams syndrome 2


title: B56_1022329.067 [Sample 88]


title: B55_1022329.137 [Sample 87]


title: B52_1022329.065 [Sample 85]


title: WS2-neuron-rep1


title: WS2-neuron-rep2


title: WS1-neuron-rep3


title: B51_1022329.064 [Sample 84]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 5


title: B64_1022329.072 [Sample 94]


title: B5_1022329.029 [Sample 83]


title: WS1-neuron-rep1


title: WS1-neuron-rep2


title: B48_1022329.062 [Sample 81]


title: B49_1022329.063 [Sample 82]


title: B45_1022329.136 [Sample 78]


title: B4_1022329.145 [Sample 73]


title: B46_1022329.060 [Sample 79]


title: B35_1022329.052 [Sample 69]


title: B47_1022329.061 [Sample 80]


title: B42_1022329.057 [Sample 75]


title: B38_1022329.135 [Sample 71]


title: B44_1022329.059 [Sample 77]

source_name: Glioblastoma


title: B34_1022329.051 [Sample 68]


title: B39_1022329.054 [Sample 72]


title: B22_1022329.042 [Sample 58]


title: B33_1022329.134 [Sample 67]


title: B32_1022329.050 [Sample 66]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 3


title: B27_1022329.046 [Sample 62]


title: B155_1022329.037 [Sample 51]

value: Neural


title: B26_1022329.045 [Sample 61]


title: B31_1022329.049 [Sample 65]


title: B30_1022329.048 [Sample 64]


title: B28_1022329.047 [Sample 63]


title: B37_1022329.053 [Sample 70]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 4


title: B24_1022329.044 [Sample 60]


title: B19_1022329.039 [Sample 54]


title: B16_1022329.133 [Sample 52]


title: B23_1022329.043 [Sample 59]


title: B21_1022329.041 [Sample 57]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 2


title: B2_1022329.028 [Sample 55]


title: B20_1022329.040 [Sample 56]


title: B152_1022329.129 [Sample 50]


title: B151_1022329.128 [Sample 49]


title: B17_1022329.038 [Sample 53]


title: B150_1022329.127 [Sample 48]


title: B133_1022329.143 [Sample 37]


title: B142_1022329.122 [Sample 42]


title: B148_1022329.126 [Sample 47]


title: B147_1022329.125 [Sample 46]


title: B138_1022329.119 [Sample 38]


title: B13_1022329.132 [Sample 35]


title: B144_1022329.142 [Sample 44]


title: B143_1022329.123 [Sample 43]


title: B141_1022329.121 [Sample 41]


title: B14_1022329.035 [Sample 40]


title: B121_1022329.111 [Sample 30]


title: B120_1022329.110 [Sample 29]


title: B126_1022329.115 [Sample 33]


title: MLS085

city: Vancouver

first: Megan

middle: K

last: Levings

address: 950 West 28th Ave

country: Canada

institute: University of British Columbia

hyb_protocol: Hybridization was performed according to Appendix A in the  FL-Ovation™ cDNA Biotin Module V2 (NuGEN) instructions with an incubation of 18h, at 45°C in the GeneChip Hybridization oven 640 (Affymetrix) and a rotation speed of 60rpm.

scan_protocol: GeneChips were then washed in a GeneChips® Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix). The microarrays were finally scanned on a GeneChip® scanner 3000 (Affymetrix).

data_processing: The data were processed using GenePattern (RMA) and custom scripts (differential expression, collapsing probes to genes, etc) as previously described (Haining et al, 2008).

source_name: Stim mTreg Donor 6

label_protocol: cDNA then underwent fragmentation and biotinylation with FL-Ovation™ cDNA Biotin Module V2 (NuGEN) according to the manufacturer’s instructions.

extract_protocol: Ex vivo and 40 h stimulated Treg and Tconv populations were resuspended in TRIzol (Invitrogen). RNA was extracted with the RNAdvance Tissue Isolation kit (Agencourt). Concentrations of total RNA were determined with a Nanodrop spectrophotometer. RNA purity was determined by Bioanalyzer 2100 traces (Agilent Technologies). Total RNA was amplified and converted to cDNA with the Ovation Pico WTA system including SPIA amplification (NuGEN) according to the manufacturer's instructions.

treatment_protocol: unstimulated: none; stimulated:40h with anti-CD3/CD28 beads (Life technologies) at 1:1 bead to cell ratio with 100U/mL IL-2 (Chiron) in Xvivo15 containing 5% human serum (both Cambrex), penicillin/streptomycin, GlutaMAX (both Life Technologies)

tag: individual

value: donor 6

tag: cell subset

value: memoryTreg

value: stimulated


title: B12_1022329.034 [Sample 28]

value: Glioblastoma (GBM) patient

value: Classical


title: MLS083

source_name: Ex vivo mTconv Donor 6

value: memoryTconv

value: unstimulated


title: MLS086

source_name: Stim nTreg Donor 7

value: donor 7

value: naiveTreg


title: B128_1022329.117 [Sample 34]

value: dead

value: FFPE


title: B131_1022329.118 [Sample 36]

value: Beva (bevacizumab monotherapy)


title: MLS082

source_name: Ex vivo nTreg Donor 7


title: B139_1022329.120 [Sample 39]

value: CCNU (Lomustine) monotherapy


title: MLS088x

source_name: Stim nTconv Donor 7

value: naiveTconv


title: MLS087

source_name: Stim mTconv Donor 6


title: B123_1022329.113 [Sample 31]


title: MLS084x

source_name: Ex vivo nTconv Donor 6


title: B118_1022329.109 [Sample 27]


title: B146_1022329.124 [Sample 45]


title: B117_1022329.108 [Sample 26]

description:
raw data file: Belob2_for_GEO_102329_French.txt
replicate of sample 9


title: B113_1022329.106 [Sample 24]

value: Proneural


title: MLS081x

source_name: Ex vivo mTreg Donor 6


title: B114_1022329.107 [Sample 25]

value: alive

value: BC 90/110 (combination treatment of beva and CCNU)


title: MLS080

source_name: Stim nTconv Donor 6

value: donor 6


title: B112_1022329.105 [Sample 23]


title: MLS077x

source_name: Stim mTreg Donor 5

value: donor 5

value: memoryTreg


title: B106_1022329.101 [Sample 18]

value: Glioblastoma (GBM) patient

value: Mesenchymal


title: B110_1022329.104 [Sample 22]


title: B101_1022329.099 [Sample 14]

value: Classical


title: B108_1022329.102 [Sample 19]


title: MLS075

source_name: Ex vivo mTconv Donor 5

value: memoryTconv

value: unstimulated


title: B105_1022329.100 [Sample 17]

source_name: Glioblastoma_BC 90/110


title: B100_1022329.096 [Sample 13]


title: B104_1022329.098 [Sample 16]


title: MLS071

source_name: Stim mTconv Donor 4

value: donor 4

value: stimulated


title: MLS074x

source_name: Ex vivo nTreg Donor 6

value: naiveTreg


title: MLS079

source_name: Stim mTconv Donor 5


title: MLS078

source_name: Stim nTreg Donor 6


title: MLS072

source_name: Stim nTconv Donor 5


title: 59AdFOT_10_4

city: MONTPELLIER

first: Sylvie

last: Dequin

address: 2 PLACE PIERRE VIALA

country: France

institute: INRA

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 4, at 10 g/L released CO2

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7

data_processing: Data normalization and statistical analysis were performed using R 3.0.3 software and the limma package. Normalization was done by the quantile method considering all arrays

organism: Saccharomyces cerevisiae

source_name: 59AdFOT_10 repetition 4

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: Yeast cells were first pre-cultured in YEPD medium in 10ml flasks at 28°C with shaking (180rpm) overnight and were then transferred to 20ml flasks containing grape must and grown in the same conditions. These pre-cultures were used to inoculate fermentations (10^6 cells/ml) in grape must. Fermentation experiments were performed at 24°C in fermenters with a working volume of 1,1l. The natural grape must used is Chardonnay Coursan 2012 which contain 230g/l of sugars (100g/L glucose and 130g/l of fructose) and 230mg/L of yeast assimilable nitrogen (free amino acids and ammonium).

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: Cells were sampled during exponential phase at 10g CO2/L released. 10^9 cells were pelleted, washed with DEPC-treated water and freeze den methanol at -80°C.

tag: strain

tag: protocol

value: released CO2 (10g/L)

tag: array

tag: block


title: B10_1022329.032 [Sample 12]

value: dead

value: FFPE


title: MLS076

source_name: Ex vivo nTconv Donor 5

value: naiveTconv


title: 59A_10_4

description: Gene expression in sample from 59A strain, biological rep 4, at 10 g/L released CO2

source_name: 59A_10 repetition 4


title: MLS070

source_name: Stim nTreg Donor 5


title: MLS073x

source_name: Ex vivo mTreg Donor 5


title: B1_1022329.130 [Sample 11]


title: MLS067x

source_name: Ex vivo mTconv Donor 4


title: B102_1022329.097 [Sample 15]

value: CCNU (Lomustine) monotherapy


title: MLS066x

source_name: Ex vivo nTreg Donor 5


title: MLS065

source_name: Ex vivo mTreg Donor 4


title: MLS068

source_name: Ex vivo nTconv Donor 4


title: 59AdFOT_5_4

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 4, at 5 g/L released CO2

source_name: 59AdFOT_5 repetition 4

value: released CO2 (5g/L)


title: MLS069x

source_name: Stim mTreg Donor 4


title: MLS048

source_name: Stim nTconv Donor 4


title: 59A_5_4

description: Gene expression in sample from 59A strain, biological rep 4, at 5 g/L released CO2

source_name: 59A_5 repetition 4


title: 59AdFOT_10_3

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 3, at 10 g/L released CO2

source_name: 59AdFOT_10 repetition 3


title: 59AdFOT_5_3

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 3, at 5 g/L released CO2

source_name: 59AdFOT_5 repetition 3


title: 59A_5_3

description: Gene expression in sample from 59A strain, biological rep 3, at 5 g/L released CO2

source_name: 59A_5 repetition 3


title: 59AdFOT_10_2

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 2, at 10 g/L released CO2

source_name: 59AdFOT_10 repetition 2


title: MLS046

source_name: Stim nTreg Donor 4


title: MLS047

source_name: Stim mTconv Donor 3

value: donor 3


title: MLS042

source_name: Ex vivo nTreg Donor 4


title: MLS039

source_name: Stim mTconv Donor 2

value: donor 2


title: MLS037

source_name: Stim mTreg Donor 2

value: memoryTreg


title: MLS045

source_name: Stim mTreg Donor 3


title: MLS040

source_name: Stim nTconv Donor 3


title: 59AdFOT_5_2

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 2, at 5 g/L released CO2

source_name: 59AdFOT_5 repetition 2


title: 59A_10_2

description: Gene expression in sample from 59A strain, biological rep 2 , at 10 g/L released CO2

source_name: 59A_10 repetition 2


title: MLS038

source_name: Stim nTreg Donor 3


title: 59A_5_2

description: Gene expression in sample from 59A strain, biological rep 2 , at 5 g/L released CO2

source_name: 59A_5 repetition 2


title: 59AdFOT_10_1

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 1, at 10 g/L released CO2

source_name: 59AdFOT_10 repetition 1


title: MLS036

source_name: Ex vivo nTconv Donor 2


title: 59AdFOT_5_1

description: Gene expression in sample from 59A FOT-deleted strain, biological rep 1 , at 5 g/L released CO2

source_name: 59AdFOT_5 repetition 1


title: MLS032

source_name: Stim nTconv Donor 2


title: MLS030

source_name: Stim nTreg Donor 2


title: MLS034

source_name: Ex vivo nTreg Donor 3


title: MLS044

source_name: Ex vivo nTconv Donor 3


title: MLS031

source_name: Stim mTconv Donor 1

value: donor 1


title: MLS028

source_name: Ex vivo nTconv Donor 1


title: MLS035

source_name: Ex vivo mTconv Donor 3


title: MLS041

source_name: Ex vivo mTreg Donor 3


title: MLS029

source_name: Stim mTreg Donor 1


title: 59A_5_1

description: Gene expression in sample from 59A strain, biological rep 1 , at 5 g/L released CO2

source_name: 59A_5 repetition 1


title: MLS026

source_name: Ex vivo nTreg Donor 2


title: MLS025

source_name: Ex vivo mTreg Donor 1


title: MLS027

source_name: Ex vivo mTconv Donor 2


title: MLS033

source_name: Ex vivo mTreg Donor 2


title: 59A_10_1

description: Gene expression in sample from 59A strain, biological rep 1 , at 10 g/L released CO2

source_name: 59A_10 repetition 1


title: MLS015

source_name: Stim mTconv Donor 7

value: donor 7


title: MLS014x

source_name: Stim nTreg Donor 1


title: MLS016

source_name: Stim nTconv Donor 1


title: MLS010

source_name: Ex vivo nTreg Donor 1


title: LNAME+AngII_03

first: Anisha

last: Gupte

address: 6565 Fannin St F8-073

department: Bioenergetics Center

institute: Houston Methodist Hospital

description: L-NAME +AngII group replicate 3

data_processing: Unmodified microarray data obtained from GenomeStudio (Illumina) was background-subtracted, log2 transformed and quantile-normalized using the lumi package within R

source_name: Mouse Heart

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 within the kit. RNA quality was assessed with an Agilent Bioanalyzer.

treatment_protocol: L-NAME (0.3 mg/ml with 1% NaCl) in drinking water 5 weeks. AngII (0.7 mg/kg/day) 4 weeks via subcutaneous micro-osmotic pump 4 weeks.

tag: gender

value: Male

tag: tissue

value: Left Ventricle

value: AngII (0.7 mg/kg/day) and L-NAME (0.3 mg/ml with 1% NaCl)


title: LNAME+AngII_01

description: L-NAME +AngII group replicate 1

tag: treatment


title: AngII_04

description: AngII group replicate 4

value: AngII (0.7 mg/kg/day)


title: LNAME+AngII_02

description: L-NAME +AngII group replicate 2


title: MLS011

source_name: Ex vivo mTconv Donor 1

value: memoryTconv

value: unstimulated


title: AngII_01

description: AngII group replicate 1


title: Joint neutrophils from isotype control treated mice - replicate 2

city: Parkville

first: CSL

last: Research

state: VIC

address: 30 Flemington Rd

country: Australia

institute: CSL Limited / bio21 Institute

description:
1184
replicate 2

data_processing: The scanner operating software, GenomeStudio, converts the signal on the array into .txt files for analysis (`none/iltp4531 Sample Probe Pro le.txt' contains sample probe measurements, and `sample table and control data/control probe pro le.txt' contains control probe measurements). Both .txt files were read  using limma (v3.18.2) read.ilmn function. Background correction, normalization, and log transformation was carried using neqc limma function.  The data was annotated using illuminaMousev2.db (v1.20.0).

source_name: joint neutrophils - control

extract_protocol: RNA was extracted using QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: C57BL/6 mice with collagen antibody-induced arthritis were injected intra-peritoneally at day 5 with 50 μg anti-G-CSFR (n = 20 mice) or control mAb (n = 10 mice). At day 7, neutrophils (CD45+ CD11bhi Ly6G+) were sorted (BD FACSAria) from pooled digests of the knee tissues, or peripheral blood, and the RNA was extracted from 3 such experiments, giving a total of 12 samples.

value: male

tag: disease state

value: collagen antibody-induced arthritis

value: control (BM4)

value: joint

tag: cell type

value: neutrophil


title: Blood neutrophils from anti-G-CSFR treated mice - replicate 1

description:
1209
replicate 1

source_name: blood neutrophils - aG-CSFR

value: aG-CSFR

value: blood


title: LNAME+AngII_04

description: L-NAME +AngII group replicate 4


title: AngII_03

description: AngII group replicate 3


title: LNAME_02

description: L-NAME group replicate 2

value: L-NAME (0.3 mg/ml with 1% NaCl)


title: Ctrl_04

description: Control group replicate 4

value: control


title: Ctrl_03

description: Control group replicate 3


title: Blood neutrophils from anti-G-CSFR treated mice - replicate 3

description:
1193
replicate 3


title: Blood neutrophils from isotype control treated mice - replicate 2

description:
1189
replicate 2

source_name: blood neutrophils - control


title: LNAME_03

description: L-NAME group replicate 3


title: Joint neutrophils from isotype control treated mice - replicate 3

description:
1183
replicate 3


title: LNAME_04

description: L-NAME group replicate 4


title: Blood neutrophils from isotype control treated mice - replicate 1

description:
1208
replicate 1


title: Joint neutrophils from anti-G-CSF treated mice - replicate 3

description:
1205
replicate 3

source_name: joint neutrophils - aG-CSFR


title: LNAME_01

description: L-NAME group replicate 1


title: Joint neutrophils from anti-G-CSF treated mice - replicate 2

description:
1215
replicate 2


title: AngII_02

description: AngII group replicate 2


title: Blood neutrophils from isotype control treated mice - replicate 3

description:
1190
replicate 3


title: Blood neutrophils from anti-G-CSFR treated mice - replicate 2

description:
1192
replicate 2


title: Joint neutrophils from anti-G-CSF treated mice - replicate 1

description:
1185_1187
replicate 1


title: Joint neutrophils from isotype control treated mice - replicate 1

description:
1182
replicate 1


title: Ctrl_02

description: Control group replicate 2


title: MRC_5_PD32-2

status: Public on Jan 18 2016

type: SRA

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

library_source: transcriptomic

data_processing:
Illumina Casava software was used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v2.0.6) vs. the H.sapiens genome GRCh37.66 obtained from Ensembl
Uniquely mapped reads were counted for each gene_id using featureCounts (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE)
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample
Genome_build: GRCh37.66
Supplementary_files_format_and_content: Excel file including raw counts and RPKM values for each sample

source_name: total RNA extracted from MRC-5 fibroblasts

growth_protocol: Cells were cultured as recommended by ATCC in Dulbeccos modified Eagles low glucose medium (DMEM) with L-glutamine (PAA Laboratories, Pasching, Austria), supplemented with 10% fetal bovine serum (PAA Laboratories). Cells were grown under normal air conditions in a 9.5% CO2 atmosphere at 37°C. For sub-culturing, the remaining medium was discarded and cells were washed in 1 x PBS (pH 7.4) (PAA Laboratories) and detached using trypsine/EDTA (PAA Laboratories). Primary fibroblasts were sub-cultured in a 1:4 (= 2 population doublings (PDs)) or 1:2 (= 1 PD) ratio. For stock purposes, cryo-conservation of the cell lines at various PDs were undertaken in cryo-conserving medium (DMEM + 10% FBS + 5% DMSO). Cells were immediately frozen at -80°C and stored for two to three days. Afterwards, cells were transferred to liquid nitrogen for long time storage. Re-freezing and re-thawing was not performed to avoid premature senescence [Honda et al., 2001]. One vial of each of the five different fibroblast cell lines (MRC-5, HFF, BJ, WI-38 and IMR-90) were obtained and maintained in culture from an early PD. On obtaining enough stock on confluent growth of the fibroblasts in 75 cm2 flasks, cells were sub-cultured into three different 75 cm2 flasks (“triplicates”) and were maintained until they were senescent in culture.

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method. Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of around 2.5 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

tag: population doublings

value: MRC-5 fibroblasts


title: MRC_5_PD32-3


title: MRC_5_PD32-1


title: 410.4 tumour cells, rep 3

city: Barcelona

first: Alexandra

last: Avgustinova

address: C/ Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

description: replicate 3

hyb_protocol: Standard Illumina hybridisation protocol

data_processing:
The data were normalised using quantile normalisation with IlluminaGUI in R
Probes that were not expressed in any of the samples were removed before normalisation to avoid adding noise to the data.

source_name: 410.4 xenograft

label_protocol: Biotinylated cRNA were prepared using Ambion TotalPrep 96-RNA amplification kit for Illumina arrays

growth_protocol: 5 x 10^5 tumour cells were inoculated orthotopically into the 4th mammary fat pad of Ub-GFP Balb/c mice. Tumours were left to grow for 2-4 weeks, until they reached an average diameter of 10 mm.

extract_protocol: RNA was extracted with Trizol reagen in accordance with the manufacturer´s. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: cells were not treated

value: 410.4 xenograft

tag: source strain

value: Balb/c

tag: host strain

value: Ub-GFP Balb/c

value: primary tumour

tag: Sex

value: female

tag: age

value: 6-8 weeks


title: Ctrl_01

description: Control group replicate 1

value: Male

value: Left Ventricle


title: Mock_infected_3

city: Charleston

first: Jeremy

last: Barth

state: SC

address: 173 Ashley Ave, BSB 627

institute: MUSC

description: Sample was prepared by combining wildtype H. pylori total RNA and AGS cell total RNA containing small RNA to simulate the infected sample RNA used in experimental treatments

hyb_protocol: Hybridization to GeneChip miRNA 2.0 arrays (Affymetrix, Santa Clara, CA) was done overnight at 45oC according to Affymetrix protocols; post hybridization washing and staining was done in Affymetrix Fluidics Stations 450 according to Affymetrix protocols

scan_protocol: GeneChips were scanned in an Affymetrix GeneChip Scanner 7G

data_processing: Scanned data (i.e., CEL files) were processed with Affymetrix miRNA QC Tool software (Version 1.0.33.0) using the following variable settings: 1) background detection, 2) BC-CG background adjustment, 3) quantile normalization, 4) small constant addition, 5) threshold inclusion, and 6) median polish summarization. Normalized expression values (log2) and detection calls for the human RNA content on the array were exported for comparative analyses.

source_name: AGS cells, mock-infected

label_protocol: Low molecular weight RNA present in the total RNA samples (100 ng) were converted to biotin-labeled target using the FlashTag® Biotin HSR kit (Genishere LLC, Hatfield, PA) according to manufacturer recommendations.

growth_protocol: Human gastric epithelial AGS cells (ATCC, Manassas, VA) were maintained in Ham's F12 medium containing 10% FBS. H. pylori wild-type strain 7.13 and isogenic Delta cagA mutant strain were cultured on Brucella-agar plates at 37oC under microaerobic conditions (5% O2, 7% CO2, 88% N2). Bacterial multiplicities of infection (MOI) were calculated. All reagents were of molecular biology grade.

extract_protocol: Cell culture medium was replaced by 1 ml RNA-Stat-60 (Tel-Test, Inc, Friendswood, TX), cells were homogenized by trituration and the homogenate was incubated for 5min at room temperature. Chloroform (200 µl) was added and the mixture shaken vigorously for 15s and then incubated at RT for 3min. The extract was centrifuged (14,500 rpm, 4oC, 15min), and the aqueous layer was recovered and combined with isopropanol (500 µl) and 1µl GenElute Linear Polyacrylamide (25 µg/ml) and then vortexed for 10s. Precipitated RNA was collected by centrifugation (14,500 rpm, 4oC, 15min), and the RNA pellet was rinsed in 70% ethanol (800 µl) and re-centrifuged (7,500 rpm, 4oC, 15min). Pelleted RNA was air-dried (15min) and triturated in nuclease-free water (30 µl).

treatment_protocol: AGS cells (5 x 105) were seeded into 6-well plates and incubated overnight in serum-free F12 medium. After addition of fresh F12 medium, aliquots of H. pylori 7.13 wild-type strain or the isogenic mutant strain Delta-cagA was added to the cells to a final MOI of 100. Cells were co-incubated at 37oC in humidified air/5% CO2 for 6 hours.

tag: infection

value: Mock


title: HPWT_infected_1

description: Sample is a combination of wildtype H. pylori RNA and AGS cell total RNA containing small RNA that was isolated from infected cell cultures

source_name: AGS cells, wildtype H plyori-infected

value: H. pylori Wildtype


title: HPWT_infected_2


title: HPCagA_infected_1

description: Sample is a combination of Delta cagA mutant H. pylori bacterial RNA and AGS cell total RNA containing small RNA that was isolated from infected cell cultures

source_name: AGS cells, Delta cagA mutant H plyori-infected

value: H. pylori Delta cagA mutant


title: HPCagA_infected_2


title: 410.4 tumour cells, rep 1

description: replicate 1

tag: sample type


title: Mock_infected_1


title: 410.4 tumour cells, rep 2

description: replicate 2


title: PM6-7A vs. pdr1 Δ

status: Public on Jan 17 2016

city: Bratislava

first: Nora

last: Toth Hervay

address: Ilkovicova 6

country: Slovakia

institute: Deparment of Microbiology and Virology,Faculty of Natural Sciences, Comenius University in Bratislava

description: samples from yeast cells grown in selective media, without any induction

hyb_protocol: 4 μg of labelled aRNA was hybridized (18 h at 45°C) in 6x SSPE with addition of formamide (10%), tween-20 (0.01%) and microarray-specific control oligos (1%, MYcroarray, USA).

scan_protocol: After washing, microarray images and two-color GPR output files were obtained using the microarray scanner InnoScan 900 and Mapix software version 7.3.1 (Innopsys, France).

data_processing: The two-color GPR files were processed using  the R version 3.0.2 and functions available in the limma package.  The two-color GPR files were imported using the read.maimages() function, background-subtracted using the minimum method and within-array-normalized using the loess method. The between-array normalisation was achieved using the Aquantile method.

label: Alexa Fluor® 647

organism: Kluyveromyces lactis

source_name: yeast wild-type cells_reference

label_protocol: 1 μg of total RNA was linearly amplified and labelled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, USA) with two different fluorescent dyes: AlexaFluor 647 and AlexaFluor 555 (Life Technologies, Germany).

growth_protocol: exponentially growing K. lactis cells

extract_protocol: Total RNA extracted using Rneasy midi kit (Qiagen GmbH, Germany) following manufacturer's instructions

treatment_protocol: grown in minimal selective media without any induction

tag: genotype

value: wildtype

label: Alexa Fluor® 555

source_name: yeast deletion mutant

tag: background strain


title: Gonad_HT_rep5

first: Noelia

middle: T

last: Díaz Blanco

state: Barcelona

address: Passeig Marítim de la Barceloneta 37-49

department: Marine Renewable Resources

institute: Institute of Marine Sciences (ICM-CSIC)

hyb_protocol: Each sample (1.65 μg) was hybridized to D. labrax array (Agilent ID 023790) at 65 °C for 17 h using Agilent’s GE Hybridization Kit. Washes were conducted as recommended by the manufacturer using Agilent’s Gene Expression Wash Pack with stabilization and drying solution.

scan_protocol: Arrays were scanned with Agilent Technologies Scanner, model G2505B. Spot intensities and other quality control features were extracted with Agilent’s Feature Extraction software version 10.4.0.0. The microarray platform GPL13443 has been validated and uploaded to the Gene Expression Omnibus (GEO)-NCBI database.

data_processing: Raw data was taken from the Feature Extraction output files and was corrected for background noise using the normexp (Ritchie et al., 2007) method. To assure comparability across samples quantile normalization (Bolstad, 2001) was used. A probe was considered reliable if its raw foreground intensity was at least two times higher than the respective background intensity and if it was neither saturated nor flagged by the Feature Extraction software. On our custom array design, most probes (78%) were represented in two (or in some cases more) identical copies. Median intensities of respective probe replicates were taken in order to yield only one expression value per probe. A probe was considered reliable if at least half of its replicates were reliable, as defined above. Differential expression analysis was carried out on all non-control probes with an empirical Bayes approach on linear models (limma) (Smyth, 2004). Results were corrected for multiple testing according to the False Discovery Rate (FDR) method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed if they had adjusted P-value < 0.05, absolute fold change > 1.2 and were reliable in all samples.  All statistical analyses were performed with the Bioconductor project (http://www.bioconductor.org/) in the R statistical environment (http://cran.rproject.org/) (Gentleman et al., 2004).

organism: Dicentrarchus labrax

source_name: Half gonad, 170 days post hatch, early high water temperature (HT)

label_protocol: RNA labelling, hybridizations, and scanning were performed according to manufacturer’s instructions. Briefly, total RNA (100 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit. After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen), quantified with the Nanodrop ND- 1000 and verified using the Bioanalyzer 2100.

growth_protocol: Rearing conditions and handling methods were as described at (Díaz et al., 2013). Both experimental groups followed the same feeding protocol; larvae were fed three times a day with Artemia AF and then with amino acid enriched Artemia EG (INVE Aquaculture, Belgium). Juveniles and adults were fed ad libitum two times a day with dry food (ProAqua S.A., Spain) of different diameters according to fish size.

extract_protocol: Total RNA was purified from 170 dph European sea bass isolated gonads by homogenizing the tissue with Trizol reagent (Invitrogen- Live Technologies, Scotland, UK). Briefly, samples were then separated into phases by chloroform, precipitated with isopropanol and washed in 75% Ethanol. The quality and concentration of the RNA were assessed by ND-1000 spectrophotometer (NanoDrop Technologies) based on A260 absorbance and checked on a 1% agarose/formaldehyde gel. Integrity of the total RNA was then verified analyzing 1 µl/sample with a Bioanalyzer 2100 with the RNA 6000 Nano LabChip kit (Agilent, Spain) before processing for microarrays to assure consistency across samples. RNA samples of 100-200 ng/µl and RINs higher than 7 were used to perform the hybridizations. Two hundred nanograms of total RNA were treated with E.coli RNAse H in order to remove complementary RNA. From this RNA 100 ng were used for the cDNA synthesis using SuperScript III RNase Transcriptase (Invitrogen, Spain) and Random hexamer (Invitrogen, Spain) following manufacturer’s instructions.

treatment_protocol: Larvae were divided in two tanks and maintained at 17ºC, a temperature known to avoid temperature effects on sex ratio (Piferrer et al., 2005; Navarro-Martín et al., 2009), for the first 20 dph. Then the thermal regime differed between the two groups. While in one tank temperature was increased to 21ºC (high temperature, HT group) in the other was decreased to 15 ºC (low temperature, LT group); in both cases temperature changes were achieved at a ratio of 0.5ºC/day. These temperatures were maintained until 60 dph when temperature in LT group was gradually raised to 21ºC to allow fish growth at normal rates. Finally, at ~220 dph, temperature started to follow the natural fluctuations to allow gonad.

value: putative females

value: gonad

value: 170 days post hatch


title: Gonad_LT_rep5

source_name: Half gonad, 170 days post hatch, early low water temperature (LT)


title: Gonad_HT_rep4


title: HPWT_infected_3


title: Gonad_HT_rep3


title: Gonad_LT_rep4


title: Complicated malaria 7

city: Pilani

first: Ashis

middle: Kumar

last: Das

state: Rajasthan

address: Vidya Vihar

department: Biological Sciences

country: India

institute: Birla Institute of Technology & Science,Pilani (Pilani Campus)

description: Gene expression of parasite isolates

hyb_protocol: The labeled cRNA samples were hybridized on to a custom P. falciparum 8x15k Array (AMADID: 24956) designed by Genotypic Technology Pvt. Ltd., Bangalore, India. 600ng of Cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanning was performed using the Agilent Microarray Scanner (Agilent, Palo Alto, CA, G Model G2565BA) at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software (Agilent Technologies).Feature extracted data was analyzed using GeneSpring GX Version 11.5 software from Agilent. Data was filtered by considering all those probes detected in at least in 4 samples out of 13 samples based on flag option. Filtered probes were normalized using quantile based normalization method.

organism: Plasmodium falciparum

source_name: P. falciparum parasites from patient's blood

label_protocol: Thirteen parasite total RNA samples  for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the samples were incubated with reverse trancription mix at 40°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C.

growth_protocol: P. falciparum isolates collected directly from infected patients with differing clinical symptoms

extract_protocol: Total RNA extracted using TriReagent (Sigma Aldrich, USA) following manufacturer's instructions

treatment_protocol: Blood was immediately (Within 15 minutes of collection) subjected to density gradient based separation (Histopaque 1077, Sigma Aldrich, USA) to separate the Peripheral Blood Mononuclear Cells (PBMCs) from the infected and uninfected erythrocytes following manufacturer’s instructions. Both fractions were washed with Phosphate buffered saline (PBS) twice and lysed using 4 volume of Tri-Reagent (Sigma Aldrich, USA) and stored at -80°C.

value: F

tag: clinical presentation

value: Jaundice


title: Complicated malaria 6

description: Gene expression of parasite isolates

value: M


title: Gonad_HT_rep2


title: Mock_infected_2


title: HPCagA_infected_3


title: Gonad_LT_rep3


title: Complicated malaria 4

description: Gene expression of parasite isolates

value: Jaundice, Anemia


title: PM6- 7A vs. PM6-7A + PDR1*

tag: strain

source_name: cells containing PDR1* gain-of-function allele


title: Endometrial cancer in different stages-4

city: Hsin-Chu

first: Wei-Yun

last: Huang

address: 75 Bo-Ai Street

department: Department of Biological Science and Technology

country: Taiwan

institute: NCTU

description:
PolyA RNA
Samples were pooled in equimolar amounts (10 samples / pool) for microarray analysis.

hyb_protocol: 45°C with 60 rpm for 16 hours in a Hybridization Oven 640 (Affymetrix).

scan_protocol: GeneChip Operating Software (GCOS) in GeneChip Scanner 3000 (Affymetrix).

data_processing: Transformation by MAS 5.0.

source_name: Advanced stage endometrial cancer

label_protocol: Double-stranded cDNA was synthesized by a chimerical oligonucleotide with oligo-dT and T7 RNA polymerase. The amplification and labeling processes were monitored using a GeneChip Eukaryotic Poly-A RNA Control Kit (Affymetrix) with exogenous positive controls that were spiked into the total RNA before cDNA synthesis. The amplified cRNA was purified and then labeled with biotin using the GeneChip IVT Labeling Kit. 20 micro-gram of biotin-labeled cRNA was added in the fragmentation buffer and heated for 35 min at 94C.

extract_protocol: Total RNA was isolated from the tissues.

value: advanced stage endometrial endometrioid adenocarcinoma (EEC)

tag: Stage

value: III and IV


title: Endometrial cancer in different stages-1

source_name: Atypical endometrial hyperplasia

tag: gender

value: female

value: atypical hyperplastic endometrium (AEH)


title: Endometrial cancer in different stages-3

source_name: Early stage endometrial cancer

tag: tissue

value: early stage endometrial endometrioid adenocarcinoma (EEC)

value: I and II


title: Complicated malaria 5

description: Gene expression of parasite isolates


title: Gonad_LT_rep2


title: Endometrial cancer in different stages-2

source_name: Normal endometrium

value: normal endometrium (NEM)


title: Complicated malaria 3

description: Gene expression of parasite isolates


title: Complicated malaria 2

description: Gene expression of parasite isolates


title: Gonad_LT_rep1


title: Gonad_HT_rep1


title: Uncomplicated malaria 5

description: Gene expression of parasite isolates

value: uncomplicated malaria


title: wild type_vs_Δrnc mutant_rep3

city: Kizugawa-shi

first: Tomoya

last: Maeda

state: Kyoto

address: 9-2 Kizugawadai

department: Molecular Microbiology and Biotechnology Group

institute: Research Institute of Innovative Technology for the Earth

description: Dye-swap array

hyb_protocol: Labeled cDNA (4.5 μg each) are mixed with 1 × hybridization buffer (6 × SSC, 0.2% SDS, 5 × Denhardt’s solution, 0.1 mg/ml denatured salmon sperm DNA) in a total volume of 340 μl, and denatured at 95˚C for 2 min. The hybridization mixture was hybridized to a microarray in an Agilent Technologies Microarray chamber at 60˚C for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 5 minutes with wash buffer 1 (2x SSC, 0.2% SDS) at room temperature , 5 minutes with wash buffer 2 (0.2x SSC, 0.2% SDS) at 60˚C, and 5 minutes with wash buffer 3 (0.2x SSC) at room temperature.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) at a resolution of 5 µm. PMT is set to 100% for Cy3 and Cy5 channels.

data_processing: The scanned images were analyzed quantified with Feature Extraction Software 10.5.5.1 (Agilent) using default parameters (protocol GE2-NonAT_105_Dec08). Feature extracted data were analyzed using GeneSpring GX v 12.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the Lowess normalization algorithm without baseline transformation.

organism: Corynebacterium glutamicum R

source_name: The wild-type strain at the exponential phase

label_protocol: The cDNAs were synthesized from RNA by using reverse transcriptase from 10 μg of total RNAs and labeled with cyanine 3 (Cy3) or cyanine 5 (Cy5) using the SuperScript Indirect cDNA Labeling system (Life Technologies).

growth_protocol: C. glutamicum strains are aerobically grown in nutrient A-rich medium containing 1% glucose at 33˚C.

extract_protocol: Total RNA was extracted from C. glutamicum cells using NucleoSpin RNA II kit (Macherey-Nagel, Germany) according to the manufacture's manual.

treatment_protocol: Two volumes of RNA Protect bacterial reagent (Qiagen) were added directly to one volume of exponentially growing cultures at an OD600 of 4 (in logarithmic phase) to stabilize cellular RNAs.

value: Wild type

source_name: rnc deletion mutant at the exponential phase

value: rnc mutant


title: Uncomplicated malaria 6

description: Gene expression of parasite isolates


title: Uncomplicated malaria 4

description: Gene expression of parasite isolates


title: wild type_vs_Δrnc mutant_rep2


title: Uncomplicated malaria 3

description: Gene expression of parasite isolates


title: THP1-MLL/AF9_knockdown-siRNA3

status: Public on Jan 16 2016

city: Munich

first: Katrin

last: Fleischmann

address: Lindwurmstrasse 2a

department: Children’s Research Center

institute: Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-Univeristät München

data_processing: LDA raw data were imported into the statistical language R version 2.11.1. The conventional method in qPCR analysis is to use housekeeper genes as references before looking at treatment effects (∆∆CT method). As it is difficult to define reliable housekeeper in the case of miRNAs, it has been shown that normalizing to the overall mean instead outperforms the reference approach. Thus, a cyclic LOESS normalization was applied to the data (separately for the A and B plates). Analysis of differential expression between MLL-AF9 knockdown and control treatments was carried out in the statistical language R with the limma package. Adjustment for multiple testing was done using the method by Benjamini and Hochberg. Log2FC, p-value of the moderated t test and p-value after correcting for multiple testing were generated. MiRNAs which showed low expression, i.e. high threshold cycle (CT values above 34.5) in both treatment groups were excluded from the analysis. MiRNAs with a p-value below 0.05 were regarded as differentially expressed. MiRNAs which were either turned “on” or “off” in both MLL-AF9 knockdown versus both non-targeting control samples (“undetermined” versus CTs below 34.5) were added to the miRNA candidate list manually. For these, no ratio can be calculated but a lower limit of differential expression is reported as previously described. Of the 664 distinct miRNAs detectable by this LDA, 72 are measured in duplicate. MiRNAs were removed from the candidate list if their replicate did not show concordant regulation.

source_name: THP1 cell line, MLL/AF9_knockdown via siRNA3

label_protocol: no labeling

growth_protocol: THP1 cells were cultured in RPMI1640, 10%FCS and 1%Pen/Strep up to day 6 of experiments and in DMEM/Ham's F12, 0.5%FCS from day 6 of experiments onwards.

extract_protocol: total RNA was isolated via miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations. 350 ng total RNA per array card were employed. Pre-amplification was performed according to supplier's protocol.

treatment_protocol: THP1 cells were treated on day 0, day 3 and day 6 with siRNAs. RNA was harvested on day 8 of experiments.

tag: cell line

tag: treatment

value: MLL-AF9 knockdown


title: THP1-MLL/AF9_knockdown-siRNA4

source_name: THP1 cell line, MLL/AF9_knockdown via siRNA4


title: THP1-control_non_targeting_siRNA#1

source_name: THP1 cell line, control non-targeting-siRNA1

value: control


title: wild type_vs_Δrnc mutant_rep1


title: Complicated malaria 1

description: Gene expression of parasite isolates


title: Uncomplicated malaria 2

description: Gene expression of parasite isolates


title: THP1-control_non_targeting_siRNA#2

source_name: THP1 cell line, control non-targeting-siRNA2


title: MDA-MB-231/E1A_Dicer knockdown-2_rep1

city: Miaoli County

first: Jen-Liang

last: Su

address: No.35, Keyan Road, Zhunan, Miaoli County 35053, Taiwan.

institute: National Health Research Institutes

description:
E1A/shD-2-rep1
Identical sample type hybridized in each channel

hyb_protocol: Labeled miRNA targets enriched by NanoSep 100K (Pall Corporation, USA) were hybridized to the  Mouse & Rat miRNA OneArray® with Phalanx hybridization buffer using OneArray® Hybridization Chamber.

scan_protocol: MiRNAs-Chips were scanned by an Axon 4000B scanner (Molecular Devices, Sunnyvale, CA, USA).

data_processing:
The signal intensity of each spot was process by R program.
Spots that passed the criteria were normalized by 75% media scaling normalization method. Normalized spot intensities were transformed to gene expression log2 ratios between the control and treatment groups.

source_name: MDA-MB-231 E1A-transfected/Dicer knockdown #2 breast cancer cells

label_protocol: MiRNAs were prepared from 2.5 μg total RNA samples and labeled using miRNA ULSTM Labeling Kit (Kreatech Diagnostics, The Netherlands).

growth_protocol: MDA-MB-231 cells were grown in Dulbecco's modified Eagle's medium (DMEM/F12) containing 10% fetal bovine serum in 37℃ with 5% CO2.

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


title: MDA-MB-231/E1A_Dicer knockdown-2_rep2

description:
E1A/shD-2-rep2
Identical sample type hybridized in each channel


title: MDA-MB-231/E1A_Dicer knockdown-1_rep1

description:
E1A/shD-1-rep1
Identical sample type hybridized in each channel

source_name: MDA-MB-231 E1A-transfected/Dicer knockdown #1 breast cancer cells


title: Uncomplicated malaria 1

description: Gene expression of parasite isolates


title: MDA-MB-231/E1A_rep1

description:
MDA-231/E1A-rep1
Identical sample type hybridized in each channel

source_name: MDA-MB-231 E1A-transfected breast cancer cells


title: MDA-MB-231/vector_rep1

description:
MDA-231-rep1
Identical sample type hybridized in each channel

source_name: MDA-MB-231 breast cancer cells


title: MDA-MB-231/vector_rep2

description:
MDA-231-rep2
Identical sample type hybridized in each channel


title: HUMAN-PVs-AF-MALE [477405_(HTA-2_0)]

city: shenyang

first: zhi

last: li

state: liaoning

address: NO. 83 wenhua road

institute: the Shenyang Northern Hospital

description: Gene expression data from myocardial sleevesof pulmonary veins in AF

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.

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

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

source_name: myocardial sleeves of pulmonary veins in AF

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

treatment_protocol: myocardial sleeves of pulmonary veins(PVs) were obtained at the time of Mitral valve surgery or Mitral valve surgery combined with Maze III surgery.A piece of atrial tissue of a maximumsize of approximately 4x3 mm（male, n =12; female, n=12）immediately snap frozen in liquid. nitrogen, and stored at −80°C.The derived site of PVs is Left atrial incision of Mitral valve surgery.No complication occurred as a consequence of tissue sampling.

value: MALE


title: HUMAN-PVs-AF-FEMALE [1001252643_(HTA-2_0)]

value: FEMALE


title: HUMAN-PVs-CON-FEMALE [502821_(HTA-2_0)]

description: Gene expression data from myocardial sleevesof pulmonary veins in non-AF

source_name: myocardial sleeves of pulmonary veins in non-AF


title: HUMAN-PVs-AF-MALE [1000663180_(HTA-2_0)]


title: HUMAN-PVs-CON-FEMALE [711470_(HTA-2_0)]


title: HUMAN-PVs-AF-MALE [4779897_(HTA-2_0)]


title: HUMAN-PVs-AF-FEMALE [706696_(HTA-2_0)]


title: HUMAN-PVs-CON-MALE [4945331_(HTA-2_0)]


title: THP1-miR-511-5p-mimic-Exp2

hyb_protocol: 1.65 µg of each Cy3-labeled cRNA sample was fragmented and prepared for hybridization (Gene Expression Hybridization Kit, Agilent Technologies, Santa Clara, CA, USA). cRNA samples were hybridized at 65°C for 17 hours on seperate Whole Human Genome Microarrays (4x44K format). Afterwards microarrays were washed with increasing stringency using Gene Expression Wash Buffers (Agilent Technologies, Santa Clara, CA, USA) followed by drying with acetonitrile (Sigma-Aldrich, St. Louis, MO, USA).

scan_protocol: Fluorescent signal intensities were detected with Scan Control 8.4.1 Software on the Agilent DNA Microarray Scanner and extracted from the images usingFeature Extraction 10.7.3.1 Software (both Agilent Technologies, Santa Clara, CA, USA). Analysis of the Agilent One-Color RNA Spike-In Plot was used to ensure equal and good performance of each single labeling and hybridization experiment.

data_processing: Green channel intensities from each data file were read for further analysis. Quality weights for each spot on every array were assigned, based on several quality measures (e.g. saturation, uniformity, population outlier) produced by Agilent Feature Extraction v10.5.1.1 (FE). Background correction was performed by FE and scaling was used for between array normalization.   Hierarchical clustering of arrays and principal component analyses were performed in collaboration with Dr. Philipp Pagel (Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universität München) with the statistical language R (R Development Core Team 2008) using packages from the Bioconductor framework (Gentleman, et al. 2004). Analysis of differential expression between knockdown and control treatments was carried out in R with the limma package (Smyth 2004) which fits a linear model for each gene and computes a moderated t-statistic and its p-value (Smyth 2005). Limma is part of the Bioconductor project (Gentleman, et al. 2004). Adjustment for multiple testing was done using the method by Benjamini and Hochberg (Benjamini, et al. 1995). Thus, logarithmic fold-change (logFC), p-value of the moderated t test and p-value after correcting for multiple testing were generated.

source_name: transfected THP1 cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) employing T7 RNA polymerase.

growth_protocol: After miR-mimic trasnfection, THP1 cells were cultured in DMEM/Ham's F12, 0.5% FCS, 1 g/L BSA for two days.

extract_protocol: total RNA was isolated via miRNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.

treatment_protocol: THP1 cells were treated once with 30 nM miRNA mimics. RNA was harvested on day 2 of experiments.

value: miR-511-5p mimic


title: OV_T5

status: Public on Jan 15 2016

city: Nantes

first: Rossana

last: Sussarellu

address: Rue de l'Ile d'Yeu

department: Ressources Biologiques et Environnement

institute: Ifremer

hyb_protocol: Hybridization was performed using the Agilent Gene expression hybridization kit (5188-5242), with 1.65 μg of labeled RNA for 16 h at 65 °C Hybridization was performed using the Agilent Gene expression hybridization kit (5188-5242), with 1.65 μg of labeled RNA, randomly onto 48 different slides for 16 h at 65 °C

scan_protocol: Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters

data_processing:
Quantile normalization was performed on background-corrected features with the limma package. Filtering step was performed according to Agilent Feature Extraction software results on spot quality and spot intensity reliability. Missing values were imputed with Impute package.
Quantile normalization was performed on background-corrected features with the limma package. Filtering step was performed according to Agilent Feature Extraction software results on spot quality and spot intensity reliability. Missing values were imputed with Impute package.

organism: Magallana gigas

label_protocol:
200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color
200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color

growth_protocol:
Standard hatchery conditions to induce gametogenesis (2 months at 17°C fed at libitum)
Standard hatchery conditions to induce gametogenesis

extract_protocol:
Total RNA extracted using Extract-all Reagent (Eurobio), 1,5 mL per 50 mg of tissue or 20000 oocytes
Total RNA extracted using Extract-all Reagent (Eurobio), 1,5 mL per 50 mg of tissue

treatment_protocol:
Polystyrene microplastic exposure at 32 µg.L-1
Gonadal maturation

value: Oocytes

value: Gamete

tag: developmental stage


title: HUMAN-PVs-CON-MALE [4958228_(HTA-2_0)]


title: OV_T4


title: HUMAN-PVs-AF-FEMALE [1002131318_(HTA-2_0)]


title: THP1-control-mimic-#1-Exp1


title: HUMAN-PVs-CON-MALE [711814_(HTA-2_0)]


title: HUMAN-PVs-CON-FEMALE [711269_(HTA-2_0)]


title: OV_T3


title: THP1-control-mimic-#1-Exp2


title: OV_T8


title: OV_T2


title: G_T3T18

value: Gonad

value: Female


title: G_T3T19


title: OV_P2


title: G_T3M44


title: G_T3T17


title: OV_P1


title: G_T3M33


title: G_T3M35


title: G_T3T1


title: G_T3M41


title: G_T3M27


title: G_T1T2


title: G_T1T1


title: G_T1M43


title: G_T1T17


title: G_T1T19


title: OV_P4


title: G_T3M25


title: G_T1M44


title: G_T1M33


title: G_T1T10


title: G_T1M26


title: G_T3M34


title: D_T3T18


title: G_T1M41


title: G_T1M37


title: D_T3T12


title: D_T3T1


title: D_T3T17


title: D_T3T11


title: G_T1M25


title: D_T3M41


title: D_T3T19


title: D_T3M35


title: MDA-MB-231/E1A_Dicer knockdown-1_rep2

description:
E1A/shD-1-rep2
Identical sample type hybridized in each channel


title: D_T3M34


title: G_T3T11


title: D_T3M25


title: D_T3M33


title: D_T1T1


title: D_T1T2


title: D_T1M44


title: D_T3M28


title: D_T1T19


title: D_T3M27


title: D_T1M43


title: D_T1T10


title: D_T3M44


title: G_T3M28


title: D_T1M41


title: THP1-miR-511-5p-mimic-Exp1


title: D_T1T17


title: D_T1M37


title: D_T1M26


title: D_T1M33


title: TX 20053

city: La Jolla

first: Sunil

last: Kurian

state: CA

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: The Gene Titan Hybridization, Wash and Stain Kit for 3' Array Plates PN 901530 (Affymetrix) is used to hybridize the fragmented aRNA  to a multi peg Gene HT U133PM Array Plate. Hybridization is carried out for 16 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). Automatic staining and washing is carried out in the Gene Titan Instrument.

scan_protocol: The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.

data_processing: Probes to Import: Interrogating Probes and Control Probes,  Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish, Probe filtering: Exclude probes with an absolute value < 4 and low variance (< 20 percentile), Median values used for probes with identical RefSeq IDs, Exclude probes without Refseq IDs (e.g. '---').

source_name: Kidney Biopsy Tissue

label_protocol: Total RNA is amplified, labeled and fragmented with GeneChip 3'IVT Plus Reagent kit PN 902416 (Affymetrix).

extract_protocol: RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX  PAXgene Blood miRNA kit PN763134 (QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer.

value: Kidney Biopsy Tissue

tag: disease state

value: normal functioning transplants TX


title: SIX1 KD, 66cl4 sh70, replicate 3

city: Salt Lake City

first: Aik Choon

last: Tan

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: Gene expression data from baseline, before treatment

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Gene 1.1 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed and normalized by using Affymetrix Power Tools (apt-probeset-summarize) with RMA.

source_name: Tumor

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

value: tumor 66cl4

value: transduced with Six1 KD sh70


title: SIX1 KD, 66cl4 sh70, replicate 2


title: TX 20068


title: D_T1M25


title: SIX1 KD, 66cl4 control, replicate 3

value: transduced with Six1 control


title: SIX1 KD, 66cl4 sh70, replicate 1


title: SIX1 KD, 66cl4 control, replicate 2


title: AR 20061

value: Interstitial fibrosis and tubular atrophy with acute rejection AR


title: TX 12948


title: TX 12960


title: TX 12946


title: SIX1 KD, 66cl4 control, replicate 1


title: ADNR 12943

value: acute dysfunction but no rejection ADNR


title: IFTA 12961

value: Interstitial fibrosis and tubular atrophy IFTA


title: TX 12944


title: AR 20020


title: TX 12935


title: AR 20024


title: TX 12894


title: TX 12893


title: TX 12936


title: MDA-MB-231/E1A_rep2

description:
MDA-231/E1A-rep2
Identical sample type hybridized in each channel


title: TX 12891


title: TX 12880


title: TX 20046


title: TX 12872


title: TX 12870


title: IFTA 12871


title: IFTA_i 12947

value: Interstitial fibrosis and tubular atrophy with inflammation IFTA_i


title: TX 12875


title: TX 12949


title: IFTA 12869


title: TX 12867


title: TX 12761


title: TX 12759


title: TX 12755


title: TX 12754


title: TX 12756


title: IFTA 12757


title: TX 12751


title: TX 12753


title: TX 12728


title: TX 12734


title: TX 12732


title: IFTA_AR 12692

value: Interstitial fibrosis and tubular atrophy with inflammation with acute rejection IFTA_AR


title: IFTA 12694


title: TX 12706


title: TX 12750


title: TX 12700


title: TX 12729


title: TX 12717


title: TX 12731


title: TX 12733


title: IFTA 12720


title: TX 12727


title: IFTA_AR 12752


title: TX 12726


title: TX 12725


title: IFTA 12686


title: TX 12730


title: TX 12704


title: TX 12432


title: AR 12317


title: IFTA 12314


title: IFTA_AR 12318


title: ADNR 12434


title: TX 12263


title: IFTA 12311


title: IFTA_AR 12313


title: TX 12012


title: ADNR 12147


title: TX 12252


title: AR 12072


title: IFTA_AR 12148


title: TX 12253


title: IFTA 12149


title: IFTA_AR 12144


title: TX 12064


title: TX 12254


title: ADNR 12146


title: TX 12251


title: TX 12067


title: TX 12011


title: IFTA_AR 12071


title: IFTA 11951


title: IFTA 12256


title: TX 11952


title: TX 11953


title: ADNR 12145


title: TX 11950


title: IFTA 11948


title: IFTA 11949


title: AR 11690


title: TX 11691


title: TX 11872


title: TX 11692


title: IFTA_AR 11584


title: AR 11593


title: ADNR 11570


title: TX 11599


title: ADNR 11571


title: AR 11449


title: IFTA_i 11946


title: AR 11450


title: TX 12760


title: TX 11597


title: ADNR 11601


title: TX 11522


title: TX 11521


title: AR 11440


title: IFTA 11416


title: ADNR 11447


title: AR 11384


title: AR 11448


title: IFTA 11383


title: AR 11443


title: TX 11444


title: AR 11421


title: IFTA_AR 11381


title: IFTA_AR 11382


title: ADNR 11497


title: IFTA_i 11446


title: AR 11380


title: ADNR 11346


title: AR 11349


title: IFTA 11282


title: TX 11327


title: IFTA_i 11332


title: ADNR 11267


title: ADNR 11338


title: TX 11160


title: TX 11331


title: ADNR 11283


title: IFTA_i 11266


title: TX 11279


title: TX 11162


title: IFTA_i 11024


title: TX 11158


title: IFTA_AR 11025


title: AR 11019


title: AR 11018


title: IFTA_AR 11013


title: AR 11027


title: IFTA 11026


title: IFTA_AR 11017


title: IFTA_AR 11016


title: IFTA_AR 11014


title: TX 10995


title: IFTA 11009


title: TX 12868


title: IFTA 11010


title: IFTA_AR 11008


title: IFTA 10993


title: IFTA_AR 11020


title: IFTA_i 11012


title: TX 10988


title: TX 10992


title: TX 10990


title: IFTA_AR 10982


title: TX 10953


title: AR 10886


title: IFTA 10884


title: AR 10906


title: ADNR 10888


title: AR 10883


title: TX 10905


title: AR 10879


title: AR 10899


title: TX 10898


title: TX 10843


title: IFTA_AR 10880


title: TX 10850


title: IFTA_AR 10849


title: AR 10777


title: AR 10821


title: AR 10774


title: TX 10871


title: IFTA 10868


title: AR 10885


title: ADNR 10737


title: IFTA 10911


title: TX 10950


title: TX 10870


title: AR 10882


title: IFTA_i 10733


title: IFTA 10845


title: ADNR 10732


title: TX 10869


title: AR 10730


title: IFTA_i 10731


title: TX 10705


title: AR 10703


title: TX 10698


title: TX 10702


title: AR 10641


title: TX 10695


title: ADNR 10638


title: IFTA_AR 10637


title: IFTA_AR 10639


title: ADNR 10643


title: IFTA 10555


title: TX 10556


title: TX 10553


title: IFTA 10636


title: TX 10557


title: ADNR 10532


title: IFTA 10530


title: AR 10503


title: ADNR 10645


title: ADNR 10531


title: TX 10518


title: ADNR 10517


title: IFTA 10508


title: IFTA 10507


title: ADNR 10534


title: TX 10516


title: AR 10535


title: AR 10536


title: TX 10486


title: AR 10502


title: IFTA 10499


title: ADNR 10495


title: ADNR 10640


title: AR 10504


title: ADNR 10441


title: AR 10438


title: TX 10482


title: ADNR 10440


title: IFTA_AR 10437


title: AR 10484


title: AR 10434


title: TX 10485


title: ADNR 10445


title: ADNR 10436


title: IFTA 10430


title: IFTA 10431


title: IFTA_AR 10433


title: IFTA_AR 10428


title: AR 10427


title: IFTA 10432


title: ADNR 10414


title: IFTA_AR 10420


title: TX 10408


title: IFTA_AR 10403


title: AR 10407


title: IFTA 10312


title: AR 10417


title: AR 10418


title: IFTA_AR 10404


title: TX 10413


title: ADNR 10308


title: AR 10411


title: AR 10306


title: IFTA 10423


title: IFTA_AR 10406


title: AR 10426


title: AR 10419


title: IFTA 10357


title: IFTA 10313


title: ADNR 10416


title: TX 10305


title: AR 10275


title: AR 10309


title: AR 10304


title: ADNR 10274


title: AR 10266


title: IFTA 10242


title: ADNR 10224


title: ADNR 10272


title: ADNR 10222


title: ADNR 10219


title: AR 10218


title: IFTA 10221


title: IFTA 10206


title: ADNR 10211


title: IFTA_i 10210


title: IFTA 10205


title: AR 10208


title: Ptf1a interneurons_P5_biological rep2

city: New York

first: Jay

last: Bikoff

institute: Columbia University

description:
FACS-isolated interneurons
Ptf1a_2_P5

hyb_protocol: The Affymetrix GeneChip Hybridization control kit and GeneChip Hybridization, Wash, and Stain kit were used to hybridize samples to Affymetrix 430 2.0 GeneChip arrays, with fluidics performed on the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: Data analysis was performed in Partek Genomics Suite version 6.6 using the GC Robust Multi-array Average (GCRMA) normalization algorithm, followed by one-way ANOVA to analyze relative fold-enrichment in V1 vs dI4 interneuron populations.

source_name: Spinal dI4/dILA interneurons

label_protocol: Purified RNA (between 1-5 ng) was amplified using the Ovation Pico WTA System (NuGEN), followed by fragmentation and biotin labeling of 5 mg of single-stranded cDNA with the Encore Biotin Module (NuGEN).

extract_protocol: After purifying spinal interneurons by FACS, RNA was isolated using the Absolutely RNA Nanoprep Kit (Stratagene) and quantified with the RiboGreen RNA quantitation kit (Invitrogen) on a 20/20n Luminometer (Turner Biosystems).

value: Spinal cord

tag: cell type

value: spinal dI4/dILA interneurons

value: Ptf1a-Cre; Rosa.lsl.YFP


title: V1 interneurons_P0_biological rep3

description:
FACS-isolated interneurons
En1_3_P0

source_name: Spinal V1 interneurons

value: spinal V1 interneurons

value: En1-Cre; Rosa.lsl.YFP


title: TX 10140


title: V1 interneurons_P0_biological rep2

description:
FACS-isolated interneurons
En1_2_P0


title: Ptf1a interneurons_P5_biological rep1

description:
FACS-isolated interneurons
Ptf1a_1_P5


title: Ptf1a interneurons_P0_biological rep3

description:
FACS-isolated interneurons
Ptf1a_3_P0


title: V1 interneurons_P5_biological rep1

description:
FACS-isolated interneurons
En1_1_P5


title: Ptf1a interneurons_P0_biological rep1

description:
FACS-isolated interneurons
Ptf1a_1_P0


title: V1 interneurons_P5_biological rep2

description:
FACS-isolated interneurons
En1_2_P5


title: TX 10165


title: P1

city: Kunming

first: Kunhua

last: Wang

state: Yunnan

address: #295 Xichang Road

department: Department of Gastrointestinal and Hernia Surgery

institute: First affiliated Hospital of Kunming Medical University

hyb_protocol: 25 μL labeled samples were mixed with 25 μL of hybridization buffer, denatured at 95°C for 2 min and incubated on ice for 2 min. Hybridization was performed at 56°C for 16-20h in Nimblegen Systems, Inc., Madison, WI, USA. Subsequently, Wash buffer kit (Exiqon) was used for array washing.

scan_protocol: Slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA).

data_processing: Scanned images were imported into GenePix Pro 6.0 software (AxonInstruments, Foster City, CA, USA) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs with intensities≥30 in all samples were chosen for the calculation of normalization factor. Expressed data were normalized using the Median normalization.

source_name: HIV-infected antiretroviral therapy-naive individual

label_protocol: miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used for miRNA labeling. 1 μg of RNA was topped up to 2 μL with water and 1 μL of CIP buffer and CIP enzyme (Exiqon) were added. The samples were mixed and incubated at 37°C for 30 min, before reaction termination at 95°C for 5 min. 3μL of labeling buffer, 1.5μL of fluorescent label (Hy3™), 2.0 μL of DMSO and 2.0 μL of labeling enzyme were added for reaction at 16°C for 1h. Terminate the reaction at 65°C for 15 min.

extract_protocol: Total RNA from each colon tissue sample was isolated using TRIzol reagent (Invitrogen) and purified with miRNeasy mini kit (Qiagen).

value: colon biopsy


title: P3


title: P2


title: V1 interneurons_P0_biological rep1

description:
FACS-isolated interneurons
En1_1_P0


title: V1 interneurons_P5_biological rep3

description:
FACS-isolated interneurons
En1_3_P5


title: Ptf1a interneurons_E12.5_biological rep3

description:
FACS-isolated interneurons
Ptf1a_3_E12


title: Ptf1a interneurons_P0_biological rep2

description:
FACS-isolated interneurons
Ptf1a_2_P0


title: V1 interneurons_E12.5_biological rep3

description:
FACS-isolated interneurons
En1_3_E12


title: N3

source_name: HIV-negative healthy individual


title: Ptf1a interneurons_E12.5_biological rep2

description:
FACS-isolated interneurons
Ptf1a_2_E12


title: N2


title: V1 interneurons_E12.5_biological rep2

description:
FACS-isolated interneurons
En1_2_E12


title: Ptf1a interneurons_E12.5_biological rep1

description:
FACS-isolated interneurons
Ptf1a_1_E12


title: N1


title: V1 interneurons_E12.5_biological rep1

description:
FACS-isolated interneurons
En1_1_E12


title: GCT44 - Yolk Sac Tumour cell line

city: Nottingham

first: Paul

middle: J

last: Scotting

address: Queen's Medical Centre

department: School of Life Sciences

institute: University of Nottingham

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Data was first preprocessed using the statistical software, R with packages provide by www.bioconductor.org. Data was preprocessed using the RMA method [66] and filtered such that probes which gave expression outputs below control background probes (recorded in the GeneChip) for all four cell lines were excluded. Fold changes in expression between each probe of each cell lines relative to Seminoma were calculated, and annotation packages were used to assign gene information to each probe set. The data was exported as a .txt file in order to be read and analysed in Excel. The Excel tool PivotTable was used to assign average expression intensity values to each gene.

source_name: Yolk Sac Tumour (Roach, 1994)

label_protocol: not provided

growth_protocol: Cell lines were cultured in Dulbecco’s Modified Eagle Medium (EC, Teratoma and YST) and RPMI-1640 media (Seminoma) (Sigma-Aldrich). containing 10% fetal bovine serum (Sigma-Aldrich). and 1% Penicillin/Streptomycin (Sigma-Aldrich).

extract_protocol: RNA extraction was performed using the RNeasy extraction kit (Qiagen) according to the manufacturer protocol. RNA was eluted with RNAse-free water.

tag: histological_subtype_primary tumor

value: Yolk Sac Tumour

tag: anatomical localisation

value: human testicular GCT


title: GCT27 - Embryocarcinoma cell line

source_name: Embryocarcinoma (Andrews, 1998)

value: Embryocarcinoma


title: NT2D1 - Teratoma cell line

source_name: Teratoma (Andrews, 1998)

value: Teratoma

value: human testicular GCT lung metastasis


title: TCam-2 - Seminoma cell line

source_name: Seminoma (de Jong, 2008)

value: Seminoma


title: C 4006

city: Copenhagen

first: Lasse

last: Folkersen

address: Artellerivej

department: Bioinformatics

country: Denmark

institute: National Genome Center

description:
Aorta intima-media from transplant donor
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: GeneChip® Fluidics Station 450

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Affymetrix Power tools 1.10.0 apt-probeset-summarize using pre-defined function RMA with no further arguments

source_name: Aorta intima-media

label_protocol: Whole Transcript Sense Target Labeling

growth_protocol: Biopsies were obtained at surgery from mammary artery and dilated and non-dilated ascending aorta.

extract_protocol: Total RNA was isolated using Trizol (BRL-Life Technologies) and RNeasy Mini kit (Qiagen, Crawley, UK) including treatment with RNase-free DNase set (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Incubated with RNAlater (Ambion, Austin, TX) and homogenized with a FastPrep using Lysing Matrix D tubes (Qbiogene, Irvine, CA).

tag: number of aortic cusps

tag: aorta dilation

value: No


title: C 4010


title: C 4002


title: C 4011


title: C 4003


title: C 4004


title: C 4007


title: C 4009


title: C 4008


title: C 4005


title: AAdv 96

description:
Aorta adventitia from patient undergoing valve surgery and/or surgery for aortic aneurysm
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Aorta adventitia

value: Yes


title: C 4012


title: AAdv 87


title: AAdv 89


title: AAdv 66


title: AAdv 51


title: AAdv 85


title: C 4000


title: C 4001


title: AAdv 77


title: AAdv 9


title: AAdv 4


title: AAdv 46


title: AAdv 55


title: AAdv 45


title: ADNR 10492

value: Kidney Biopsy Tissue

value: acute dysfunction but no rejection ADNR


title: AAdv 3


title: AAdv 49


title: AAdv 286


title: AAdv 28


title: AAdv 225


title: AAdv 188

value: Borderline


title: AAdv 266


title: AAdv 32


title: AAdv 301


title: AAdv 297


title: AAdv 283


title: AAdv 199


title: AAdv 232


title: AAdv 184


title: AAdv 191


title: AAdv 131


title: AAdv 11


title: AAdv 13


title: AAdv 177


title: AAdv 120


title: AAdv 105


title: AAdv 116


title: AAdv 161


title: AAdv 100


title: AMed 85

description:
Aorta intima-media from patient undergoing valve surgery and/or surgery for aortic aneurysm
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: AMed 9


title: AMed 87


title: AAdv 112


title: AMed 8


title: AMed 66


title: AMed 56


title: AMed 96


title: AMed 58


title: AMed 53


title: AMed 49


title: AMed 46