title: SQ20B_HNSCC_control_rep2_CTXSurival28.65

first: Elana

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

institute: University of Maryland, Baltimore

description:
940CC0014-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: fRMA normalization with R/Bioconductor package fRMA v1.7.2.

source_name: HNSCC cell line SQ20B

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

value: HNSCC (head and neck squamous cell carcinoma)

tag: 7 day cetuximab cell survival rate

tag: treated with

value: none (control)


title: human bone marrow MSCs

status: Public on Jun 12 2017

type: RNA

city: Taipei

first: Pei-Lun

last: Lai

address: 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan

department: Genomic research center

country: Taiwan

institute: Acdemia Sinica

description: Gene expression data from BMMSCs

hyb_protocol: After aRNA fragmentation, 12.5 ug of fragmented aRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0 Array. Affymetrix Fluidics Station 450 was used for gene chips washing and staining.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and use Gene Spring Software 12 to normalize data (RMA mode).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Bone marrow MSCs purchased from LONZA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (GeneChip® 3’ IVT Express Kit, Affymetrix).

growth_protocol: Human fibroblasts were used to generate iMSCs. We used fibroblasts within ten passages. The iMSC medium consisted of Dulbecco's modified Eagle's medium/LG (Invitrogen, Carlsbad, CA, USA) with 10% FBS.

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

treatment_protocol: Fibroblasts were plated on 10-cm plates and treated with drugs in 6 days for iMSC generation then compared the transcriptomic profiles with primary BMMSCs and fibroblasts.

tag: cell type

value: BMMSCs


title: human iMSCs from 56-year-old female fibroblasts

description: Gene expression data from iMSCs (56-year-old female)

scan_protocol: GeneChip® Human Genome U133 Plus 2.0 Array

source_name: iMSCs generated from 56-year-old female

value: iMSCs


title: human iMSCs from 42-year-old female fibroblasts

description: Gene expression data from iMSCs (42-year-old female)

source_name: iMSCs generated from 42-year-old female


title: human neonatal  fibroblasts

description: Gene expression data from CRL2097

source_name: fibroblasts isolated from neonatal foreskin

value: Fibroblasts


title: COPD 4

type: genomic

city: Kansas City

first: Isaac Kirubakaran

last: Sundar

state: KS

address: 3901 Rainbow Blvd.

department: Internal Medicine

country: USA

institute: University of Kansas Medical Center

description:
COPD lung parenchyma tissue
C.4

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing:
The data was analyzed through Illumina's GenomeStudio methylation module (v1.9.0).
Unmethylated and methylated signal intensities in series supplementary file

label: Cy3 and Cy5

molecule: genomic DNA

source_name: COPD lung tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Lung tissues were collected snap frozen and stored at -80 °C. Genomic DNA was extracted from lung tissue. Briefly, 1 ?g genomic DNA was bisulfite-converted using EZ DNA Methylation Kit (Zymo Research, Irvine, CA). The bisulfite-converted DNA samples were assayed using Infinium HumanMethylation450 BeadChip array from Illumina (San Diego, CA) following the manufacturer’s instructions.

tag: tissue

value: lung parenchyma

tag: Sex

value: M

tag: age

tag: fev%

tag: fev/fvc%


title: human aldult fibroblasts_42y

description: Gene expression data from 42-year-old female

source_name: dermal fibroblasts from 42-year-old female


title: COPD 2

description:
COPD lung parenchyma tissue
C.2

value: F

tag: pack years


title: SQ20B_HNSCC_control_rep1_CTXSurival28.65

city: Baltimore

middle: Judith

state: MD

department: Institute for Genome Sciences

description:
940CC0013-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: COPD 1

description:
COPD lung parenchyma tissue
C.1


title: human aldult fibroblasts_56y

description: Gene expression data from 56-year-old female

source_name: dermal fibroblasts from 56-year-old female


title: human iMSCs from CRL2097

description: Gene expression data from iMSCs (CRL2097)

source_name: iMSCs generated from neonatal foreskin


title: Smoker 6

description:
Smoker lung parenchyma tissue
S.6

source_name: Smoker lung tissue


title: Smoker 7

description:
Smoker lung parenchyma tissue
S.7


title: wt bone marrow monocyte, cultured, 8 days, infected (rep3)

city: Marburg

first: Wilhelm

last: Bertrams

address: Hans-Meerwein-Str. 2

department: Institute for Lung Research

country: Germany

institute: Philipps University Marburg

description: Sample name: wt_0p25_3

data_processing: Raw Ct data are shown in Non-normalized_data.txt. U6 snRNA (average of 4 values) yielding deltaCt values was used for normalization presented in in normalized_data.txt. Fold changes were calculated with the the ddCt method (2^-ddCt) and presented in fold-change_data.txt

label: FAM/NFQ-MGB

organism: Mus musculus

source_name: bone marrow (femur/tibia)

label_protocol: RNA was reverse transcribed with the Life Technologies miR RT kit wiith megaplex primers. Reverse transcribed RNA was then run on a TLDA plate (TaqMan® Array Rodent MicroRNA A Card v2.0 [catalog number 4398967]) with FAM-labelled primers

growth_protocol: Bone marrow monocytes were cultured for 6 days in RPMI with 10% FCS, 1 % GlutaMAX and 0.1 % beta-mercaptoethanol. 20ng/ml M-CSF was given on day 1 and 4, 20 ng/ml GM-CSF was given on day 6

extract_protocol: Total RNA was isolated by cell lysis in Trizol and subsequent phenol/chloroform precipitation

treatment_protocol: On day 7, cells were infected with Legionella Pneumophila MOI 0.25 for 24 h or mock treated

value: bone marrow

tag: maturation to macrophage

value: 20 ng/ml M-CSF on day 1 and 4, 20 ng/ml GM-CSF on day 6

tag: stimulus

value: Legionella Pneumophila MOI 0.25, for 24h on day 7


title: MyD88-/- bone marrow monocyte, cultured, 8 days, infected (rep1)

description: Sample name: MyD88_0p25_1


title: MyD88-/- bone marrow monocyte, cultured, 8 days, infected (rep2)

description: Sample name: MyD88_0p25_2


title: MyD88-/- bone marrow monocyte, cultured, 8 days (rep3)

description: Sample name: MyD88_ctrl_3

value: mock


title: Smoker 4

description:
Smoker lung parenchyma tissue
S.4


title: Smoker 5

description:
Smoker lung parenchyma tissue
S.5


title: SCC25_HNSCC_control_rep3_CTXSurival7.61

description:
940CC0018-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line SCC25


title: SCC25_HNSCC_control_rep1_CTXSurival7.61

description:
940CC0016-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: wt bone marrow monocyte, cultured, 8 days, infected (rep2)

description: Sample name: wt_0p25_2


title: MyD88-/- bone marrow monocyte, cultured, 8 days, infected (rep3)

description: Sample name: MyD88_0p25_3


title: Smoker 3

description:
Smoker lung parenchyma tissue
S.3


title: wt bone marrow monocyte, cultured, 8 days, infected (rep1)

description: Sample name: wt_0p25_1


title: Smoker 2

description:
Smoker lung parenchyma tissue
S.2


title: SCC25_HNSCC_control_rep2_CTXSurival7.61

description:
940CC0017-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: 93VU147T_HNSCC_control_rep1_CTXSurival35.57

description:
940CC0004-20080828-Hu133.CEL
Gene expression data from the HNSCC cell line 93VU147T replicate 1.

source_name: HNSCC cell line 93VU147T


title: HaCaT_Keratinocyte_control_rep3_CTXSurival32.57

description:
940CC0127-20090811-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

value: HaCaT

value: Keratinocyte


title: Smoker 1

description:
Smoker lung parenchyma tissue
S.1


title: Non-smoker 8

description:
Non-smoker lung parenchyma tissue
NS.8

source_name: Non-smoker lung tissue


title: Non-smoker 6

description:
Non-smoker lung parenchyma tissue
NS.6


title: MyD88-/- bone marrow monocyte, cultured, 8 days (rep2)

description: Sample name: MyD88_ctrl_2


title: wt bone marrow monocyte, cultured, 8 days (rep2)

description: Sample name: wt_ctrl_2


title: HaCaT_Keratinocyte_control_rep2_CTXSurival32.57

description:
940CC0126Rep-20090811-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: wt bone marrow monocyte, cultured, 8 days (rep3)

description: Sample name: wt_ctrl_3


title: 93VU147T_HNSCC_control_rep3_CTXSurival35.57

description:
940CC0006-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: HaCaT_Keratinocyte_control_rep1_CTXSurival32.57

description:
940CC0126-20090811-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: Non-smoker 5

description:
Non-smoker lung parenchyma tissue
NS.5


title: MyD88-/- bone marrow monocyte, cultured, 8 days (rep1)

description: Sample name: MyD88_ctrl_1


title: 93VU147T_HNSCC_control_rep2_CTXSurival35.57

description:
940CC0005-20080828-Hu133.CEL
Gene expression data from the HNSCC cell line 93VU147T replicate 2.


title: Non-smoker 7

description:
Non-smoker lung parenchyma tissue
NS.7


title: wt bone marrow monocyte, cultured, 8 days (rep1)

description: Sample name: wt_ctrl_1


title: Non-smoker 4

description:
Non-smoker lung parenchyma tissue
NS.4


title: Non-smoker 3

description:
Non-smoker lung parenchyma tissue
NS.3


title: Non-smoker 1

description:
Non-smoker lung parenchyma tissue
NS.1


title: SQ20B_HNSCC_control_rep3_CTXSurival28.65

description:
940CC15-20080916-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: NIKS HPV18-positive replicate 2

status: Public on Jun 11 2017

city: Aurora

first: Dohun

last: Pyeon

state: CO

department: Immunology and Microbiology

institute: University of Colorado School of Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 2.0 Plus. GeneChips were washed and stained in the GeneChip Hybridization Oven 640 and GeneChip Fluidics Station.

scan_protocol: GeneChips were scanned using the GeneChip Scanner

data_processing: Gene expression data quality was validated using QC plots observing RNA degradation and log density distribution for all probes for each sample. The data were filtered based on mas5 present/absent calls, where transcripts were discarded if they had at least one absent call. After filtering, 27,146 transcripts remained. Transcript expression was normalized using RMA

label: Biotin

source_name: Stabily transfected with HPV18 genome under G418 selection

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

growth_protocol: Cells were grown in E Complete medium co-cultured with mitomycin C-treated NIH 3T3 mouse feeder fibroblast cells

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen)

treatment_protocol: Cells maintaining HPV genomes were transiently transfected and selected with G418

value: Skin

tag: gender

value: Male


title: NIKS HPV16-positive E7-deficient replicate 3

source_name: Stabily transfected with HPV-16ΔE7 genome under G418 selection


title: Non-smoker 2

description:
Non-smoker lung parenchyma tissue
NS.2


title: NIKS HPV16-positive E7-deficient replicate 1


title: NIKS HPV18-positive replicate 1


title: NIKS HPV16-positive E7-deficient replicate 2


title: NIKS HPV18-positive replicate 3


title: 90pc_contMO_rep1

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

description: 0.75 pmol standard control morpholino (GeneTools)

hyb_protocol: Labelled cDNA was hybridized to Agilent zebrafish V3 expression microarrays according to manufacturers protocol.

scan_protocol: Microarrays were scanned using a GenePix 4000B scanner with GenePix Pro 6 software.

data_processing: Spot intensities were extracted using GenePix Pro 6 software and median spot intensities were normalized using the qspline algorithm in oneChannelGUI.

label: Alexa Fluor 647

organism: Danio rerio

source_name: Whole 90% epiboly stage embryo

label_protocol: Alexa Fluor 647 labelled cDNA was produced from 15µg total RNA using Invitrogen Superscript Plus Direct cDNA labelling system according to manufacturers protocol.

growth_protocol: Embyos were maintained in E3 embryo medium at 28.5 degrees celcius

extract_protocol: 200 embryos were lysed in 1ml Trizol and total RNA extracted according to manufacturers protocol. RNA was then cleaned using QIAGEN Rneasy columns.

tag: strain

value: AB

tag: developmental stage

value: 90% epiboly


title: 90pc_doubleMO_rep2

description: 0.5 pmol anti-tbx16 morpholino; 0.25 pmol anti-ta morpholino


title: NIKS HPV16-positive replicate 3

source_name: Stabily transfected with HPV16 genome under G418 selection


title: 90pc_doubleMO_rep3


title: NIKS HPV16-positive replicate 2


title: 90pc_contMO_rep2


title: 90pc_doubleMO_rep1


title: shield_doubleMO_rep3

source_name: Whole shield stage embryo

value: shield


title: shield_contMO_rep3


title: NIKS HPV16-positive replicate 1


title: shield_doubleMO_rep2


title: shield_doubleMO_rep1


title: shield_contMO_rep2


title: NIKS replicate 2

source_name: HPV-negative


title: NIKS replicate 3


title: 90pc_contMO_rep3


title: shield_contMO_rep1


title: NIKS replicate 1


title: NIKS HPV18-positive replicate 2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 Beadchip using standard Illumina protocol

scan_protocol: Beadchips were scanned using illumina Iscan

data_processing: Data were processed and beta values calculated using Genome Studio software

label: biotin, dinitrophenyl

extract_protocol: Genomic DNA was isulated using Dneasy (Qiagen) and bisulfite converted using EZ DNA Methylation Kit (Zymo) according to the manufacturer's instructions.


title: NIKS replicate 1


title: Sox9_WT_rep6

status: Public on Jun 10 2017

city: Potsdam

first: Thomas

last: Lufkin

state: NY

address: 8 Clarkson Avenue

department: Biology

institute: Clarkson University

description: Array Content = MouseWG-6_V1_1_R4_11234304_A.bgx.xml

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The illumina output for Genespring was imported into Genespring 11 (Agilent Technologies). The data was then normalised using log2 transformation and  percentile shift normalization at the 75th percentile, following the routine method used for Illumina array by Genespring.

source_name: E13.5 axial and appendicular skeleton

label_protocol: Biotinylated cRNA for Sox9 samples were prepared with the Ambion MessageAmp kit for Illumina arrays. Biotinylated cRNA for Sox6 and Sox5/Sox6 samples were prepared with the Epicentre TargetAmp-Nano Labeling Kit for Illumina arrays.

extract_protocol: Total RNA was extracted from the sorted cells 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 Bioanalyzer.

treatment_protocol: E13.5 embryos with internal organs removed and enriched for their axial and appendicular skeleton were dissociated into single cells for fluorescent activated cell sorting.

value: Skeletal

tag: genotype/variation

tag: Stage

value: E13.5 embryo


title: NIKS HPV18-positive replicate 3


title: Sox9_KO_rep1


title: Sox9_WT_rep5


title: Sox9_WT_rep4


title: Sox9_KO_rep2


title: Sox9_WT_rep3


title: Sox9_WT_rep1


title: Sox9_KO_rep4


title: NIKS HPV16-positive replicate 3


title: NIKS replicate 3


title: Sox9_KO_rep3


title: NIKS replicate 2


title: NIKS HPV16-positive replicate 1


title: NIKS HPV16-positive replicate 2


title: NIKS HPV18-positive replicate 1


title: Sox9_WT_rep2


title: 327NL

city: Shanghai

first: Hongbin

last: Ji

address: YueYang Rd

country: China

institute: SIBCB

hyb_protocol: Affymetrix standard procedures

scan_protocol: Affymetrix standard procedures

data_processing: RMA-sketch

source_name: ADC adjacent normal

label_protocol: Affymetrix standard procedures

extract_protocol: Trizol extraction of total RNA

treatment_protocol: frozen

value: lung ADC adjacent normal


title: 202NL


title: 316NL


title: 363

source_name: ADC

value: lung adenocarcinomas


title: 178NL


title: 123NL


title: 512


title: 105NL


title: 129NL


title: 439


title: 181


title: 411NL


title: 262


title: 136


title: 368


title: 105


title: 345


title: 374


title: 385


title: 278


title: 399


title: 212


title: 426


title: 485


title: 355


title: 230


title: 244


title: 224


title: 123


title: 182


title: 347


title: 397


title: 380


title: 178


title: 370


title: 243


title: 511


title: 272


title: 168


title: 373


title: 175


title: 329


title: 339


title: 491


title: 163


title: 180NL


title: 327


title: 262NL


title: 267


title: 411


title: 198


title: 291


title: 197


title: 187


title: 316


title: 481


title: 382


title: 336


title: 259


title: 309


title: 128


title: 218


title: 180


title: 318


title: 231


title: 421


title: 276


title: 393


title: 194


title: 269


title: 300


title: 275


title: 202-2


title: 305


title: 324


title: 203


title: 277


title: NonRecurrence132

city: WARREN

first: nien

last: wei

state: NJ

address: 9 northridge way

institute: Auspex Diagnostics

hyb_protocol: The hybridization cocktails contains 3.75 ug of the fragmented, end-labeled cDNA were applied to the Affy Human Gene 2.0 ST arrays. Hybridization was performaed for 17 hours, and the arrays were washed and stained with GeneChip Fluidicd Station 450.

scan_protocol: Arrays were scanned using Affymetrix  GCS 3000 7G and GeneChip Operating sofware v. 1.4 to produce Cel intensity files.

data_processing: Affymetrix Expression Console is used to extract data

source_name: surgical tumor tissue

label_protocol: Samples were fragmented and labeled using NuGen Encore Biotin kit

extract_protocol: Total RNA from patient samples were extracted on the Qiasymphony using Qiasymphony RNA kit

value: colorectal cancer

tag: recurrence status

value: NonRecurrence


title: NonRecurrence133


title: NonRecurrence138


title: 154


title: NonRecurrence137


title: NonRecurrence134


title: 249


title: NonRecurrence130


title: NonRecurrence136


title: 325


title: NonRecurrence131


title: 448


title: NonRecurrence127


title: NonRecurrence126


title: NonRecurrence125


title: 280


title: NonRecurrence129


title: 338


title: NonRecurrence124


title: NonRecurrence122


title: NonRecurrence121


title: 97


title: 129


title: 245


title: NonRecurrence112


title: NonRecurrence118


title: NonRecurrence116


title: NonRecurrence123


title: 240


title: NonRecurrence120


title: NonRecurrence119


title: NonRecurrence135


title: NonRecurrence113


title: NonRecurrence115


title: NonRecurrence103


title: NonRecurrence114


title: NonRecurrence108


title: NonRecurrence107


title: NonRecurrence111


title: NonRecurrence128


title: NonRecurrence105


title: NonRecurrence104


title: NonRecurrence101


title: NonRecurrence117


title: NonRecurrence109


title: NonRecurrence106


title: NonRecurrence102


title: NonRecurrence110


title: NonRecurrence98


title: NonRecurrence99


title: NonRecurrence100


title: NonRecurrence94


title: NonRecurrence95


title: NonRecurrence85


title: NonRecurrence87


title: NonRecurrence86


title: NonRecurrence88


title: NonRecurrence84


title: NonRecurrence92


title: NonRecurrence91


title: NonRecurrence89


title: 412


title: NonRecurrence93


title: NonRecurrence83


title: NonRecurrence73


title: NonRecurrence78


title: NonRecurrence90


title: NonRecurrence81


title: NonRecurrence76


title: NonRecurrence82


title: NonRecurrence74


title: NonRecurrence77


title: NonRecurrence72


title: NonRecurrence75


title: NonRecurrence79


title: NonRecurrence96


title: NonRecurrence80


title: NonRecurrence71


title: NonRecurrence70


title: NonRecurrence69


title: NonRecurrence67


title: NonRecurrence65


title: NonRecurrence66


title: NonRecurrence68


title: NonRecurrence59


title: NonRecurrence63


title: NonRecurrence50


title: NonRecurrence51


title: NonRecurrence52


title: NonRecurrence55


title: NonRecurrence49


title: NonRecurrence97


title: NonRecurrence64


title: NonRecurrence62


title: NonRecurrence60


title: NonRecurrence56


title: NonRecurrence53


title: NonRecurrence54


title: NonRecurrence48


title: NonRecurrence61


title: NonRecurrence58


title: NonRecurrence46


title: NonRecurrence47


title: NonRecurrence43


title: NonRecurrence44


title: NonRecurrence41


title: NonRecurrence57


title: NonRecurrence42


title: NonRecurrence38


title: NonRecurrence39


title: NonRecurrence36


title: NonRecurrence40


title: NonRecurrence34


title: NonRecurrence45


title: NonRecurrence37


title: NonRecurrence26


title: NonRecurrence31


title: NonRecurrence35


title: NonRecurrence24


title: NonRecurrence32


title: NonRecurrence27


title: NonRecurrence25


title: NonRecurrence16


title: NonRecurrence18


title: NonRecurrence17


title: NonRecurrence28


title: NonRecurrence13


title: NonRecurrence33


title: NonRecurrence29


title: NonRecurrence23


title: NonRecurrence20


title: NonRecurrence21


title: NonRecurrence19


title: NonRecurrence30


title: NonRecurrence22


title: NonRecurrence12


title: NonRecurrence10


title: NonRecurrence11


title: NonRecurrence14


title: NonRecurrence15


title: NonRecurrence9


title: NonRecurrence8


title: NonRecurrence6


title: NonRecurrence7


title: Recurrence96

value: Had Recurrence


title: NonRecurrence1


title: Recurrence91


title: Recurrence87


title: NonRecurrence2


title: NonRecurrence3


title: Recurrence94


title: Recurrence88


title: NonRecurrence4


title: Recurrence86


title: Recurrence97


title: Recurrence92


title: Recurrence85


title: NonRecurrence5


title: Recurrence90


title: Recurrence93


title: Recurrence83


title: Recurrence95


title: Recurrence82


title: Recurrence75


title: Recurrence84


title: Recurrence80


title: Recurrence89


title: Recurrence77


title: Recurrence74


title: Recurrence78


title: Recurrence76


title: Recurrence81


title: Recurrence73


title: Recurrence79


title: Recurrence72


title: Recurrence71


title: Recurrence70


title: Recurrence69


title: Recurrence68


title: Recurrence52


title: Recurrence53


title: Recurrence57


title: Recurrence64


title: Recurrence60


title: Recurrence61


title: Recurrence58


title: Recurrence48


title: Recurrence45


title: Recurrence67


title: Recurrence55


title: Recurrence65


title: Recurrence63


title: Recurrence54


title: Recurrence41


title: Recurrence43


title: Recurrence40


title: Recurrence56


title: Recurrence47


title: Recurrence59


title: Recurrence50


title: Recurrence49


title: Recurrence46


title: Recurrence66


title: Recurrence44


title: Recurrence62


title: Recurrence38


title: Recurrence51


title: Recurrence42


title: Recurrence39


title: Recurrence36


title: Recurrence33


title: Recurrence35


title: Recurrence30


title: Recurrence37


title: Recurrence29


title: Recurrence26


title: Recurrence34


title: Recurrence31


title: Recurrence32


title: Recurrence28


title: Recurrence27


title: Recurrence24


title: Recurrence18


title: Recurrence21


title: Recurrence25


title: Recurrence19


title: Recurrence14


title: Recurrence20


title: Recurrence22


title: Recurrence23


title: Recurrence16


title: Recurrence17


title: Recurrence15


title: Recurrence11


title: Recurrence12


title: Recurrence13


title: Recurrence8


title: Recurrence10


title: Recurrence6


title: Recurrence1


title: Recurrence7


title: Recurrence3


title: FX-NonRecurrence101


title: Recurrence4


title: Recurrence2


title: Recurrence9


title: Recurrence5


title: FX-NonRecurrence98


title: FX-NonRecurrence100


title: FX-NonRecurrence102


title: FX-NonRecurrence99


title: FX-NonRecurrence94


title: FX-NonRecurrence88


title: FX-NonRecurrence91


title: FX-NonRecurrence93


title: FX-NonRecurrence90


title: FX-NonRecurrence89


title: FX-NonRecurrence87


title: FX-NonRecurrence85


title: FX-NonRecurrence92


title: FX-NonRecurrence96


title: FX-NonRecurrence97


title: FX-NonRecurrence86


title: FX-NonRecurrence81


title: FX-NonRecurrence84


title: FX-NonRecurrence82


title: FX-NonRecurrence83


title: FX-NonRecurrence80


title: FX-NonRecurrence76


title: FX-NonRecurrence77


title: FX-NonRecurrence73


title: FX-NonRecurrence78


title: FX-NonRecurrence74


title: FX-NonRecurrence75


title: FX-NonRecurrence72


title: FX-NonRecurrence71


title: FX-NonRecurrence70


title: FX-NonRecurrence69


title: FX-NonRecurrence79


title: FX-NonRecurrence61


title: FX-NonRecurrence66


title: FX-NonRecurrence67


title: FX-NonRecurrence62


title: FX-NonRecurrence58


title: FX-NonRecurrence68


title: FX-NonRecurrence64


title: FX-NonRecurrence65


title: FX-NonRecurrence59


title: FX-NonRecurrence56


title: FX-NonRecurrence50


title: FX-NonRecurrence55


title: FX-NonRecurrence57


title: FX-NonRecurrence46


title: FX-NonRecurrence54


title: FX-NonRecurrence47


title: FX-NonRecurrence44


title: FX-NonRecurrence63


title: FX-NonRecurrence43


title: FX-NonRecurrence53


title: FX-NonRecurrence51


title: FX-NonRecurrence52


title: FX-NonRecurrence42


title: FX-NonRecurrence41


title: FX-NonRecurrence48


title: FX-NonRecurrence49


title: FX-NonRecurrence45


title: FX-NonRecurrence60


title: FX-NonRecurrence38


title: FX-NonRecurrence37


title: FX-NonRecurrence40


title: FX-NonRecurrence39


title: FX-NonRecurrence34


title: FX-NonRecurrence30


title: FX-NonRecurrence31


title: FX-NonRecurrence32


title: FX-NonRecurrence28


title: FX-NonRecurrence27


title: FX-NonRecurrence29


title: FX-NonRecurrence25


title: FX-NonRecurrence24


title: FX-NonRecurrence26


title: FX-NonRecurrence21


title: FX-NonRecurrence36


title: FX-NonRecurrence22


title: FX-NonRecurrence35


title: FX-NonRecurrence23


title: FX-NonRecurrence16


title: FX-NonRecurrence17


title: FX-NonRecurrence19


title: FX-NonRecurrence20


title: FX-NonRecurrence12


title: FX-NonRecurrence18


title: FX-NonRecurrence15


title: FX-NonRecurrence13


title: FX-NonRecurrence11


title: FX-NonRecurrence14


title: FX-NonRecurrence6


title: FX-NonRecurrence9


title: FX-NonRecurrence7


title: FX-NonRecurrence10


title: FX-NonRecurrence95


title: FX-NonRecurrence3


title: FX-Recurrence60


title: FX-Recurrence54


title: FX-Recurrence57


title: FX-Recurrence59


title: FX-Recurrence47


title: FX-Recurrence64


title: FX-Recurrence61


title: FX-Recurrence44


title: FX-NonRecurrence1


title: FX-NonRecurrence33


title: FX-Recurrence50


title: FX-NonRecurrence2


title: FX-Recurrence56


title: FX-NonRecurrence4


title: FX-NonRecurrence5


title: FX-Recurrence53


title: FX-Recurrence49


title: FX-Recurrence55


title: FX-Recurrence58


title: FX-NonRecurrence8


title: FX-Recurrence51


title: FX-Recurrence46


title: FX-Recurrence63


title: FX-Recurrence62


title: FX-Recurrence52


title: FX-Recurrence45


title: FX-Recurrence48


title: FX-Recurrence42


title: FX-Recurrence43


title: FX-Recurrence22


title: FX-Recurrence36


title: FX-Recurrence26


title: FX-Recurrence27


title: FX-Recurrence34


title: FX-Recurrence28


title: FX-Recurrence38


title: FX-Recurrence39


title: FX-Recurrence40


title: FX-Recurrence33


title: FX-Recurrence35


title: FX-Recurrence37


title: FX-Recurrence32


title: FX-Recurrence21


title: FX-Recurrence20


title: FX-Recurrence30


title: FX-Recurrence31


title: FX-Recurrence17


title: FX-Recurrence29


title: FX-Recurrence19


title: FX-Recurrence12


title: FX-Recurrence24


title: FX-Recurrence14


title: FX-Recurrence16


title: FX-Recurrence23


title: FX-Recurrence18


title: FX-Recurrence15


title: FX-Recurrence9


title: FX-Recurrence8


title: FX-Recurrence5


title: FX-Recurrence11


title: FX-Recurrence3


title: FX-Recurrence7


title: FX-Recurrence10


title: 5FU-NonRecurrence119


title: FX-Recurrence6


title: 5FU-NonRecurrence115


title: FX-Recurrence4


title: FX-Recurrence2


title: FX-Recurrence1


title: FX-Recurrence13


title: 5FU-NonRecurrence116


title: 5FU-NonRecurrence109


title: 5FU-NonRecurrence110


title: 5FU-NonRecurrence117


title: 5FU-NonRecurrence107


title: 5FU-NonRecurrence114


title: 5FU-NonRecurrence118


title: 5FU-NonRecurrence102


title: 5FU-NonRecurrence105


title: 5FU-NonRecurrence113


title: 5FU-NonRecurrence112


title: 5FU-NonRecurrence111


title: 5FU-NonRecurrence108


title: 5FU-NonRecurrence103


title: 5FU-NonRecurrence100


title: 5FU-NonRecurrence104


title: 5FU-NonRecurrence95


title: 5FU-NonRecurrence96


title: 5FU-NonRecurrence106


title: 5FU-NonRecurrence101


title: 5FU-NonRecurrence98


title: 5FU-NonRecurrence91


title: 5FU-NonRecurrence88


title: FX-Recurrence25


title: 5FU-NonRecurrence99


title: 5FU-NonRecurrence84


title: 5FU-NonRecurrence83


title: 5FU-NonRecurrence82


title: 5FU-NonRecurrence97


title: 5FU-NonRecurrence80


title: 5FU-NonRecurrence79


title: 5FU-NonRecurrence94


title: 5FU-NonRecurrence87


title: 5FU-NonRecurrence92


title: 5FU-NonRecurrence90


title: FX-Recurrence41


title: 5FU-NonRecurrence78


title: 5FU-NonRecurrence89


title: 5FU-NonRecurrence70


title: 5FU-NonRecurrence81


title: 5FU-NonRecurrence93


title: 5FU-NonRecurrence86


title: 5FU-NonRecurrence72


title: 5FU-NonRecurrence67


title: 5FU-NonRecurrence76


title: 5FU-NonRecurrence68


title: 5FU-NonRecurrence85


title: 5FU-NonRecurrence71


title: 5FU-NonRecurrence75


title: 5FU-NonRecurrence64


title: 5FU-NonRecurrence66


title: 5FU-NonRecurrence63


title: 5FU-NonRecurrence73


title: 5FU-NonRecurrence62


title: 5FU-NonRecurrence65


title: 5FU-NonRecurrence77


title: 5FU-NonRecurrence59


title: 5FU-NonRecurrence74


title: 5FU-NonRecurrence57


title: 5FU-NonRecurrence69


title: 5FU-NonRecurrence60


title: 5FU-NonRecurrence61


title: 5FU-NonRecurrence58


title: 5FU-NonRecurrence55


title: 5FU-NonRecurrence51


title: 5FU-NonRecurrence54


title: 5FU-NonRecurrence44


title: 5FU-NonRecurrence50


title: 5FU-NonRecurrence53


title: 5FU-NonRecurrence39


title: 5FU-NonRecurrence41


title: 5FU-NonRecurrence38


title: 5FU-NonRecurrence52


title: 5FU-NonRecurrence56


title: 5FU-NonRecurrence42


title: 5FU-NonRecurrence48


title: 5FU-NonRecurrence43


title: 5FU-NonRecurrence45


title: 5FU-NonRecurrence49


title: 5FU-NonRecurrence36


title: 5FU-NonRecurrence40


title: 5FU-NonRecurrence31


title: 5FU-NonRecurrence47


title: 5FU-NonRecurrence33


title: 5FU-NonRecurrence30


title: 5FU-NonRecurrence20


title: 5FU-NonRecurrence37


title: 5FU-NonRecurrence13


title: 5FU-NonRecurrence34


title: 5FU-NonRecurrence10


title: 5FU-NonRecurrence27


title: 5FU-NonRecurrence17


title: 5FU-NonRecurrence35


title: 5FU-NonRecurrence46


title: 5FU-NonRecurrence24


title: 5FU-NonRecurrence14


title: 5FU-NonRecurrence23


title: 5FU-NonRecurrence21


title: 5FU-NonRecurrence32


title: 5FU-NonRecurrence12


title: 5FU-NonRecurrence11


title: 5FU-NonRecurrence22


title: 5FU-NonRecurrence19


title: 5FU-NonRecurrence28


title: 5FU-NonRecurrence29


title: 5FU-NonRecurrence16


title: 5FU-NonRecurrence26


title: 5FU-NonRecurrence18


title: 5FU-NonRecurrence8


title: 5FU-NonRecurrence7


title: 5FU-NonRecurrence9


title: 5FU-NonRecurrence3


title: 5FU-NonRecurrence4


title: 5FU-NonRecurrence15


title: 5FU-NonRecurrence5


title: 5FU-NonRecurrence2


title: 5FU-Recurrence71


title: 5FU-NonRecurrence25


title: 5FU-NonRecurrence1


title: 5FU-Recurrence73


title: 5FU-Recurrence66


title: 5FU-NonRecurrence6


title: 5FU-Recurrence69


title: 5FU-Recurrence70


title: 5FU-Recurrence64


title: 5FU-Recurrence72


title: 5FU-Recurrence68


title: 5FU-Recurrence65


title: 5FU-Recurrence67


title: 5FU-Recurrence60


title: 5FU-Recurrence62


title: 5FU-Recurrence63


title: 5FU-Recurrence52


title: 5FU-Recurrence59


title: 5FU-Recurrence61


title: 5FU-Recurrence57


title: 5FU-Recurrence53


title: 5FU-Recurrence46


title: 5FU-Recurrence51


title: 5FU-Recurrence50


title: 5FU-Recurrence58


title: 5FU-Recurrence55


title: 5FU-Recurrence49


title: 5FU-Recurrence56


title: 5FU-Recurrence42


title: 5FU-Recurrence45


title: 5FU-Recurrence48


title: 5FU-Recurrence43


title: 5FU-Recurrence54


title: 5FU-Recurrence41


title: 5FU-Recurrence47


title: 5FU-Recurrence39


title: 5FU-Recurrence35


title: 5FU-Recurrence37


title: 5FU-Recurrence40


title: 5FU-Recurrence36


title: 5FU-Recurrence38


title: 5FU-Recurrence34


title: 5FU-Recurrence44


title: 5FU-Recurrence29


title: PDX-ET-743-1 [miRNA]

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

hyb_protocol: labeled RNA were hybridized on Human miRNA Microarray Kit Release 16.0, 8x60K

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 10.7).

data_processing: raw data were then processed using the Bioconductor package Limma (Linear models for microarray analysis).

source_name: PDX ET-743

label_protocol: One hundred ng of total RNA were labeled using the miRNA Complete Labeling and Hyb Kit

growth_protocol: MT-CHC01 cells were cultured in KODMEM-F12 with glutammine, Hepes and P/S

extract_protocol: Total RNA extracted using Trizol and Absolute RNA miRNA kit (Agilent) following manufacturer's instructions

treatment_protocol: For in vitro experiment: 24 hours at 5 nM of ET-743. In Vivo: 3 weeks of treatement with ET-743 at the dose of 0.15 mg/Kg/weekly i.v.

tag: cell/tissue type

value: intrahepatic cholangiocarcinoma paired patient derived xenograft (ICC PDX)

value: ET-743 (0.15 mg/Kg weekly i.v., three administrations)


title: 5FU-Recurrence26


title: PDX-ET-743-2 [miRNA]

tag: treated with


title: 5FU-Recurrence25


title: 5FU-Recurrence33


title: 5FU-Recurrence27


title: 5FU-Recurrence20


title: 5FU-Recurrence32


title: 5FU-Recurrence31


title: PDX-NT2 [miRNA]

source_name: PDX NT

value: PBS for 24hrs (untreated control)


title: 5FU-Recurrence22


title: 5FU-Recurrence19


title: 5FU-Recurrence17


title: 5FU-Recurrence21


title: 5FU-Recurrence18


title: MT-CHC01-ET-743-2 [miRNA]

source_name: MT-CHC01 ET-743

tag: cell line

value: intrahepatic cholangiocarcinoma cell line

value: 5 nM ET-743 for 24 hrs


title: 5FU-Recurrence24

tag: tissue


title: 5FU-Recurrence30


title: 5FU-Recurrence23


title: 5FU-Recurrence12


title: 5FU-Recurrence28


title: 5FU-Recurrence16


title: 5FU-Recurrence13


title: Non_AMS_7

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

institute: 3rd Military Medical University

description: No

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.  a, The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: Plasma

label_protocol: After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C c, Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.  Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: Plasma

tag: bmi

tag: Sex


title: Non_AMS_6

description: No

tag: age

value: Male


title: MT-CHC01-NT2 [miRNA]

source_name: MT-CHC01 NT


title: 5FU-Recurrence9


title: 5FU-Recurrence8


title: MT-CHC01-ET-743-1 [miRNA]


title: 5FU-Recurrence15


title: 5FU-Recurrence3


title: 5FU-Recurrence14


title: AMS_12

description: No


title: 5FU-Recurrence2


title: 5FU-Recurrence1


title: PDX-NT1 [miRNA]


title: 5FU-Recurrence11


title: Non_AMS_8

description: No


title: AMS_9

description: No


title: kidney in db/db mice, biological rep2

city: Beijing

first: Haojun

last: Zhang

state: Beijing

address: 2 YingHua Dongjie, Chaoyang District

department: Institute of Clinical Medical Sciences

institute: China-Japan Friendship Hospital

description: Gene expression data from kidney in db/db mice

hyb_protocol: 15µg fragmented cRNA, with contol oligo B2 and eukaryotic hybridization controls (bioB, bioC, bioD, cre) was hybridized to the Affymetrix Mouse Genome 430 2.0 array at 45℃ for 16 hours. After hybridization, the GeneChip arrays were washed, and then stained with streptavidin phycoerythrinonan (SAPE) with Affymetrix Fluidics Station 450

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

data_processing: Microarray data were analyzed using Affymetrix Expression Console and Transcriptome Analysis Software(TAC) 3.0 and normalized using the Robust Multiarray Average (RMA) method.

source_name: kidney in db/db mice

label_protocol: 100ng of total RNA was used for cDNA synthesis, and produce biotin-tagged cRNA with GeneChip IVT Labeling kit (Affymetrix).

value: kidney

tag: genotype

value: db/db

value: male

tag: background strain

value: 22 weeks


title: kidney in db/db mice, biological rep1


title: 5FU-Recurrence5


title: AMS_6

description: No


title: Non_AMS_9

description: No


title: Non_AMS_2

description: No


title: Non_AMS_4

description: No


title: Non_AMS_3

description: No


title: AMS_8

description: No


title: 5FU-Recurrence10


title: kidney in db/m mice, biological rep2

description: Gene expression data from kidney in db/m mice

source_name: kidney in db/m mice

value: db/m


title: kidney in db/m mice, biological rep1


title: AMS_7

description: No


title: MT-CHC01-NT1 [miRNA]


title: 5FU-Recurrence7


title: AMS_1

description: No


title: AMS_13

description: No


title: kidney in db/db mice, biological rep3


title: 5FU-Recurrence6


title: AMS_11

description: No


title: Non_AMS_5

description: No


title: Non_AMS_1

description: No


title: AMS_2

description: No


title: AMS_10

description: No


title: Fins_control_non_infected_fish_biological replicate1

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

hyb_protocol: The slides were pre-treated with 1% BSA fraction V, 5 X SSC, 0.1% SDS for 30 min. at 50 ºC and washed with 2 X SSC (3 min) and 0.2 X SSC (3 min) and hybridized overnight in cocktail containing 1.3 X Denhardt's, 3 X SSC, 0.3% SDS, 2.1 ug/ul polyadenylate and 1 ug/ul yeast tRNA.

scan_protocol: Signal was captured and processed using an Agilent scanner (G2565B, Agilent Technologies). The scanner images were segmented by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information

source_name: Fins of six SVCV non infected fish

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: Adult zebrafish of  2-3 g (~ 4 cm in length) were obtained from a local fish pet shop to study a situation that more closely resembles the variability of natural populations. Zebrafish were maintained at 24-26 ºC in 30 l aquaria with tap-dechlorinated carbon-filtered water with 1 g of CaCl2, 1 g of NaHCO3 and 0.5 g of Instant Ocean sea salts added to water resulting in a conductivity of 200-300 µS pH of 7.8-8.2. The aquaria were provided with biological filters and fish fed with a commercial feed diet. For each experiment, groups of adult zebrafish were moved to 2 l aquaria provided with biological filters.

extract_protocol: RNA was extracted using the RNAeasyPlus kit (Qiagen, Hilden, Germany).

treatment_protocol: To infect zebrafish with SVCV, cell culture medium containing  7.1±2 x107 pfu/ml was added to 2 l water tanks and fish were exposed to the virus for 90 minutes. Mock-infected zebrafish were incubated with cell culture medium in parallel experiments.

value: fin

tag: number

value: 6 fish per group


title: IL10_pos

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

institute: CIMA

description: Gene expression data from IL-10+ dendritic cells

hyb_protocol: Labeled sense cDNA was hybridized to the GeneChip® Mouse Gene 2.0 ST Arrays, washed and stained on a GeneChip® Fluidics 450 workstation (Affymetrix) according to the manufacturer protocols.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000 7G

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

source_name: Splenic IL-10+ DCs from VertX mice vaccinated with OVA+Imiquimod

label_protocol: The sense cDNA was prepared from 2 ng of total RNA using the Affymetrix GeneChip® WT Pico Kit. The sense strand cDNA was then fragmented and biotinylated according to the manufacturer's instructions.

growth_protocol: Splenic IL-10+ and IL-10- DC were purified by using anti-CD11c-conjugated magnetic beads (Miltenyi) followed by staining with CD11c-APC antibodies and separation with a FACSAria flow cytometer according to their expression of IL-10 (GFP).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions.

treatment_protocol: Vert-X mice (B6(Cg)-Il10tm1.1Karp/J) were immunized subcutaneously with OVA protein (0.5 mg/mouse) combined with Imiquimod cream (Meda-Aldara™; topical application; 2.5 mg/mouse).  Two days later, spleens were harvested and pooled for cell purification.

value: Vert-X; B6(Cg)-Il10tm1.1Karp/J

tag: immunized with

value: OVA + Imiquimod

tag: time point

value: 2 days after immunization

tag: cell type

value: spleen

value: Splenic IL-10+ dendritic cells

value: Positive


title: Fins_control_non_infected_fish_biological replicate3


title: Fins_SVCV resistant fish_biological replicate2

source_name: Fins of six SVCV resistant fish 30 days post inoculation


title: kidney in db/m mice, biological rep3

tag: gender


title: 5FU-Recurrence4

value: colorectal cancer

value: Had Recurrence


title: AMS_3

description: No

value: Plasma


title: Patient X_107

city: Yokohama-shi, Tsurumi-ku

first: Ryo

last: Matoba

state: Kanagawa-ken

country: Japan

institute: DNAChipResearchInc

hyb_protocol: A total of 600 ng of Cy3 labeled RNA was hybridized to custom-made microarrays at 60C for 17 hours and subsequently washed according to the Agilent standard hybridization protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505B Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data with low signal intensities were excluded from additional investigation, and with each sample, the intensity values were subjected to Quantile Equalization algorithm to correct background noise and for normalization.

source_name: retrospective training study_recurrent case

label_protocol:
After monitoring the RNA using 260nm absorbance, one microgram total RNA was converted to cDNA, and was amplified using the Low RNA Input Fluorescent Labeling Kit (Agilent Technologies, Santa Clara, CA).
The cRNA was labeled with Cyanine 3(Cy3)-CTP during in vitro transcription.

extract_protocol: The tumor specimens were cut into approximately 8.0 mm square pieces within 2 hours of surgical resection, immediately put into RNAlaterTM (Ambion, Austin, TX), and stored at -80ºC until use. Total RNA was extracted using TRIzol reagent (Invitrogen, San Diego, CA) as described in the manufacturer’s protocol.

value: Male

tag: stage (dukes)

value: B

tag: study group

value: retrospective training study

tag: recurrency

value: recurrent


title: Sox5Sox6_KO_rep4

description: Array Content = MouseWG-6_V2_0_R2_11278593_A.bgx.xml

tag: strain

value: Skeletal

tag: genotype/variation

tag: Stage

value: E13.5 embryo


title: Patient X_112

tag: tissue


title: AMS_5

description: No

tag: bmi


title: Fins_SVCV infected fish_biological replicate2

source_name: Fins of six SVCV infected fish 2 days post infection

value: fin


title: AMS_4

description: No

tag: Sex


title: IL10_neg

description: Gene expression data from IL-10- dendritic cells

source_name: Splenic IL-10- DCs from VertX mice vaccinated with OVA+Imiquimod

value: Negative


title: Fins_SVCV infected fish_biological replicate3

value: 6 fish per group


title: Patient X_089

source_name: retrospective training study_recurrent-free case

tag: age

value: recurrent-free


title: Fins_control_non_infected_fish_biological replicate2


title: Fins_SVCV resistant fish_biological replicate1


title: Patient X_093


title: Patient X_121


title: Sox5Sox6_KO_rep1

source_name: E13.5 axial and appendicular skeleton


title: Patient X_083

value: Female


title: Sox5Sox6_KO_rep2


title: Patient X_091


title: Sox5Sox6_KO_rep3


title: Sox6_het_rep1


title: Patient X_090


title: Patient X_082


title: Patient X_081


title: Fins_SVCV infected fish_biological replicate1


title: Patient X_080


title: Patient X_087


title: Patient X_076


title: Patient X_077


title: Patient X_084


title: Patient X_078


title: Patient X_079


title: Sox6_het_rep3


title: Sox6_het_rep4


title: Sox6_het_rep2


title: Patient X_073


title: Patient X_072


title: Patient X_074


title: Patient X_075


title: Patient X_069


title: Patient X_070


title: 320-pDC-CTRL

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

scan_protocol: Whole-genome transcriptional profiling was performed using Illumina Human HT-12 microarrays (SanDiego, CA) as per manufacturer’s instructions. These were performed by the microarray facility at the Diamantina Institute, University of Queensland.

data_processing: Background correction and normalization was performed using the neqc () function available in limma, which uses the normal-exponential convolution model for background correction followed by quantile normalization.

source_name: PBMC

label_protocol: Total RNA samples were biotinylated and amplified using the Ilumina® TotalPrepTM RNA Amplification Kit (Ambion, Austin, TX, USA) as per manufacturer’s instructions with a standardized input amount of 500 ng.

growth_protocol: PBMC were isolated by density gradient centrifugation and cultured at 2X106 cell/ml in media (RPMI 1640 supplemented with 2% heat-inactivated fetal bovine serum,  penicillin, streptomycin and  glutamine) as previously described.  Briefly, 250 μl/well cell resuspension was cultured in a 96-well U-bottom plate, with 8 replicates in each group. The cells were rested at 37°C with 5% CO2 and 95% humidity overnight and then subsequently stimulated with HRV16 or left unstimulated, and further incubated for 24 hrs.

extract_protocol: Following culture, plates were centrifuged at 750Xg for 5 minutes and the supernatants were pooled and harvested for cytokine quantification by enzyme-linked immunosorbent assay (ELISA). The cell pellets were pooled and resuspended in 200 μl of RNA protect, and stored in -80°C for RNA extraction using the RNeasy mini kit (QIAGEN, Australia). Total RNA from PBMC samples preserved in 200 μl of RNAprotect was extracted by RNeasy mini Kit together with RNase free DNase set (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Intact PBMC and pDC depleted PBMC were stimulated in the presence or absence of HRV16 for 24 hrs.

tag: sampleID

tag: sampletype

tag: treatment

value: Control

value: PBMC


title: 320-pDC-RV16

hyb_protocol: Whole-genome transcriptional profiling was performed using Illumina Human HT-12 microarrays (SanDiego, CA) as per manufacturer’s instructions.


title: 320-PBMC-CTRL


title: 320-PBMC-RV16


title: 316-PBMC-CTRL


title: 316-PBMC-RV16


title: Patient X_066


title: 322-pDC-RV16


title: 322-pDC-CTRL


title: 316-pDC-CTRL


title: Patient X_003


title: Patient X_067


title: Patient X_068


title: Patient X_005


title: 284-PBMC-RV16


title: Patient X_011


title: 316-pDC-RV16


title: 322-PBMC-RV16


title: Patient X_008


title: 284-PBMC-CTRL


title: 322-PBMC-CTRL


title: Patient T_222


title: Patient T_059

source_name: retrospective training study


title: 284-pDC-CTRL


title: Patient T_024


title: 283-PBMC-RV16


title: 284-pDC-RV16


title: 283-pDC-RV16


title: Patient S_159


title: Patient S_121


title: Patient S_119


title: Patient S_094


title: Patient S_070


title: Patient R_467


title: Patient S_041


title: 299-PBMC-RV16


title: 299-pDC-RV16


title: Patient S_015


title: 308-pDC-RV16


title: 307-pDC-RV16


title: 308-pDC-CTRL


title: 308-PBMC-RV16


title: Patient O_455


title: Patient R_118


title: 307-pDC-CTRL


title: 308-PBMC-CTRL


title: 299-pDC-CTRL


title: Patient R_359


title: Patient R_016


title: 307-PBMC-RV16


title: 283-PBMC-CTRL


title: Patient O_410


title: Patient O_265


title: 306-PBMC-RV16


title: Patient O_209


title: 307-PBMC-CTRL


title: 299-PBMC-CTRL


title: 306-PBMC-CTRL


title: Patient O_261


title: 306-pDC-RV16


title: 306-pDC-CTRL


title: Patient O_197


title: Patient O_194


title: 305-pDC-CTRL


title: Patient O_171


title: 305-PBMC-RV16


title: 305-pDC-RV16


title: Patient O_158


title: Patient O_130


title: Patient O_157


title: Patient O_134


title: Patient O_135


title: 298-pDC-RV16


title: 298-pDC-CTRL


title: 298-PBMC-CTRL


title: Patient O_128


title: 305-PBMC-CTRL


title: 298-PBMC-RV16


title: Patient O_088


title: 203 C-1 Replicate 2

city: Oxford

first: Julius

last: Muller

state: Oxfordshire

address: ORCRB, Roosevelt Drive

department: Nuffield Department of Medicine

institute: The Jenner Institute, University of Oxford

description: Replicate 2

data_processing: Probes were background corrected using negative control probes followed by quantile normalization using the neqc method of Shi et al. (2010) [PMID:20929874].

source_name: Whole Blood

label_protocol: Biotinylated cRNA were prepared with the Ambion Total Prep RNA amplification kit

extract_protocol: Whole blood was collected in PAXgene Blood RNA tubes (PreAnalytiX) and processed according to the manufacturer’s protocol. The purity and quantity of the isolated total RNA was assessed using an Agilent Bioanalyser prior to storage at -20oC until required. Globin mRNA was subsequently depleted using the GLOBINclear Kit (Ambion). Depleted RNA was then amplified using the TotalPrep RNA Amplification Kit (Illumina) and the resulting cDNA was used as a template for the synthesis of biotin-labelled cRNA.

tag: subject id

value: baseline

value: Whole Blood


title: Patient O_082

value: colorectal cancer


title: 306 D3 Replicate 1

description: Replicate 1

tag: time point

value: 72 hrs


title: 202 D1 Replicate 2

description: Replicate 2

value: 24 hrs


title: Patient O_012

value: Male

value: B


title: Patient O_074

value: retrospective training study

value: recurrent


title: Patient O_042


title: 201 D4 Replicate 1

description: Replicate 1

value: 96 hrs


title: Patient O_009


title: 306 C-1 Replicate 1

description: Replicate 1


title: 204 C-1 Replicate 1

description: Replicate 1


title: Patient O_032


title: Patient N_038


title: Patient O_004


title: 211 D2 Replicate 2

description: Replicate 2

value: 48 hrs


title: Patient N_043


title: Patient N_035


title: Patient S_132


title: Patient N_031


title: Patient N_028


title: Patient N_034


title: 312 D2 Replicate 1

description: Replicate 1


title: 211 D2 Replicate 1

description: Replicate 1


title: Patient N_027


title: 302 D3 Replicate 1

description: Replicate 1


title: 202 D1 Replicate 1

description: Replicate 1


title: 205 D2 Replicate 1

description: Replicate 1


title: 207 C-1 Replicate 1

description: Replicate 1


title: 210 D4 Replicate 1

description: Replicate 1


title: 203 C-1 Replicate 1

description: Replicate 1


title: 302 D4 Replicate 1

description: Replicate 1


title: Patient N_025


title: Patient M_225


title: Patient M_182


title: Patient M_161


title: Patient N_005


title: 283-pDC-CTRL


title: 310 C-1 Replicate 1

description: Replicate 1


title: Patient N_022


title: 208 C-1 Replicate 1

description: Replicate 1


title: 204 D1 Replicate 1

description: Replicate 1


title: 307 D1 Replicate 1

description: Replicate 1


title: 205 C-1 Replicate 1

description: Replicate 1


title: 306 D2 Replicate 1

description: Replicate 1


title: 211 C-1 Replicate 1

description: Replicate 1


title: 201 D2 Replicate 1

description: Replicate 1


title: Patient M_020


title: Patient M_010


title: Patient M_041


title: Patient M_049


title: Patient K_057


title: Patient K_038


title: Patient K_030


title: Patient I_097


title: 206 D2 Replicate 1

description: Replicate 1


title: Patient K_020


title: 307 D2 Replicate 1

description: Replicate 1


title: 210 D2 Replicate 1

description: Replicate 1


title: Patient I_090


title: 308 D1 Replicate 1

description: Replicate 1


title: Patient I_082


title: 204 D2 Replicate 1

description: Replicate 1


title: Patient I_068


title: 310 D2 Replicate 1

description: Replicate 1


title: Patient I_069


title: Patient I_070


title: 308 D3 Replicate 1

description: Replicate 1


title: 211 D1 Replicate 1

description: Replicate 1


title: 209 D2 Replicate 1

description: Replicate 1


title: Patient I_063


title: Patient I_025


title: 204 D4 Replicate 1

description: Replicate 1


title: Patient I_019


title: 209 D3 Replicate 1

description: Replicate 1


title: 205 D1 Replicate 1

description: Replicate 1


title: 212 D2 Replicate 1

description: Replicate 1


title: 311 C-1 Replicate 1

description: Replicate 1


title: Patient H_338


title: Patient H_304


title: Patient H_238


title: 203 D2 Replicate 1

description: Replicate 1


title: Patient H_560


title: 304 D1 Replicate 1

description: Replicate 1


title: Patient H_140


title: Patient H_142


title: 305 D1 Replicate 1

description: Replicate 1


title: 203 D4 Replicate 1

description: Replicate 1


title: Patient H_149


title: 304 C-1 Replicate 1

description: Replicate 1


title: 208 D4 Replicate 1

description: Replicate 1


title: Patient H_232


title: 304 D3 Replicate 1

description: Replicate 1


title: Patient H_119


title: Patient H_028


title: Patient H_129


title: Patient H_096


title: 207 D4 Replicate 1

description: Replicate 1


title: 306 D1 Replicate 1

description: Replicate 1


title: 212 D1 Replicate 1

description: Replicate 1


title: 305 D4 Replicate 1

description: Replicate 1


title: 207 D3 Replicate 1

description: Replicate 1


title: 209 C-1 Replicate 1

description: Replicate 1


title: Patient H_021


title: Patient H_009


title: Patient H_018


title: 203 D3 Replicate 1

description: Replicate 1


title: Patient C_209


title: Patient C_204


title: Patient C_202


title: Patient C_481


title: Patient H_003


title: 302 D2 Replicate 1

description: Replicate 1


title: Patient C_201


title: Patient C_187


title: 201 D3 Replicate 1

description: Replicate 1


title: 201 D1 Replicate 1

description: Replicate 1


title: Patient C_188


title: Patient C_190


title: Patient C_166


title: 208 D3 Replicate 1

description: Replicate 1


title: 210 D1 Replicate 1

description: Replicate 1


title: Patient C_174


title: 205 D3 Replicate 1

description: Replicate 1


title: 202 D3 Replicate 1

description: Replicate 1


title: 311 D1 Replicate 1

description: Replicate 1


title: Patient C_160


title: 209 D1 Replicate 1

description: Replicate 1


title: 305 D3 Replicate 1

description: Replicate 1


title: 307 C-1 Replicate 1

description: Replicate 1


title: 304 D2 Replicate 1

description: Replicate 1


title: 304 D4 Replicate 1

description: Replicate 1


title: 202 D4 Replicate 1

description: Replicate 1


title: 307 D4 Replicate 1

description: Replicate 1


title: 307 D3 Replicate 1

description: Replicate 1


title: Patient C_155


title: Patient C_141


title: Patient C_122


title: Patient C_131


title: 207 D2 Replicate 1

description: Replicate 1


title: Patient C_107


title: Patient C_103


title: Patient C_084


title: Patient C_073


title: Patient C_135


title: Patient C_080


title: Patient C_093


title: Patient C_085


title: 208 D1 Replicate 1

description: Replicate 1


title: Patient C_068


title: Patient C_070


title: 311 D4 Replicate 1

description: Replicate 1


title: 312 D4 Replicate 1

description: Replicate 1


title: 305 D2 Replicate 1

description: Replicate 1


title: Patient C_064


title: 302 C-1 Replicate 1

description: Replicate 1


title: 310 D4 Replicate 1

description: Replicate 1


title: 308 D4 Replicate 1

description: Replicate 1


title: 305 C-1 Replicate 1

description: Replicate 1


title: 211 D3 Replicate 1

description: Replicate 1


title: Patient C_137


title: 208 D2 Replicate 1

description: Replicate 1


title: 312 D3 Replicate 1

description: Replicate 1


title: 212 C-1 Replicate 1

description: Replicate 1


title: 209 D4 Replicate 1

description: Replicate 1


title: 202 C-1 Replicate 1

description: Replicate 1


title: 212 D4 Replicate 1

description: Replicate 1


title: Patient C_057


title: Patient C_030


title: Patient C_028


title: Patient C_041


title: Patient C_048


title: Patient C_050


title: Patient C_051


title: Patient C_040


title: Patient S_257

source_name: prospect study_recurrent-free case

value: prospect


title: Patient C_021


title: Patient C_001


title: 203 D1 Replicate 1

description: Replicate 1


title: Patient S_240


title: 207 D1 Replicate 1

description: Replicate 1


title: 312 D1 Replicate 1

description: Replicate 1


title: 310 D1 Replicate 1

description: Replicate 1


title: 204 D3 Replicate 1

description: Replicate 1


title: Patient R_279


title: 308 D2 Replicate 1

description: Replicate 1


title: Patient R_276


title: Patient R_278


title: 206 D1 Replicate 1

description: Replicate 1


title: 206 D4 Replicate 1

description: Replicate 1


title: 306 D4 Replicate 1

description: Replicate 1


title: 212 D3 Replicate 1

description: Replicate 1


title: 202 D2 Replicate 1

description: Replicate 1


title: 310 D3 Replicate 1

description: Replicate 1


title: 311 D2 Replicate 1

description: Replicate 1


title: 210 C-1 Replicate 1

description: Replicate 1


title: Patient R_254

source_name: prospect study_recurrent case


title: Patient R_225


title: Patient R_261


title: 210 D3 Replicate 1

description: Replicate 1


title: Patient R_264


title: Patient R_193


title: Patient R_206


title: 312 C-1 Replicate 1

description: Replicate 1


title: 206 C-1 Replicate 1

description: Replicate 1


title: 311 D3 Replicate 1

description: Replicate 1


title: 206 D3 Replicate 1

description: Replicate 1


title: 302 D1 Replicate 1

description: Replicate 1


title: 211 D4 Replicate 1

description: Replicate 1


title: Patient R_083


title: Patient R_162


title: Patient R_187


title: Patient R_105


title: Patient R_085


title: Patient R_235


title: Patient R_182


title: Patient R_184


title: Patient R_214


title: 205 D4 Replicate 1

description: Replicate 1


title: Patient R_114


title: Patient O_437


title: BCBL + dhC16

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip v4.0 from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalized using the cubic spline algorithm (GenomeStudio) and background removed with the GenomeStudio's Detection P-value algorithm

source_name: PEL cell-line

label_protocol: cRNA was labeled with the TargetAmp Nano Labeling kit for Illumina Expression BeadChip (Epicentre Catalog Number TAN07924)

growth_protocol: The cells were cultured in RPMI 1640 medium (ATCC) supplemented with 20% FBS. All cells were cultured at 37°C in 5% CO2. All experiments were carried out using cells harvested at low (< 20) passages.

extract_protocol: RNA was extracted using  RNeasy Mini kit (Qiagen) including the DNAseI treatment

treatment_protocol: The cells were treated with vehicle control or dhC16-Cer (40 µM) for 24 h

tag: cell line

value: PEL cell line BCBL-1


title: Patient N_024

tag: gender

value: recurrent-free


title: BCBL

value: vehicle


title: 308 C-1 Replicate 1

description: Replicate 1


title: 201 C-1 Replicate 1

description: Replicate 1


title: Patient N_073

value: Female

tag: stage (dukes)


title: Patient O_419

tag: study group


title: Patient O_386

tag: recurrency


title: Patient O_313


title: Patient O_394


title: Patient N_123


title: Patient C_328


title: Patient C_348


title: Patient N_016


title: Patient O_217


title: Patient C_306


title: Patient C_276


title: Patient C_284


title: Patient C_273


title: Patient C_279


title: Patient C_257


title: Patient C_233


title: Patient C_097


title: Patient C_063


title: Patient N_059


title: Patient C_250


title: Patient T_477


title: Patient C_281


title: Patient T_479


title: Esophageal squamous cell carcinoma_FFPE_Sample38

first: Jianming

last: Ying

address: Panjianyuan Nanli 17, Chaoyang District, Beijing, China

department: Pathology

institute: Cancer Hospital Chinese Academy of Meidcal Sciences

hyb_protocol: Briefly, the 75 ng FFPE DNA were hybridized to MIP probes and allowed to anneal 58°C overnight (16-18h) after denaturation at 95°C for 5 min. Then each sample was split into two tubes and gap fill reaction was performed by adding dATP (A) and dTTP (T) (A/T) in one tube and dGTP (G) and dCTP (C) (G/C) to another. After removing the uncircularised MIP probes through exonuclease treatment, the cleavage enzyme was added to linearize the gap-filled circular MIP Probes. Then the circular MIP probes were amplified by first and second round PCR. The enriched product was digested by HaeIII enzyme and the 44bp fragments were hybridized to the OncoScan™ Array for 16-18h

scan_protocol: The hybridized arrays were washed, stained using the GeneChip® Fluidics Station 450 and scanned through GeneChip® Scanner 3000 7G

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software. The CEL file generated after scanning, was converted to OSCHP files through Oncoscan Console Software 1.1 (Biodiscovery, Inc., CA USA). Further the OSCHP file was analyzed through Affymetrix TuScan algorithm (a modified ASCAT algorithm) using the Nexus Express for Oncoscan software version 3.0 (Biodiscovery, Inc., CA USA). The TuScan algorithm creates segmentation to differentiate between adjacent clusters of probes and determines the copy number changes.

label_protocol: Biotin labelled fragmented DNA were prepared according to the standard OncoScan™ Array protocol  (Affymetrix).

extract_protocol: Genomic DNA was extracted from esophageal squamous cell carcinoma FFPE samplesusing the Qiagen QIAamp DNA Mini kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and Qubit® 2.0 Fluorometer.

value: esophageal squamous cell carcinoma

tag: tissue type

value: FFPE

tag: tnm stage

tag: tumor differentiation

value: moderately differentiated

tag: clinical outcome

value: metastasis

value: female


title: Esophageal squamous cell carcinoma_FFPE_Sample34

tag: tissue

value: non-metastasis

value: male


title: Esophageal squamous cell carcinoma_FFPE_Sample32


title: Esophageal squamous cell carcinoma_FFPE_Sample35

value: well differentiated


title: Patient C_027

value: B

value: colorectal cancer


title: Patient C_042

value: Male


title: Patient C_015


title: Patient C_031


title: Esophageal squamous cell carcinoma_FFPE_Sample33


title: Esophageal squamous cell carcinoma_FFPE_Sample36


title: Esophageal squamous cell carcinoma_FFPE_Sample37


title: Patient S_277

value: recurrent


title: Patient S_271

value: prospect


title: Patient S_604


title: Esophageal squamous cell carcinoma_FFPE_Sample31


title: Patient S_558


title: Esophageal squamous cell carcinoma_FFPE_Sample30


title: Patient R_146


title: Patient R_134


title: Esophageal squamous cell carcinoma_FFPE_Sample29


title: Patient R_241


title: Patient R_130


title: Patient R_140


title: Esophageal squamous cell carcinoma_FFPE_Sample26


title: Esophageal squamous cell carcinoma_FFPE_Sample27

value: poor differentiated


title: Patient R_101

value: recurrent-free


title: Esophageal squamous cell carcinoma_FFPE_Sample25


title: Patient O_473


title: 102326-72 HBV liver

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

description: Liver gene expression data from chronic HBV infection

scan_protocol: Standard Ilumina iScan N240 scanning protocol

data_processing: Primary gene expression data was processed and analyzed using Illumina's Genomestudio v.2010.2 software. Data was normalized using the quantile method

source_name: HBV liver

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy FFPE Kit following the protocol provided by the manufacturer.

value: M

tag: ethnicity

value: nonCau


title: 102326-70 HBV liver

value: F

value: Cau


title: 102326-71 HBV liver


title: 102326-69 HBV liver


title: Esophageal squamous cell carcinoma_FFPE_Sample24

value: esophageal squamous cell carcinoma

value: FFPE

tag: age


title: Esophageal squamous cell carcinoma_FFPE_Sample28

value: moderately differentiated


title: Patient N_011

value: Female


title: Patient O_347


title: Patient O_092


title: Esophageal squamous cell carcinoma_FFPE_Sample21

value: metastasis

value: male


title: Patient O_416

value: B


title: Patient O_331

value: colorectal cancer


title: Esophageal squamous cell carcinoma_FFPE_Sample23

value: well differentiated

value: female


title: Patient O_476

value: Male

value: prospect


title: Patient O_468

value: recurrent-free


title: Patient M_168


title: Esophageal squamous cell carcinoma_FFPE_Sample20


title: 102326-66 HBV liver


title: 102326-67 HBV liver


title: 102326-68 HBV liver


title: 102326-64 HBV liver


title: 102326-63 HBV liver


title: Esophageal squamous cell carcinoma_FFPE_Sample18

value: non-metastasis


title: Esophageal squamous cell carcinoma_FFPE_Sample19


title: 102326-61 HBV liver

value: nonCau


title: Esophageal squamous cell carcinoma_FFPE_Sample22


title: Esophageal squamous cell carcinoma_FFPE_Sample17


title: Patient M_120


title: 102326-65 HBV liver

value: F


title: Esophageal squamous cell carcinoma_FFPE_Sample15


title: Patient M_094


title: Esophageal squamous cell carcinoma_FFPE_Sample14


title: Esophageal squamous cell carcinoma_FFPE_Sample16


title: 102326-59 HBV liver


title: 102326-62 HBV liver

value: Cau


title: 102326-60 HBV liver


title: 102326-58 HBV liver


title: Esophageal squamous cell carcinoma_FFPE_Sample13

value: esophageal squamous cell carcinoma


title: Patient H_231

value: recurrent


title: Patient M_112


title: Patient H_615


title: Patient K_206


title: Patient H_213


title: Esophageal squamous cell carcinoma_FFPE_Sample11

value: FFPE


title: 102326-57 HBV liver

value: M


title: 102326-55 HBV liver


title: Esophageal squamous cell carcinoma_FFPE_Sample10

value: moderately differentiated

value: metastasis


title: Patient H_220

value: B


title: 102326-54 HBV liver


title: Patient H_023

value: Female

value: colorectal cancer


title: Patient H_145


title: Esophageal squamous cell carcinoma_FFPE_Sample9

value: male


title: Esophageal squamous cell carcinoma_FFPE_Sample12

value: female


title: Patient T_107

value: prospect


title: Esophageal squamous cell carcinoma_FFPE_Sample7

value: poor differentiated


title: Patient H_306

value: Male

value: recurrent-free


title: Esophageal squamous cell carcinoma_FFPE_Sample8


title: 102326-50 HBV liver

value: nonCau


title: 102326-52 HBV liver


title: 102326-48 HBV liver

value: F

value: Cau


title: Esophageal squamous cell carcinoma_FFPE_Sample5

value: esophageal squamous cell carcinoma


title: 102326-49 HBV liver


title: Esophageal squamous cell carcinoma_FFPE_Sample6

value: FFPE

value: non-metastasis


title: Esophageal squamous cell carcinoma_FFPE_Sample3

value: well differentiated


title: Esophageal squamous cell carcinoma_FFPE_Sample4

value: moderately differentiated


title: Esophageal squamous cell carcinoma_FFPE_Sample2

value: metastasis


title: Patient S_230

value: Female

value: B


title: Esophageal squamous cell carcinoma_FFPE_Sample1


title: 102326-47 HBV liver

value: M


title: Patient R_292

value: recurrent

value: colorectal cancer


title: Patient R_048

value: prospect


title: Patient R_043

value: Male


title: Patient S_141

value: recurrent-free


title: Patient S_116


title: Patient S_037


title: Patient S_033


title: Patient R_031


title: 102326-44 HBV liver

value: nonCau


title: Patient S_002


title: Patient S_099


title: 102326-34 HBV liver


title: Patient S_113


title: 102326-43 HBV liver


title: 102326-41 HBV liver

value: F


title: 102326-35 HBV liver


title: 102326-42 HBV liver


title: 102326-36 HBV liver

value: Cau


title: Patient T_064


title: 102326-40 HBV liver


title: patient 22 (cancer tissues vs paired nontumor samples )

city: chongqing

first: Jing

last: Xiong

state: chongqing

address: Medical College Road, Yuzhong District, Chongqing, No. 1

institute: chongqing medical university

description: tumor and nontumor samples are obtained from the same patient

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by lowess normalization.

source_name: RCC cancer tissues

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

growth_protocol: 5 patients were informed and have declared written informed consent that their samples can be used for research. Patients received retroperitoneal laparoscopic radical nephrectomy, retroperitoneal laparoscopic partial nephrectomy, cytoreductiv enephrectomy at The First Affiliated Hospital of Chongqing Medical University

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: All the samples were rapidly and carefully frozen in liquid nitrogen after resection until use. None of the patients had been pretreated with radiotherapy or chemotherapy prior to surgery.

value: tumor

source_name: RCC paired nontumor samples

value: nontumor samples


title: 102326-37 HBV liver


title: 102326-45 HBV liver


title: Patient O_507


title: patient 26 (cancer tissues vs paired nontumor samples )


title: Patient R_017


title: Patient O_308


title: patient 25 (cancer tissues vs paired nontumor samples )


title: Patient R_010


title: patient 6 (cancer tissues vs paired nontumor samples )


title: 102326-39 HBV liver


title: Patient O_305


title: Patient O_298


title: Patient O_302


title: 102326-46 HBV liver


title: 102326-38 HBV liver


title: Patient O_295


title: 102326-30 HBV liver


title: 102326-33 HBV liver


title: Patient O_251


title: 102326-27 HBV liver


title: Patient O_256


title: 102326-26 HBV liver


title: 102326-28 HBV liver


title: Patient O_246


title: Patient O_107


title: 102326-29 HBV liver


title: 102326-25 HBV liver


title: 102326-31 HBV liver


title: Patient O_079


title: 102326-20 HBV liver


title: Patient O_108


title: Patient O_117


title: Patient O_087


title: 102326-19 HBV liver


title: 102326-15 HBV liver


title: 102326-24 HBV liver


title: 102326-22 HBV liver


title: Patient O_069


title: 102326-14 HBV liver


title: 102326-18 HBV liver


title: 102326-32 HBV liver


title: PC-3M-2B4_rep4

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

description: SAMPLE 8

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

source_name: The low metastatic line human prostate epithelial cell line

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

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

value: prostate

tag: cell type

value: prostate epithelial

tag: metastasis status


title: patient 5 (cancer tissues vs paired nontumor samples )


title: Patient O_062


title: PC-3M-2B4_rep2

description: SAMPLE 6

value: The low metastatic line human prostate epithelial cell line


title: PC-3M-2B4_rep3

description: SAMPLE 7


title: Patient O_070


title: Patient O_059


title: 102326-12 HBV liver


title: 53KOSTS_shRb_secondary_2

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

institute: Kanazawa University

hyb_protocol: Hybridization were performed using the miRNA complete labeling and hybridization kit (Agilent) according to the manufacturer's instructions.  Washing were performed using Gene expression buffer 1 and 2 (Agilent) according to the manufacture's recommendations.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1  (Agilent). The data were normalized by quantile method with GeneSpring 12.6.1 GX software (Agilent).

source_name: 53KOSTS, shRb, secondary

label_protocol: Cyanine-3 (Cy3) labeled miRNA was prepared from 100 ng total RNA using the miRNA complete labeling and hybridization kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Minced pieces of soft tissue sarcoma samples derived from p53 knocked out mice were digested with 300 U/ml collagenase, 100 U/ml hyaluronidase and 100 μg/ml DNase I in α-modified Eagle’s medium with 10% fetal bovine serum, and then cells were cultured in α-modified Eagle’s medium with 10% fetal bovine serum.

extract_protocol: Total RNA was extracted by using the miRNeasy Mini Kit (Qiagen, Tokyo, Japan) following the manufacturer's recommendations. The quality of the RNA samples was assessed by using the 2100 Bioanalyzer 2100 (Agilent, Santa Clara, USA). The RNA integrity number (RIN) of each total RNA sample was 10.

treatment_protocol: p53 null mice derived soft tissue sarcoma cells were transduced with Rb shRNA (TRCN0000042543, sigma) or control shRNA (SHC002, Sigma), selected by 2 ug/ml puromycin. Cells cultured under monolayer conditions were detached with trypsin-EDTA, and filtered through a 40 μm cell strainer. The cells were then inoculated into 1% methylcellulose containing αMEM supplemented with B27 (Life Technologies, Carlsbad, USA), 10 ng/ml human EGF (PeproTech, Rocky Hill, USA) and 10 ng/ml human bFGF (PeproTech), and without serum, at a density of 5 x 10e3 cells per well on 6-well-type ultra-low attachment plate (EZ-BindShut II, AGC Techno Glass, Shizuoka, Japan). After 10 - 14 days incubation, spheres were collected and passaged once in 2D condition.

tag: shRNA

tag: culture

value: secondary

value: sphere-forming cells derived from Rb depleted p53 knocked out mouse derived sarcoma cells


title: 102326-16 HBV liver


title: Patient O_021

value: Female

value: B


title: Patient O_008


title: 53KOSTS_shRb_secondary_3


title: Patient M_107


title: 102326-07 HBV liver

value: M


title: 53KOSTS_shRb_2

source_name: 53KOSTS, shRb, primary

value: primary

value: Rb depleted p53 knocked out mouse derived sarcoma cells


title: 53KOSTS_shRb_1


title: 102326-13 HBV liver


title: 53KOSTS_Nontarget_2

source_name: 53KOSTS, Non-target, primary

value: Non-target

value: p53 knocked out mouse derived sarcoma cells


title: 102326-08 HBV liver


title: 102326-17 HBV liver


title: Patient M_090

value: Male

value: prospect

value: recurrent-free

value: colorectal cancer


title: 53KOSTS_shRb_secondary_1


title: 102326-11 HBV liver

value: Cau


title: 102326-10 HBV liver

value: F


title: PC-3M-2B4_rep1

description: SAMPLE 5

value: prostate

value: prostate epithelial


title: Patient M_083


title: 102326-06 HBV liver


title: 102326-05 HBV liver


title: 53KOSTS_Nontarget_1


title: Patient M_080


title: Patient M_085


title: PC-3M-1E8_rep3

description: SAMPLE 3

source_name: The highly metastatic human prostate epithelial cell line


title: PC-3M-1E8_rep2

description: SAMPLE 2

value: The highly metastatic human prostate epithelial cell line


title: 102326-09 HBV liver


title: Patient M_082

value: recurrent


title: PC-3M-1E8_rep1

description: SAMPLE 1


title: PC-3M-1E8_rep4

description: SAMPLE 4


title: HCC827_mock_2

city: Tokushima

first: Kiyoshi

last: Masuda

address: 3-18-15 Kuramoto-cho

department: Department of Human Genetics

institute: Institute of Biomedical Sciences, Tokushima University Graduate School

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Oligo Microarrays (G4851B) 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 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HCC827 lung adenocarcinoma, control cell 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

value: lung adenocarcinoma


title: Patient M_072

value: B


title: HCC827_WT_1

source_name: HCC827 lung adenocarcinoma, TRIM58 expressing cell 1


title: 102326-03 HBV liver


title: HCC827_mock_1

source_name: HCC827 lung adenocarcinoma, control cell 1


title: HCC827_WT_2

source_name: HCC827 lung adenocarcinoma, TRIM58 expressing cell 2


title: Patient M_025


title: Patient M_038


title: A549_WT_3

source_name: A549 lung adenocarcinoma, TRIM58 expressing cell 3


title: Patient M_017


title: 102235-20 HBV liver

value: M


title: Patient K_145


title: Patient M_013

value: Female


title: Patient M_012


title: 102235-17 HBV liver


title: 102326-01 HBV liver


title: A549_WT_1

source_name: A549 lung adenocarcinoma, TRIM58 expressing cell 1


title: 102235-24 HBV liver


title: A549_mock_1-2

source_name: A549 lung adenocarcinoma, control cell 1


title: A549_WT_2

source_name: A549 lung adenocarcinoma, TRIM58 expressing cell 2


title: 102235-23 HBV liver


title: A549_mock_1-1


title: Patient K_117

source_name: prospect study_recurrent-free case


title: A549_mock_3

source_name: A549 lung adenocarcinoma, control cell 3


title: 102235-16 HBV liver

source_name: HBV liver


title: 102235-15 HBV liver


title: 102235-12 HBV liver


title: A549_mock_2

source_name: A549 lung adenocarcinoma, control cell 2


title: Patient K_110


title: Patient K_092


title: 102235-11 HBV liver


title: Patient K_053


title: Patient K_069


title: Patient H_263


title: Patient K_087

source_name: prospect study_recurrent case


title: Patient H_244


title: 102235-14 HBV liver


title: Patient H_214


title: Patient H_242


title: Patient H_196


title: Patient H_236


title: Patient K_013


title: Patient H_092


title: Patient H_103


title: Patient H_098


title: CHC001 PDX ET-743 - replicate 1

hyb_protocol: Six hundred ng of labeled RNA were hybridized on SurePrint G3 Human Gene Expression 8x60K v2 glass arrays;

source_name: CHC001 PDX ET-743 - replicate 1

label_protocol: 100 ng of total RNA were amplified and labeled using Low Input Quick Amp Labeling Kit, one-color kit (Agilent Technologies);

growth_protocol: MT-CHC01 cells were cultured in KODMEM-F12 with 10% fbs, glutammine, Hepes and P/S

extract_protocol: Total RNA extracted using Trizol AND Absolute RNA miRNA kit (Agilent) following manufacturer's instructions

value: CHC001 PDX ET-743 (0.15 mg/Kg weekly i.v., three administrations)

tag: treatment

value: ET-743 at the dose of 0.15 mg/Kg/weekly for three weeks


title: CHC001 PDX ET-743 - replicate 2

source_name: CHC001 PDX ET-743 - replicate 2

tag: cell line


title: MT-CHC01-ET743-1

source_name: MT-CHC01 ET-743

value: ET-743 at the dose of 5 nM for 24 hours


title: RC301_4h_PA14_rep2

city: Durham

first: Alejandro

last: Aballay

state: NC

address: 265 Jones Building

department: Molecular Genetics and Microbiology

institute: Duke University Medical Center

hyb_protocol: cRNA was fragmented and added to 44 K feature Agilent C. elegans Gene Expression Microarray V2 slides (Agilent Technologies, Santa Clara, CA). Hybridization was performed in the Agilent rotisserie Hybridization Oven for 17 hours.

scan_protocol: Arrays were subsequently washed and scanned with the Agilent B scanner according to standard Agilent protocols (Agilent Technologies, Santa Clara, CA).

data_processing: Microarray data was analyzed using Partek Genomics Suite (St. Louis, MO). Raw data was preprocessed, including background correction, normalization, and summarization using robust multiarray average analysis, and expression data were log2 transformed for a subsequent analysis. Please note that sample data table contains gProcessedSignal values.

organism: Caenorhabditis elegans

source_name: RC301 animals, 4 hours, PA14

label_protocol: Total RNA was assessed for quality with an Agilent 2100 Bioanalyzer G2939A (Agilent Technologies, Santa Clara, CA) and a Nanodrop 8000 spectrophotomer (Thermo, Wilmington, DE). Total RNA was converted Cy-3-labeled, linearly amplified cRNA using the Low Input Quick Amp (LIQA) Labeling One-Color Microarray-Based Gene Expression Analysis Kit (Agilent Technologies, Santa Clara, CA) according to the manufacterer protocols by the Duke Microarray Facility.

growth_protocol: DA650 and RC301 animals were synchronized by treating gravid adults with sodium hydroxide and bleach. Synchronized L1 animals were grown at 20°C on NGM plates seeded with E. coli OP50 for 48 hours.

extract_protocol: Animals were wahed from the P. aeruginosa containing plates and flash-frozen in Trizol (Life Technologies, Carlsbad, CA). Total RNA from three biological replicates was extracted using the RNeasy Plus Universal Kit (Qiagen, Netherlands). Residual genomic DNA was removed by DNase treatment (Ambion, Austin, TX).

treatment_protocol: After 48 hours of growth on E. coli OP50, animals were rinsed off the plates with M9, washed three times with M9, concentrated and transferred to plates containing modified NMG media seeded with Pseudomonas aeruginosa strain PA14. The animals were incubated with the pathogen for 4 hours at 25°C.

tag: strain

value: Young adult

tag: gender

value: hermaphrodite

tag: incubated with

value: P. aeruginosa strain PA14 for 4hrs

value: whole animal


title: CHC001 PDX NT - replicate 2

source_name: CHC001 PDX NT - replicate 2

value: CHC001 PDX NT (PBS)

value: PBS


title: RC301_4h_PA14_rep3


title: CHC001 PDX NT - replicate 1

source_name: CHC001 PDX NT - replicate 1


title: Patient H_091

value: Male

tag: stage (dukes)

tag: study group

value: prospect

tag: recurrency

value: recurrent-free

value: colorectal cancer


title: Patient H_012


title: RC301_4h_PA14_rep1


title: DA650_4h_PA14_rep3

source_name: DA650 animals, 4 hours, PA14


title: MT-CHC01-NT1

source_name: MT-CHC01 NT


title: DA650_4h_PA14_rep1


title: Patient H_011


title: DA650_4h_PA14_rep2