title: ILC cell line SUM44PE

status: Public on Jan 05 2016

city: Amsterdam

first: Inès

last: Goossens-Beumer

address: Science Park 406

institute: Agendia NV

hyb_protocol: A total of 750 ng of cy3-labeled cDNA was hybridized to custom 44K arrays at 65°C for 17 hours, and subsequently washed according to the standard Agilent hybridization protocol.

scan_protocol: Arrays were scanned with a dual laser scanner (Agilent Technologies). Image analysis of the scanned arrays was performed to quantify fluorescent intensities using Feature Extraction software version 9.5 (Agilent Technologies). The Feature Extraction process included within-array normalization, which was performed using the Lowess correction method using a linear polynomial (locally weighted linear least square regression; the current default method for normalisation of Agilent microarrays).

data_processing: Background correction was applied to feature signal intensities using an offset of 10. All probe intensities <1 were set as missing values. Log 2 transformed probe intensities were quantile normalized using the R package limma. Batch-effect (see manuscript) adjustment was performed using R package ComBat. Genes with multiple probes were summarized by the first principle component of a correlating subset (see manuscript for more detail).

source_name: ILC breast cancer cell line

label_protocol: Two-hundred nanogram total RNA was reversed transcibed, amplified and labeled with Cy3 using the QuickAmp Labeling kit (Agilent Technologies), and subsequently purified using the Qiagen RNeasy micro kit.

extract_protocol: Total RNA was isolated from fresh frozen tissue using Qiazol. After DNAse treatment samples were purified using the Qiagen RNeasy micro kit.

value: ILC breast cancer cell line SUM44PE


title: TMD_F_88_EDL [exon-level]

type: RNA

city: Houston

first: Mario

last: Sirito

state: TX

address: 1515 Holcombe blvd

department: Cancer Genetics

country: USA

institute: M. D. Anderson Cancer Center

description: TMD_SKM_FIN061_861001_HUEX1ST_20060224_TN.CEL

hyb_protocol: Sample hybridization, washing and scanning was performed according to manufacturer’s recommendations.

scan_protocol: Scanning was performed using the Affymetrix GeneChip Scanner according to manufacturer’s recommendations. Images were processed using GCOS manager v1.4.0.036 and GCDO v5.0.9.

data_processing:
CEL files were analyzed using the Partek Genomics Suite (Partek Inc., St. Louise, MO), employing the workflow for exon arrays, and aligned to genome Build hg18.  Only the core set of probes (as defined by Affymetrix) were included.  Intensities were quartile normalized with RMA background correction but without GC correction.
probe_group_file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Skeletal muscle- extensor hallucis/digitorum longus

label_protocol: RNA was processed for hybridization using Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay for preparation of single-stranded (ss) target DNA

growth_protocol: Not applicable

extract_protocol: RNA was extracted using the TriZol Reagent according to the manufacturer's suggestions (Invitrogen, Carlsbad, CA) and further purified using the RNeasy kit (Qiagen Inc., Valencia, CA).  The quality and integrity of the RNA was then analyzed on an Agilent Bio- Analyzer (RNA 6000 Nano LabChip).  Total cellular RNA samples with a RIN (RNA integrity number) >7 were used for further microarray studies

treatment_protocol: Not applicable

tag: diagnosis

value: Tibial muscular Dystophy

tag: gender

value: F

tag: age (yrs)


title: N_M_43_x_04 [exon-level]

description:
N_KL_055_EA_HUEX1ST_20050910_VN.CEL
Ambion

source_name: Skeletal muscle

value: Normal

value: M


title: N_M_85_x [exon-level]

description:
N_KL_045_EA_HuEX1ST_20050831_TN.CEL
Stratagene


title: TMD_M_58_EDL [exon-level]

description: TMD_SKM_FIN060_860001_HUEX1ST_20060224_TN.CEL


title: BMD_M_26_BB [exon-level]

description: BMD_SKM_USOH023_240001_HUEX1ST_20060224_TN.CEL

source_name: Skeletal Muscle-biceps brachi

value: Becker Muscular Dystrophy


title: N_M_43_x_03 [exon-level]

description:
N_KL_038_EA_HuEX1ST_20050831_TN.CEL
Ambion


title: ILC cell line ZR7530

country: Netherlands

tag: tissue

value: ILC breast cancer cell line ZR7530


title: ILC cell line SkBr5

value: ILC breast cancer cell line SkBr5


title: DM2_F_55_BB [exon-level]

value: Myotonic Dystrophy Type 2


title: DM1_x_x_x [exon-level]

value: Myotonic Dystrophy Type 1

value: Not available


title: DM1_M_21_x [exon-level]

description:
DM1_KL_054_EA_HUEX1ST_20051215_TN.CEL
Homozygous mutation


title: DM2_F_50_BB [exon-level]


title: N_F_61_x [exon-level]

description:
N_KL_037_EA_HUEX1ST_20050820_VN.CEL
Stratagene


title: DM2_F_37_VL [exon-level]

source_name: Skeletal Muscle- vastus lateralis


title: BMD_M_50_D [exon-level]

description: BMD_SKM_USOH020_237001_HUEX1ST_20060224_TN.CEL

source_name: Skeletal Muscle-Deltoid


title: DM2_M_51_BB [exon-level]


title: ILC cell line OCUBM

value: ILC breast cancer cell line OCUBM


title: ILC cell line OCUBF

value: ILC breast cancer cell line OCUBF


title: DM2_F_43_D [exon-level]


title: DM2_M_39_BB [exon-level]


title: ILC cell line MDAMB468

value: ILC breast cancer cell line MDAMB468


title: ILC cell line MDAMB453

value: ILC breast cancer cell line MDAMB453


title: DM2_F_43_BB [exon-level]


title: DMD_M_20_G [exon-level]

description: DMD_SKM_USOH024_241001_HUEX1ST_20060224_TN.CEL

source_name: Skeletal muscle-gastrocnemius

value: Duchenne Muscular Dystrophy


title: DM1_F_x_BB [exon-level]


title: DM1_F_x_D [exon-level]


title: ILC cell line MDAMB134VI

value: ILC breast cancer cell line MDAMB134VI


title: DM2_F_51_BB [exon-level]


title: DM1_F_54_x [exon-level]


title: ILC cell line MDAMB330

value: ILC breast cancer cell line MDAMB330


title: DM1_F_29_BB [exon-level]


title: DM2_F_58_BB [exon-level]


title: ILC cell line HCC2218

value: ILC breast cancer cell line HCC2218


title: DM1_F_55_D [exon-level]

value: F


title: ILC cell line MPE600

value: ILC breast cancer cell line MPE600


title: ILC cell line HCC1187

value: ILC breast cancer cell line HCC1187


title: BMD_M_45_BB [exon-level]

description: BMD_SKM_USOH022_239001_HUEX1ST_20060224_TN.CEL

value: Becker Muscular Dystrophy

value: M


title: DM1_M_25_x [exon-level]


title: DM2_F_65_BB [exon-level]


title: ILC cell line CAMA1

value: ILC breast cancer cell line CAMA1


title: ILC cell line EVSAT

value: ILC breast cancer cell line EVSAT


title: ILC breast cancer patient RL8096

source_name: Primary ILC breast cancer

value: Primary ILC breast cancer


title: ILC breast cancer patient RL8099


title: ILC breast cancer patient RL8094


title: ILC breast cancer patient RL8092


title: ILC breast cancer patient RL8090


title: ILC breast cancer patient RL8085


title: ILC breast cancer patient RL8083


title: ILC breast cancer patient RL8089


title: ILC cell line SkBr3

value: ILC breast cancer cell line SkBr3


title: ILC breast cancer patient RL8081


title: ILC breast cancer patient RL8080


title: ILC breast cancer patient RL8078


title: ILC breast cancer patient RL8072


title: ILC breast cancer patient RL8074


title: ILC breast cancer patient RL8070


title: ILC breast cancer patient RL8076


title: ILC breast cancer patient RL8068


title: ILC breast cancer patient RL8066


title: ILC breast cancer patient RL8060


title: ILC breast cancer patient RL8058


title: ILC breast cancer patient RL8054


title: ILC breast cancer patient RL8098


title: ILC breast cancer patient RL8049


title: ILC breast cancer patient RL8052


title: ILC breast cancer patient RL8051


title: ILC breast cancer patient RL8048


title: ILC breast cancer patient RL8047


title: ILC breast cancer patient RL8087


title: ILC breast cancer patient RL8045


title: ILC breast cancer patient RL8043


title: ILC breast cancer patient RL8044


title: ILC breast cancer patient RL8042


title: ILC breast cancer patient RL8041


title: ILC breast cancer patient RL8040


title: ILC breast cancer patient RL8039


title: ILC breast cancer patient RL8038


title: ILC breast cancer patient RL8037


title: ILC breast cancer patient RL8036


title: ILC breast cancer patient RL8033


title: ILC breast cancer patient RL8032


title: ILC breast cancer patient RL8031


title: ILC breast cancer patient RL8063


title: ILC breast cancer patient RL8056


title: ILC breast cancer patient RL8030


title: ILC breast cancer patient RL8027


title: ILC breast cancer patient RL8026


title: ILC breast cancer patient RL8025


title: ILC breast cancer patient RL8023


title: ILC breast cancer patient RL8022


title: ILC breast cancer patient RL8021


title: ILC breast cancer patient RL8020


title: ILC breast cancer patient RL8019


title: ILC breast cancer patient RL8017


title: ILC breast cancer patient RL8034


title: ILC breast cancer patient RL8016


title: ILC breast cancer patient RL8011


title: ILC breast cancer patient RL8013


title: ILC breast cancer patient RL8009


title: ILC breast cancer patient RL8008


title: s1D.H4c.Cy3

city: Urbana

first: Eunsoo

last: Choe

state: Illinois

address: s-306 Turner hall 1102 S. Goodwin Ave.

institute: USDA-ARS

description:
biological replication 3 of 3
raw data in Cy3 channel of 002_D.gpr

hyb_protocol: Labeled samples were hybridized to custom designed Agilent maize 4x44K arrays.

scan_protocol: Axon 4000B microarray scanner (Molecular Devices, Sunnyvale, CA) at 5 μm resolution. Spotfinding was carried out using GenePix 6.1 image analysis software (Molecular Devices, Sunnyvale, CA).

data_processing: R (R Development Core Team, 2014) (v 3.1.0) using the Limma package (v 3.20.1) were used for data processing. Median foreground values from the 8 arrays were read into R, and any spots that had been manually flagged (-100 values) were given a weight of zero (Smyth and Speed, 2003). The individual Cy5 and Cy3 values were all normalized together using the quantile method and then log2-transformed.The mixed effects statistical model were fit on the 39,091 probes while accounting for array as random. The expression values from the probes were compared with the positive and negative controls and 30,190 probes were selected based on expression values > 6.25 on the log2 scale in at least 2 samples out of 16 samples.

organism: Zea mays

source_name: Low-yielding hyrbid L1

label_protocol: Seventy-five ng of total RNA was labeled using the Agilent 2-color Low Input Quickamp Whole Transcriptome Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's protocols.

growth_protocol: Six shrunken2 (sh2) sweet corn hybrids were grouped to high- and low-yielding groups based on kernel mass per hectare in 2012. They were grown under high plant density at the University of Illinois Vegetable Crop Research Farm near Urbana, IL in 2013.

extract_protocol: Total RNA was extracted using RNeasy mini kit (Qiagen, Hilden, North Rhine-Westphalia, Germany).

treatment_protocol: Plant density was at 71,700 plants per hectare, the optimal plant density of the most crowding stress tolerant hybrid and 13,700 plants per hectare above normal. High plant density resulted 90% yield increase in high-yielding group compared with low-yielding group.

tag: hybrid

tag: yield group

value: Low

value: leaf at R1


title: ILC breast cancer patient RL8003


title: ILC breast cancer patient RL8007


title: s2B.H2b.Cy3

description:
biological replication 2 of 3
raw data in Cy3 channel of 003_B.gpr

source_name: High-yielding hybrid H2

value: High


title: s1D.H5b.Cy5

description:
biological replication 2 of 3
raw data in Cy5 channel of 002_D.gpr

source_name: Low-yielding hyrbid L2


title: s1C.H6b.Cy5

description:
biological replication 2 of 2
raw data in Cy5 channel of 002_C.gpr

source_name: Low-yielding hyrbid L3


title: s2D.H3b.Cy5

description:
biological replication 2 of 2
raw data in Cy5 channel of 003_D.gpr

source_name: High-yielding hybrid H3


title: s2C.H6a.Cy3

description:
biological replication 1 of 2
raw data in Cy3 channel of 003_C.gpr


title: s2D.H5c.Cy3

description:
biological replication 3 of 3
raw data in Cy3 channel of 003_D.gpr


title: s2B.H4b.Cy5

description:
biological replication 2 of 3
raw data in Cy5 channel of 003_B.gpr


title: s2A.H1c.Cy3

description:
biological replication 3 of 3
raw data in Cy3 channel of 003_A.gpr

source_name: High-yielding hybrid H1


title: s1C.H3a.Cy3

description:
biological replication 1 of 2
raw data in Cy3 channel of 002_C.gpr


title: s2A.H5a.Cy5

description:
biological replication 1 of 3
raw data in Cy5 channel of 003_A.gpr


title: ILC breast cancer patient RL1130


title: ILC breast cancer patient RL1129


title: s1A.H1a.Cy3

description:
biological replication 1 of 3
raw data in Cy3 channel of 002_A.gpr


title: s1B.H4a.Cy3

description:
biological replication 1 of 3
raw data in Cy3 channel of 002_B.gpr


title: N_M_43_x_04 [gene-level]

description:
N_KL_055_EA_HUEX1ST_20050910_VN.CEL
Ambion

data_processing:
CEL files were analyzed using the Partek Genomics Suite (Partek Inc., St. Louise, MO), employing the workflow for exon arrays, and aligned to genome Build hg18.  Only the core set of probes (as defined by Affymetrix) were included.  Intensities were quartile normalized with RMA background correction but without GC correction.
probe_group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset_file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

value: Normal


title: s2C.H2c.Cy5

description:
biological replication 3 of 3
raw data in Cy5 channel of 003_C.gpr


title: s1B.H1b.Cy5

description:
biological replication 2 of 3
raw data in Cy5 channel of 002_B.gpr


title: s1A.H2a.Cy5

description:
biological replication 1 of 3
raw data in Cy5 channel of 002_A.gpr


title: ILC breast cancer patient RL1127


title: ILC breast cancer patient RL1126


title: N_M_85_x [gene-level]

description:
N_KL_045_EA_HuEX1ST_20050831_TN.CEL
Stratagene


title: N_M_43_x_03 [gene-level]

description:
N_KL_038_EA_HuEX1ST_20050831_TN.CEL
Ambion


title: ILC breast cancer patient RL1124


title: ILC breast cancer patient RL1123


title: TMD_M_58_EDL [gene-level]

description: TMD_SKM_FIN060_860001_HUEX1ST_20060224_TN.CEL

value: Tibial muscular Dystophy


title: ILC breast cancer patient RL1122


title: TMD_F_88_EDL [gene-level]

description: TMD_SKM_FIN061_861001_HUEX1ST_20060224_TN.CEL


title: N_F_61_x [gene-level]

description:
N_KL_037_EA_HUEX1ST_20050820_VN.CEL
Stratagene


title: ILC breast cancer patient RL1116


title: ILC breast cancer patient RL1114


title: DMD_M_20_G [gene-level]

description: DMD_SKM_USOH024_241001_HUEX1ST_20060224_TN.CEL

value: Duchenne Muscular Dystrophy


title: BMD_M_26_BB [gene-level]

description: BMD_SKM_USOH023_240001_HUEX1ST_20060224_TN.CEL


title: ILC breast cancer patient RL1120


title: ILC breast cancer patient RL1110


title: ILC breast cancer patient RL1111


title: ILC breast cancer patient RL1112


title: ILC breast cancer patient RL1107


title: BMD_M_45_BB [gene-level]

description: BMD_SKM_USOH022_239001_HUEX1ST_20060224_TN.CEL


title: DM2_F_55_BB [gene-level]

value: Myotonic Dystrophy Type 2


title: BMD_M_50_D [gene-level]

description: BMD_SKM_USOH020_237001_HUEX1ST_20060224_TN.CEL


title: DM2_M_51_BB [gene-level]


title: DM2_F_37_VL [gene-level]


title: ILC breast cancer patient RL1121


title: ILC breast cancer patient RL1104


title: DM2_F_65_BB [gene-level]


title: ILC breast cancer patient RL1102


title: DM2_F_43_D [gene-level]


title: DM2_F_50_BB [gene-level]


title: DM2_F_51_BB [gene-level]


title: ILC breast cancer patient RL1100


title: ILC breast cancer patient RL1099


title: ILC breast cancer patient RL1098


title: ILC breast cancer patient RL1105


title: ILC breast cancer patient RL1097


title: ILC breast cancer patient RL1096


title: ILC breast cancer patient RL1095


title: DM2_F_58_BB [gene-level]


title: ILC breast cancer patient RL1094


title: DM2_F_43_BB [gene-level]


title: ILC breast cancer patient RL1089


title: DM2_M_39_BB [gene-level]


title: ILC breast cancer patient RL1088


title: ILC breast cancer patient RL8101


title: DM1_F_55_D [gene-level]

value: Myotonic Dystrophy Type 1


title: ILC breast cancer patient RL1101


title: DM1_M_21_x [gene-level]

description:
DM1_KL_054_EA_HUEX1ST_20051215_TN.CEL
Homozygous mutation


title: ILC breast cancer patient RL1087


title: ILC breast cancer patient RL1086


title: DM1_F_x_BB [gene-level]

value: F

value: Not available


title: ILC breast cancer patient RL1085


title: DM1_F_29_BB [gene-level]


title: ILC breast cancer patient RL1090


title: ILC breast cancer patient RL1084


title: DM1_M_25_x [gene-level]


title: L-Glu

city: ATLANTA

first: GUOQING

last: LI

state: GEORGIA

address: 161 Jessie Hill Jr. Drive

department: BIOLOGY

institute: GEORGIA STATE UNIVERSITY

description: Gene expression data from PAO1 at 20mM L-Glu

scan_protocol: Affymetrix Protocol:Scan-M10

data_processing: Microarray Suite 5.0 software

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 in MMP supplemented with L-Glu

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 10 ug total RNA

growth_protocol: Overnight grown cultures of P. aeruginosa PAO1 were used to inoculate 10 ml minimal medium P and grown at 37ºC with shaking at 300rpm.Cells were harvested when the optical density at 600 nm reached 0.4~0.6 by centrifugation for 5 minutes at 4C.

extract_protocol: Total RNA was isolated by the hot phenol method, followed by DNase I treatment and column RNA purification (Qiagen). Labeled cDNA probes were prepared in accordance with the protocol provided by the manufacturer (Affymetrix). cDNA was synthesized by annealing random primers (Invitrogen) to purified total RNA and subsequent extension with reverse transcriptase (SuperScript II; Invitrogen).

treatment_protocol: P. aeruginosa PAO1 was grown in minimal medium P in the presence of L-Glutamate at 20 mM with or without D-Arg at 20mM.

tag: strain


title: D-Arg_01

description: Gene expression data from PAO1 at 20mM L-Glu & 20mM D-Arg

source_name: PAO1 in MMP supplemented with L-Glu and D-Arg_01


title: DM1_F_54_x [gene-level]


title: ILC breast cancer patient RL1080


title: DM1_F_x_D [gene-level]


title: ILC breast cancer patient RL1079


title: D-Arg_02

source_name: PAO1 in MMP supplemented with L-Glu and D-Arg_02


title: MCF-7/ADR cells, biological rep2

city: Shanghai

first: Cun

last: Wang

address: No. 25/Ln 2200 Xie-Tu Road, Shanghai 200032, China

country: China

institute: Shanghai Cancer Institute

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

source_name: MCF-7/ADR cells

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

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

treatment_protocol: MCF-7 and MCF-7/ADR cells were cultured in RPMI-1640 medium with 10% fetal calf serum. MCF-7/ADR cells were cultured in the presence of a low concentration of Dox (1 µg/ml) and passaged for 1 week in drug-free medium before the experiments.

tag: disease state

value: Breast cancer

tag: cell line


title: BCP1+PF-2341066

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 for 14h at 58°C

scan_protocol: Standard Illumina protocols for HumanHT-12 V4 chips from Illumina using the Illumina BeadArray Reader

data_processing: Background signal was removed using the Detection P value algorithm. Signals were normalized using the cubic spline algorithm. Differential expression was determined using the Illumina Custom Algorithm. Ratios were determined as the fraction between the treatments and the Control group

source_name: Primary effusion lymphoma cell-line BCP1

label_protocol: cRNA was labeled with the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, TX),

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: Total RNA was extracted with TriZol

treatment_protocol: The cells were treated with vehicle control or c-MET inhibitor PF-2341066 (0.8 µM) for 24 h

tag: treatment


title: ILC breast cancer patient RL1078


title: BC1+Vehicle

source_name: Primary effusion lymphoma cell-line BC1

value: Vehicle


title: DM1_x_x_x [gene-level]

source_name: Skeletal muscle


title: ILC breast cancer patient RL1083


title: MCF-7 cells, biological rep2

source_name: MCF-7 cells

growth_protocol: RPMI-1640 medium with 10% fetal calf serum.


title: MCF-7 cells, biological rep3


title: BCBL1+PF-2341066

source_name: Primary effusion lymphoma cell-line BCBL1


title: BC1+PF-2341066


title: MCF-7/ADR cells, biological rep3


title: ILC breast cancer patient RL1077


title: BSA_R61A

city: Caen Cedex

first: Brigitte

last: Sola

address: CHU Côte de Nacre

department: UFR de médecine

country: France

institute: Université de Caen

hyb_protocol: Hybridation was performed according to manufacturer's instructions

scan_protocol: Scan was performed according to manufacturer's instructions

data_processing: Data processing was done according to IGBMC's protocols (Strasbourg, France)

label: Biotin

source_name: RPMI 8226 cells, one day after 6Gy C-ions irraidations, sample 1

label_protocol: Labelling was performed according to manufacturer's instructions

growth_protocol: RPMI 8226 cells were were cultured at 37°C under 5% CO2 in RPMI 1640 medium (Lonza SPRL, Verviers, Belgium) supplemented with 10% fetal calf serum (FCS, PAA Laboratories GmbH, Pashing, Austria), 2 mM L-glutamine and antibiotics (Lonza).

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

treatment_protocol: 0 or 6 Gy dose of C-ion irradiations

value: RPMI 8226


title: BSA_R61C

source_name: RPMI 8226 cells, one day after 6Gy C-ions irraidations, sample 3


title: BSA_R61B

source_name: RPMI 8226 cells, one day after 6Gy C-ions irraidations, sample 2


title: BCBL1+Vehicle

value: +vehicle


title: MCF-7/ADR cells, biological rep1


title: UHRF1 KD+S674A 03

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

hyb_protocol: standard Affymetrix Protocol

scan_protocol: standard Affymetrix Protocol

data_processing: The data were analyzed with Partek Genomics Suite 6.6. Robust Multi-Array Average (RMA) was used as normalization method. One-way ANOVA modeling was used to obtain differentailly expressed probes acorss different groups.

source_name: HeLa cells stably expressing UHRF1 shRNA reconstituted with UHRF1 S674A

label_protocol: standard Affymetrix Protocol

growth_protocol: cells were cultured in DMEM (Dulbecco's Modified Eagle Medium) higlucose medium supplemented with 10% Fetal Bovine Serum (FBS).

extract_protocol: Total RNA of the cells were extracted using PARIS™ Kit(Ambion AM1921)

treatment_protocol: HeLa cells were treated with shRNAs targeting control or UHRF1. Reconstituting with WT or S674A mutant were performed in UHRF1 depleted cells.

tag: cell type

value: HeLa

tag: genotype/variation

value: UHRF1-depleted cells

tag: shRNA


title: BCP1+Vehicle


title: MCF-7 cells, biological rep1


title: ILC breast cancer patient RL1075

source_name: Primary ILC breast cancer

value: Primary ILC breast cancer


title: BSA_R01B

source_name: RPMI 8226 cells, one day after 0Gy C-ions irraidations, sample 2


title: BSA_R01C

source_name: RPMI 8226 cells, one day after 0Gy C-ions irraidations, sample 3


title: UHRF1 KD+S674A 02

value: UHRF1 shRNA reconstituted with UHRF1 S674A


title: ILC breast cancer patient RL1074


title: UHRF1 KD+S674A 01


title: BSA_R01A

source_name: RPMI 8226 cells, one day after 0Gy C-ions irraidations, sample 1


title: ILC breast cancer patient RL1073


title: UHRF1 KD+WT 03

source_name: HeLa cells stably expressing UHRF1 shRNA reconstituted with UHRF1 WT

value: UHRF1 shRNA reconstituted with UHRF1 WT


title: ILC breast cancer patient RL1070


title: ILC breast cancer patient RL1067


title: ILC breast cancer patient RL1066


title: U251M2 GBM Treated with V-4084 - repeat 3 - mAdbID:128257

city: Baltimore

first: Maria

middle: Libera

last: Ascierto

address: 5500 Orleans Street

department: Oncology

institute: Johns Hopkins

description: mAdb experiment ID: 128257

hyb_protocol: Affymetrix Hybridization Protocol Other: Biotinylated cDNA was hybridized to GeneChip Human Gene 1.0 ST Arrays and MoGene-1_0-st-v1 (Affymetrix, Santa Clara, CA) and stained on a Genechip Fluidics Station 450 (Affymetrix), according to the manufacturer's instructions.

scan_protocol: Affymetrix Scanning Protocol Other: Arrays were scanned on a GeneChip Scanner 3000 (Affymetrix).

data_processing:
Data Processing Protocol
Calculation Method: Global gene expression profiling was analyzed using BRBArrayTools developed by the Biometric Research Branch, NCI (http://linus.nci.nih.gov/BRB-ArrayTools.html) and the Partek Genomics Suite (St Louis, MO). RMA (Robust Multiarray Average) normalization was used for intensity calculations.

source_name: U251M2 GBM Treated with V-4084

label_protocol:
Affymetrix WT Terminal Labeling Kit
Other: RNA quality and quantity was estimated using Nanodrop (Thermo Scientific, Pittsburgh, PA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). First- and second-strand cDNA were synthesized from 200 ng of total RNA with an Ambion® WT Expression Kit according to the manufacturer's instructions. cDNAs were fragmented and biotinylated (Affymetrix WT Terminal Labeling Kit).

extract_protocol:
miRNeasy minikit
Other: Total mRNA was extracted using miRNeasy minikit (Qiagen, Valencia, CA) according to the manufacturer's protocol.

treatment_protocol:
Treatment type: small molecule
Agent: V-4084
Treatment dose: 0.01 M
Treatment time: 7 days
In-vitro treatment: V-4084 is a small molecule compound that selectively inhibits MET kinase activity. For in vitro study, compounds were diluted in dimethyl sulfoxide (DMSO) at 0.01 M, separated into small aliquots (5 ul), and kept at –80C until use. GBM cells were treated for 7 days with V-4084.

value: brain tumor

value: glioblastoma (GBM) cells

value: Glioblastoma


title: U251M2 GBM Treated with V-4084 - repeat 1 - mAdbID:128255

description: mAdb experiment ID: 128255


title: DBM2 GBM Treated with V-4084 - repeat 3 - mAdbID:128251

description: mAdb experiment ID: 128251

source_name: SF295 GBM Treated with V-4084


title: U251M2 GBM Treated with Vehicle - repeat 2 - mAdbID:128253

description: mAdb experiment ID: 128253

source_name: U251M2 GBM Treated with Vehicle

treatment_protocol:
Treatment type: compound
Agent: dimethyl sulfoxide (DMSO)
Treatment time: 7 days
In-vitro treatment: Vehicle used was dimethyl sulfoxide (DMSO) for 7 days.


title: ILC breast cancer patient RL1064


title: U251M2 GBM Treated with V-4084 - repeat 2 - mAdbID:128256

description: mAdb experiment ID: 128256


title: DBM2 GBM Treated with V-4084 - repeat 1 - mAdbID:128249

description: mAdb experiment ID: 128249


title: UHRF1 KD 03

source_name: HeLa cells stably expressing UHRF1 shRNA

value: UHRF1 shRNA


title: U251M2 GBM Treated with Vehicle - repeat 3 - mAdbID:128254

description: mAdb experiment ID: 128254


title: U251M2 GBM Treated with Vehicle - repeat 1 - mAdbID:128252

description: mAdb experiment ID: 128252


title: ILC breast cancer patient RL1063


title: UHRF1 KD+WT 02


title: UHRF1 KD+WT 01


title: DBM2 GBM Treated with Vehicle - repeat 3 - mAdbID:128248

description: mAdb experiment ID: 128248

source_name: DBM2 GBM Treated with Vehicle


title: UHRF1 KD 02


title: ILC breast cancer patient RL1062


title: U87M2 GBM Treated with V-4084 - repeat 2 - mAdbID:128244

description: mAdb experiment ID: 128244

source_name: U87M2 GBM Treated with V-4084


title: DBM2 GBM Treated with V-4084 - repeat 2 - mAdbID:128250

description: mAdb experiment ID: 128250


title: DBM2 GBM Treated with Vehicle - repeat 1 - mAdbID:128246

description: mAdb experiment ID: 128246


title: UHRF1 KD 01


title: DBM2 GBM Treated with Vehicle - repeat 2 - mAdbID:128247

description: mAdb experiment ID: 128247


title: ILC breast cancer patient RL1061


title: U87M2 GBM Treated with V-4084 - repeat 1 - mAdbID:128243

description: mAdb experiment ID: 128243


title: U87M2 GBM Treated with V-4084 - repeat 3 - mAdbID:128245

description: mAdb experiment ID: 128245


title: UHRF1-Ctrl 02

source_name: HeLa cells stably expressing control shRNA

value: control cells

value: control shRNA


title: ILC breast cancer patient RL1057


title: ILC breast cancer patient RL1058


title: UHRF1-Ctrl 01


title: UHRF1-Ctrl 03


title: U118 GBM Treated with V-4084 - repeat 3 - mAdbID:128239

description: mAdb experiment ID: 128239

source_name: U118 GBM Treated with V-4084


title: U87M2 GBM Treated with Vehicle - repeat 1 - mAdbID:128240

description: mAdb experiment ID: 128240

source_name: U87M2 GBM Treated with Vehicle


title: ILC breast cancer patient RL1056


title: U87M2 GBM Treated with Vehicle - repeat 3 - mAdbID:128242

description: mAdb experiment ID: 128242


title: ILC breast cancer patient RL1055


title: ILC breast cancer patient RL1054


title: U87M2 GBM Treated with Vehicle - repeat 2 - mAdbID:128241

description: mAdb experiment ID: 128241


title: ILC breast cancer patient RL1052


title: U118 GBM Treated with Vehicle - repeat 3 - mAdbID:128236

description: mAdb experiment ID: 128236

source_name: U118 GBM Treated with Vehicle


title: SF295 GBM Treated with V-4084 - repeat 2 - mAdbID:128233

description: mAdb experiment ID: 128233


title: U118 GBM Treated with V-4084 - repeat 1 - mAdbID:128237

description: mAdb experiment ID: 128237


title: ILC breast cancer patient RL1048


title: U118 GBM Treated with Vehicle - repeat 2 - mAdbID:128235

description: mAdb experiment ID: 128235


title: ALCL75

type: genomic

city: Marseille

first: Mohamed

last: BELHOCINE

address: 163, Avenue de Luminy

institute: INSERM

hyb_protocol: Labeled products were purified with Microcon YM-30 filters (Millipore, Billerica, MA). Patient and normal control DNAs (reference) were mixed and hybridized with Human Cot I DNA (Invitrogen) at 65°C for 24 hours. The sandwiched slides were hybridized for 24 hours at 65°C with 15 rotations per minute and washed according to the Agilent protocol.

scan_protocol: Agilent Technologies Scanner G2505C US84600241

data_processing: Log2 ratios were determined with Agilent Feature Extraction software (v 9.1.3.1). Results were visualized and analyzed with Agilent’s CGH Analytics v3.5 software.

molecule: genomic DNA

source_name: Tumoral biopsy

label_protocol: SurePrint G3 Human CGH Microarray Kit 4×180K (ref G4449A) was used according to the manufacturer's recommendations

extract_protocol: Frozen tumor samples were retrieved from CHU de Toulouse tumor tissue bank, in accordance with institutional review board‐approved protocols (DC 2009‐989) and in accordance with the Helsinki Declaration of 1975, as revised in 2000. The percentage of malignant cells was assessed on frozen sections by ALK1 or CD30 staining and was greater than 40% for all selected cases.Total DNA extraction was performed from 10 frozen sections of tumor biopsies (10 μm thickness each), using the QIAamp DNA Mini kit (Qiagen, Courtaboeuf, France), following the manufacturer’s protocol.

value: tumor

value: F

value: healthy control DNA


title: U118 GBM Treated with V-4084 - repeat 2 - mAdbID:128238

description: mAdb experiment ID: 128238


title: ILC breast cancer patient RL1047


title: ALCL68


title: MEMORY 3

city: Pittsburgh

last: Chikina

state: PA

address: 3501 5th ave

institute: University of Pittsburgh

description:
6189772039_F
replicate 3

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing: lumi R package

organism: Mus musculus

source_name: MEMORY, spleen

label_protocol: Illumina protocol

growth_protocol: ex vivo

extract_protocol: d8 and d18 post NP-CGG immunization of transfer recipients 3x10e5 live CD19+ NP+ kappa light chain- CD38- CD95+ splenic GCBC were sorted per sample

value: BALB/cJ

value: spleen

value: Memory B-cell population


title: MEMORY 2

description:
6189772039_E
replicate 2


title: LATE 2

description:
6189772039_B
replicate 2

source_name: LATE, spleen

value: Late GC B-cell population


title: U118 GBM Treated with Vehicle - repeat 1 - mAdbID:128234

description: mAdb experiment ID: 128234


title: SF295 GBM Treated with V-4084 - repeat 1 - mAdbID:128232

description: mAdb experiment ID: 128232


title: SF295 GBM Treated with Vehicle - repeat 1 - mAdbID:128230

description: mAdb experiment ID: 128230

source_name: SF295 GBM Treated with Vehicle


title: ILC breast cancer patient RL1046

source_name: Primary ILC breast cancer


title: ALCL49


title: ILC breast cancer patient RL1044


title: LATE 1

description:
6189772039_A
replicate 1


title: NAIVE 2

description:
6189772028_B
replicate 2

source_name: NAIVE, spleen

value: Naive B-cell population


title: SF295 GBM Treated with Vehicle - repeat 2 - mAdbID:128231

description: mAdb experiment ID: 128231


title: EARLY 3

description:
6189772028_F
replicate 3

source_name: EARLY, spleen

value: Early GC B-cell population


title: NAIVE 3

description:
6189772028_C
replicate 3


title: ALCL45

value: M


title: ALCL47


title: ILC breast cancer patient RL1043

value: Primary ILC breast cancer


title: EARLY 1

description:
6189772028_D
replicate 1


title: MEMORY 1

description:
6189772039_D
replicate 1


title: LATE 3

description:
6189772039_C
replicate 3


title: EARLY 2

description:
6189772028_E
replicate 2


title: ALCL46


title: ALCL41


title: ALCL54


title: ILC breast cancer patient RL1039


title: Mouse Treated with U251M2 GBM with Vehicle - repeat 1 - mAdbID:128284

description: mAdb experiment ID: 128284

source_name: Mouse Treated with U251M2 GBM and Vehicle

treatment_protocol:
Treatment type: small molecule
Agent: MC 400, Tween 80
Treatment dose: 0.5% (MC 400), 0.05% (Tween 80)
Treatment time: 7 days
In-vivo treatment: For all subcutaneous tumor, each GBM cell line (5 x 10(5) cells in 100 ul of PBS) was subcutaneously inoculated into the flank region of nude mice to initiate tumor growth. Vehicle treatment was 0.5% MC 400 with 0.05% Tween 80 for 7 days.

value: brain tumor

tag: other


title: ILC breast cancer patient RL1038


title: ILC breast cancer patient RL1037


title: ILC breast cancer patient RL1034


title: Mouse Treated with U251M2 GBM with V-4084 - repeat 2 - mAdbID:128282

description: mAdb experiment ID: 128282

source_name: Mouse Treated with U251M2 GBM and V-4084

treatment_protocol:
Treatment type: small molecule
Agent: V-4084
Treatment dose: 30 mg/kg
Treatment time: 7 days
In-vivo treatment: V-4084 is a small molecule compound that selectively inhibits MET kinase activity. For all subcutaneous tumor, each GBM cell line (5 x 10(5) cells in 100 ul of PBS) was subcutaneously inoculated into the flank region of nude mice to initiate tumor growth. Tumors were harvested after 7 days of treatment with V-4084 (vehicle used was 0.5% MC 400 with 0.05% Tween 80).

value: glioblastoma (GBM) cells


title: Mouse Treated with DBM2 GBM with V-4084 - repeat 3 - mAdbID:128283

description: mAdb experiment ID: 128283

source_name: Mouse Treated with DBM2 GBM and V-4084

value: Glioblastoma

value: For all subcutaneous tumor, each GBM cell line (5 x 10(5) cells in 100 ul of PBS) was subcutaneously inoculated into the flank region of nude mice to initiate tumor growth.


title: Mouse Treated with U251M2 GBM with V-4084 - repeat 1 - mAdbID:128281

description: mAdb experiment ID: 128281


title: ILC breast cancer patient RL1033


title: Mouse Treated with DBM2 GBM with Vehicle - repeat 3 - mAdbID:128278

description: mAdb experiment ID: 128278

source_name: Mouse Treated with DBM2 GBM and Vehicle


title: ILC breast cancer patient RL1032


title: Mouse Treated with DBM2 GBM with V-4084 - repeat 1 - mAdbID:128279

description: mAdb experiment ID: 128279


title: Mouse Treated with U251M2 GBM with Vehicle - repeat 2 - mAdbID:128285

description: mAdb experiment ID: 128285


title: Mouse Treated with DBM2 GBM with Vehicle - repeat 1 - mAdbID:128276

description: mAdb experiment ID: 128276


title: Mouse Treated with DBM2 GBM with V-4084 - repeat 2 - mAdbID:128280

description: mAdb experiment ID: 128280


title: ALCL39


title: Mouse Treated with U251M2 GBM with Vehicle - repeat 3 - mAdbID:128286

description: mAdb experiment ID: 128286


title: Mouse Treated with U87M2 GBM with V-4084 - repeat 2 - mAdbID:128274

description: mAdb experiment ID: 128274

source_name: Mouse Treated with U87M2 GBM and V-4084


title: ALCL37


title: Mouse Treated with U87M2 GBM with V-4084 - repeat 3 - mAdbID:128275

description: mAdb experiment ID: 128275


title: Mouse Treated with DBM2 GBM with Vehicle - repeat 2 - mAdbID:128277

description: mAdb experiment ID: 128277


title: ALCL35


title: ALCL33


title: Mouse Treated with U87M2 GBM with V-4084 - repeat 1 - mAdbID:128273

description: mAdb experiment ID: 128273


title: Mouse Treated with U87M2 GBM with Vehicle - repeat 3 - mAdbID:128272

description: mAdb experiment ID: 128272

source_name: Mouse Treated with U87M2 GBM and Vehicle


title: Mouse Treated with U87M2 GBM with Vehicle - repeat 2 - mAdbID:128271

description: mAdb experiment ID: 128271


title: Mouse Treated with U87M2 GBM with Vehicle - repeat 1 - mAdbID:128270

description: mAdb experiment ID: 128270


title: ALCL32


title: ILC breast cancer patient RL1028


title: Mouse Treated with U118 GBM with V-4084 - repeat 3 - mAdbID:128269

description: mAdb experiment ID: 128269

source_name: Mouse Treated with U118 GBM and V-4084


title: ILC breast cancer patient RL1029


title: ALCL30


title: GRO (3) spt16 35ºC

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Third replica: Run-on labelling for spt16 G132D mutant 35min.

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

data_processing:
Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate.
Value was the result of the local background sustraction to the raw data. In Processed data, we normalized using ArrayStat software (Median Absolute Deviation). For TR the average value for each gene was corrected by percentage of uridines present in each probe-coding strand.

organism: Saccharomyces cerevisiae

source_name: spt16 G132D mutant cells 35ºC.

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were permeabilized with 20 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix.

growth_protocol: Yeast strains grown in SC-ura to exponential phase and treated with α-factor for synchronization

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: spt16 G132D mutant (DMY2) background BY4741.


title: GRO (2) spt16 35ºC

description: Second replica: Run-on labelling for spt16 G132D mutant 35min.


title: ILC breast cancer patient RL1024


title: ILC breast cancer patient RL1023


title: GRO (1) spt16 35ºC

description: First replica: Run-on labelling for spt16 G132D mutant 35min.


title: ILC breast cancer patient RL1022


title: Mouse Treated with U118 GBM with V-4084 - repeat 1 - mAdbID:128267

description: mAdb experiment ID: 128267


title: Mouse Treated with U118 GBM with Vehicle - repeat 3 - mAdbID:128266

description: mAdb experiment ID: 128266

source_name: Mouse Treated with U118 GBM and Vehicle


title: ALCL29


title: ILC breast cancer patient RL1025


title: GRO (2) spt16 30ºC

description: Second replica: Run-on labelling for spt16 G132D mutant 30min.

source_name: spt16 G132D mutant cells 30ºC.


title: Mouse Treated with U118 GBM with Vehicle - repeat 1 - mAdbID:128263

description: mAdb experiment ID: 128263


title: ILC breast cancer patient RL1020


title: Mouse Treated with SF295 GBM with V-4084 - repeat 3 - mAdbID:128262

description: mAdb experiment ID: 128262

source_name: Mouse Treated with SF295 GBM and V-4084


title: Mouse Treated with U118 GBM with V-4084 - repeat 2 - mAdbID:128268

description: mAdb experiment ID: 128268


title: Mouse Treated with U118 GBM with Vehicle - repeat 2 - mAdbID:128264

description: mAdb experiment ID: 128264


title: ILC breast cancer patient RL1021


title: Mouse Treated with SF295 GBM with V-4084 - repeat 2 - mAdbID:128261

description: mAdb experiment ID: 128261


title: ALCL26

source_name: Tumoral biopsy


title: ILC breast cancer patient RL1017


title: ALCL24


title: ALCL28


title: GRO (3) spt16 30ºC

description: Third replica: Run-on labelling for spt16 G132D mutant 30min.


title: GRO (1) spt16 30ºC

description: First replica: Run-on labelling for spt16 G132D mutant 30min.


title: NAIVE 1

description:
6189772028_A
replicate 1


title: ALCL27


title: ALCL25


title: Mouse Treated with SF295 GBM with V-4084 - repeat 1 - mAdbID:128260

description: mAdb experiment ID: 128260


title: ILC breast cancer patient RL1016


title: ALCL22


title: GRO (1) wt 35ºC

description: First replica: Run-on labelling for WT BY4741 35min.

source_name: Wild type cells 35ºC.

value: BY4741 wild type


title: GRO (3) wt 35ºC

description: Third replica: Run-on labelling for WT BY4741 35min.


title: ALCL21

value: tumor


title: ALCL23

value: F


title: ILC breast cancer patient RL1015


title: GRO (3) wt 30ºC

description: Third replica: Run-on labelling for WT BY4741 30min.

source_name: Wild type cells 30ºC.


title: GRO (2) wt 35ºC

description: Second replica: Run-on labelling for WT BY4741 35min.


title: ILC breast cancer patient RL1014

source_name: Primary ILC breast cancer


title: GRO (2) wt 30ºC

description: Second replica: Run-on labelling for WT BY4741 30min.


title: Mouse Treated with SF295 GBM with Vehicle - repeat 2 - mAdbID:128259

description: mAdb experiment ID: 128259

source_name: Mouse Treated with SF295 GBM and Vehicle


title: ILC breast cancer patient RL1011


title: ILC breast cancer patient RL1009


title: ILC breast cancer patient RL1008


title: ILC breast cancer patient RL1007


title: ILC breast cancer patient RL1001


title: Mouse Treated with SF295 GBM with Vehicle - repeat 1 - mAdbID:128258

description: mAdb experiment ID: 128258


title: Mtl1-MYC ChIP in wt cells

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: Mtl1-MYC ChIP wt  V3

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

organism: Schizosaccharomyces pombe

source_name: Mtl1 ChIP DNA

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were first grown at 30˚C to OD600=~0.2 and then shifted to 37˚C for 5 hours.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam,ab1220), c-myc antibody (Covance, MMS-150R) or with GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. For Red1-MYC, Mtl1-MYC and CFP-Mmi1 ChIP, cells were further crosslinked with DMA for 45 min at 30˚C.

value: wild type

tag: growth stage

value: log. growing cells

tag: chip antibody

value: c-myc antibody (Covance, MMS-150R)

tag: fraction

value: Mtl1-MYC immunoprecipitated DNA

source_name: Whole-cell extract DNA

value: Whole-cell extract DNA


title: ALCL44

value: healthy control DNA


title: ALCL18


title: Mtl1-MYC ChIP in dhp1-2 cells

description: Mtl1-MYC ChIP dhp1-2 V3

value: dhp1-2 mutant


title: CFP-Mmi1 ChIP in wt cells

description: GFP-Mmi1 ChIP wt  V3

source_name: Mmi1 ChIP DNA

value: GFP antibody (Abcam, ab290)

value: CFP-Mmi1 immunoprecipitated DNA


title: CFP-Mmi1 ChIP in dhp1-2 cells

description: GFP-Mmi1 ChIP dhp1-2 V3


title: H3K9me2 ChIP in ∆rrp6 dhp1-2 cells

description: H3K9me2 ChIP ∆rrp6 dhp1-2 V3

source_name: H3K9me2 ChIP DNA

value: {delta}rrp6 dhp1-2 mutant

value: H3K9me2 (Abcam,ab1220)

value: H3K9me2 immunoprecipitated DNA


title: ALCL15

value: M


title: ALCL20


title: GRO (1) wt 30ºC

description: First replica: Run-on labelling for WT BY4741 30min.


title: ALCL13


title: Red1-MYC ChIP in dhp1-2 cells

description: Red1-MYC ChIP dhp1-2 V3

source_name: Red1 ChIP DNA

value: Red1-MYC immunoprecipitated DNA


title: H3K9me2 ChIP in ∆rrp6 cells

description: H3K9me2 ChIP ∆rrp6 V3

value: {delta}rrp6 mutant


title: ALCL17

value: tumor


title: ALCL19


title: ILC breast cancer patient RL1004

value: Primary ILC breast cancer


title: Red1-MYC ChIP in wt cells

description: Red1-MYC ChIP wt  V3

value: wild type


title: begin self-pruning-biological rep1_(Citrus)

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

description: citrus

hyb_protocol: The microarray experiment was performed according to the method described in the Affymetrix GeneChip Expression Analysis Overview.

organism: Citrus sinensis

growth_protocol: Plants of sweet orange (Citrus Sinensis Osbeck cv. Cara Cara Navel Orange) were grown under natural environmental conditions

extract_protocol: Total RNA was isolated using Trizol reagent (Invitrogen, USA).

value: shoot meristems

tag: cultivar

value: Cara Cara Navel Orange


title: ALCL12

tag: gender


title: ALCL11

value: F


title: ALCL14


title: ALCL16


title: before self-pruning-biological rep2_(Citrus)

department: College of Horticulture and Forestry Science

description: citrus

scan_protocol: The microarray experiment was performed according to the method described in the Affymetrix GeneChip Expression Analysis Overview.


title: Near-infrared treatment

city: Matsumoto

first: Yohei

last: Tanaka

state: Nagano

department: Plastic Surgery

country: Japan

institute: Clinica Tanaka

description: Gene expression after near-infrared treatment

hyb_protocol: Hybridization mixtures were prepared by adding 2x Hybridization Buffer and mixing well by pipetting. Hybridization was carried out at 65°C for 17 hours. Washing was performed using the Agilent Stabilization and Drying Solution.

scan_protocol: Slides were scanned using an Agilent Technologies Microarray Scanner (Agilent Technologies), and images were processed by Agilent Feature Extraction software (Agilent Technologies) with background correction.

data_processing: Data were imported into GeneSpring and normalization was performed 75 percentile shift. After normalization and data filtering of the raw date output files, log-fold changes in gene expression in NIR irradiated group compared with control were analyzed to determine up-regulated and down-regulated genes, using a 2-fold change as the cut-off using GeneSpring GX 11.0 software (Agilent Technologies). Up-regulated and down-regulated genes were further clustered into functional gene groups using ontology analysis with GeneSpring GX 11.0 software.

source_name: human corneal epithelial cell

label_protocol: Cy3-labeled cRNA samples were synthesized using an Agilent Low Input Quick Amp Labeling kit, according to the manufacturer's instructions (Agilent Technologies). For each time point, 50 ng of total RNA was used to generate first-strand cDNA. After the denaturation step (10 min at 65°C) and cRNA synthesis step (2 hr at 40°C), the reactions were incubated at 70°C for 15 minutes to inactivate the AffinityScript enzyme. For the labeling reactions, cRNA samples were each mixed with 6 μL of Transcription Master Mix cocktail containing Cy3-CTP, and incubated at 40°C for 2 hours. Purification was performed using Qiagen RNeasy mini spin columns (Qiagen). Labeled cRNA were quantified on a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE) and quality was also checked by Agilent 2100 bioAnalyzer series II (Agilent Technologies).

growth_protocol: Human corneal cells were prepared from normal human corneal epithelial tissue by enzymatic digestion, which was supplied from Rocky Mountain Lyons Eye Bank (CO, USA) after concluding the material transfer agreement. The medium was changed every 2 days until the cultures became subconfluented. The subconfluented corneal cells were subcultured with trypsin and seeded on a cell culture insert containing a microporous membrane with 0.4 μm pore size. Corneal cells were cultivated between an air and liquid interface to form a multilayered, highly corneal epithelium-like structure. All cells were grown at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNAs were extracted in QIAzol reagent (Qiagen, Hilden, Germany) and spin-column purified using RNeasy Mini spin column (Qiagen). The RNA was extracted from control and irradiated group, which consists of six whole individual 3-dimensional reconstructed human corneal epithelial models. Quantity and quality of RNA samples were then measured using UV absorbance (NanoDrop Technologies, Wilmington, DE) and quality was also assessed using an Agilent 2100 bioAnalyzer series II (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The NIR device emits an NIR spectrum between 1100 and 1800 nm, with water filtering to remove wavelengths between 1400 and 1500 nm, and simulates solar NIR radiation that reaches the human tissues on the Earth’s surface. To avoid thermal effects, the sapphire contact cooling tip was set to a fixed temperature of 20°C. We performed 5 rounds of NIR irradiation at 10 J ⁄cm2.

value: human corneal epithelial model


title: Near-infrared treatment with UV cut

description: Gene expression after near-infrared treatment with UV cut


title: ALCL9

value: healthy control DNA


title: No treatment

description: Gene expression of no treatment control


title: H3K9me2 ChIPin dhp1-2 cells

description: H3K9me2 ChIP dhp1-2 V3

value: dhp1-2 mutant

value: log. growing cells

value: Whole-cell extract DNA


title: H3K9me2 ChIP in wt cells

description: H3K9me2 ChIP wt  V3


title: WT_colon_2

city: Philadelphia

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalized without background subtraction using Illumina GenomeStudio V1.8

source_name: Intestinal epithelium

label_protocol: Biotin labeled complementary RNA (cRNA) was made using the EpiCentre TargetAmp-Nano kit

growth_protocol: Ifnar1-/- mice were crossed with Csnk1a1lox/lox mice which bear floxed Csnk1a1 and Vil1-Cre-ERT2 to generate Csnk1a1lox/lox; Ifnar1+/+ or Csnk1a1lox/lox; Ifnar1+/+ mice bearing Vil1-Cre-ERT2 (Vil1-Cre-ERT2 in genotype identification is omitted for simplicity). Genotyping was performed from the tail of 4-week-old pups according to standard protocol with described primers.

extract_protocol: RNA was extracted using the Qiagen miRneasy kit

treatment_protocol: Mice were injected intraperitoneally (120 mg/kg) on two consecutive days with Tamoxifen. At day 5 after the last injection, mice were euthanized. Intestinal epithelial cells (IEC) were isolated from the middle part of the small intestine in Hank’s balanced salt solution containing 5 mM EDTA at 4 °C for 30 min.

value: colon

value: Intestinal epithelium

tag: genotype

value: Csnk1a1_delta_gut Ifnar1+/+


title: ALCL10

tag: tissue


title: ALCL5

value: M


title: ALCL4


title: ALCL7


title: ALCL3


title: before self-pruning-biological rep1_(Citrus)

description: citrus

data_processing: The microarray experiment was performed according to the method described in the Affymetrix GeneChip Expression Analysis Overview.


title: ALCL6


title: Near-infrared treatment with UV+near-infrared cut

description: Gene expression after near-infrared treatment with UV+near-infrared cut


title: IFNAR1ko_colon_2

value: Csnk1a1_delta_gut Ifnar1-/-


title: After self-pruning-biological rep2_(Citrus)

description: citrus

label_protocol: The microarray experiment was performed according to the method described in the Affymetrix GeneChip Expression Analysis Overview.


title: IFNAR1ko_colon_1


title: After self-pruning-biological rep1_(Citrus)

description: citrus


title: hm24h-rep3

status: Public on Jan 04 2016

city: wuhan

first: Lin

last: xian

state: Hubei

address: shizishan street,number 1

department: College of Veterinary Medicine

institute: Huazhong Agricutural University

description: Gene expression after 24h in H5N1-infected U251

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides.

data_processing: Data were extracted with Feature Extraction software  10.7  (Agilent  technologies,  Santa  Clara,  CA,  US).  Raw  data  were  normalized by  Quantile  algorithm,  Gene  Spring  Software  11.0  (Agilent  technologies,  Santa  Clara, CA, US).

source_name: U251 cells, 24hpi, H5N1 infection, replicate3

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

growth_protocol: U251 cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum, amd incubated in 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted usingTRIZOL Reagent (Cat#15596-018， Lifetechnologies, Carlsbad,  CA,  US)following  the  manufacturer’ s  instructions  and  check ed  for  a  RIN number  to  inspect  RNA  integration  by  an  Agilent  Bioanalyzer  2100  (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini  kit  (Cat#74106, QIAGEN,  GmBH,  Germany)  and  RNase-Free  DNase  Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: U251 cells were inoculated with H5N1 at MOI 1.0 or not infected. After 40 min adsorption, cells were washed once using warm phosphate-buffered saline (PBS) and then incubated in DMEM containing 0.2% FBS at 37℃. At time points 6, 12, and 24 hpi, total RNA was extracted.

value: U251 astrocyte cell line

tag: infection

tag: time

value: 24 hpi


title: hm24h-rep1

source_name: U251 cells, 24hpi, H5N1 infection, replicate1


title: hm12h-rep1

description: Gene expression after 12h in H5N1-infected U251

source_name: U251 cells, 12hpi, H5N1 infection, replicate1

value: 12 hpi


title: WT_colon_1

tag: strain

value: Csnk1a_delta_gut Ifnar1+/+


title: hm6h-rep3

description: Gene expression after 6h in H5N1-infected U251

source_name: U251 cells, 6hpi, H5N1 infection, replicate3

value: 6 hpi


title: hm24h-rep2

source_name: U251 cells, 24hpi, H5N1 infection, replicate2


title: ALCL2

source_name: Tumoral biopsy

value: tumor


title: hm12h-rep2

source_name: U251 cells, 12hpi, H5N1 infection, replicate2


title: hm12h-rep3

source_name: U251 cells, 12hpi, H5N1 infection, replicate3


title: hm6h-rep2

source_name: U251 cells, 6hpi, H5N1 infection, replicate2


title: hm6h-rep1

source_name: U251 cells, 6hpi, H5N1 infection, replicate1


title: con12h-rep3

description: Gene expression after 12h in control-infected U251

source_name: U251 cells, 12hpi, control infection, replicate3

value: control


title: ALCL1


title: begin self-pruning-biological rep2_(Citrus)

description: citrus

value: shoot meristems

value: Cara Cara Navel Orange


title: con24h-rep2

description: Gene expression after 24h in control-infected U251

source_name: U251 cells, 24hpi, control infection, replicate2


title: con12h-rep1

source_name: U251 cells, 12hpi, control infection, replicate1


title: con24h-rep1

source_name: U251 cells, 24hpi, control infection, replicate1


title: con6h-rep1

description: Gene expression after 6h in control-infected U251

source_name: U251 cells, 6hpi, control infection, replicate1


title: con12h-rep2

source_name: U251 cells, 12hpi, control infection, replicate2


title: con6h-rep3

source_name: U251 cells, 6hpi, control infection, replicate3


title: con24h-rep3

source_name: U251 cells, 24hpi, control infection, replicate3


title: con6h-rep2

source_name: U251 cells, 6hpi, control infection, replicate2


title: 6368

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: main population (MP)

hyb_protocol: Purified and labeled cRNA (28 pmol of Cy3 labeled cRNA) was hybridised on the array followed by (manual) washing, according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, arrays were scanned using the Agilent DNA MicroArray Scanner with surescan High-Resolution Technology and probe signals were quantified using Agilent’s Feature Extraction software (version 10.1.1.1).

data_processing: Data as processed by the Agilent’s Feature Extraction software (version 10.1.1.1 - feature gProcessedSignal). Data was base 2 log-transformed and a quantile normalization was applied. Control probes and probes below backrgound were removed. Data from replicate probes were averaged.

source_name: PACA Tx 19/12 MP

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 5-50 ng of total RNA was amplified in a 2-cycle amplification reaction as described by Baugh et al. During the second in vitro transcription reaction, the sample was amplified and labeled with 2.4µl Cyanine 3-CTP (Cy3) according to Agilent’s protocol.

extract_protocol: RNA was extracted using the Rneasy Micro Kit (Qiagen), according to the instructions of the manufacturer

value: female

tag: age

value: 45.5 years

value: pancreatic cancer

tag: tumor stage

tag: tumor grade


title: 6366

description: main population (MP)

source_name: PaCaTX  1/7/08 MP

value: male

value: 53.6 years


title: 6367

description: side population (SP)

source_name: PaCaTX  1/7/08 SP


title: 6363

description: side population (SP)

source_name: Paca Txpt 3/4/08 SP

value: 77.8 years


title: Bhlhe40-GFPpos TH17 cells rep2

city: St. Louis

first: Chih-Chung

last: Lin

state: MO

address: 660 S. Euclid Ave. Box 8118

department: Pathology and Immunology

description: Gene expression data from FACS-sorted Bhlhe40-GFPpos TH17 cells

hyb_protocol: Hybridization was performed by standard methods at the GTAC at Washington University School of Medicine.

scan_protocol: GeneChips were scanned at the GTAC at Washington University School of Medicine.

data_processing: Array data were imported into Arraystar 5 software (DNAstar) and then normalized using the robust multi-array analysis method with quantile normalization.

source_name: Bhlhe40-GFPpos TH17 rep2

label_protocol: RNA was amplified (Ovation Pico SL WTA System V2, Nugen), labeled (Encore Biotin Module, Nugen), and fragmented.

growth_protocol: Purified naïve splenic CD4 T cells from Bhlhe40-GFP reporter mice were cultured for 4 days in TH17 condition

extract_protocol: Total RNA was isolated by the E.Z.N.A. MicroElute Total RNA Kit, Omega Bio-Tek.

treatment_protocol: Stimulation with PMA and ionomycin for 4 hours prior to collection of total RNA

value: spleen

tag: cell type

value: purified CD4 T cells

value: Bhlhe40-GFP reporter

tag: background strain

value: C57BL/6 (10 generation backcross)

value: 10 wks old


title: Bhlhe40-GFPpos TH17 cells rep1

institute: Washington University School of Medicine

source_name: Bhlhe40-GFPpos TH17 rep1


title: 6365

description: side population (SP)

source_name: PaCaTXpt 26/6/08 SP


title: 6362

description: main population (MP)

source_name: Paca Txpt 3/4/08 MP


title: Bhlhe40-GFPpos TH17 cells rep3

source_name: Bhlhe40-GFPpos TH17 rep3

value: 17 wks old


title: 6361

description: side population (SP)

source_name: Paca Tx 4/11 SP2

value: 78.4 years


title: Bhlhe40-GFPneg TH17 cells rep2

description: Gene expression data from FACS-sorted Bhlhe40-GFPneg TH17 cells

source_name: Bhlhe40-GFPneg TH17 rep2


title: 6369

description: side population (SP)

source_name: PACA Tx 19/12 SP


title: Bhlhe40-GFPneg TH17 cells rep3

source_name: Bhlhe40-GFPneg TH17 rep3


title: 6360

description: main population (MP)

source_name: Paca Tx 4/11 MP1


title: PTPROt/TCL1, biological replicate 1

city: Columbus

first: Tasneem

last: Motiwala

address: 420 W. 12th Ave

institute: The Ohio State University

description:
gene expression data from PTPROt/TCL1 double Tg mice
PTPROt/TCL1 double Tg 1

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50 mg/ml), Affymetrix Eukaryotic Hybridization Controls (affymetrix) and Oligo B2, 3 nM (Affymetrix). Heat 65oC for 5 mins, 99oC for 5 mins, 45oC for 5 mins, centrifuge topr speed for 5 mins. Hybridize 16 hrs at 45o at 60 rpm. Fluidics washing is FS450_0002

scan_protocol: Affymetrix Gebe CHIP Scanner 3000 7G using AGCC

data_processing: The data were analyzed through Bioconductor package, RMA method was used as the background-correction and normalization.

source_name: splenic CD19 cells from PTPROt/TCL1 double Tg mice

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: RNA was extracted using Trizol (Invitrogen) according to manufacturer's protocol. It was further purified using PCI/CI extraction. RNA quality was assessed using Nanodrop ND1000 and RNA Nano Bioanayzer prior to use for microarray.

value: CD19 cells

tag: genotype/variation

value: PTPROt/TCL1 double Tg


title: 6364

description: main population (MP)

source_name: PaCaTXpt 26/6/08 MP1


title: TCL1, biological replicate 4

description:
gene expression data from TCL1 Tg mice
TCL1 Tg 4

source_name: splenic CD19 cells from TCL1 Tg mice

value: TCL1 Tg


title: PTPROt, biological replicate 4

description:
gene expression data from PTPROt Tg mice
PTPROt Tg 4

source_name: splenic CD19 cells from PTPROt Tg mice

value: PTPROt Tg


title: PTPROt/TCL1, biological replicate 3

description:
gene expression data from PTPROt/TCL1 double Tg mice
PTPROt/TCL1 double Tg 3

value: female


title: PTPROt, biological replicate 3

description:
gene expression data from PTPROt Tg mice
PTPROt Tg 3


title: PTPROt, biological replicate 2

description:
gene expression data from PTPROt Tg mice
PTPROt Tg 2


title: PTPROt/TCL1, biological replicate 2

description:
gene expression data from PTPROt/TCL1 double Tg mice
PTPROt/TCL1 double Tg 2


title: TCL1, biological replicate 3

description:
gene expression data from TCL1 Tg mice
TCL1 Tg 3


title: TCL1, biological replicate 1

description:
gene expression data from TCL1 Tg mice
TCL1 Tg 1


title: TCL1, biological replicate 2

description:
gene expression data from TCL1 Tg mice
TCL1 Tg 2


title: NTg, biological replicate 1

description:
gene expression data from NTg mice
NTg 1

source_name: splenic CD19 cells from NTg mice

value: NTg


title: NTg, biological replicate 4

description:
gene expression data from NTg mice
NTg 4


title: NTg, biological replicate 3

description:
gene expression data from NTg mice
NTg 3


title: NTg, biological replicate 2

description:
gene expression data from NTg mice
NTg 2


title: PTPROt, biological replicate 1

description:
gene expression data from PTPROt Tg mice
PTPROt Tg 1


title: CKO_F

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description:
isolated luminal uterine epithelium from 3.5dpc ALK3 cKO mice
9576

hyb_protocol: For microarray analyses, labeled cRNA was hybridized to Illumina Mouse WG-6 v.2.0 by the Genomics and Proteomics Core at Texas Children Hospital (Houston, TX).

scan_protocol: According to Illumina protocol.

data_processing: Array data were quantile normalized. Differentially expressed genes were defined, using two-sided t-test and fold change (on log-transformed data).

source_name: CKO

label_protocol: According to Illumina protocol.

growth_protocol: Mice carrying the Alk3 floxed allele were previously generated by Drs. Mishina and Behringer [PMID:11857780]. Briefly, loxP sites were inserted into the Alk3 locus spanning exon 2, which encodes portion of the extracellular domain.  To generate Alk3 cKO mice, Alk3flox/flox mice were bred to mice carrying the Pgr-cre knockin allele (Pgrcre/+)  to obtain Alk3flox/flox Pgrcre/+ females (cKO mice). The mice were maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background. For the embryo attachment experiments, we used males with a transgene containing the enhanced green fluorescent protein gene (EGFP) under the control of the CMV-IE enhancer/chicken β-actin/rabbit β-globin hybrid promoter (mouse line FVB.Cg-Tg(CAG-EGFP)B5Nagy/J).

extract_protocol: Uterine tissues were collected and immediately frozen in dry ice. RNA was extracted using the QIAGEN RNEasy Kit by homogenizing the tissue with an OMNI-TH disrupter following the manufacturer’s protocol.

tag: genetic background

value: hybrid C57BL/6J and 129S5/SvEvBrd

value: luminal uterine epithelium

value: Alk3 cKO

value: F


title: CKO_E

description:
isolated luminal uterine epithelium from 3.5dpc ALK3 cKO mice
9574

value: E


title: Control_B

description:
isolated luminal uterine epithelium from 3.5dpc control mice
9599

source_name: Control

value: Control

value: B


title: CKO_D

description:
isolated luminal uterine epithelium from 3.5dpc ALK3 cKO mice
9415

value: D


title: Control_C

description:
isolated luminal uterine epithelium from 3.5dpc control mice
9602

value: C


title: Kidney_Normal_Sample 13

city: Royal Oak

first: Bryan

last: Thibodeau

state: MI

address: 3811 West 13 Mile Road

department: BioBank

institute: Beaumont Research Institute

description: Gene expression data from normal kidney adjacent to clear cell renal cell carcinoma

hyb_protocol: Hybridization to Affymetrix Human Gene 1.0 ST Arrays as well as washing and staining (with GeneChip® Fluidics Station 450, Affymetrix) were performed following manufacturer protocols.

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

data_processing:
The CEL files containing the raw intensity data from the Affymetrix GeneChip arrays were imported into Partek Genomics Suite and normalized using the robust multichip average with a guanine-cytosine content background correction, quantile normalization, log2-transformation, and median polish probeset summarization.
HuGene-1_0-st-v1
HuGene-1_0-st-v1

source_name: Normal kidney, adjacent to tumor

label_protocol: Using the Ambion® WT Expression Kit (Affymetrix, Santa Clara, CA), total RNA was used to generate purified sense cDNA ready for fragmentation and labeling. Fragmentation and terminal labeling was done according to manufacturer’s protocols using the GeneChip® WT Terminal Labeling and Controls Kit.

extract_protocol: RNA was isolated from fresh frozen tissue using E.Z.N.A. Total RNA Kit I (Omega bio-tek, Norcross, GA) which included an on-column DNase treatment. Tissue was homogenized into lysis buffer using the gentleMACS dissociator (Miltenyi Biotec Inc., Auburn, CA) and the manufacturer’s “Homogenization of tissue for total RNA isolation” protocol. RNA was quantitated using a Nanodrop spectrophotomer (Thermo Fisher Scientific Inc.) and quality determined on an Agilent Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA).

treatment_protocol: Patients undergoing either partial or radical nephrectomy at William Beaumont Hospital (Royal Oak, MI) were consented prior to surgery with local IRB oversight. Samples were collected at time of surgery and stored at -80°C according to CAP (College of American Pathologist)-accredited standard operating procedures.

value: normal kidney

tag: fuhrman grade

tag: analysis group

value: normal

tag: patient id


title: Kidney_Normal_Sample 14


title: Kidney_Normal_Sample 11


title: Kidney_Normal_Sample 12


title: Kidney_Normal_Sample 10


title: EL clone, biological rep2

city: Frederick

first: Steven

middle: X.

last: Hou

state: Maryland

address: 1050 Boyles St. Bldg. 560

description:
Gene expression data from EL clone derived from prostate cancer cell line Du145
DU145-EL-2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HuGene-1_0-st-v1.

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

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: EL clone

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

growth_protocol: cells were curture with RPMI 1640 with 10% FBS

extract_protocol: total RNA was extracted with RNeasy® Mini Kit from Qiagen according to the manufacturer's instructions.

tag: disease state

value: prostate cancer

tag: subclone

value: EL

tag: subclone source

tag: tumorigenicity

value: higher tumorigenicity ability


title: Control_A

description:
isolated luminal uterine epithelium from 3.5dpc control mice
9594

tag: tissue

value: A


title: EL clone, biological rep1

description:
Gene expression data from EL clone derived from prostate cancer cell line Du145
DU145-EL-1


title: ML clone, biological rep2

description:
Gene expression data from ML clone derived from prostate cancer cell line Du145
DU145-ML-2

source_name: ML clone

value: ML

value: lower tumorigenicity ability


title: ML clone, biological rep1

description:
Gene expression data from ML clone derived from prostate cancer cell line Du145
DU145-ML-1


title: Kidney_Normal_Sample 8


title: Kidney_Normal_Sample 7


title: Kidney_Normal_Sample 9


title: Kidney_Normal_Sample 2


title: Kidney_Normal_Sample 5


title: ccRCC_HighGrade_Sample 16

description: Gene expression data from high grade clear cell renal cell carcinoma

source_name: clear cell renal cell carcinoma, high grade

value: clear cell renal cell carcinoma

value: Grade 4

value: High Grade


title: Kidney_Normal_Sample 6


title: ccRCC_HighGrade_Sample 14

value: Grade 3


title: Kidney_Normal_Sample 3


title: ccRCC_HighGrade_Sample 13


title: Kidney_Normal_Sample 4


title: ccRCC_HighGrade_Sample 11


title: Kidney_Normal_Sample 1


title: ccRCC_HighGrade_Sample 10


title: ccRCC_HighGrade_Sample 12


title: ccRCC_HighGrade_Sample 9


title: ccRCC_HighGrade_Sample 8


title: ccRCC_HighGrade_Sample 6


title: ccRCC_HighGrade_Sample 15


title: ccRCC_HighGrade_Sample 4


title: ccRCC_HighGrade_Sample 1


title: ccRCC_LowGrade_Sample 13

description: Gene expression data from low grade clear cell renal cell carcinoma

source_name: clear cell renal cell carcinoma, low grade

value: Grade 2

value: Low Grade


title: ccRCC_HighGrade_Sample 7


title: ccRCC_HighGrade_Sample 3


title: ccRCC_LowGrade_Sample 11


title: ccRCC_LowGrade_Sample 9


title: ccRCC_LowGrade_Sample 8


title: ccRCC_HighGrade_Sample 5


title: ccRCC_LowGrade_Sample 7


title: ccRCC_LowGrade_Sample 4

value: Grade 1


title: ccRCC_LowGrade_Sample 10


title: ccRCC_LowGrade_Sample 3


title: ccRCC_LowGrade_Sample 12


title: ccRCC_LowGrade_Sample 6


title: ccRCC_HighGrade_Sample 2


title: Kidney_Benign_Sample 6

description: Gene expression data from benign kidney disease

source_name: non-functional kidney

value: non-functional kidney

value: Benign


title: ccRCC_LowGrade_Sample 1


title: Kidney_Benign_Sample 5

source_name: oncocytoma

value: oncocytoma


title: ccRCC_LowGrade_Sample 5


title: Kidney_Benign_Sample 2


title: Hepatocytes_ JNKΔhepa_repl1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

description:
Hepa_JNK1ΔhepaJNK2-/-_1
Replicate 1

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

source_name: Primary hepatocytes, JNKΔhepa double-knockout mouse

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT Expression Kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Constitutive Jnk2 knockout mice (Jnk2-/-) were purchased from Harlan Laboratories (Bar Harbor, ME). Jnk1f/f (C57BL/6) mice were crossed with transgenic mice expressing cre-recombinase under control of albumin promoter and alpha-fetoprotein enhancer elements (Albf-Cre) to generate hepatocyte-specific Jnk1 knockout mice (Jnk1Δhepa), previously characterized in our lab (PMID: 24037431). JNKΔhepa double-knockout mice were obtained by crossing Jnk1Δhepa and Jnk2-/- mice. Matching male Jnk1f/fJnk2+/+ littermates were used as wildtype (WT) controls.

extract_protocol: Total RNA was isolated using RNeasy Micro Kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice had free acces to standard laboratory chow and water. Mice were used at the age between 7 and 8 wks.

tag: strain/background

value: JNKΔhepa double-knockout

tag: Sex

value: male

value: 7-8 wks

value: primary hepatocytes

tag: mouseid


title: Hepatocytes_WT_repl3

description:
Hepa_WT_3
Replicate 3

source_name: Primary hepatocytes, Jnk1f/fJnk2+/+ (WT) mouse

value: Jnk1f/fJnk2+/+ (WT)

tag: age


title: Kidney_Benign_Sample 1


title: ccRCC_LowGrade_Sample 2


title: Hepatocytes_ JNKΔhepa_repl2

description:
Hepa_JNK1ΔhepaJNK2-/-_2
Replicate 2


title: Hepatocytes_ JNKΔhepa_repl3

description:
Hepa_JNK1ΔhepaJNK2-/-_3
Replicate 3


title: Liver_ JNKΔhepa_repl3

description:
Liv_JNK1ΔhepaJNK2-/-_3
Replicate 3

source_name: liver, JNKΔhepa double-knockout mouse

value: liver


title: Liver_WT_repl3

description:
Liv_WT_3
Replicate 3

source_name: liver, Jnk1f/fJnk2+/+ (WT) mouse


title: Liver_WT_repl2

description:
Liv_WT_2
Replicate 2


title: PTPROt/TCL1, biological replicate 4

description:
gene expression data from PTPROt/TCL1 double Tg mice
PTPROt/TCL1 double Tg 4

source_name: splenic CD19 cells from PTPROt/TCL1 double Tg mice

tag: gender

value: female

tag: strain

value: spleen

value: CD19 cells

value: PTPROt/TCL1 double Tg


title: SK-ChA-1_ITL_50Mw_rep2

city: Amsterdam

first: Perry

middle: D

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

hyb_protocol: 750 ng of the obtained biotinylated cRNA samples was hybridized according to the Illumina Manual “Direct Hybridization Assay Guide”

scan_protocol: Samples were scanned using the Illumina iScan array scanner.

data_processing: Data were retrieved using Illumina's GenomeStudio v2011.1 software. Analyses were carried out with Bioconductor packages in the statistical software package R (version 3.0.0). Normexp-by-control background correction, quantile normalization, and log2 transformation (Shi et al, NAR, 2010) were performed on the Illumina sample and control probe profiles using the limma package (version 3.16.5), function neqc.

label_protocol: Biotinylated cRNA was prepared using the Illumina TotalPrep RNA amplification kit (Ambion, Inc., Austin, TX) according to the manufacturer’s specifications with an input of 200 ng total RNA.

growth_protocol: Human perihilar cholangiocarcinoma (SK-ChA-1) cells were maintained at standard culture conditions (37˚C, 5% CO2 and 95% air). SK-ChA-1 cells were cultured in Roswell Park Memorial Institute (RPMI) 1640 culture medium supplemented with 10% fetal bovine serum (FBS) (v/v) (Gibco, Invitrogen, Carlsbad, CA), 1% penicillin/streptomycin (v/v), 1% L-glutamine (v/v) (both from Lonza, Walkersville, MD), and 1×10-5% β-mercaptoethanol (v/v) (Sigma-Aldrich). The cells were passaged weekly at a 1:10 ratio.

extract_protocol: Total cellular RNA was extracted from SK-ChA-1 cells using 1 mL of TRIzol (Life Technologies, Bleiswijk, the Netherlands) according to the manufacturer’s protocol. RNA quality and integrity was determined using the Agilent BioAnalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Cells were harvested using Accutase (Innovative Cell Technologies, San Diego, CA) and seeded in 6-wells culture plates (Corning Life Sciences, Tewksbury, MA) at a density of 0.5×106 cells/well. After reaching confluence, cells were washed with PBS and incubated with ZnPC-ITLs (500 µM final lipid concentration) in serum-free RPMI 1640 medium (1.5 mL final volume per well) for 30 minutes at 37°C in the dark. Control cells received an equal volume of PBS. In case of PDT, cells were irradiated with a 671-nm diode laser (CNI, Changchun, China) at a laser power of either 50 or 500 mW until a cumulative light dose of 15 J/cm2 was reached. Cells were maintained at 37°C in a dark room during PDT.

tag: cell line

tag: treatment

value: ITL

tag: irradiation

value: 50 mW

tag: slide

value: K


title: Hepatocytes_WT_repl2

description:
Hepa_WT_2
Replicate 2

tag: genotype/variation


title: Hepatocytes_WT_repl1

description:
Hepa_WT_1
Replicate 1


title: SK-ChA-1_ITL_50Mw_rep3

value: L


title: SK-ChA-1_ITL_0Mw_rep1

value: 0 Mw

value: D


title: SK-ChA-1_ITL_500Mw_rep1

value: G


title: SK-ChA-1_ITL_0Mw_rep3

value: F


title: SK-ChA-1_ITL_500Mw_rep2

value: H


title: SK-ChA-1_control_0Mw_rep3

value: control

value: C


title: SK-ChA-1_ITL_50Mw_rep1

value: J


title: SK-ChA-1_control_0Mw_rep1

value: A


title: SK-ChA-1_control_0Mw_rep2

value: B


title: SK-ChA-1_ITL_500Mw_rep3

value: I


title: Pgc1b knockout, biological replicate 3

city: Barcelona

first: Josep M

last: Mercader

state: Catalunya

address: C/Jordi Girona 29 08034

department: Life Science Department

institute: Barcelona Supercomputing Center

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays using the Affymetrix Hybridization Kit following the manufacturer's instructions for the 49/64 format array. Washing and staining of arrays were carried out using a GeneChip Fluidics 450 Workstation using protocol WS2v5_450.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).

data_processing: Softwares/tools used for the data processing were Affymetrix GeneChip® Operating Software (GCOS) and Partek Genomic Suite 6.5. For the creation of the summarized log-signal, the Robust Multichip Average (RMA) with Quantile Normalisation and Median Polish for probe set summarisation were used.

source_name: heart, Pgc1b knockout

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2), and subsequently the Affymetrix One-cycle kit was used to convert and amplify RNA to cRNA, which was then labelled and fragmented using the Affymetrix IVT Labelling Kit according to the manufacturer's instructions.

growth_protocol: Hearts were quickly collected and snap frozen in liquid nitrogen from wild-type and PGC-1β KO mice on a mixed background (sv129 and C57BL/6) generated as previously reported (Lelliott et al. 2006 (PMID 17090215)). Animal procedures were performed in accordance with the UK Home Office regulations and the UK Animal Scientrific Procedures Act [A(sp)A 1986]. Animals were housed in a temperature-controlled room with a 12-h light/dark cycle. Food and water were available ad libitum.

extract_protocol: Total RNA was extracted with a combination of Trizol and the RNeasy Mini Kit (Qiagen).

value: mixed background (sv129 and C57BL/6)

tag: genotype

value: Pgc1b knockout

value: heart

tag: date


title: Pgc1b knockout, biological replicate 2


title: Pgc1b knockout, biological replicate 1


title: Insulin treatment, biological replicate 3

hyb_protocol: 8 µg of cDNA was hybridized per microarray for 16 hours of hybridization at 45ºC. Washing and staining of microarrays were performed using a Fluidics Station 450 (Affymetrix, Santa Clara, CA).

data_processing: We applied quantile normalization. For each gene, we selected the 50% of the probes with the highest interquartile-range across samples, and applied RMA summarization to the selected probes. We used the Bioconductor software.

source_name: C2C12 cells, insulin

label_protocol: 25 ng total RNA was amplified using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2), and subsequently labeled using the GeneChip Mapping 10K Xba Assay Kit (Affymetrix; catalog # 900441) according to the manufacturer's instructions.

growth_protocol: Briefly, C2C12 cells were cultured in Dulbecco's Modified Eagle Media (DMEM) supplemented with 10% fetal bovine serum, and penicillin/streptomycin. To induce differentiation, media was replenished by DMEM containing 2% (v/v) of horse serum with penicillin/streptomycin.  Myotubes between days 4 and 7 following the induction of differentiation were used for experiments.

treatment_protocol: For chronic insulin treatment, cells were either left untreated or incubated with 100 nM insulin in DMEM for 48h in fusion medium to induce an insulin-resistance state. Medium was changed every 24h.

tag: cell type

value: differentiated myotubes

value: chronic insulin


title: Infected with lentiviruses encoding DOR siRNA, biological replicate 4

description: AFF008_V8_Si6 D2H_190207

data_processing: We used quantile normalization followed by RMA summarization, as implemented in Bioconductor.

source_name: Confluent C2C12 myoblasts, DOR RNAi

growth_protocol: Confluent C2C12 myoblasts previously infected with lentiviruses encoding scrambled RNA or DOR siRNA were allowed to differentiate in 5% horse serum-containing medium for 4 days.

treatment_protocol: Lentiviruses encoding scrambled or DOR siRNA were used. Fifteen million C2C12 myoblasts grown on 12-well plates were transduced at moi 100 and cells were amplified during 5-7 days. Transduced cells (GFP-positive) were then sorted with a MoFlo® flow cytometer (DakoCytomation®, Summit v 3.1 software), obtaining between 93-99% GFP-positive cells.

value: confluent myoblasts

value: DOR RNAi


title: Infected with lentiviruses encoding scrambled RNA, biological replicate 3

description: AFF008_V5_SCR D2 D_190207

source_name: Confluent C2C12 myoblasts, scrambled RNAi

value: scrambled RNAi


title: Wild-type control, biological replicate 3

source_name: heart, WT

value: wild-type


title: Wild-type control, biological replicate 2


title: Infected with lentiviruses encoding DOR siRNA, biological replicate 3

description: AFF008_V6_Si6 D2 D_190207


title: Bhlhe40-GFPneg TH17 cells rep1

description: Gene expression data from FACS-sorted Bhlhe40-GFPneg TH17 cells

source_name: Bhlhe40-GFPneg TH17 rep1

value: spleen

value: purified CD4 T cells

value: Bhlhe40-GFP reporter

tag: background strain

value: C57BL/6 (10 generation backcross)

value: 10 wks old


title: SK-ChA-1_ITL_0Mw_rep2

value: ITL

value: 0 Mw

value: E


title: Liver_WT_repl1

description:
Liv_WT_1
Replicate 1

value: Jnk1f/fJnk2+/+ (WT)

value: male

value: 7-8 wks

value: liver


title: Infected with lentiviruses encoding scrambled RNA, biological replicate 2

description: AFF008_V3_SCR D2C_190207


title: Wild-type control, biological replicate 1

value: mixed background (sv129 and C57BL/6)

value: heart


title: Infected with lentiviruses encoding DOR siRNA, biological replicate 2

description: AFF008_V4_Si6 D2C_190207

value: confluent myoblasts

value: DOR RNAi


title: Insulin treatment, biological replicate 1

value: differentiated myotubes

value: chronic insulin


title: Infected with lentiviruses encoding scrambled RNA, biological replicate 4

description: AFF008_V7_SCR D2H_190207

value: scrambled RNAi


title: Insulin treatment, biological replicate 2


title: Untreated control, biological replicate 2

source_name: C2C12 cells, control


title: Untreated control, biological replicate 3


title: Liver_ JNKΔhepa_repl1

description:
Liv_JNK1ΔhepaJNK2-/-_1
Replicate 1

value: JNKΔhepa double-knockout


title: Infected with lentiviruses encoding scrambled RNA, biological replicate 1

description: AFF008_SCR D2A_190207


title: L7

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description:
Leiomyoma patient No.7
2555 miRNAs were spotted on each array.

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

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

data_processing: The raw data of each spot was normalized by quantile normalization (Bolstad BM, et al. Bioinformatics 2003; 19: 185-193). In short, the raw data of each spot was processed by substitution with a mean+2SD of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Any miRNAs which showed values equal to 0 or less than 0 after the substitution above were deleted, where 2555 miRNAs were narrowed down to 758 miRNAs. The quantile normalization was performed further on the data according to the literature above written by Bolstad, et al.

source_name: Leiomyoma tissues

label_protocol: Extracted total RNA was labeled with Hy3 using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Vedbaek, Denmark)

growth_protocol: No culture performed.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Qiagen).

treatment_protocol: No treatment performed.

tag: location of tumors

value: Stomach

tag: diagnosis

value: Leiomyoma


title: Infected with lentiviruses encoding DOR siRNA, biological replicate 1

description: AFF008_Si6 D2 A_190207


title: L6

description:
Leiomyoma patient No.6
2555 miRNAs were spotted on each array.

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.  The data matrix includes quantile normalized signal intensity for 758 genes that could be detected in all samples


title: L5

description:
Leiomyoma patient No.5
2555 miRNAs were spotted on each array.

value: Esophagus


title: L4

description:
Leiomyoma patient No.4
2555 miRNAs were spotted on each array.


title: Nup98HoxA9#9

city: Ibaraki

first: Masahiro

last: Oka

state: Osaka

address: 7-6-8 Saito-Asagi

institute: National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN)

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: ES cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was prepared from indicated ES cell lines using TRIzol reagent TRIzol reagent. The quality of RNA was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  (Invitrogen Life Technologies) following manufacture's infomarion.

tag: sample type

value: ES expressing Nup98HoxA9

tag: clone


title: L3

description:
Leiomyoma patient No.3
2555 miRNAs were spotted on each array.


title: Parental ES (EB3)

value: ES (parental)


title: G6

description:
GIST patient No.6
2555 miRNAs were spotted on each array.

source_name: GIST tissues

value: GIST


title: G5

description:
GIST patient No.5
2555 miRNAs were spotted on each array.


title: L2

description:
Leiomyoma patient No.2
2555 miRNAs were spotted on each array.


title: G9

description:
GIST patient No.9
2555 miRNAs were spotted on each array.


title: L1

description:
Leiomyoma patient No.1
2555 miRNAs were spotted on each array.


title: Kidney_Benign_Sample 4

source_name: renal cyst

tag: tissue

value: renal cyst

tag: fuhrman grade

tag: analysis group

value: Benign

tag: patient id


title: G8

description:
GIST patient No.8
2555 miRNAs were spotted on each array.


title: G4

description:
GIST patient No.4
2555 miRNAs were spotted on each array.

value: Rectum


title: Nup98HoxA9#1


title: G1

description:
GIST patient No.1
2555 miRNAs were spotted on each array.


title: Kidney_Benign_Sample 3

source_name: oncocytoma

value: oncocytoma


title: HoxA9-Ct

value: ES expressing HoxA9-Ct


title: G3

description:
GIST patient No.3
2555 miRNAs were spotted on each array.


title: G2

description:
GIST patient No.2
2555 miRNAs were spotted on each array.


title: Untreated control, biological replicate 1

tag: cell line


title: G7

description:
GIST patient No.7
2555 miRNAs were spotted on each array.


title: Liver_ JNKΔhepa_repl2

description:
Liv_JNK1ΔhepaJNK2-/-_2
Replicate 2

tag: strain/background

tag: Sex

value: male

tag: age

value: 7-8 wks

value: liver

tag: mouseid


title: adjacent cancer [4366-]

city: Shanghai

first: Yi-Zhou

last: Jiang

state: Shanghai

address: No. 270 Dong-An Road

institute: Fudan University Shanghai Cancer Center

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G

data_processing:
The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method (ExpressionConsole 1.3.1)
probe group file: HTA-2_0.r1.pgf
meta-probeset file: HTA-2_0.r1.Psrs.mps

source_name: breast_normal tissue

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: Total RNA was isolated from cells at indicated time point with Trizol

tag: gender

value: female

tag: tissue type

value: normal breast tissue


title: adjacent cancer [4700-]


title: adjacent cancer [4563-]


title: adjacent cancer [4155-]


title: adjacent cancer [4483-]


title: adjacent cancer [4311-]


title: adjacent cancer [4160-]


title: adjacent cancer [3995-2]


title: adjacent cancer [4442-]


title: adjacent cancer [4136-]


title: adjacent cancer [4439-]


title: adjacent cancer [4232-]


title: adjacent cancer [4660-]


title: adjacent cancer [4132-]


title: adjacent cancer [4367-]


title: adjacent cancer [4659-]


title: adjacent cancer [4603-]


title: adjacent cancer [4252-]


title: adjacent cancer [4143-]


title: adjacent cancer [4737-]


title: adjacent cancer [4638-]


title: adjacent cancer [4318-]


title: adjacent cancer [4559-]


title: adjacent cancer [4783-]


title: adjacent cancer [4083-]


title: adjacent cancer [4467-]


title: adjacent cancer [4448-]


title: adjacent cancer [4557-]


title: adjacent cancer [4346-]


title: cancer [4793+]

tag: age (yrs)

tag: menopause status (0=pre, 1=post)

tag: size (cm)

tag: tumor grade

tag: positive lymph nodes

value: triple negative breast cancer (TNBC)


title: adjacent cancer [4119-]


title: adjacent cancer [4803-]


title: cancer [4803+]


title: cancer [4773+]


title: adjacent cancer [4162-]


title: cancer [4660+]


title: cancer [4747+]


title: cancer [4736+]


title: cancer [4769+]


title: cancer [4791+]


title: cancer [4737+]


title: cancer [4783+]


title: cancer [4799+]


title: cancer [4714+]


title: cancer [4708+]


title: cancer [4827+]


title: cancer [4638+]


title: cancer [4702+]


title: cancer [4563+]


title: cancer [4603+]


title: cancer [4700+]


title: cancer [4584+]


title: cancer [4639+]


title: cancer [4591+]


title: cancer [4601+]


title: cancer [4624+]


title: cancer [4659+]


title: cancer [4367+]


title: cancer [4448+]


title: cancer [4467+]


title: cancer [4346+]


title: cancer [4557+]


title: cancer [4474+]


title: cancer [4559+]


title: cancer [4439+]


title: cancer [4483+]


title: cancer [4412+]


title: cancer [4366+]


title: cancer [4167+]


title: cancer [4170+]


title: cancer [4442+]


title: cancer [4252+]


title: cancer [4232+]


title: cancer [4143+]


title: cancer [4267+]


title: cancer [4318+]


title: cancer [4136+]


title: cancer [4311+]


title: cancer [4160+]


title: cancer [4132+]


title: cancer [4119+]