title: Seedlings -control rep.3 [re-analysis]

city: Little Rock

first: Mariya

last: Khodakovskaya

state: AR

address: 2801 S. University Avenue

department: Biology

institute: University of Arkansas at Little Rock

description:
Gene expression data from tomato seedlings (11 day-old) (cv. Micro-Tom)
EA09092_280570_Tomato_NL-3

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Tomato Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400. Hybridization reactions to Affymetrix Maize GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

scan_protocol: Scanning of the Affymetrix Tomato GeneChip expression arrays were done using the services of Expression Analysis Inc. (http://www.expressionanalysis.com/).

data_processing: Data extraction was also performed by Expression Analysis Inc.  Expression values were calculated using the Affymetrix GeneChip Operating System (GCOS) and were based on the difference of the PM (Perfect Match) signal and MM (Mismatch) signal at each of the probe pairs.  The fluorescent signal values from each array were normalized to achieve similar overall intensity between arrays.  The fluorescent signal values of any hybridization reaction were then multiplied by a scaling factor to make their (trimmed) mean intensity equal to 500.  The scaling factor is unique to each hybridization reaction and is in general below 10

organism: Solanum lycopersicum

source_name: 11 day old seedlings

label_protocol: Complimentary RNA (cRNA) was produced according to Affymetrix Eukaryotic two-cycle target labeling assay as specified in the GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com/support/technical/manual/expression_manual.affx).

growth_protocol: Tomato seeds were collected after 1 day of placement on regular MS medium or medium supplemented with Helical MWCNT. Another part was germinated germinated on on regular MS medium or medium supplemented with Helical MWCNT and 11 days of cultivation.

extract_protocol: Seeds and seedlings were isolated and immediately frozen in liquid nitrogen. The harvested seeds and seedlings  were then transferred to the laboratory and grinded to a fine powder in mortars and pestles using liquid nitrogen.  Total RNA was extracted using a RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: No special treatments before harvesting were carried out.

tag: cultivar

value: cv. Micro-Tom

value: Seedlings

tag: growth medium

value: regular MS agar medium


title: myometrium_primary cell culture_30 hours_rep 6

status: Public on May 30 2016

type: RNA

city: Nottingham

first: Marios

last: Georgiou

address: Queen's Medical Centre

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

description: pregnant, term no labor

hyb_protocol: Standard NASC hybridization protocol

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: The raw CEL files were normalized using the RMA background correction with quantile normalization, log base 2 transformation and mean probe-set summarization with adjustment for GC content. Differentially expressed genes (DEG) were identified by a two-way ANOVA, and p-values were adjusted using the FDR (false-discovery rate) method to correct for multiple comparisons. DEG were considered significant if p-value was £ 0.05 at a fold change (FC) of < -2 and > 2 with FDR <0.5.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: myometrium, passage 4 primary cells, 30 hours

label_protocol: Total RNA according to the standard Affymetrix protocol (WT Expression Kit User Manual, 2010, Affymetrix).

growth_protocol: Tissue was immediately plated in DMEM (as per treatment protocol). Cells were cultured in DMEM supplemented with 10% fetal calf serum and penicillin/streptomycin. Once confluent at passage 4, the media was refreshed to DMEM supplemented with penicillin/streptomycin alone and cultured as per 'treatment protocol'.

extract_protocol: Trizol extraction of total RNA was performed using a Trizol® Plus RNA Purification kit (Thermo Fisher Scientific, Ambion, Abgene Ltd., West Sussex, UK)

treatment_protocol: Tissue and cells were cultured for a period of 30 hours in DMEM supplemented with penicillin/streptomycin

tag: sample type

value: primary cell culture

tag: tissue

value: myometrium


title: Seedlings-Helical MWCNTs (25 ug/ml) rep.1

country: USA

description:
Gene expression data from tomato seedlings (20day-old) (cv. Micro-Tom)
EA09092_280571_Tomato_NL-4

source_name: 11 day old seedlings_exposed to Helical MWCNT

tag: genotype/variation

value: wild type

tag: age

value: MS medium supplemented with Helical MWCNTs (25 ug/ml)


title: colonic mucosa from control group 1

city: Hangzhou

first: Shiyi

last: Wang

state: Zhejiang Province

address: No. 54, Youdian Road

department: Department of Gastroenterology

country: China

institute: The First Affiliated Hospital of Zhejiang Chinese Medical University

description:
Coding and non-coding gene expression data of colonic mucosa from control group 1.
con1_(HTA-2_0)

hyb_protocol: After fragmentation, samples were hybridized in GeneChip® Hybridization Oven 645 according to the user manual of GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: After the wash protocols completing, the probe arrays were scanned by using the GeneChip® Scanner 3000 7G according to instructions for scanning probe arrays.

data_processing: The data were analyzed and standardized by SST-RMA algorithm using Affymetrix Expression Console™ Software (version 1.3).

source_name: Control_human colonic mucosa

label_protocol: Biotinylated samples were prepared according to the user manual of GeneChip® WT Terminal Labeling Kit.

growth_protocol: Fresh specimens of colon tissues form control patients were washed with RNAase free water and put into RNAlater(Qiagen) immediately and frozen in -80℃.

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

treatment_protocol: Fresh specimens of colon tissues form MC's patients were washed with RNAase free water and put into RNAlater(Qiagen) immediately and frozen in -80℃.

tag: subject group

value: control patient group

value: colon biopsies from endoscopy


title: myometrium_cell line_30 hours_rep 3

source_name: myometrium, cell line, 30 hours

value: cell line


title: ifng + dexa_2

city: Cologne

first: Mario

last: Fabri

address: Kerpener Strasse 62

department: Dermatology

country: Germany

institute: University of Cologne

hyb_protocol: Agilent Gene Expression Hybridization Kit

scan_protocol: Agilent G2595C Scanner

data_processing:
Genespring XII
Normalization: Shift to 75 percentile

source_name: ifng + dexa_2

label_protocol: Agilent low-Input QuickAmp Labeling Kit

extract_protocol: Trizol for RNA isolation

tag: cell type

value: Monocyte-derived macrophages

tag: agent

value: dexamethasone/interferon-gamma


title: colonic mucosa from control group 5

description:
Coding and non-coding gene expression data of colonic mucosa from control group 5.
con5_(HTA-2_0)


title: ifng_2

value: interferon-gamma


title: Seedlings-Helical MWCNTs (25 ug/ml) rep.3

description:
Gene expression data from tomato seedlings (11 day-old) (cv. Micro-Tom)
EA09092_280573_Tomato_NL-6


title: Seedlings-Helical MWCNTs (25 ug/ml) rep.2

description:
Gene expression data from tomato seedlings (20day-old) (cv. Micro-Tom)
EA09092_280572_Tomato_NL-5


title: media_3

value: media


title: myometrium_explant_30 hours_rep 6

description: pregnant, term no labor

source_name: myometrium, explant, 30 hours

value: tissue


title: colonic mucosa from control group 2

description:
Coding and non-coding gene expression data of colonic mucosa from control group 2.
con2_(HTA-2_0)


title: media_2


title: ifng + dexa_1

source_name: ifng + dexa_1


title: myometrium_cell line_30 hours_rep 2


title: Pre- and postnatal saccharin2

city: New Haven

first: Marina

last: Picciotto

state: CT

address: 301 Cedar Street Congess place/YPI 4th floor

department: Psychiatry

institute: Yale University

description: Gene expression data from adult female mouse brain recevied saccharin or nicotine during gestational period

hyb_protocol: Samples are hybridized to arrays for 16 hours at 45C. The standard array is then washed and stained using the fluidics station and then scanned.

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

data_processing: The data were analyzed with limma R package as linear regression fitting.

organism: Mus musculus

source_name: Female mouse received nicotine during gestational period

label_protocol: Single stranded cDNA is then converted into double stranded cDNA and purified using the Affymetrix Cleanup Module. An in vitro transcription (IVT) reaction is then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA.

growth_protocol: NIH Guide for Care and Use of Laboratory Animals. C57BL/6J mice (Jackson Laboratories, Bar Harbor, ME) used in the developmental nicotine exposure studies acclimated for 1 week, had ad libitum food and water and a 12-h light–dark cycle (lights on at 7AM).

extract_protocol: Mouse tissue samples were transferred to Trizol reagent  and disrupted with a Dounce tissue homogenizer. Chloroform was added and samples were centrifuged. The aqueous phase was transferred to a column from an RNeasy tissue kit (Qiagen, Redwood City, CA) and RNA was isolated according to the manufacturer's recommendations. Subsequently, RNAs from 4 animals were pooled to obtain 5 pools per experimental group (20 subjects total).

treatment_protocol: Saccharin or Nicotine soultion delivered to pregnant mice from the conception. Nicotine and saccharin water weand from offspring 21 day old. The animal let live undisturbed by 90 day old

value: brain

tag: tissue compartment

value: cerebral cortex

value: 90 day old


title: myometrium_cell line_30 hours_rep 1


title: ifng_1


title: dexa_2

value: dexamethasone


title: Seedlings -control rep.2 [re-analysis]

description:
Gene expression data from tomato seedlings (11 day-old) (cv. Micro-Tom)
EA09092_280569_Tomato_NL-2

value: cv. Micro-Tom

value: Seedlings

value: regular MS agar medium


title: Seedlings -control rep.1 [re-analysis]

description:
Gene expression data from tomato seedlings (11 day-old) (cv. Micro-Tom)
EA09092_280568_Tomato_NL-1

value: wild type


title: Pre- and postnatal saccharin1


title: myometrium_snap frozen immediately_rep 6

description: pregnant, term no labor

source_name: myometrium, 0 hours

value: myometrium


title: Pre- and postnatal nicotine 1

source_name: Female mouse received saccharin during gestational period


title: dexa_1


title: Pre- and postnatal nicotine 2


title: media_1


title: macrophage-Ctrl siRNA

city: shang hai

first: Qian

last: Zhang

address: xiangyin road 800

institute: Second military medical university

description: Gene expression after 48hr in Control siRNA transfected peritoneal macrophages

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: peritoneal macrophages transfected with Control siRNA

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: mouse peritoneal macrophages transfected with Dnmt3a siRNA and 48 hr later extracted total RNA

value: peritoneal macrophages

tag: gender

value: male


title: myometrium_snap frozen immediately_rep 5

description: pregnant, term no labor


title: Seeds -control rep.3 [re-analysis]

description:
Gene expression data from tomato seeds (1day-old) (cv. Micro-Tom)
EA09092_278468_Tomato_NS-3

source_name: Seeds_1 day after placement on MS medium

value: 1 day after placement of medium

value: Seeds


title: myometrium_explant_30 hours_rep 5

description: pregnant, term no labor


title: Seeds -control rep.2 [re-analysis]

description:
Gene expression data from tomato seeds (1day-old) (cv. Micro-Tom)
EA09092_278467_Tomato_NS-2


title: Seeds -control rep.1 [re-analysis]

description:
Gene expression data from tomato seeds (1day-old) (cv. Micro-Tom)
EA09092_278466_Tomato_NS-1


title: Seeds-Helical MWCNTs (25 ug/ml) rep.2

description:
Gene expression data from tomato seedlings (11 day-old) (cv. Micro-Tom)
EA09092_278470_Tomato_NS-5

source_name: Seeds_1 day after placement on MS medium+Helical MWCNT

value: MS medium supplemented with Helical MWCNTs (25 ug/ml)


title: myometrium_primary cell culture_30 hours_rep 5

description: pregnant, term no labor

value: primary cell culture


title: myometrium_primary cell culture_30 hours_rep 3

description: pregnant, term no labor


title: myometrium_explant_30 hours_rep 3

description: pregnant, term no labor


title: myometrium_snap frozen immediately_rep 4

description: pregnant, term no labor


title: Seeds-Helical MWCNTs (25 ug/ml) rep.1

description:
Gene expression data from tomato seeds (1day-old) (cv. Micro-Tom)
EA09092_278469_Tomato_NS-4


title: macrophage-Dnmt3a siRNA

description: Gene expression after 48hr in Dnmt3a siRNA transfected peritoneal macrophages

source_name: peritoneal macrophages transfected with Dnmt3a siRNA


title: tr.2

city: New York

first: Timothy

middle: Cragin

state: NY

address: 1130 St. Nicholas Av

department: Medicine

institute: Columbia University

hyb_protocol: 12 μg of RNA dissolved in 300 μL of buffer was hybridized to Mouse Genome 430A. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm (v.2.30.0) as implemented in Biobase (v.1.28.0)/Affy (v.1.36.0)/Bioconductor/R (v.2.15.2).

source_name: Gr1+Cd11b+ splenic cells from Tff2-/- mice treated with Tff2 and Csf2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water. Tff2-/- mice (n=4, males, 16 weeks old) on C57BL/6 background were given 3% DSS water for 5 days following plain water and sacrificed on day 14 later. Splenic Cd11b+Gr1+ cell were sorted with a BD FACSAria Flow Cytometer and split into two halves.

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

treatment_protocol: One half was cultured for 7 days at density 1x106 cells/ml in 3 ml complete RPMI-1640 medium (10% fetal calf serum, ES grade, Invitrogen) supplemented with Csf2 (5 nM) alone while another half with an addition of 3 µM mouse recombinant Tff2.

tag: strain background

value: 16  wks

tag: treated with

value: 5nM Csf2 + 3 µM mouse recombinant Tff2

value: spleen

value: Gr1+Cd11b+ cells


title: tr.4


title: myometrium_explant_30 hours_rep 2

description: pregnant, term no labor

value: tissue


title: ctrl.4

source_name: Gr1+Cd11b+ splenic cells from Tff2-/- mice treated with Csf2

value: 5nM Csf2


title: tr.1


title: myometrium_primary cell culture_30 hours_rep 2

description: pregnant, term no labor


title: ctrl.3


title: myometrium_primary cell culture_30 hours_rep 4

description: pregnant, term no labor


title: ctrl.1


title: tr.3


title: myometrium_snap frozen immediately_rep 2

description: pregnant, term no labor


title: 6 days +p

city: Jena

first: khabat

last: vahabi

state: Deutschland

address: Dornburger Straße 159

department: plant physiology

institute: Friedrich-Schiller-Universität

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

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

organism: Arabidopsis thaliana

source_name: Arabidopsis root after 6 days  interaction with fungi control (with fungi)

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

growth_protocol: Arabidopsis thaliana WT (ecotype Columbia-0) seeds were surface-sterilized and placed on Petri dishes containing MS nutrient medium (Murashige and Skoog 1962). After cold treatment at 4°C for 48 h, plates were incubated for 10 days at 22°C under continuous illumination (65 μmol m-2 sec-1, light from the top). Piriformospora indica was cultured for three weeks at 22-24°C on Aspergillus-minimal medium (Hill and Kaefer 2001; Johnson et al. 2011: Section A, B)

extract_protocol: Total RNA was isolated from both roots and shoots of WT seedlings after 2 and 6 days of co-cultivation with P. indica using RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Twelve day-old (48 h cold treatment and 10 days of illumination) Arabidopsis seedlings of equal sizes were selected for co-cultivation experiments. They were transferred to PNM plates with a nylone membrane on the top (Johnson et al. 2011, Section C1 - Method 1) and expose to a fungal (KM) plug or a KM plug without fungal hyphae (5 mm in diameter). The plags were placed 3 cm away from the closest root part . The light intensity (80 ± 5 μmol m-2 sec-1) was checked every third day to ensure that both P. indica- and mock-treated seedlings receive equal amounts of light.

value: root

tag: genotype

value: Columbia wild type

value: 16 days


title: heart_Cell_exp1_VTS2_rep1

status: Public on May 29 2016

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
977
Gene expression data after treatment.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomics Suite.

label: Biotin

source_name: heart in chronic heart failure, treated with cardiac progenitor cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip Whole Transcript (WT) Sense Target labelling assay kit, Affymetrix).

growth_protocol: Nude mice underwent left anterior descending artery ligation (permanent) to induce a MI. Three weeks later, mice were in chronic heart failure. Mice with sufficiently decreased cardiac function (ejection fraction < 50%) were included in the study.

extract_protocol: Total RNA was extracted from explanted, frozen whole hearts by phenol chloroform extraction (Trizol reagent).

treatment_protocol: Mice were randomly allocated among four treatment groups: cardiovascular progenitor cells, the total extracellular vesicles secreted by those cardiovascular progenitor cells in 48 hours, alpha-MEM control, and sham. Cell-treated mice each received 500000 cells. EV-treated mice each received the EV secreted by 500000 cells. Cell grafts were done by injecting 10uL of suspension at each of three sites within the peri-infarcted myocardium. This was accomplished by closed chest, trans-cutaneous, echo-guided injections. Sham-operated animals were anesthetised and the needle inserted three times into the myocardium without injection.

tag: phenotype

value: immunodeficient (nude)

value: excised heart

tag: disease state

value: chronic heart failure

tag: treatment

value: cardiac progenitor cells

tag: time point

value: 6 weeks after treatment


title: myometrium_primary cell culture_30 hours_rep 1

description: pregnant, term no labor

source_name: myometrium, passage 4 primary cells, 30 hours

value: myometrium


title: heart_Cell_exp1_VTS1_rep1

description:
695
Gene expression data after treatment.


title: myometrium_explant_30 hours_rep 4

description: pregnant, term no labor


title: heart_Ves_exp1_VTS2_rep1

description:
610
Gene expression data after treatment.

source_name: heart in chronic heart failure, treated with extracellular vesicles

value: cardiac progenitor cell-secreted extracellular vesicles (EVs)


title: ctrl.2

value: male


title: 6 days -p

source_name: Arabidopsis root after 6 days, control (without fungi)


title: myometrium_explant_30 hours_rep 1

description: pregnant, term no labor


title: 2 days +p

source_name: Arabidopsis root after 2 days  interaction with fungi control (with fungi)

value: 12 days


title: heart_Ctrl_exp1_VTS1_rep1

description:
634
Gene expression data after treatment.

source_name: heart in chronic heart failure, treated with alpha-MEM control

value: alpha-MEM control


title: heart_Ctrl_exp9_VTS3_rep1

description:
301
Gene expression data after treatment.


title: 2 days -p

source_name: Arabidopsis root after 2 days, control (without fungi)


title: heart_Sham_exp9_VTS3_rep1

description:
286
Gene expression data after treatment.

source_name: heart in chronic heart failure, sham operated

value: sham operated


title: myometrium_snap frozen immediately_rep 1

description: pregnant, term no labor

source_name: myometrium, 0 hours


title: heart_Ves_exp9_VTS3_rep1

description:
300
Gene expression data after treatment.


title: heart_Cell_exp9_VTS3_rep1

description:
308
Gene expression data after treatment.


title: pre-vaccination blood sample from donor R155

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

institute: Northwestern University

description:
P162_R155_prevax
pre-vaccination blood transcriptional profilling

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using Genome Studio software (Illumina).

data_processing: Raw probe intensities were preprocessed using the R (version 3.2.1) statistical language. Missing values were imputed using the KNN algorithm implemented in the R package impute (version 1.42.0). Log2 transformation was performed for variance stabilisation and followed by quantile normalization as implemented in Bioconductor software package limma (version 3.24.15).

organism: Macaca mulatta

source_name: Blood sample from donor R155

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: total RNA was extracted using Agencourt RNAdvance Blood Kit. The isolated total RNA was checked for quantity and quality using a NanoDrop 2000c (Thermo Fisher Scientific) and an Experion Electrophoresis System. Samples with an RQI classification ≥7.0 were selected to proceed downstream to amplification. Samples were normalized at 50ng for input and amplified using Illumina TotalPrep RNA amplification kits (Ambion) according to the manufacturer’s protocol.

tag: donor

tag: vaccination group

tag: vaccination time

value: pre-vaccination

tag: time after immunization

value: pre

tag: number of siv challenge to infection

value: Blood


title: post-1st immunization blood sample from donor P899

description:
P162_P899_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P899

value: post-1st immunization

value: 24 hours

tag: tissue


title: post-1st immunization blood sample from donor R163

description:
P162_R163_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor R163


title: pre-vaccination blood sample from donor P899

description:
P162_P899_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P901

description:
P162_P901_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)

source_name: Blood sample from donor P901

value: post-3rd immunization


title: post-3rd immunization blood sample from donor R163

description:
P162_R163_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P901

description:
P162_P901_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P901

description:
P162_P901_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-1st immunization blood sample from donor R159

description:
P162_R159_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor R159


title: pre-vaccination blood sample from donor P898

description:
P162_P898_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P898


title: post-1st immunization blood sample from donor R155

description:
P162_R155_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor R163

description:
P162_R163_prevax
pre-vaccination blood transcriptional profilling


title: heart_Ves_exp1_VTS1_rep1

description:
608
Gene expression data after treatment.

value: immunodeficient (nude)


title: Seeds-Helical MWCNTs (25 ug/ml) rep.3

description:
Gene expression data from tomato seedlings (11 day-old) (cv. Micro-Tom)
EA09092_278471_Tomato_NS-6

source_name: Seeds_1 day after placement on MS medium+Helical MWCNT

tag: cultivar

value: cv. Micro-Tom

tag: genotype/variation

value: wild type

tag: age

value: 1 day after placement of medium

value: Seeds

tag: growth medium

value: MS medium supplemented with Helical MWCNTs (25 ug/ml)


title: pre-vaccination blood sample from donor R159

description:
P162_R159_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P891

description:
P162_P891_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P891


title: post-3rd immunization blood sample from donor P898

description:
P162_P898_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-1st immunization blood sample from donor P897

description:
P162_P897_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P897

value: neg


title: post-3rd immunization blood sample from donor R155

description:
P162_R155_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P897

description:
P162_P897_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P898

description:
P162_P898_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P894

description:
P162_P894_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P894


title: post-1st immunization blood sample from donor P894

description:
P162_P894_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P899

description:
P162_P899_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-1st immunization blood sample from donor P891

description:
P162_P891_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P894

description:
P162_P894_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-3rd immunization blood sample from donor P897

description:
P162_P897_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-3rd immunization blood sample from donor R159

description:
P162_R159_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P891

description:
P162_P891_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P888

description:
P162_P888_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P888


title: pre-vaccination blood sample from donor P890

description:
P162_P890_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P890


title: post-3rd immunization blood sample from donor P890

description:
P162_P890_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: myometrium_snap frozen immediately_rep 3

description: pregnant, term no labor

tag: sample type

value: tissue

value: myometrium


title: post-1st immunization blood sample from donor P884

description:
P162_P884_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P884


title: post-1st immunization blood sample from donor P890

description:
P162_P890_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P884

description:
P162_P884_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P884

description:
P162_P884_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P868

description:
P162_P868_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P868


title: post-3rd immunization blood sample from donor P868

description:
P162_P868_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P857

description:
P162_P857_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P857


title: pre-vaccination blood sample from donor P888

description:
P162_P888_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P858

description:
P162_P858_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)

source_name: Blood sample from donor P858


title: post-3rd immunization blood sample from donor P888

description:
P162_P888_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P864

description:
P162_P864_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P864


title: post-1st immunization blood sample from donor P853

description:
P162_P853_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P853


title: post-1st immunization blood sample from donor P858

description:
P162_P858_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-1st immunization blood sample from donor P864

description:
P162_P864_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P853

description:
P162_P853_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P853

description:
P162_P853_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P877

description:
P162_P877_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P877


title: post-1st immunization blood sample from donor P857

description:
P162_P857_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P857

description:
P162_P857_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P877

description:
P162_P877_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P877

description:
P162_P877_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P858

description:
P162_P858_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P864

description:
P162_P864_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P868

description:
P162_P868_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P847

description:
P162_P847_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P847


title: post-3rd immunization blood sample from donor P852

description:
P162_P852_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)

source_name: Blood sample from donor P852


title: post-3rd immunization blood sample from donor P839

description:
P162_P839_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)

source_name: Blood sample from donor P839


title: pre-vaccination blood sample from donor P839

description:
P162_P839_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P842

description:
P162_P842_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P842


title: pre-vaccination blood sample from donor P843

description:
P162_P843_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P843


title: post-3rd immunization blood sample from donor P842

description:
P162_P842_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-3rd immunization blood sample from donor P838

description:
P162_P838_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)

source_name: Blood sample from donor P838


title: post-1st immunization blood sample from donor P852

description:
P162_P852_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P842

description:
P162_P842_prevax
pre-vaccination blood transcriptional profilling


title: pre-vaccination blood sample from donor P838

description:
P162_P838_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P843

description:
P162_P843_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P852

description:
P162_P852_prevax
pre-vaccination blood transcriptional profilling


title: pre-vaccination blood sample from donor P837

description:
P162_P837_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P837


title: post-1st immunization blood sample from donor P838

description:
P162_P838_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P843

description:
P162_P843_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-1st immunization blood sample from donor P787

description:
P162_P787_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P787


title: post-3rd immunization blood sample from donor P837

description:
P162_P837_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P773

description:
P162_P773_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P773


title: pre-vaccination blood sample from donor P847

description:
P162_P847_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P837

description:
P162_P837_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P787

description:
P162_P787_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P839

description:
P162_P839_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P773

description:
P162_P773_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-3rd immunization blood sample from donor P847

description:
P162_P847_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-3rd immunization blood sample from donor P787

description:
P162_P787_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P833

description:
P162_P833_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P833


title: post-1st immunization blood sample from donor P833

description:
P162_P833_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P833

description:
P162_P833_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-1st immunization blood sample from donor P773

description:
P162_P773_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P770

description:
P162_P770_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P770


title: post-3rd immunization blood sample from donor P770

description:
P162_P770_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P767

description:
P162_P767_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P767


title: post-3rd immunization blood sample from donor P767

description:
P162_P767_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-1st immunization blood sample from donor P753

description:
P162_P753_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P753


title: post-3rd immunization blood sample from donor P753

description:
P162_P753_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P742

description:
P162_P742_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P742


title: post-1st immunization blood sample from donor P770

description:
P162_P770_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P753

description:
P162_P753_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P708

description:
P162_P708_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P708


title: pre-vaccination blood sample from donor P755

description:
P162_P755_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P755


title: post-1st immunization blood sample from donor P755

description:
P162_P755_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-1st immunization blood sample from donor P726

description:
P162_P726_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P726


title: pre-vaccination blood sample from donor P708

description:
P162_P708_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P742

description:
P162_P742_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P692

description:
P162_P692_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P692


title: post-1st immunization blood sample from donor P700

description:
P162_P700_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P700


title: post-3rd immunization blood sample from donor P755

description:
P162_P755_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P700

description:
P162_P700_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P692

description:
P162_P692_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P742

description:
P162_P742_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-3rd immunization blood sample from donor P700

description:
P162_P700_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P726

description:
P162_P726_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P767

description:
P162_P767_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-1st immunization blood sample from donor P708

description:
P162_P708_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P734

description:
P162_P734_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P734


title: pre-vaccination blood sample from donor P692

description:
P162_P692_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P734

description:
P162_P734_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-1st immunization blood sample from donor P734

description:
P162_P734_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P668

description:
P162_P668_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P668


title: post-3rd immunization blood sample from donor P726

description:
P162_P726_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P668

description:
P162_P668_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P668

description:
P162_P668_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-1st immunization blood sample from donor P662

description:
P162_P662_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P662


title: pre-vaccination blood sample from donor P661

description:
P162_P661_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P661


title: post-3rd immunization blood sample from donor P639

description:
P162_P639_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P639


title: post-1st immunization blood sample from donor P639

description:
P162_P639_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P662

description:
P162_P662_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P661

description:
P162_P661_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-3rd immunization blood sample from donor P662

description:
P162_P662_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P639

description:
P162_P639_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P636

description:
P162_P636_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P636


title: pre-vaccination blood sample from donor P628

description:
P162_P628_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P628


title: pre-vaccination blood sample from donor P625

description:
P162_P625_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P625


title: pre-vaccination blood sample from donor P636

description:
P162_P636_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P636

description:
P162_P636_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-1st immunization blood sample from donor P615

description:
P162_P615_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P615


title: post-1st immunization blood sample from donor P621

description:
P162_P621_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P621


title: post-3rd immunization blood sample from donor P621

description:
P162_P621_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P621

description:
P162_P621_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P628

description:
P162_P628_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: pre-vaccination blood sample from donor P615

description:
P162_P615_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P435

description:
P162_P435_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P435


title: post-3rd immunization blood sample from donor P625

description:
P162_P625_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-3rd immunization blood sample from donor P615

description:
P162_P615_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: pre-vaccination blood sample from donor P435

description:
P162_P435_prevax
pre-vaccination blood transcriptional profilling


title: post-1st immunization blood sample from donor P436

description:
P162_P436_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P436


title: post-1st immunization blood sample from donor P625

description:
P162_P625_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-1st immunization blood sample from donor P628

description:
P162_P628_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P436

description:
P162_P436_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P436

description:
P162_P436_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-3rd immunization blood sample from donor P435

description:
P162_P435_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-1st immunization blood sample from donor P431

description:
P162_P431_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor P431


title: pre-vaccination blood sample from donor P382

description:
P162_P382_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P382


title: post-3rd immunization blood sample from donor P382

description:
P162_P382_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/Alum boosting (week 12)


title: post-3rd immunization blood sample from donor P263

description:
P162_P263_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P263


title: post-3rd immunization blood sample from donor P431

description:
P162_P431_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)


title: post-1st immunization blood sample from donor P382_rep1

description:
P162_P382_post1st_rep1
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: post-1st immunization blood sample from donor P263

description:
P162_P263_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: pre-vaccination blood sample from donor P431

description:
P162_P431_prevax
pre-vaccination blood transcriptional profilling


title: post-3rd immunization blood sample from donor P120

description:
P162_P120_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P120


title: post-3rd immunization blood sample from donor M935

description:
P162_M935_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor M935


title: post-1st immunization blood sample from donor P382

description:
P162_P382_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)


title: louis-00379: Brain_CG_5

status: Public on May 28 2016

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: Brain

tag: diseasestate

value: Classic glioblastoma

tag: survival (days)

tag: vital status

value: Alive

tag: organismpart

value: Brain

tag: biosourcetype


title: louis-00379: Brain_NG_7

scan_protocol: See mage-tab files linked to series entry for additional details

value: Non-classic glioblastoma


title: MSCD-SF-Cre-GFP P16

city: Silver Spring

first: BIJU

last: ISSAC

address: 503 Robert Grant Ave, Rm 2W123

department: Military HIV Research Program

institute: Walter Reed Army Institute of Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was preprocessed on GeneSpring GX 13.0 from Agilent. Raw data was quantile normalized and log2 transformed

source_name: Mouse bone marrow

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

growth_protocol: Transduced MSCD-SF were cultured in complete DMEM for 2 days and subconfluent cells were harvested.

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

treatment_protocol: No additional treatment except lentivirus trnasduction described in overall design

tag: genotype

tag: strain

value: C57 BL6 background

value: 6~8 weeks

value: bone marrow


title: louis-00379: Brain_CO_2

data_processing: See mage-tab files linked to series entry for additional details

value: Classic anaplastic oligodendroglioma


title: MSCD-SF-Cre-GFP P19


title: MSCD-SF-GFP2 P20


title: pre-vaccination blood sample from donor M935

description:
P162_M935_prevax
pre-vaccination blood transcriptional profilling

tag: donor

tag: vaccination group

value: pre-vaccination

value: pre

value: Blood


title: louis-00379: Brain_NO_9

label_protocol: See mage-tab files linked to series entry for additional details


title: louis-00379: Brain_NO_13

extract_protocol: See mage-tab files linked to series entry for additional details

value: Dead


title: pre-vaccination blood sample from donor P120

description:
P162_P120_prevax
pre-vaccination blood transcriptional profilling

tag: vaccination time

tag: time after immunization


title: post-1st immunization blood sample from donor P120

description:
P162_P120_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

value: post-1st immunization

value: 24 hours

tag: number of siv challenge to infection

tag: tissue


title: MSCD-SF-GFP2 P16


title: louis-00379: Brain_NG_13


title: louis-00379: Brain_CO_1


title: louis-00379: Brain_NG_10


title: louis-00379: Brain_CG_3


title: louis-00379: Brain_NG_14


title: louis-00379: Brain_CG_7


title: louis-00379: Brain_NO_6


title: louis-00379: Brain_CG_6


title: IRF4KO_GMIL4_MoDC_2

city: Saint Louis

first: Carlos

middle: Gustavo

last: Briseno

state: Missouri

address: 660 S Euclid

institute: Washington University School of Medicine

hyb_protocol: Hybed onto Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Standard Affymetrix protocol

data_processing: Data was processed using RMA summarization and quartile normalization using Arraystar ver. 5

source_name: IRF4 C57Bl/6

label_protocol: Ambion WT Expression kit, Genechip WT Terminal Labeling and Controls Kit

growth_protocol: WT Ly6Chi BM monocytes were differentiated into Mo-DCs by culturing in GM-CSF alone or GM-CSF and IL-4 for 72 hours. IRF4KO Ly6Chi BM monocytes were differentiated into Mo-DCs by culturing in GM-CSF and IL-4 for 72 hours. Splenocytes were harvested by digestion with Collagenase B and Dnase I. BM marrow cells were harvested by crushing of femurs and tibias.

extract_protocol: WT and IRF4KO Mo-DCs were sorted as Ly-6Clo CD11c+, WT BM monocytes were gated as Ter-119– CD45.2+ MHC-IIlo Ly-6G– CD115+. Monocyte subsets were sorted as Ly-6ChiTremL4– and Ly-6Clo TremL4+. WT CD24+ DCs were sorted as B220– CD11c+ MHCII+ Sirp-a– CD24+

treatment_protocol: Mice were analyzed at steady state

tag: gender

value: Female

tag: cell type

value: Mo-DC

tag: treatment

value: Ly6ChiTremL4- bone marrow monocytes GM-CSF + IL-4 for 72 hours


title: IRF4KO_GMIL4_MoDC


title: WT_GMOnly_MoDC_2

source_name: WT C57Bl/6

value: WT

value: Ly6ChiTremL4- bone marrow monocytes GM-CSF for 72 hours


title: WT_GM_IL4_MoDC_2


title: louis-00379: Brain_CG_11

value: Classic glioblastoma

value: Brain


title: post-3rd immunization blood sample from donor P661

description:
P162_P661_post3rd
transcriptional profilling of blood taken 24h post-ALVAC-SIV/gp120/MF59 boosting (week 12)

source_name: Blood sample from donor P661

value: post-3rd immunization


title: louis-00379: Brain_NO_5


title: louis-00379: Brain_NG_12

value: Non-classic glioblastoma


title: louis-00379: Brain_CG_2


title: louis-00379: Brain_NO_11

value: Alive


title: louis-00379: Brain_NO_1


title: louis-00379: Brain_NG_8


title: louis-00379: Brain_NO_7


title: louis-00379: Brain_CO_4

value: Classic anaplastic oligodendroglioma


title: louis-00379: Brain_CG_1


title: louis-00379: Brain_NG_9


title: louis-00379: Brain_NG_3


title: louis-00379: Brain_NO_14


title: louis-00379: Brain_NG_6


title: louis-00379: Brain_CO_5


title: louis-00379: Brain_NG_1


title: louis-00379: Brain_NO_12


title: louis-00379: Brain_CG_10


title: louis-00379: Brain_CG_13


title: louis-00379: Brain_NO_4


title: louis-00379: Brain_CG_12


title: louis-00379: Brain_NG_2


title: louis-00379: Brain_NO_2


title: louis-00379: Brain_CG_14


title: louis-00379: Brain_CG_8


title: louis-00379: Brain_NO_15


title: louis-00379: Brain_NO_8


title: louis-00379: Brain_CG_4


title: louis-00379: Brain_CG_9


title: louis-00379: Brain_CO_3


title: louis-00379: Brain_CO_6


title: louis-00379: Brain_NG_11


title: louis-00379: Brain_NG_5


title: louis-00379: Brain_CO_7


title: louis-00379: Brain_NG_4


title: louis-00379: Brain_NO_10


title: louis-00379: Brain_NO_3


title: Ing

city: Shanghai

first: Hao

last: Ying

address: 320 YUEYANG ROAD

department: INS

institute: SIBS,CAS

hyb_protocol: miRNA array hybridization was performed using miRCURYTM Array Hybridization buffer and Wash buffer

scan_protocol: Axon GenePix 4000B microarray scanner and GenePix pro V6.0 were used for miRNA array scanning and analysis.

data_processing: GenePix pro V6.0 is used to read the raw intensity of the image. The intensity of green signal is calculated after background subtraction and four Replicated spots of each probe on the same slide have been calculated the median. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data = (Foreground-Background) / median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

source_name: inguinal adipose tissue

label_protocol: miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon) was used for miRNA labeling.

extract_protocol: Brown adipose tissue, inguinal adipose tissue, epidydimal adipose tissue, gastrocnemius muscle, and soleus muscle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. RNasey Mini Kit(Qiagen p/n 74104) was used to obtain 1 ug of total RNA for miRNA labeling.

value: inguinal adipose tissue

tag: age

value: post natal month 2-3


title: Ep

source_name: epidydimal adipose tissue

value: epidydimal adipose tissue


title: Gas

source_name: gastrocnemius muscle

value: gastrocnemius muscle


title: Bat

source_name: brown adipose tissue

value: brown adipose tissue


title: E058 in vivo, biological rep1

city: Yangzhou

first: Qingqing

last: Gao

state: Jiangsu

address: Yangzhou wenhui Road 12

department: Colledge of Veterianry medicine

institute: Yangzhou university

description: Gene expression profile of APEC O2 strain E058 in vivo

hyb_protocol: The GeneChip® E. coli Genome 2.0 Array (Affymetrix) was hybridized with the labeled cDNA.

scan_protocol: The microarray was washed and scanned with the GeneChip® Scanner 3000 (Affymetrix)

organism: Escherichia coli APEC O2

source_name: bacteria harvested from blood of chickens

label_protocol: The cDNA was labeled with GeneChip® DNA Labeling Reagent (Affymetrix)

growth_protocol: To prepare the in vitro samples, APEC strain E058 was grown statically at 37 °C in 10 mL of LB broth until the absorbance at 600 nm (A600) reached 0.4. To prepare the in vivo samples, the bacteria was harvested from cardiac blood  in 1-day-old chickens at 5 hours post infection.

extract_protocol: Total RNA from both the in vitro and in vivo samples of APEC E058 was extracted with the RNAiso Plus kit (Takara, Dalian, China) and further purified with NucleoSpin RNA Clean-up (Macherey-Nagel, Germany), according to the manufacturers’ instructions.

treatment_protocol: The in vitro bacterial samples were harvested by centrifugation (5000 × g, 10 min, 4 °C) and the pellet was frozen at −70 °C until RNA extraction. The in vivo bacterial samples were harvested with two-step centrifugation. We first centrifuged the collected anticoagulated blood samples at low speed to remove the abundant red and white blood cells and collected the upper serum layer. We then used high-speed centrifugation to precipitate the bacteria from the serum.

tag: condition

value: in vivo


title: Sol

source_name: soleus muscle

value: soleus muscle


title: E058 in vitro, biological rep1

description: Gene expression profile of APEC O2 strain E058 in vitro

source_name: bacteria grown in LB in vitro

value: in vitro


title: E058 in vivo, biological rep3


title: E058 in vivo, biological rep2


title: E058 in vitro, biological rep2


title: HCT116_SB590885

city: Kolkata

first: Gaurisankar

last: Sa

state: West Bengal

address: p-1/12, CIT Scheme VII M

department: Molecular Medicine

country: India

institute: Bose Institute

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: HCT116 p53+/+ cells

growth_protocol: Cells were grown in DMEM with PS and 10%FBS.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with

treatment_protocol: 80% confluent cells were treated with control vehicle or 10nM SB590885

tag: cell line


title: HCT116_CONTROL


title: Primary tumor breast - BCPT0025 piece 2

city: Stockholm

first: John

last: Lövrot

address: Cancer Center Karolinska

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Fragmented and biotinylated cRNA (10 μg) was hybridized at 45C for 16 h to a high density oligonucleotide custom made Affymetrix array chip (Human Cancer G110 Array). The arrays were then washed, stained with streptavidin-phycoerythrin (SAPE, final concentration of 10 μg/ml).

scan_protocol: The arrays were scanned according to the manufacturer’s instructions (Affymetrix Genechip® Technical Manual, 2001). The scanned images were inspected for the presence of obvious defects (artifacts or scratches) on the array. In case of visible microarray artifacts, the sample was rehybridized and rescanned on new chips using the same fragmented probe.

data_processing: Probe intensities were extracted, background corrected, normalized and summarized to probeset expression using the rma function in the R/Bioconductor package affy with the default settings

source_name: Primary tumor breast

label_protocol: Preparation of in vitro transcription (IVT) products and oligonucleotide array hybridization and scanning were performed according to the Affymetrix protocol (Santa Clara, CA, USA). In brief, the amount of starting total RNA for each probe preparation varied between 2 and 5 μg. IVT reactions were performed in batches to generate biotinylated cRNA targets, which were subsequently chemically fragmented at 95C for 35 min.

extract_protocol: Extraction of total RNA from frozen tumors was carried out using the Qiagen RNeasy Mini Kit (Qiagen, Germany). The integrity of the RNA extracts was tested on an Agilent 2100 Bioanalyzer (Agilent Technologies, Rockville, MD), measuring the 28S: 18S ribosomal RNA ratio. RNA extracts of high quality were stored at -70C until microarray analyses.

tag: ID

tag: piece

tag: setnr

tag: case-control status

value: Primary tumor breast


title: Primary tumor breast - BCPT0460 piece 2


title: Primary tumor breast - BCPT0044 piece 2


title: Primary tumor breast - BCPT0520 piece 2


title: Primary tumor breast - BCPT0276 piece 2


title: Primary tumor breast - BCPT0075 piece 2


title: Primary tumor breast - BCPT0867 piece 2


title: Primary tumor breast - BCPT0135 piece 2


title: Primary tumor breast - BCPT0315 piece 2


title: Primary tumor breast - BCPT0146 piece 2


title: Primary tumor breast - BCPT0774 piece 2


title: Primary tumor breast - BCPT0263 piece 2


title: pre-vaccination blood sample from donor P263

description:
P162_P263_prevax
pre-vaccination blood transcriptional profilling

source_name: Blood sample from donor P263

value: pre-vaccination

value: pre

value: Blood


title: Primary tumor breast - BCPT0492 piece 2


title: Primary tumor breast - BCPT0177 piece 2


title: Primary tumor breast - BCPT0397 piece 2


title: Primary tumor breast - BCPT0414 piece 2


title: Primary tumor breast - BCPT0978 piece 2


title: Primary tumor breast - BCPT0446 piece 2


title: Primary tumor breast - BCPT0422 piece 2


title: Primary tumor breast - BCPT0823 piece 2


title: Primary tumor breast - BCPT0732 piece 2


title: Primary tumor breast - BCPT0328 piece 2


title: Primary tumor breast - BCPT0628 piece 2


title: Primary tumor breast - BCPT0597 piece 2


title: Primary tumor breast - BCPT0029 piece 2


title: Primary tumor breast - BCPT0753 piece 2


title: Primary tumor breast - BCPT0889 piece 2


title: Primary tumor breast - BCPT0919 piece 2


title: Primary tumor breast - BCPT0777 piece 2


title: Primary tumor breast - BCPT0779 piece 2


title: Primary tumor breast - BCPT0209 piece 2


title: Primary tumor breast - BCPT0296 piece 2


title: Primary tumor breast - BCPT0904 piece 2


title: Primary tumor breast - BCPT0020 piece 2


title: Primary tumor breast - BCPT0247 piece 2


title: Primary tumor breast - BCPT0830 piece 2


title: Primary tumor breast - BCPT0550 piece 2


title: Primary tumor breast - BCPT0685 piece 2


title: Primary tumor breast - BCPT0879 piece 2


title: Primary tumor breast - BCPT0540 piece 2


title: Primary tumor breast - BCPT0916 piece 2


title: Primary tumor breast - BCPT0382 piece 2


title: Primary tumor breast - BCPT0013 piece 2


title: Primary tumor breast - BCPT0267 piece 2


title: Primary tumor breast - BCPT0423 piece 2


title: Primary tumor breast - BCPT0220 piece 2


title: HDFa_G2_2

city: Budapest

first: Vince

middle: Kornél

last: Grolmusz

address: Szentkirályi 46.

country: Hungary

institute: Semmelweis University

hyb_protocol: After RNA purification, labeled RNA was hybridized to Agilent 8×15K Human miRNA Microarray Release 12.0. slides, according to the manufacturer’s instructions.

scan_protocol: After washing, array scanning and feature extraction was performed by Agilent DNA Microarray Scanner and Feature Extraction Software 11.0.1.

data_processing: Data processing of raw microarray data was performed by GeneSpring software 12.6 following Agilent's recommendation. Total gene signal normalization at the 75th percentile of raw signal values and baseline transformation at the median of all samples following Agilent's recommendation.

source_name: HDFa

label_protocol: Total RNA (100 ng) was labeled with Cy3 and amplified using Low Input Quick Amp Labeling Kit according to the manufactureer's instructions.

extract_protocol: Total RNA was isolated using miRNesay Mini Kit (Qiagen), accordig to the manufacturer's instructions

value: HDFa

tag: cell cycle phase


title: HDFa_G1_2


title: HDFa_S_3

value: S


title: HDFa_G1_1


title: HDFa_S_2


title: HDFa_S_1


title: H295R_S_1


title: Primary tumor breast - BCPT0102 piece 2


title: H295R_G1_3


title: Primary tumor breast - BCPT0591 piece 2


title: Primary tumor breast - BCPT0249 piece 2


title: Primary tumor breast - BCPT0950 piece 2


title: H295R_G1_2


title: Primary tumor breast - BCPT0803 piece 2


title: Primary tumor breast - BCPT0848 piece 2


title: Primary tumor breast - BCPT0203 piece 2


title: Primary tumor breast - BCPT0409 piece 2


title: Primary tumor breast - BCPT0541 piece 2


title: Primary tumor breast - BCPT0885 piece 2


title: Primary tumor breast - BCPT0744 piece 2


title: post-1st immunization blood sample from donor M935

description:
P162_M935_post1st
transcriptional profilling of blood taken 24h post-ALVAC-SIV priming (week 0)

source_name: Blood sample from donor M935

tag: donor

value: post-1st immunization

value: 24 hours


title: H295R_S_2


title: Primary tumor breast - BCPT0997 piece 2


title: Primary tumor breast - BCPT0412 piece 2


title: HDFa_G2_1


title: H295R_G2_3


title: H295R_G2_1


title: Primary tumor breast - BCPT0972 piece 2


title: Primary tumor breast - BCPT0970 piece 2


title: H295R_G1_1


title: Primary tumor breast - BCPT0817 piece 2


title: H295R_G2_2


title: Primary tumor breast - BCPT0456 piece 2


title: Primary tumor breast - BCPT0186 piece 2


title: Primary tumor breast - BCPT0786 piece 2


title: H295R_G1_2

hyb_protocol: After RNA purification, labeled RNA was hybridized to Agilent Whole Human Genome Microarray slides, according to the manufacturer’s instructions.

scan_protocol: Agilent scanner, FE SW 11.0.1

label_protocol: Low Input QuickAmp Ver. 6.7

extract_protocol: Total RNA was isolated using miRNeasy Mini Kit (Qiagen), according to the manufacturer's instructions


title: Primary tumor breast - BCPT0741 piece 2


title: Primary tumor breast - BCPT0727 piece 2


title: H295R_G1_3


title: Primary tumor breast - BCPT0703 piece 2


title: Primary tumor breast - BCPT0164 piece 2


title: Primary tumor breast - BCPT0620 piece 2


title: Primary tumor breast - BCPT0983 piece 2


title: Primary tumor breast - BCPT0006 piece 2


title: H295R_G2_1


title: H295R_G1_1


title: H295R_S_2


title: H295R_G2_2


title: H295R_G2_3


title: Primary tumor breast - BCPT0512 piece 2

description: This tumor is an outlier when comparing gene-expression data for the original RNA (piece 1) and the re-extracted RNA (piece 2). It is one of two tumors from a bilateral BC patient.


title: HDFa_S_2

label_protocol: Total RNA (100 ng) was labeled with Cy3 and amplified using Low Input Quick Amp Labeling Kit according to the manufacturer's instructions.


title: Primary tumor breast - BCPT0893 piece 2


title: Primary tumor breast - BCPT0211 piece 2


title: HDFa_S_3


title: Primary tumor breast - BCPT0886 piece 2


title: Primary tumor breast - BCPT0026 piece 2


title: Primary tumor breast - BCPT0156 piece 2


title: Primary tumor breast - BCPT0469 piece 2


title: H295R_S_1


title: HDFa_G1_2


title: Primary tumor breast - BCPT0704 piece 2


title: HDFa_G2_3


title: Primary tumor breast - BCPT0260 piece 2


title: HDFa_S_1


title: liu-00258: C99 cy5 OSE cy3 745 610_635_nm

source_name: adenocarcinoma sporadic 99

tag: diseasestate

value: Ovarian Adenocarcinoma

tag: Sex

value: female

tag: organismstatus

value: premortem

tag: diseasestage

tag: genotype

value: sporadic

tag: developmentalstage

value: Adult

tag: individual

value: sporadic 99

tag: age (years)

tag: histology

value: adenocarcinoma (not otherwise specified)

tag: tumorgrading

tag: organismpart

value: Ovary

source_name: Ovarian surface epithelial cell line

value: Normal

tag: cellline

value: ovarian surface epithelial cell line


title: HDFa_G1_1

tag: cell line


title: Primary tumor breast - BCPT0363 piece 2

tag: ID

tag: piece

tag: setnr

tag: tissue

value: Primary tumor breast


title: Primary tumor breast - BCPT0488 piece 2

tag: case-control status


title: HeLa_G1_3

source_name: HeLa

value: HeLa

tag: cell cycle phase


title: HDFa_G2_1


title: HeLa_G1_2


title: liu-00258: C95 cy5 OSE cy3 710 620_635_nm

source_name: adenocarcinoma sporadic 95

tag: diseasestate

tag: Sex

tag: organismstatus

value: sporadic 95

value: serous


title: Primary tumor breast - BCPT0534 piece 2


title: Primary tumor breast - BCPT0595 piece 2


title: HeLa_S_2

value: S


title: HeLa_S_1


title: HeLa_G2_1


title: liu-00258: C87 cy5 OSE cy3 710 605_635_nm

source_name: adenocarcinoma sporadic 87

tag: diseasestage

tag: genotype

tag: developmentalstage

value: sporadic 87


title: Primary tumor breast - BCPT0535 piece 2


title: Primary tumor breast - BCPT0573 piece 2


title: Primary tumor breast - BCPT0536 piece 2


title: HeLa_G2_3


title: HDFa_G2_2

value: HDFa


title: Primary tumor breast - BCPT0569 piece 2


title: Primary tumor breast - BCPT0884 piece 2


title: liu-00258: C84 cy5 OSE cy3 710 620_635_nm

source_name: adenocarcinoma sporadic 84

value: Ovarian Adenocarcinoma

tag: individual

value: sporadic 84

tag: age (years)

tag: histology


title: HeLa_G2_2


title: liu-00258: C85 cy5 vs OSEcy3 770 630_635_nm

source_name: adenocarcinoma sporadic 85

value: female

value: premortem

value: sporadic 85

tag: tumorgrading

tag: organismpart

tag: cellline


title: liu-00258: C79 cy5 OSE cy3 675 600_635_nm

source_name: adenocarcinoma sporadic 79

value: sporadic

value: Adult

value: sporadic 79


title: Primary tumor breast - BCPT0436 piece 2

tag: ID

tag: piece


title: Primary tumor breast - BCPT0309 piece 2

tag: setnr

tag: tissue


title: Primary tumor breast - BCPT0681 piece 2

tag: case-control status


title: Primary tumor breast - BCPT0487 piece 2


title: Primary tumor breast - BCPT0151 piece 2


title: liu-00258: C77 cy5 vs OSEcy3 760 740_630_nm_635_nm

source_name: adenocarcinoma sporadic 77

tag: diseasestate

value: sporadic 77

value: Ovary

value: Normal


title: liu-00258: C49 cy5 OSE cy3_635_nm

source_name: adenocarcinoma sporadic 49

tag: Sex

value: sporadic 49

value: endometrioid

value: ovarian surface epithelial cell line


title: liu-00258: C46 cy5 OSE cy3 570 520_635_nm

source_name: adenocarcinoma sporadic 46

tag: organismstatus

value: sporadic 46

value: adenocarcinoma (not otherwise specified)


title: liu-00258: C16 cy5 OSE cy3 580 520_635_nm

source_name: adenocarcinoma sporadic 16

tag: diseasestage

value: sporadic 16

value: serous


title: liu-00258: C17 cy5 OSE cy3 590 520_635_nm

source_name: adenocarcinoma sporadic 17

value: Ovarian Adenocarcinoma

tag: genotype

value: sporadic 17


title: Primary tumor breast - BCPT0169 piece 2

source_name: Primary tumor breast

value: Primary tumor breast


title: Primary tumor breast - BCPT0736 piece 2


title: HeLa_G1_1

tag: cell line

value: HeLa

tag: cell cycle phase


title: liu-00258: C41 cy5 OSE cy3 690 580_635_nm

source_name: adenocarcinoma sporadic 41

value: female

value: premortem

value: sporadic

tag: developmentalstage

tag: individual

value: sporadic 41

tag: age (years)


title: liu-00258: C15 cy5 OSE cy3 660 600_635_nm

source_name: adenocarcinoma sporadic 15

value: Adult

value: sporadic 15

tag: histology

tag: tumorgrading

tag: organismpart

value: Ovary


title: liu-00258: C123 cy5 vs OSEcy3 740_630_nm_635_nm

source_name: adenocarcinoma sporadic 123

value: sporadic 123

value: Normal

tag: cellline


title: liu-00258: C42 cy5 OSE cy3 570 520_635_nm

source_name: adenocarcinoma sporadic 42

value: sporadic 42

value: ovarian surface epithelial cell line


title: liu-00258: C20 cy5 OSE cy3 680 580_635_nm

source_name: adenocarcinoma sporadic 20

value: sporadic 20

value: adenocarcinoma (not otherwise specified)

source_name: Ovarian surface epithelial cell line


title: liu-00258: C118 cy5 vs OSEcy3 765 620_635_nm

source_name: adenocarcinoma sporadic 118

value: Ovarian Adenocarcinoma

value: sporadic 118


title: liu-00258: C114cy5 vs OSEcy3 725 635_635_nm

source_name: adenocarcinoma sporadic 114

value: sporadic 114

value: serous


title: liu-00258: C117 cy5 vs OSEcy3 800 620_635_nm

source_name: adenocarcinoma sporadic 117

value: female

value: sporadic 117

value: endometrioid


title: liu-00258: C105 cy5 OSE cy3 810 620_635_nm

source_name: adenocarcinoma sporadic 105

value: premortem

value: sporadic

value: sporadic 105


title: liu-00258: C100 cy5 OSE cy3 740 620_635_nm

source_name: adenocarcinoma sporadic 100

value: Adult

value: sporadic 100

value: Ovary


title: liu-00258: B79 cy5 OSE cy3 690 560_635_nm

source_name: adenocarcinoma BRCA1-79

value: Normal


title: liu-00258: C1 cy5 OSE cy3 590 550_635_nm

source_name: adenocarcinoma sporadic 1

value: sporadic 1

value: ovarian surface epithelial cell line


title: liu-00258: C110 cy5 vs OSEcy3 730 580_635_nm

source_name: adenocarcinoma sporadic 110

value: sporadic 110

value: adenocarcinoma (not otherwise specified)


title: liu-00258: C111 cy5 vs OSEcy3 720 620_635_nm

source_name: adenocarcinoma sporadic 111

value: Ovarian Adenocarcinoma

value: sporadic 111


title: liu-00258: b74 cy5 OSE cy3 560 510_635_nm

source_name: adenocarcinoma BRCA1-74

value: serous


title: liu-00258: C107 cy5 vs OSEcy3 740 630_635_nm

source_name: adenocarcinoma sporadic 107

value: female

value: sporadic 107


title: liu-00258: C102 cy5 OSE cy3 825 620_635_nm

source_name: adenocarcinoma sporadic 102

value: sporadic 102


title: liu-00258: B80 cy5 vs OSEcy3 730 630_635_nm

source_name: adenocarcinoma BRCA1-80

value: premortem

value: endometrioid/clear cell


title: liu-00258: B78 cy5 vs OSEcy3 730 640_635_nm

source_name: adenocarcinoma BRCA1-78


title: liu-00258: B77 cy5 OSE cy3 660 590_635_nm

source_name: adenocarcinoma BRCA1-77


title: liu-00258: C103 cy5 OSE cy3 730 620_635_nm

source_name: adenocarcinoma sporadic 103

value: sporadic

value: sporadic 103


title: liu-00258: B70 cy5 OSE cy3 720 570_635_nm

source_name: adenocarcinoma BRCA1-70

value: IC

value: Adult

value: clear cell

source_name: Ovarian surface epithelial cell line


title: liu-00258: B62 cy5 OSE cy3 600 540_635_nm

source_name: adenocarcinoma BRCA1-62

value: endometrioid

value: Ovary

value: Normal


title: liu-00258: B63 cy5 OSE cy3 680 580_635_nm

source_name: adenocarcinoma BRCA1-63

value: ovarian surface epithelial cell line


title: liu-00258: B64 cy5 OSE cy3 590 550_635_nm

source_name: adenocarcinoma BRCA1-64

value: Ovarian Adenocarcinoma


title: liu-00258: B60 cy5 OSE cy3 620 520_635_nm

source_name: adenocarcinoma BRCA1-60


title: liu-00258: B55 cy5 OSE cy3 640 540_635_nm

source_name: adenocarcinoma BRCA1-55


title: liu-00258: B54 cy5 OSE cy3 710 605_635_nm

source_name: adenocarcinoma BRCA1-54


title: liu-00258: B61 cy5 OSE cy3 610 540_635_nm

source_name: adenocarcinoma BRCA1-61

value: adenocarcinoma (not otherwise specified)


title: liu-00258: B52-2 cy5 OSE cy3 720 620_635_nm

source_name: adenocarcinoma BRCA1-52-2

value: serous


title: liu-00258: B41 cy5 OSE cy3 710 605_635_nm

source_name: adenocarcinoma BRCA1-41

value: female


title: liu-00258: B40 cy5 OSE cy3 670 615_635_nm

source_name: adenocarcinoma BRCA1-40


title: cell_A3_rep3

city: Wu Xi

first: Dong-Xu

last: He

address: Jiangnan University

department: Jiangnan University

institute: National Engineering Laboratory for Cereal Fermentation Technology

description: gene expression

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to OE Human lncRNA Microarray V4.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions


title: liu-00258: B39 cy5 OSE cy3 700 610_635_nm_635_nm

source_name: adenocarcinoma BRCA1-39


title: cell_W3_rep3

description: gene expression


title: cell_A2_rep2

description: gene expression


title: cell_A1_rep1

description: gene expression


title: cell_W1_rep1

description: gene expression


title: cell_W2_rep2

description: gene expression


title: liu-00258: B36 cy5 OSE cy3 660 570_635_nm

source_name: adenocarcinoma BRCA1-36


title: 13D1592_genomic DNA from peripheral blood 42

type: genomic

city: Amsterdam

first: Peter

last: Henneman

state: Noord Holland

address: Meibergdreef 9

department: Clinical Genetics

country: Netherlands

institute: Academic Medical Center Amsterdam

hyb_protocol: Bisulfite converted DNA was hybridized to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

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

data_processing:
Minfi (v1.16.0) for reading the data; MethylAid (v1.14.0) for quality control - Due to failing the QC, samples Crohn100, Crohn32 and Crohn75 were removed from the processed data
non_normalized.txt contains unmethylated and methylated signal intensities
Average M values normalized using the functional normalization method implemented in minfi

label: Cy5 and Cy3

molecule: genomic DNA

source_name: heathy control_peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: Peripheral blood was drawn and stored in EDTA to prevent coagulation. Erythrocytes were lysed before proteins were aggregated out of the sample. Genomic DNA was extracted through ethanol precipitation, after which the DNA was dissolved in tris-ethylenediaminetetraacetic buffer (Tris-EDTA) and stored at 4°C.

tag: gender

value: Female

tag: disease state

value: Control

tag: age (yr)

tag: atnf usage at time of phlebotomy

value: No

value: peripheral blood


title: 13D0390_genomic DNA from peripheral blood 32

tag: tissue


title: 13D1593_genomic DNA from peripheral blood 43


title: 13D0046_genomic DNA from peripheral blood 29


title: Preadipocytes treated with DMIOA+Retinoic Acid (RA), biological replicate 2

city: Winnipeg

first: Alemu

middle: Regassa

last: Hunde

state: Manitoba

address: 12 Dafoe Road

department: Animal Science

country: Canada

institute: University of Manitoba

description: Gene expression data from preadipocytes isolated from laying hen, treated with DMIOA+RA

hyb_protocol: Following fragmentation, 12.5 µg of biotinylated total RNA were hybridized for 16 hours at 45C on Affymetrix Chicken Genome Array. Genechips were washed and stained using Fluidics station 450 (Affymetrix).

scan_protocol: The stained chips were scanned using Scanner 3000 (Affynetrix)

data_processing: Data were background corrected and normalised using GC-RMA

organism: Gallus gallus

source_name: Adipose tissue

label_protocol: 15 µg of biotinylated aRNA were prepared according to the standard Affymetrix protocol (3' IVT Express Kit user manual, Affymetrix)

growth_protocol: The isolated preadipoctes were incubated in FBS containing 10% DMEM in an incubator with 5% CO2

extract_protocol: Total RNA was extracted using TriZol according to the manufacturer's instructions.

treatment_protocol: Confluent preadipocytes were treated with adipogeneic cocktail (DMIOA) and DMIOA+10 μM Retinoic Acid

tag: cell type

value: Preadipocytes


title: Preadipocytes treated with DMIOA+Retinoic Acid (RA), biological replicate 3


title: liu-00258: B2-8 cy5 vs OSEcy3 805 620_635_nm

source_name: adenocarcinoma BRCA2-8

tag: diseasestate

tag: Sex

tag: organismstatus

value: premortem

tag: diseasestage


title: 11D5316_genomic DNA from peripheral blood 27


title: liu-00258: B2-9 cy5 vs OSEcy3 745 620_635_nm

source_name: adenocarcinoma BRCA2-9

tag: genotype

tag: developmentalstage


title: 13D0403_genomic DNA from peripheral blood 35


title: Preadipocytes treated with DMIOA+Retinoic Acid (RA), biological replicate 1


title: 13D1591_genomic DNA from peripheral blood 41


title: Preadipocytes treated with DMIOA, biological replicate 3 (2)

description: Gene expression data from preadipocytes isolated from laying hen, treated with DMIOA


title: 13D1474_genomic DNA from peripheral blood 38


title: 12D4543_genomic DNA from peripheral blood 28


title: 10D4351_genomic DNA from peripheral blood 24


title: liu-00258: B2-5 cy5 vs OSEcy3 725 630_635_nm

source_name: adenocarcinoma BRCA2-5

tag: individual

tag: age (years)

source_name: Ovarian surface epithelial cell line


title: 13D0391_genomic DNA from peripheral blood 33


title: 10D0578_genomic DNA from peripheral blood 22


title: 13D1588_genomic DNA from peripheral blood 39


title: 13D1589_genomic DNA from peripheral blood 40


title: 09D5523_genomic DNA from peripheral blood 21


title: 09D4345_genomic DNA from peripheral blood 20


title: 13D0769_genomic DNA from peripheral blood 36


title: 13D1471_genomic DNA from peripheral blood 37


title: 13D0060_genomic DNA from peripheral blood 30


title: 11D3702_genomic DNA from peripheral blood 26


title: liu-00258: B2-3 cy5 vs OSEcy3 770 610_635_nm

source_name: adenocarcinoma BRCA2-3

tag: histology

tag: tumorgrading


title: 13D0061_genomic DNA from peripheral blood 31


title: liu-00258: B2-7 cy5 vs OSEcy3 750 620_635_nm

source_name: adenocarcinoma BRCA2-7

tag: organismpart

tag: cellline


title: Crohn84_genomic DNA from peripheral blood 17

source_name: Crohn’s Disease_peripheral blood

tag: gender

tag: disease state

value: Crohn


title: 10D3526_genomic DNA from peripheral blood 23

tag: age (yr)

tag: atnf usage at time of phlebotomy


title: Crohn99_genomic DNA from peripheral blood 18

tag: tissue


title: Preadipocytes treated with DMIOA, biological replicate 1 (2)

tag: cell type


title: Crohn52_genomic DNA from peripheral blood 13

value: Yes


title: 13D0396_genomic DNA from peripheral blood 34


title: liu-00258: B2-23 cy5 vs OSEcy3 750 610_635_nm

source_name: adenocarcinoma BRCA2-23

tag: diseasestate

tag: Sex

value: Adult


title: Non-treated control preadipocytes, biological replicate 2 (2)

description: Gene expression data from preadipocytes isolated from laying hen, control


title: liu-00258: B2-22cy5 OSE cy3 770 620_635_nm

source_name: adenocarcinoma BRCA2-22

tag: organismstatus

tag: diseasestage


title: liu-00258: B2-24 cy5 vs OSEcy3 740 590_635_nm

source_name: adenocarcinoma BRCA2-24

tag: genotype

tag: developmentalstage

value: serous/clear cell features


title: 10D5119_genomic DNA from peripheral blood 25


title: Non-treated control preadipocytes, biological replicate 3 (2)


title: Crohn51_genomic DNA from peripheral blood 12


title: Non-treated control preadipocytes, biological replicate 1 (2)


title: wet_e

city: Beijing

first: Haowei

last: Yue

address: School of Environment

institute: Tsinghua University

description: GeoChip data for soil sample collected at increased precipitation, replicate 5

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: uncultured soil microorganism

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

extract_protocol: Soil DNA was extracted by freeze-grinding mechanical lysis as previously described (Zhou et al 1996). Freshly extracted DNA was purified twice using 0.5% low melting point agarose gel followed by phenol-chloroform-butanol extraction. DNA quality and quantity were assessed by the ratios of 260 nm/280 nm and 260 nm/230 nm, and final DNA contents were quantified with a PicoGreen method using a FLUO star Optima .

tag: sample type

value: Soil microbes in Tibet grassland

tag: precipitations

value: increased precipitation; 50%


title: wet_d

description: GeoChip data for soil sample collected at increased precipitation, replicate 4


title: wet_c

description: GeoChip data for soil sample collected at increased precipitation, replicate 3


title: Crohn63_genomic DNA from peripheral blood 14


title: Crohn67_genomic DNA from peripheral blood 15


title: wet_b

description: GeoChip data for soil sample collected at increased precipitation, replicate 2


title: Preadipocytes treated with DMIOA, biological replicate 2 (2)


title: liu-00258: B2-25 cy5 OSE cy3 715 620_635_nm

source_name: adenocarcinoma BRCA2-25

tag: individual

tag: age (years)

tag: histology

tag: tumorgrading

value: Ovary

value: Normal

value: ovarian surface epithelial cell line


title: liu-00258: B2-21cy5 OSE cy3 800 620_635_nm

source_name: adenocarcinoma BRCA2-21

value: Ovarian Adenocarcinoma

value: adenocarcinoma (not otherwise specified)

tag: organismpart

tag: cellline


title: liu-00258: B2-20 cy5 OSE cy3 750 620_635_nm

source_name: adenocarcinoma BRCA2-20

value: female

value: serous


title: Crohn34_genomic DNA from peripheral blood 9

tag: gender

value: Female

tag: disease state

tag: age (yr)

tag: atnf usage at time of phlebotomy

value: No


title: liu-00258: B2-2 cy5 vs OSEcy3 700 610_635_nm

source_name: adenocarcinoma BRCA2-2

tag: diseasestate

tag: Sex


title: wet_f

description: GeoChip data for soil sample collected at increased precipitation, replicate 6


title: liu-00258: B2-1cy5 vs OSEcy3 720 605_635_nm

source_name: adenocarcinoma BRCA2-1

tag: organismstatus

tag: diseasestage


title: wet_a

description: GeoChip data for soil sample collected at increased precipitation, replicate 1


title: dry_f

description: GeoChip data for soil sample collected at decreased precipitation, replicate 6

value: decreased precipitation; -50%


title: liu-00258: B2-16 cy5 OSE cy3 720 620_635_nm

source_name: adenocarcinoma BRCA2-16

value: premortem

tag: genotype

tag: developmentalstage


title: liu-00258: B2-10 cy5 vs OSEcy3 750 630_635_nm

source_name: adenocarcinoma BRCA2-10


title: Crohn47_genomic DNA from peripheral blood 10

value: Crohn

tag: tissue

value: peripheral blood


title: dry_c

description: GeoChip data for soil sample collected at decreased precipitation, replicate 3

tag: sample type

tag: precipitations


title: Crohn135_genomic DNA from peripheral blood 4


title: dry_a

description: GeoChip data for soil sample collected at decreased precipitation, replicate 1


title: control_d

description: GeoChip data for soil sample collected at control precipitation, replicate 4

value: 0%; control precipitation


title: dry_e

description: GeoChip data for soil sample collected at decreased precipitation, replicate 5


title: dry_d

description: GeoChip data for soil sample collected at decreased precipitation, replicate 4


title: control_e

description: GeoChip data for soil sample collected at control precipitation, replicate 5


title: control_f

description: GeoChip data for soil sample collected at control precipitation, replicate 6


title: control_b

description: GeoChip data for soil sample collected at control precipitation, replicate 2


title: dry_b

description: GeoChip data for soil sample collected at decreased precipitation, replicate 2


title: Crohn150_genomic DNA from peripheral blood 6

value: Yes


title: Crohn13_genomic DNA from peripheral blood 3


title: control_a

description: GeoChip data for soil sample collected at control precipitation, replicate 1

value: Soil microbes in Tibet grassland


title: liu-00251: TCGA-02-0069-01A-01R-0202-01

status: Public on May 27 2016

source_name: Brain

value: GLIOBLASTOMA MULTIFORME

value: Brain

tag: individual

tag: clinical diagnosis

value: GBM

tag: pathologic status

value: NOT SPECIFIED

tag: histologic diagnosis

tag: tissue anatomic site


title: control_c

description: GeoChip data for soil sample collected at control precipitation, replicate 3


title: 09D1004_genomic DNA from peripheral blood 19

source_name: heathy control_peripheral blood

tag: gender

tag: disease state

value: Control


title: liu-00258: B2-4 cy5 vs OSEcy3 720 630_635_nm

source_name: adenocarcinoma BRCA2-4

value: Ovarian Adenocarcinoma

value: Adult

tag: age (years)

tag: histology

tag: tumorgrading

tag: organismpart

value: Ovary

value: Normal

tag: cellline

value: ovarian surface epithelial cell line


title: liu-00251: TCGA-08-0531-01A-01R-0280-01

tag: diseasestate

value: MALIGNANT

value: PARIETAL LOBE


title: liu-00251: TCGA-06-0644-01A-02R-0306-01


title: Crohn114_genomic DNA from peripheral blood 2

value: Female

value: Crohn

tag: age (yr)

tag: atnf usage at time of phlebotomy

value: No


title: liu-00251: TCGA-02-0080-01A-01R-0202-01

value: TEMPORAL LOBE


title: liu-00251: TCGA-06-0166-01A-01R-0233-01


title: liu-00251: TCGA-02-0006-01B-01R-0177-01


title: liu-00251: TCGA-06-0187-01A-01R-0233-01


title: liu-00251: TCGA-08-0356-01A-01R-0298-01


title: liu-00251: TCGA-06-0240-01A-02R-0233-01


title: liu-00251: TCGA-06-0124-01A-01R-0219-01


title: liu-00251: TCGA-08-0511-01A-01R-0280-01


title: Crohn50_genomic DNA from peripheral blood 11

tag: tissue

value: peripheral blood


title: liu-00251: TCGA-02-0451-01A-01R-0280-01

value: GLIOBLASTOMA MULTIFORME


title: liu-00251: TCGA-02-0047-01A-01R-0177-01

value: Brain


title: liu-00251: TCGA-06-0414-01A-01R-0280-01

value: GBM


title: liu-00251: TCGA-06-0208-01B-01R-0233-01

value: FRONTAL LOBE


title: liu-00251: TCGA-06-0184-01A-01R-0233-01


title: liu-00251: TCGA-06-0195-01B-01R-0233-01


title: liu-00251: TCGA-02-0074-01A-01R-0202-01


title: liu-00251: TCGA-06-0208-01A-01R-0233-01


title: liu-00251: TCGA-02-0271-01A-01R-0280-01

value: NOT SPECIFIED


title: liu-00251: TCGA-06-0176-01A-02R-0233-01


title: liu-00251: TCGA-02-0026-01B-01R-0298-01


title: Crohn140_genomic DNA from peripheral blood 5


title: liu-00251: TCGA-06-0125-01A-01R-0219-01


title: liu-00251: TCGA-06-0194-01A-01R-0280-01


title: liu-00251: TCGA-06-0156-01A-02R-0233-01

value: GLIOBLASTOMA

value: OCCIPITAL LOBE


title: Crohn154_genomic DNA from peripheral blood 7


title: liu-00251: TCGA-08-0392-01A-01R-0298-01

value: OVERLAPPING LESION OF BRAIN


title: liu-00251: TCGA-06-0176-01A-03R-0233-01


title: liu-00251: TCGA-06-0156-01A-03R-0233-01


title: liu-00251: TCGA-02-0338-01A-01R-0280-01


title: liu-00251: TCGA-02-0001-01C-01R-0177-01


title: liu-00251: TCGA-08-0347-01A-01R-0298-01


title: liu-00251: TCGA-02-0038-01A-01R-0177-01


title: liu-00251: TCGA-06-0156-01A-01R-0233-01


title: liu-00251: TCGA-02-0104-01A-01R-0298-01


title: liu-00251: TCGA-02-0317-01A-01R-0280-01


title: liu-00251: TCGA-06-0219-01A-01R-0233-01


title: liu-00251: TCGA-08-0375-01A-01R-0298-01


title: liu-00251: TCGA-06-0130-01A-01R-0219-01


title: liu-00251: TCGA-06-0177-01A-01R-0280-01


title: liu-00251: TCGA-02-0113-01A-01R-0202-01


title: liu-00251: TCGA-02-0048-01A-01R-0298-01


title: liu-00251: TCGA-02-0290-01A-01R-0280-01


title: liu-00251: TCGA-06-0412-01A-01R-0280-01


title: liu-00251: TCGA-08-0346-01A-01R-0298-01


title: liu-00251: TCGA-08-0522-01A-01R-0280-01


title: liu-00251: TCGA-08-0345-01A-01R-0306-01


title: liu-00251: TCGA-02-0068-01A-01R-0298-01


title: liu-00251: TCGA-08-0521-01A-01R-0280-01


title: liu-00251: TCGA-06-0185-01A-01R-0233-01