title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1545

source_name: Control_blood draw

value: Control

value: F


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1547

status: Public on May 15 2016

type: genomic

city: Duarte

first: Nancy

last: Chen

state: CA

address: 1500 Duarte Road

department: Diabetes

country: USA

institute: City of Hope

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were scanned by Illumina iScan machine using standard recommended Illumina scanner setting

data_processing:
Bioconductor R pachage "Minfi" was used to process data including background substraction, control normalization and Subset-quantile Within Array (SWAN) normalization.
GEO.Monos.processed.data.txt: Average beta after data processing
GEO.Monos.signal.intensities.data.txt: unmethylated and methylated signal intensities

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Case_blood draw

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA extraction and purification method uses sodium dodecylsulfate cell lysis followed by salt precipitation method for protein removal using commercial uregene® reagents (Gentra System, Inc., Minneapolis, MN) in the Molecular Diagnostics Section of the EDIC Central Biochemistry Laboratory.

tag: cell type

tag: sample group

value: Case

tag: gender

value: M

tag: age

value: monocyte

tag: collection time


title: IL-6 stimulation treated group 2

status: Public on May 16 2016

type: RNA

city: Changsha

first: Weiguo

last: Ren

state: Hunan

address: No.216, Tongzipo, Yuelu District

country: China

institute: hird Xiangya Hospital of Central South University

description: Expression data for xenograft tumor treated with IL-6

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix® Multispecies miRNA 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Raw data were normalized with the RMA algorithm by Gene Spring Software 13.0 (Agilent）

label: biotin

molecule: total RNA

source_name: colon adenocarcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

growth_protocol: The human colon adenocarcinoma cell lines HCT116 were cultured inDulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum, 100 units/m of penicillin and streptomycin. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

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

treatment_protocol: Male BALB/c athymic nude mice (4–5 weeks old) were injected in right armpit subcutaneously with 1×107 of HCT116 cells, in a volume of 2ml of PBS, Once the tumor size reached approximately 5 mm in diameter, the mice were randomly divided into groups: 1) PBS control group with tumors untreated; 2) IL-6 stimulation treated group, 3) Combined CUL4A  siRNA with IL-6 stimulation treated group.30 ul siRNA/oligofectamine mixture containing 400 pmol siRNA or/and 600pg IL-6 every four days. After a month, the mice were sacrificed and the tumor tissues were taken.

tag: cell line

tag: agent


title: Brain_Wild Type PUS1_Indiv1

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

institute: University of South Carolina

description:
Gene expression of Brain tissue
G: US10130359_252800516690_S01_GE2_107_Sep09_1_1.txt

hyb_protocol: 300 ng of Cy3-labelled cRNA and 300 ng of Cy5-labelled cRNA was mixed and 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 instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A-028005) 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 immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using two color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channels set to 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid 028005_D_F_20130207) to obtain background- and dye-corrected (LOWESS) signal intensities.  Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

organism: Mus musculus

source_name: Brain, Wild Type PUS1 Individual 1

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA was prepared from 200 ng 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 a NanoDrop 2000c Spectrophotometer.

growth_protocol: The tissue samples were from mice that were 14 to 16 weeks old.

extract_protocol: Total RNA was isolated from frozen brain tissue (cross section of whole brain) using the mirVanaTM PARISTM kit.

tag: strain

value: C57BL/6J with backcrosses for 5 generations before experimentation

tag: tissue

value: Brain

tag: genotype/variation

value: Wild Type PUS1

value: Female


title: PBS control group 1 with tumors untreated

description: Expression data for xenograft tumor treated with PBS

value: PBS


title: immunophenotypic HSPCs from placenta, replicate 2

city: Los Angeles

first: Hanna

middle: Katri Annikki

last: Mikkola

address: 621 Charles E Young Drive South, 2204, Mailbox 160606

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
Sample name: PL_R2
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: R package Limma provided through Bioconductor was used for assessing differential expression (> 2-fold and p-value <0.05). Robust Multiarray Averaging was used to obtain absolute expression mRNA levels.

source_name: human placenta, CD34+CD38-CD90+43+

label_protocol: Standard Affymetrix protocol.

growth_protocol:
[EB differentiation] H1 ESCs were cultured in Iscoves modified Dulbecco’s medium (Invitrogen) supplemented with 15% non-heat inactivated defined fetal bovine serum (Hyclone), 2mM L-glutamine, 1% MEM non-essential amino acids (Invitrogen), 0.3 uM 2-mercaptoethanol (Invitrogen) and 1% penicillin/streptomycin (10,000 U/ml, Invitrogen). At Day 4 of EB differentiation, cultures were supplemented with 10 ng/ml bone morphogenetic protein-4 (BMP-4) (R&D Systems), 50 ng/ml FLT-3 ligand (Peprotech) and 300 ng/ml stem cell factor (SCF) (Peprotech). At day 12, BMP-4 was removed from the culture medium.
[HSPC culture] CD34+ embryoid body-derived cells were co-cultured for 2 weeks on OP9-M2 co-culture and CD34+ fetal liver cells were co-cultured for 2 or 5 weeks on OP9-M2 co-culture, when not sorted immediately from fresh fetal liver tissue or embryoid bodies

extract_protocol: RNA was purified from sorted cells using RNeasy Mini Kit (QIAGEN), according to manufacturer's instructions.

treatment_protocol: cells in culture were cultured at 37C and 5% CO2 in alpha-MEM (Invitrogen), 20% FBS (Hyclone), 2 mM L-glutamine and 1% penicillin/streptomycin (10,000 U/ml, Invitrogen) supplemented with SCF (25 ug/ml, Peprotech), Flt-3 (25 ug/ml, Peprotech) and TPO (25 ug/ml, Peprotech)

value: HSPC

tag: cell source

value: Placenta


title: immunophenotypic HSPCs from embryoid bodies, replicate 1

description:
Sample name: EB_R1
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells

source_name: embryoid bodies, CD34+CD38-CD90+CD43+

value: Embryoid body cells


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1540


title: Adherent sorted live CD34+ cell, biological replicate 2

city: Lund

first: Justyna

middle: Marta

last: Rak

state: Sverige

address: Solvegatan 19

department: Laboratory Medicine

country: Sweden

institute: Lund University

description: Gene expression data from adherent cells

hyb_protocol: Hybridized at 45C for 16 hours in Affymetrix GeneChip Hybridization Oven 645

scan_protocol: Scanned in  Affymetrix 7G scanner

data_processing: RMA

source_name: human cord-blood derived CD34+ cells

label_protocol: Ambion MessageAmp(tm) Premier RNA Amplification kit was used and followed its user manual

growth_protocol: Human CD34 positive cells were grown in serum-free expansion medium (SFEM) supplemented with SCF, TPO and FLT3L at 100ng/ml

extract_protocol: Total RNA was extracted from cells stabilized in RLT buffer according to the “Purification of total RNA from animal cells using spin technology” protocol of the Qiagen RNeasy Micro Kit.

treatment_protocol: On day 4 of the culture cells were submitted to adhesion assay on MSC-layers, adherent and non-adherent cell fractions were collected. From the two fractions live CD34+ cells were sorted into RLT buffer from Qiagen for subsequent RNA extraction and analysis.

value: human cord-blood derived CD34+ cells

tag: genotype

value: human, normal karyotype

value: Less than 24h old cordblood from uncomplicated births


title: immunophenotypic HSPCs from fetal liver co-cultured for 2 weeks on OP9-M2 stroma, replicate 3

description:
Sample name: FL-OP9 2wks_R3
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells

source_name: 2 weeks co-cultured human fetal liver, CD34+CD38-CD90+CD45+

value: Fetal Liver co-cultured 2 weeks on OP9-M2


title: Adherent sorted live CD34+ cell, biological replicate 3


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1538

value: Control


title: Non-adherent sorted live CD34+ cell, biological replicate 2


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1535

value: F


title: immunophenotypic HSPCs from fetal liver co-cultured for 5 weeks on OP9-M2 stroma, replicate 2

description:
Sample name: FL-OP9 5wks_R2
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells

source_name: 5 weeks co-cultured human fetal liver, CD34+CD38-CD90+CD45+

value: Fetal Liver co-cultured 5 weeks on OP9-M2


title: Non-adherent sorted live CD34+ cell, biological replicate 3


title: Adherent sorted live CD34+ cell, biological replicate 1


title: immunophenotypic HSPCs from embryoid bodies, replicate 2

description:
Sample name: EB_R2
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1528

value: M


title: immunophenotypic HSPCs from fetal liver co-cultured for 5 weeks on OP9-M2 stroma, replicate 1

description:
Sample name: FL-OP9 5wks_R1
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1527

value: Case

value: monocyte


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1529


title: immunophenotypic HSPCs from fresh fetal liver, replicate 2

description:
Sample name: FL_R2
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells

source_name: human fetal liver, CD34+CD38-CD90+CD45+

value: Fetal Liver


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1526


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1533


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1524


title: immunophenotypic HSPCs from fetal liver co-cultured for 2 weeks on OP9-M2 stroma, replicate 2

description:
Sample name: FL-OP9 2wks_R2
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: immunophenotypic HSPCs from fresh fetal liver, replicate 3

description:
Sample name: FL_R3
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: immunophenotypic HSPCs from placenta, replicate 1

description:
Sample name: PL_R1
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: immunophenotypic HSPCs from fresh fetal liver, replicate 1

description:
Sample name: FL_R1
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: immunophenotypic HSPCs from embryoid bodies co-cultured for 2 weeks on OP9-M2 stroma, replicate 1

description:
Sample name: EB-OP9_R1
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells

source_name: 2 weeks co-cultured embryoid body cells, CD34+CD38-CD90+CD45+

value: Embryoid body cells co-cultured 2 weeks on OP9-M2


title: immunophenotypic HSPCs from fetal liver co-cultured for 2 weeks on OP9-M2 stroma, replicate 1

description:
Sample name: FL-OP9 2wks_R1
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1519


title: Non-adherent sorted live CD34+ cell, biological replicate 1


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1516


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1513


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1512


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1518


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1505


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1506


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1496


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1502


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1497


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1504


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1490


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1494


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1501


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1492


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1489


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1507


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1488


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1491


title: immunophenotypic HSPCs from embryoid bodies co-cultured for 2 weeks on OP9-M2 stroma, replicate 2

description:
Sample name: EB-OP9_R2
Gene expression for population enriched for immunophenotypic human hematopoietic stem cells


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1511


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1509


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1482


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1481


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1480


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1477


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1473


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1476


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1475


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1470


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1495


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1468


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1466


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1462


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1454


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1455


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1459


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1460


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1458


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1446


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1483


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1445


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1487


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1467


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1444


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1479


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1485


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1452


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1451


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1550

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1550

data_processing:
Bioconductor R pachage "Minfi" was used to process data including background substraction, control normalization and Subset-quantile Within  Array (SWAN) normalization.
GEO.WB.processed.data.txt: Average beta after data processing
GEO.WB.signal.intensities.data.txt: unmethylated and methylated signal intensities

extract_protocol: The DNA extraction and purification method uses sodium dodecylsulfate cell lysis followed by salt precipitation method for protein removal using commercial uregene® reagents (Gentra System, Inc., Minneapolis, MN) in the Molecular Diagnostics Section of the  EDIC Central Biochemistry Laboratory.

tag: participant id

value: whole blood

value: EDIC baseline (1993-94)


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1540

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1540


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1539

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1539


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1547

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1547


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1538

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1538


title: DNA-methylations on monocytes of DCCT/EDIC participant ID 1443


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1529

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1529


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1528

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1528


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1527

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1527


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1524

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1524


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1519

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1519


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1518

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1518


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1521

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1521


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1513

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1513


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1512

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1512


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1509

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1509


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1545

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1545


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1516

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1516


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1506

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1506


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1504

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1504


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1492

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1492


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1507

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1507


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1533

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1533


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1502

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1502


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1496

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1496


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1491

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1491


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1497

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1497


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1501

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1501


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1495

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1495


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1489

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1489


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1494

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1494


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1490

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1490


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1535

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1535


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1488

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1488


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1526

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1526


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1487

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1487


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1485

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1485


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1483

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1483


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1511

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1511


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1481

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1481


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1480

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1480


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1479

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1479


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1482

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1482


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1477

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1477


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1470

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1470


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1473

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1473


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1475

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1475


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1466

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1466


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1467

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1467


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1468

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1468


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1459

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1459


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1462

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1462


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1476

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1476


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1458

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1458


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1460

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1460


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1455

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1455


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1454

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1454


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1452

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1452


title: Saos2-p21WAF1/Cip1 Tet-OFF_rep4

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

hyb_protocol: The microarray hybridization was performed based on the manufacturer’s standard protocols.

scan_protocol: The arrays were scanned by the Affymetrix Scanner 3000(Affymetrix)

data_processing: The data were analyzed with analyzed using Partek Genomics Suite. RMA normalization was performed.

source_name: Saos2-p21WAF1/Cip1 Tet-OFF

label_protocol: The sample labeling was performed based on the manufacturer’s standard protocols.

growth_protocol: Saos2 Tet-ON p21WAF1/Cip1 (human osteosarcoma) carrying Tet-ON were maintained in DMEM (Invitrogen) with 10% FCS (Invitrogen), 2mM l-glutamine (Invitrogen), and 100 μg/ml penicillin and streptomycin (Invitrogen) at 37°C and 5% CO2.

treatment_protocol: For p21WAF1/Cip1 expression induction, Saos2 p21WAF1/Cip1 cells were treated with 2μg/ml Doxycycline (Applichem).

value: human osteosarcoma


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1446

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1446


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1451

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1451


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1505

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1505


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1445

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1445


title: Saos2-p21WAF1/Cip1 Tet-OFF_rep1


title: Saos2-p21WAF1/Cip1 Tet-OFF_rep2


title: Saos2-p21WAF1/Cip1 Tet-ON_rep4

source_name: Saos2-p21WAF1/Cip1 Tet-ON


title: Saos2-p21WAF1/Cip1 Tet-ON_rep2


title: Saos2-p21WAF1/Cip1 Tet-ON_rep3


title: Saos2-p21WAF1/Cip1 Tet-ON_rep1


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1443

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1443


title: DNA-methylations on Whole blood of DCCT/EDIC participant ID 1444

description:
Genomic DNA was originally obtained for EDIC genetic study and provided by DCCT/EDIC study
WB_methyl_EDIC_1444


title: IRG 23_HIV seropositive therapy Naïve (ART-N)

city: Chandigarh

first: Sunil

middle: K

last: Arora

address: 4th Floor Research Block:A

department: Immunopathology

country: India

institute: PGIMER

description: Gene Expression data

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

scan_protocol: Affymetrix Gene Chip 3000 Scanner was used for Scanning as per the manufacturer’s protocol

data_processing: All the scanned array images were visually inspected at Affymetrix AGCC portal. After image acquisition of microarray experiments raw data sets were extracted from all Cel file (raw intensity file). These raw data sets were separately analyzed using the GeneSpring GX12.1 software. All the microarray raw data (cel files) were preprocessed using RMA (Robust Multichip Average) algorithm that consists of three steps: a background adjustment, normalization and finally summarization.

label: Biotin

source_name: HIV seropositive therapy Naïve (ART-N)

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: RNA Extraction by Qiagen kit as per manufactors protocol

tag: subject status

value: HIV-1 subtype C infected patient

tag: subject group

value: HIV seropositive therapy Naïve (ART-N)

tag: cd4 count

value: CD4 Count <250

value: Peripheral Blood


title: IRG 12_HIV seropositive therapy Responder (ART-R)

description: Gene Expression data

value: CD4 Count >400


title: IRG 22_Healthy Control (HC)

description: Gene Expression data

source_name: Healthy Control (HC)

value: Healthy Subject

value: Healthy Control (HC)


title: IRG 17_HIV seropositive therapy Responder (ART-R)

description: Gene Expression data


title: IRG 24_HIV seropositive therapy Naïve (ART-N)

description: Gene Expression data


title: IRG 11_HIV seropositive therapy Responder (ART-R)

description: Gene Expression data


title: IRG 18_HIV seropositive therapy Naïve (ART-N)

description: Gene Expression data


title: IRG 16_HIV seropositive on therapy immunolgical failure (ART-IF)

description: Gene Expression data


title: IRG 10_HIV seropositive therapy Responder (ART-R)

description: Gene Expression data


title: IRG 15_HIV seropositive on therapy immunolgical failure (ART-IF)

description: Gene Expression data


title: IRG 7_HIV seropositive on therapy immunolgical failure (ART-IF)

description: Gene Expression data


title: blood-PP-PIDOPT1847

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Following fragmentation, 49 ul representing 5 micrograms of cDNA were diluted into 171 microlitres of Affymetrix hybridization cocktail, and 200 microlitres hybridized for 16 hr at 45 C in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data from .CEL files were summarized and normalized using the RMA algorithm. During pre-processing of the RMA normalized data, we removed VNP PID4015 from downstream statistical analyses as PCA revealed it was an outlier to both VNP and PP groups.

source_name: blood-PP

label_protocol: 50 ng of total RNA was amplified, labeled and hybridized to Affymetrix Human U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA) using the NuGEN Ovation RNA Amplification System V2, Ovation WB Reagent and Encore Biotin Module according to manufacturer’s specifications (NuGEN Inc, San Carlos, CA). 3.8 ug of Nugen amplified cDNA was fragmented by incubation in Nugen Fragmentation buffer at 37 C for 30 min, followed by incubation at 95 C for 2min. Fragmented cDNA was labelled using the Nugen Encore Biotin Module according to manufacturer's instructions.

growth_protocol: HIV-infected viremic non-progressor (VNP) and putative progressor (PP) samples were sampled from the UCSF SCOPE and OPTIONS cohorts, respectively. VNPs were defined as having confirmed HIV-1 infection for at least 9 years with sustained plasma HIV RNA levels >10,000 copies/ml and maintenance of peripheral blood CD4+ T cell counts >500 cells/mm3 and a CD4% (of all lymphocytes) >15% (Table 1). Recently HIV-infected PPs were defined as having plasma HIV RNA levels >10,000 copies/mL, CD4+ T cell counts >400 cells/mm3 and having been initially infected with HIV 2-24 months prior to the index visit (Table 1). The estimated date of initial HIV infection was calculated according to published algorithms that incorporate “de-tuned” anti-HIV-1 antibody ELISA results [46,47] or by a documented sero-conversion window of <6 months. All participants were required to be antiretroviral therapy (ART)-naïve. HIV-infected viremic non-progressors and viremic progressor samples for nef analysis were collected as described in Table 3.

extract_protocol: RNA from whole was extracted using the PAXgene RNA Isolation Kit according to manufacturer's instructions.

tag: pid

tag: hiv patient class

value: Putative Progressor


title: IRG 9_HIV seropositive therapy Naïve (ART-N)

description: Gene Expression data

value: CD4 Count >250


title: blood-PP-PIDOPT1690


title: blood-PP-PIDOPT1836


title: blood-PP-PIDOPT1831


title: IRG 6_HIV seropositive on therapy immunolgical failure (ART-IF)

description: Gene Expression data


title: IRG 5_Healthy Control (HC)

description: Gene Expression data


title: blood-PP-PIDOPT1793


title: blood-PP-PIDOPT1845


title: IRG 20_HIV seropositive on therapy immunolgical failure (ART-IF)

description: Gene Expression data


title: IRG 1_HIV seropositive therapy Naïve (ART-N)

description: Gene Expression data


title: blood-PP-PIDOPT1712


title: NaF_miR9_3

city: Mexico

first: Sandra

middle: Lorena

last: Romero-Cordoba

state: Mexico

address: Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan. México, D.F.

department: Cancer Genomics

country: Mexico

institute: National Instute of Genomic Medicine

description: replicate 3 batch 2

hyb_protocol: Standard illumina protocol

scan_protocol: Standard illumina protocol

data_processing: Image files were quantified in BeadStudio Version 3.3.8 (Illumina) and raw data were analyzed (variance stabilizing transformation, log2 transformation and quantile normalization) in R statistical environment using the lumi package implemented in Bioconductor. To reduce the non-biological experimental variation or batch effects we applied combat adjustment method (http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html) to the normalized data. To define the differentially expressed genes within NFs/miR-9 and NFs/control, an adjusted T Test was performed with limma library: significant genes were selected based on a minimum log2 fold change of 0.7 and P.value < 0.05. Unsupervised hierarchical clustering analysis for the differentially expressed genes was performed with gplots in R

source_name: Immortalized Normal Fibroblasts

label_protocol: Standard illumina protocol

growth_protocol: Cultured in FGM-2 medium supplemented with serum maintained at 37 °C under 5% CO2

extract_protocol: Total RNA was isolated using QIAzol®Lysis Reagent (QIAGEN Sciences, Germantown, USA) according to the manufacturer’s instruction

treatment_protocol: 25 nM of miR-9 precursor or control (Pre-miR precursor molecules , Life Technologies)  were transfected for 24hrs using Lipofectamine 2000 (Life Technologies) according to the manufacturer’s instruction.

tag: treatment

value: Transiently transfected with miR-9

value: Adjacent normal breast tissue


title: IRG 21_Healthy Control (HC)

description: Gene Expression data


title: IRG 13_HIV seropositive on therapy immunolgical failure (ART-IF)

description: Gene Expression data


title: IRG 4_Healthy Control (HC)

description: Gene Expression data


title: IRG 2_HIV seropositive therapy Responder (ART-R)

description: Gene Expression data


title: blood-VNP-PID4020

source_name: blood-VNP

value: Viremic Non Progressor


title: IRG 8_HIV seropositive on therapy immunolgical failure (ART-IF)

description: Gene Expression data


title: kidney samples_control_group1

status: Public on May 14 2016

city: Shanghai China

first: linghong

last: shen

address: 1630 Dongfang Road

institute: Department of Cardiology, Renji Hospital                                  Shanghai Jiaotong University School of Medicine

description:
AT
miRNA profile in rat kidney

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After 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).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 9.5.3 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 10.0 (Agilent technologies, Santa Clara, CA, US).

organism: Rattus norvegicus

source_name: rat kidney samples of control group

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

growth_protocol: standard rat chow, specific pathogen free

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: male Sprague-Dawley rats (250-300g) were deprived of water for 3 days and then given furosemide by intramuscularly injection at a dose of 10 mg/kg. For CI-AKI group, a nonionic low-osmolar contrast medium, Omnipaque (350 mg I/ML, GE Healthcare, Shanghai, China) at a dose of 10 ml/kg, was subsequently administered via tail vein over the course of 5 min. For control group, the same amount of normal saline was given. Peripheral blood and kidney samples were harvest at 8h after contrast medium/normal saline administration.

value: Sprague-Dawley

tag: gender

value: male

tag: treated with

value: normal saline

value: kidney


title: kidney samples_control_group4

description:
HT
miRNA profile in rat kidney


title: plasma samples_CI-AKI_group4

description:
Gu
miRNA profile in rat plasma

source_name: rat plasma samples of CI-AKI group

value: contrast medium

value: plasma


title: kidney samples_control_group3

description:
ET
miRNA profile in rat kidney


title: kidney samples_control_group2

description:
CT
miRNA profile in rat kidney


title: NaF_miR9_2

description: replicate 2 batch 1


title: kidney samples_CI-AKI_group3

description:
FT
miRNA profile in rat kidney

source_name: rat kidney samples of CI-AKI group


title: blood-VNP-PID1597

value: whole blood


title: NaF_miR9_1

description: replicate 1 batch 1


title: kidney samples_CI-AKI_group1

description:
BT
miRNA profile in rat kidney


title: NaF_Con_2

description: replicate 2 batch 2

value: Transiently transfected with control


title: NaF_Con_3

description: replicate 3 batch 2


title: NaF_Con_1

description: replicate 1 batch 1


title: plasma samples_CI-AKI_group1

description:
Au
miRNA profile in rat plasma


title: plasma samples_CI-AKI_group2

description:
Cu
miRNA profile in rat plasma


title: plasma samples_control _group1

description:
Bu
miRNA profile in rat plasma

source_name: rat plasma samples of control group


title: plasma samples_control_group4

description:
Hu
miRNA profile in rat plasma


title: blood-VNP-PID1208


title: blood-VNP-PID1662


title: plasma samples_CI-AKI_group3

description:
Eu
miRNA profile in rat plasma


title: plasma samples_control _group2

description:
Du
miRNA profile in rat plasma


title: kidney samples_CI-AKI_group2

description:
DT
miRNA profile in rat kidney


title: blood-VNP-PID1587


title: kidney samples_CI-AKI_group4

description:
GT
miRNA profile in rat kidney


title: plasma samples_control_group3

description:
Fu
miRNA profile in rat plasma


title: bone marrow_normal_2

city: Hefei

first: Xiaohu

last: Zheng

state: Anhui

address: Huang Shan Road

department: School of Life Sciences

institute: University of Science and Technology of China

description: SAMPLE 4

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bitt. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, GeneSpring Software 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: bone marrow_normal

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA 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-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: No treatment.Freshly bone marrow mononuclear cells from acute myeloid leukemias and healthy volunteers were to microarray analysis.

value: healthy donors

tag: cell type

value: bone marrow mononuclear cells


title: bone marrow_normal_1

description: SAMPLE 3


title: genomic DNA from vaginal fluid of 20F15008

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

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

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

data_processing: BeadStudio software v3.2

source_name: vaginal fluid of 20F15008

extract_protocol: genomic DNA was extracted using QIAamp DNA Investigator Kit and Mini Kit

tag: age

value: Female

tag: ethnicity

value: Korean-Asian

tag: sample type

value: vaginal fluid


title: genomic DNA from vaginal fluid of 20F15007

source_name: vaginal fluid of 20F15007


title: BV-2_cells+LPS+HF100_1

city: KUALA LUMPUR

first: PUI MUN

last: CHAN

state: WILAYAH PERSEKUTUAN

address: DEPARTMENT OF BIOMEDICAL SCIENCE

department: DEPARTMENT OF BIOMEDICAL SCIENCE

country: Malaysia

institute: UNIVERSITY OF MALAYA

hyb_protocol: The amount of the resulting fluorescently labelled cRNA was quantified with the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1. The Cy3-labelled samples were hybridized with the microrray (Mus musculus Genome Oligo Microarray; Agilent), comprising over 60,000 Mus musculus genes and transcripts, for 17 hours at 65°C before washing and scanning.

scan_protocol: The scanning was done using an Agilent G4900DA SureScan Microarray Scanner.

data_processing: Data were extracted from resulting images (Feature Extraction Software; Agilent). The Agilent GeneSpring GX 13.0 was used for analysis of the datasets. Biological replicate samples were sorted according to four conditions: cells only (control), cells induced with 1 µg/mL of LPS, cells treated with 100 µg/mL of HF, and cells induced with 1 µg/mL of LPS and treated with 100 µg/mL of HF. Filtering of the datasets was performed (filter by flags present in all samples) by selecting only genes that are detectable in all samples. Fold change differences between control and induced and/or treated samples were calculated using cut-offs of 2-fold with significant values of p < 0.05.

source_name: BV-2 cells induced with 1 µg/mL of LPS and treated with 100 µg/mL of HF

label_protocol: Twenty five nanogram of total RNA from each sample was amplified and labelled with fluorescent dye (Cy3, Low Input Quick Amp Labelling Kit, One Colour; Agilent) according to the manufacturer’s protocol.

growth_protocol: BV-2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM; Gibco) supplemented with 5% fetal bovine serum (Gibco), 1% penicillin-streptomycin (Gibco), 0.5% fungizone (Gibco), 0.1% gentamycin (Gibco), 0.1% insulin (Sigma), 1% non-essential amino acid (NEAA; Gibco). The cells were maintained in humidified incubator with 5% CO2 at 37°C.

extract_protocol: Cells were harvested and the RNA was isolated using Absolutely RNA Miniprep Kit according to the protocol provided by the manufacturer (Agilent).

treatment_protocol: BV-2 cells (2.5 X 1 000 000 cells) were seeded in 25cm3 flask and allowed for attachment overnight at 37°C in humidified atmosphere containing 5% CO2. The cells were then treated with or without 100 µg/mL of HF and co-incubated with or without 1 µg/mL of LPS for 24 hours.

tag: cells


title: Dmp1-Cre targeted CAR cells, biological rep 1

city: St. Louis

first: Daniel

middle: C

last: Link

state: MO

address: 660 South Euclid Avenue

department: Internal Medicine

institute: Washington University in St Louis

description: Gene expression data from Dmp1-Cre targeted CAR cells

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with Affymetrix Expression Console 1.4 using default analysis settings. The processing/normalization algorithm is RMA.

source_name: FACS sorted Dmp1-Cre targeted CAR cells from mouse bone marrow

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

growth_protocol: Mice were kept in regular mouse facility, standard mouse food and water were provided

extract_protocol: FACS sorted cells were directly collected in RLT lysis buffer and total RNA were extracted using Qiagen Rnesay Micro Kit (Cat# 74004, Qiagen)

treatment_protocol: Mice were killed using CO2 chamber, bone marrow were then harvested from femur and tibia.

tag: strain

tag: tissue

value: Bone marrow

value: Dmp1-Cre Cxcl12-gfp/+

value: 7 weeks after birth


title: Dmp1-Cre non-targeted CAR cells, biological rep 2

description: Gene expression data from Dmp1-Cre non-targeted CAR cells

source_name: FACS sorted Dmp1-Cre non-targeted CAR cells from mouse bone marrow

tag: genotype


title: Dmp1-Cre targeted CAR cells, biological rep 2


title: bone marrow_AML_1

description: SAMPLE 1

source_name: bone marrow _AML

value: aute myeloid leukemia (AML) patient


title: BV-2_cells+HF100_2

source_name: BV-2 cells treated with 100 µg/mL of HF

value: treated with 100 µg/mL of HF


title: BV-2_cells+HF100_1


title: Dmp1-Cre non-targeted CAR cells, biological rep 3


title: Dmp1-Cre non-targeted CAR cells, biological rep 1


title: bone marrow_AML_2

description: SAMPLE 2

value: male


title: genomic DNA from vaginal fluid of 30F15005

source_name: vaginal fluid of 30F15005


title: BV-2_cells only_1

source_name: BV-2 cell only


title: BV-2_cells only_2


title: BV-2_cells+LPS+HF100_2

value: induced with 1 µg/mL of LPS and treated with 100 µg/mL of HF


title: BV-2_cells+LPS_1

source_name: BV-2 cells induced with 1 µg/mL of LPS

value: induced with 1 µg/mL of LPS


title: Namalwa_Oct-1X

city: Moscow

first: Elizaveta

last: Pankratova

address: Vavilova st. 32

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: Oct-1X overexpressing cell line

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: Namalwa cell line, transfected with Oct-1X

label_protocol: biotin-UTP-labelled cRNA was were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: The human cell line Namalwa was maintained in DMEM with 10% FCS 100 U/ml penicilin and 100 mkg/ml streptomicin

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

treatment_protocol: The constructs pL-Oct-1A-3FLAG (C-end) or pL-Oct-1L-3FLAG or pL-Oct-1X-3FLAG (C-end)  were generated by inserting a copy of human Oct-1 isoforms coding sequences into the pLenti6/V5-D_TOPO expression vector (Invitrogene) and transduced into Namalwa cells. Blasticidin was used to selected and maintain the stably transduced cells.

tag: forced overexpression protein


title: Dmp1-Cre targeted CAR cells, biological rep 3


title: BV-2_cells+LPS_2


title: genomic DNA from menstual blood day2 of 20F15008

source_name: menstrual blood of 20F15008

value: menstrual blood


title: Namalwa_Oct-1A

description: Oct-1A overexpressing cell line

source_name: Namalwa cell line, transfected with Oct-1A


title: Tibial MSC at passage 0, bioloogical rep 3

city: Columbus

first: Zongyang

last: Sun

state: Ohio

address: 305 W 12th Ave

department: Orthodontics

institute: The Ohio State University

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Bioarray Eukaryotic Hybridization Controls (Affymetrix) and Oligo B2, 3nM (Affymetrix). Then, heated at 65°C for 5 minutes, 99°C for 5 minutes, 45°C for 5 minutes, and centrifuged with top speed for 5 minutes, followed by hybridization for 16 hours at 45°C at 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450_0002.

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

data_processing: Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console. Data visualization and filtering was performed in Transcriptome Analysis console version 3.0.

organism: Sus scrofa

source_name: Porcine bone marrow aspirated from tibia

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

growth_protocol: Mesenchymal stem cells were isolated from bone marrow by whole blood plating on T75 flasks, and cultured in alpha-MEM supplemented with 20% FBS, 1% L-Glutamine, and 1% Pen/Strep.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer's protocol. RNA quality and concentration was determined by Agilent 2100 Bioanalyzer (Agilent Technologies).

value: female

value: American Yorkshire

value: primary culture of porcine bone marrow MSC


title: WTpancreas_caerulein0week_rep3

city: BEIJING

first: XIAFEI

last: HONG

state: BEIJING

address: DONGDAN SANTIAO

institute: Peking Union Medical College Hospital

hyb_protocol: 10 μg of cDNA was fragmented and hybridized to the GeneChip Mouse Genome 430 2.0 Array. The DNA chips were washed, stained using the GeneChip® Fluidics Station 450

scan_protocol: The scanning process used the GeneChip® Scanner 3000 7G

data_processing: Software: R 3.1.0; algorithm: Robust Multi-array Average (RMA) and Gene Set Enrichment Analysis (GSEA)

source_name: Wild-type pancreas without caerulein intra-abdominal injection

label_protocol: Biotinlabeled cDNA was obtained from 250ng total RNA with Gene AmpPCR System 9700

growth_protocol: The mice were housed in a 12/12-hour light/dark cycle

extract_protocol: Total RNA was extracted from tissue with miRNeasy Mini Kit and RNase-Free Dnase Set

treatment_protocol: Caerulein was intra-abdominally injected to induce acute pancreatitis

tag: background strain

tag: Sex

value: Male

value: pancreas


title: WTpancreas_caerulein0week_rep1

value: Female


title: KrasG12Dpancreas_caerulein1week_rep3

source_name: KrasG12D mutated pancreas caerulein intra-abdominal injection for 1 week


title: WTpancreas_caerulein0week_rep2


title: Tibial MSC at passage 0, bioloogical rep 2


title: WTpancreas_caerulein0week_rep4


title: KrasG12Dpancreas_caerulein1week_rep1


title: Namalwa_Oct-1L

description: Oct-1L overexpressing cell line

source_name: Namalwa cell line, transfected with Oct-1L


title: WTpancreas_caerulein0week_rep5


title: Namalwa_control

description: control sample

source_name: Namalwa cell line


title: Tibial MSC at passage 0, bioloogical rep 1


title: WTpancreas_caerulein0week_rep6


title: Mandibular MSC at passage 0, biological rep 3

source_name: Porcine bone marrow aspirated from mandibular symphysis


title: KrasG12Dpancreas_caerulein1week_rep2


title: genomic DNA from menstual blood day1 of 30F15005

source_name: menstrual blood of 30F15005

value: Korean-Asian


title: Mandibular MSC at passage 0, biological rep 2


title: KrasG12Dpancreas_caerulein2week_rep3

source_name: KrasG12D mutated pancreas caerulein intra-abdominal injection for 2 weeks


title: genomic DNA from menstual blood day3 of 30F15005


title: KrasG12Dpancreas_caerulein2week_rep1


title: KrasG12Dpancreas_caerulein2week_rep2


title: genomic DNA from menstual blood day3 of 20F15008


title: genomic DNA from menstual blood day2 of 30F15005


title: genomic DNA from menstual blood day1 of 20F15008


title: genomic DNA from menstual blood day3 of 20F15007

source_name: menstrual blood of 20F15007


title: genomic DNA from menstual blood day1 of 20F15007


title: mIMCD-VPS33B-3

status: Public on May 13 2016

city: London

first: Paul

last: Gissen

state: London

address: Gower Street

department: LMCB

country: United Kingdom

institute: UCL

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Affymetrix Mogene 2.0 arrays. 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: RMA processing using 'oligo' Bioconductor package in R

source_name: mouse IMCD, VPS33B shRNA

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

growth_protocol: mIMCD3 cells (American Type Culture Collection CRL2123) were cultured in a 1:1 mix of DMEM and Ham's F-12 medium, supplemented with 10% FBS

extract_protocol: Extraction of total RNA was performed using the RNAeasy Microkit (Qiagen, UK)

treatment_protocol: Non-silencing hairpins were used as controls. Plasmid shRNA constructs (VPS33B; V2MM_91195 and VIPAR; V2LMM_9377) were purchased from Open Biosystems. mIMCD-3 cells were transfected with 4 µg of plasmid with recovery (48 h) before transfected cells were selected using 1.5 µg/ml puromycin. Individual clones were selected to reduce variability. Level of knockdown was assessed by protein blotting (VPS33B) or quantitative real time PCR (VIPAR).

tag: cell line

value: kidney

tag: transfection

value: VPS33B shRNA


title: mIMCD-VPS33B-1


title: mIMCD-PLOD3-1

source_name: mouse IMCD, PLOD3 shRNA

value: PLOD3 shRNA


title: mIMCD-VPS33B-2


title: mIMCD-VIPAR-1

source_name: mouse IMCD, VIPAR shRNA

value: VIPAR shRNA


title: mIMCD-VIPAR-3


title: mIMCD-wildtype-3

source_name: mouse IMCD, wild type


title: mIMCD-wildtype-1


title: mIMCD-PLOD3-3


title: mIMCD-control-1

source_name: mouse IMCD, control shRNA

value: control shRNA


title: genomic DNA from menstual blood day2 of 20F15007

label_protocol: Standard Illumina Protocol


title: mIMCD-control-3


title: NIH3T3 PGC7 pre cloning

city: Setagaya

first: Keisuke

last: Oboki

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Center for Medical Research Cooperation

country: Japan

institute: TOKYO METROPOLITAN INSTITUTE of MEDICAL SCIENCE

description: Gene expression data from NIH3T3 overexpressed PGC8/Stella pre-cloned cells.

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

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

source_name: NIH3T3 cells with PGC7, pre cloning.

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

growth_protocol: NIH3T3 cells and B16F10 cellswere maintained in Dulbecco’s modified Eagle’s Minimum Essential Medium supplemented with 100 U/mL penicillin, streptomycin sulfate, and 10% fetal bovine serum.

extract_protocol: RNeasy Total RNA Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Target cells were incubated in the virus/polybrene-containing supernatants overnight. After infection, the cells were replaced with fresh medium.

tag: genotype/variation


title: B16F10 PGC7 clone-1

description: Gene expression data from B16F10 overexpressed PGC7/Stella cloned cells (#1).

source_name: B16F10 cells with PGC7, clone-1

value: overexpressed PGC8/Stella pre-cloned cells


title: mIMCD-PLOD3-2


title: NIH3T3 PGC7 clone-2

description: Gene expression data from NIH3T3 overexpressed PGC7/Stella cloned cells (#2).

source_name: NIH3T3 cells with PGC7, clone-2


title: B16F10 PGC7 clone-2

description: Gene expression data from B16F10 overexpressed PGC7/Stella cloned cells (#2).

source_name: B16F10 cells with PGC7, clone-2


title: B16F10 ctrl

description: Gene expression data from B16F10 cells.

source_name: B16F10 cells control

value: control


title: B16F10 PGC7 clone-3

description: Gene expression data from B16F10 overexpressed PGC7/Stella cloned cells (#3).

source_name: B16F10 cells with PGC7, clone-3


title: mIMCD-control-2


title: mIMCD-wildtype-2


title: NIH3T3 PGC7 clone-1

description: Gene expression data from NIH3T3 overexpressed PGC7/Stella cloned cells (#1).

source_name: NIH3T3 cells with PGC7, clone-1


title: mIMCD-VIPAR-2


title: BJEL_SNP_Affy_250K

city: Illkirch; Strasbourg

first: Valeriya

last: Malysheva

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description: Immortalized BJEL fibroblast cells (pretransformed)

hyb_protocol: DNA was hybridized to each array according to the manufacturer's instructions at 49°C during 16hr, washed and stained on GeneChip Fluidics Station 450

scan_protocol: The arrays were scanned using Affymetrix GCS3000-7G

data_processing: For each array the .CEL file was generated using Affymetrix GeneChip Command Console version 3.2 (AGCC v4.1). Analysis of copy number and Loss of heterozygosity were performed using Genotyping Console 4.2.0.26. BJEL and BJELM samples were compared in a pairwise manner with BJ sample.

label_protocol: According to manufacturer (Affymetrix)

growth_protocol: BJEL cells were cultured in monolayer conditions Dulbecco’s modified Eagle’s medium (DMEM)/M199 (4:1) (with 4.5 g/l glucose) supplemented with 10% of heat inactivated fetal calf serum (FCS), G-418 (400 µg/µl) and Hygromycin (400 µg/µl).

extract_protocol: Genomic DNA was extracted from cells using the QIAamp DNA Mini Kit cat. No. 51304

value: BJEL

value: foreskin fibroblast cells


title: NIH3T3 ctrl

description: Gene expression data from NIH3T3 cells.

source_name: NIH3T3 cells control


title: BJELM_SNP_Affy_250K

description: Transformed BJELM fibroblast cells (cancer cells)

growth_protocol: BJELM cells were cultured in monolayer conditions Dulbecco’s modified Eagle’s medium (DMEM)/M199 (4:1) (with 4.5 g/l glucose) supplemented with 10% of heat inactivated fetal calf serum (FCS),G-418 (400 µg/µl), Hygromycin (400 µg/µl) and puromycin (1 µg/ml) and continuously grown with 10-6 M 4-hydroxytamoxyfen (4-OHT).

value: BJELM


title: ERa_KOHmz_E2_rep5

city: Rennes

first: Raphaël

last: Métivier

address: Campus de Beaulieu

institute: CNRS UMR 6290

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE microarray (8X60K, Design 028005)  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min), Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028005_D_F_20120201). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a weight of 1 for 20 or with a weight of 1 in all 3 microarrays from at least one experimental group. At this step, 35195 spots out of 62976 were selected. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 32526 rows each corresponding to a unique ProbeName (provided as data Matrix) and 20 columns (individuals).

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 µg of total RNA exhibiting a RIN>9 using the One-Color Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts). Dye incorporation and cRNA yield were checked with the Biospec nano spectrophotometer (Shimadzu).

growth_protocol: Wild-type breeders (ERWT) were obtained from the same parents as were the ERKO mice. Genotyping was systematically performed on DNA prepared from breedings’ tails. Mice were housed in cages in groups of 5 and kept in a temperature-controlled facility on an artificial 12h light-dark cycle.

extract_protocol: RNAs were isolated from livers of ERWT or ERKO ovariectomized mice treated or not with E2 following tissue homogenization using a Precellys tissue homogenizer (Bertin Technology). Total RNAs were prepared using GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich). Integrity and purity of the RNAs were controlled on an Experion apparatus (Biorad).

treatment_protocol: Mice were ovariectomized at 4 weeks of age and were treated by oral gavage with placebo (P, castor oil 5% EtOH) or estradiol (E2, 1mg/kg) at 9 weeks of age. Folllowing anesthesia by injection of ketamine (100 mg/kg) and xylazine (10 mg/kg) by intraperitoneal route, mice were sacrificed 4 hours after gavage. Blood was collected by retroorbital prelevement and liver sample was snap-frozen in liquid nitrogen and stored at -80°C.

value: liver

value: ERa-/-

tag: treatment


title: ERa_KOHmz_PLB_rep2

source_name: ERa-/-, placebo, 718

value: placebo


title: BJ_SNP_Affy_250K

description: Primary human BJ foreskin fibroblasts (normal cells)

growth_protocol: BJ cells were cultured in monolayer conditions Dulbecco’s modified Eagle’s medium (DMEM)/M199 (4:1) (with 4.5 g/l glucose) supplemented with 10% of heat inactivated fetal calf serum (FCS).

value: BJ


title: ERa_WT_PLB_rep3

source_name: ERa+/+, placebo, 777

value: ERa+/+


title: ERa_KOHmz_PLB_rep5

source_name: ERa-/-, placebo, 788


title: ERa_KOHmz_PLB_rep4

source_name: ERa-/-, placebo, 773


title: ERa_WT_PLB_rep5

source_name: ERa+/+, placebo, 2082


title: ERa_WT_PLB_rep4

source_name: ERa+/+, placebo, 785


title: ERa_KOHmz_E2_rep2


title: ERa_WT_E2_rep4


title: ERa_KOHmz_E2_rep3


title: ERa_WT_E2_rep1


title: ERa_WT_E2_rep3


title: ERa_WT_PLB_rep1

source_name: ERa+/+, placebo, 753


title: ERa_KOHmz_E2_rep1


title: ERa_KOHmz_PLB_rep3

source_name: ERa-/-, placebo, 720


title: ERa_WT_PLB_rep2

source_name: ERa+/+, placebo, 761


title: ERa_WT_E2_rep2


title: ERa_KOHmz_E2_rep4


title: SNU5_CONTROL_Rep3

city: houston

first: Rebecca

middle: Dunbar

last: Schroeder

state: Texas

address: 4425 stillbrooke dr

institute: MD Anderson Cancer Center

description: SAMPLE 9

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

growth_protocol: MKN45 were maintained in RPMI-1640 medium supplemented with 10% FBS (HyClone/Thermo Scientific, Waltham, MA), minimum essential medium (MEM) vitamins, sodium pyruvate (Mediatech/Corning Cellgro, Manassas, VA), L-glutamine, non-essential amino acids, penicillin/streptomycin (Lonza, Switzerland), and HEPES buffer. SNU-5 cells were cultured in Iscove's modified Dulbecco's medium supplemented with 10% FBS, MEM vitamins, L-glutamine, sodium pyruvate, non-essential amino acids, penicillin/streptomycin, and HEPES. All cells were grown at 37° C in 5% CO2

extract_protocol: Total RNA from cell pellets was isolated using the mirVana miRNA isolation kit (Ambion, Inc)

treatment_protocol: 1uM crizotinib (MET inhibitor)

value: Gastric Cancer Cell line

value: none (control)


title: SNU5_TREAT_Rep3

description: SAMPLE 10

value: 1uM crizotinib for 24 hrs


title: MKN45_TREAT_Rep3

description: SAMPLE 12


title: MKN45_CONTROL_Rep3

description: SAMPLE 11


title: Mandibular MSC at passage 0, biological rep 1

source_name: Porcine bone marrow aspirated from mandibular symphysis

tag: gender

value: female

value: American Yorkshire

value: Bone marrow

value: primary culture of porcine bone marrow MSC


title: SNU5_CONTROL_Rep2

description: SAMPLE 7

tag: treated with


title: SNU5_TREAT_Rep1

description: SAMPLE 6

tag: cell type


title: SNU5_TREAT_Rep2

description: SAMPLE 8


title: SNU5_CONTROL_Rep1

description: SAMPLE 5


title: MKN45_TREAT_Rep2

description: SAMPLE 4


title: MKN45_CONTROL_Rep2

description: SAMPLE 3


title: MKN45_CONTROL_Rep1

description: SAMPLE 1


title: MKN45_TREAT_Rep1

description: SAMPLE 2


title: Normal_crypt_02

city: South San Francisco

first: Omar

last: Kabbarah

state: California

address: 1 DNA Way

department: Oncology Biomarker Development

institute: Genentech Inc

hyb_protocol: Affymetrix HG-U133A GeneChips were hybridized according to the manufacturer’s instructions.

data_processing: Normalized expression values were obtained by quantile normalization and calculation of the robust multichip average (RMA) expression measure using the affy Bioconductor package (Gautier L et al, Bioinformatics, 2004; package version 1.46.1).

source_name: Normal crypt epithelium

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

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

value: Male

tag: tissue type

value: Normal crypt epithelium

tag: tumor stage

tag: age (yrs)

tag: site

value: Rt colon


title: Normal_surface_08

source_name: Normal surface epithelium

value: Female

value: Normal surface epithelium


title: Normal_surface_07

value: colon


title: Normal_crypt_08


title: Normal_crypt_01

value: sigmoid


title: Normal_crypt_07


title: Normal_surface_06


title: Normal_surface_01


title: Metastasis_07

source_name: Metastasis

value: Metastasis

value: ovary


title: Normal_surface_05


title: Normal_crypt_06


title: Normal_surface_02


title: Normal_crypt_04


title: Metastasis_09

value: liver


title: Normal_crypt_05


title: Metastasis_08


title: Metastasis_01


title: Metastasis_06


title: Metastasis_05


title: Metastasis_02


title: ERa_KOHmz_PLB_rep1

source_name: ERa-/-, placebo, 716

value: ERa-/-

value: placebo


title: Carcinoma_15

source_name: Carcinoma

value: Carcinoma

value: transverse


title: Metastasis_11

value: lymph node


title: ERa_WT_E2_rep5

value: ERa+/+


title: Carcinoma_13

value: rectum


title: Carcinoma_17


title: Carcinoma_14

value: Male


title: Metastasis_10


title: Metastasis_03


title: Metastasis_04


title: Carcinoma_18


title: Carcinoma_12


title: Carcinoma_16

value: Lt colon


title: Carcinoma_11


title: Carcinoma_03

value: Rt colon


title: Carcinoma_10

value: Female


title: Carcinoma_05


title: Adenoma_16

source_name: Adenoma

value: Adenoma


title: Carcinoma_04

value: cecum


title: Adenoma_20


title: Carcinoma_02

value: sigmoid


title: Carcinoma_09


title: Carcinoma_08


title: Adenoma_17


title: Adenoma_14


title: Normal_liver_04 [methylation]

hyb_protocol: Fragmented DNA was dispensed onto the multichannel HumanMethylation BeadChips and hybridization performed in an Illumina Hybridization oven for 20 h.

scan_protocol: BeadChips were coated and then imaged on an Illumina iScan Reader and images were processed with GenomeStudio software methylation module (version 1.8 or later).

data_processing:
Raw data was preprocessed using the Bioconductor methylumi software package (Davis et al, 2015; version 2.14.0)
Normalized M-values; background correction and quantile normalization were performed with the lumiMethyB and lumiMethyN functions, respectively, from the lumi Bioconductor package (version 2.15.5)

source_name: Normal liver adjacent to liver metastasis

label_protocol: BeadChips were washed, primer extended, and stained as per manufacturer protocols.

extract_protocol: DNA  was extracted usingQiagen  DNeasy Blood and Tissue kit according to the manufacturer's instructions. The target was prepared and hybridized according to the Illumina Infinium HD Methylation Assay, Manual Protocol (Illumina Part # 15019522 Rev. A). Bisulfite Conversion: A bisulfite conversion reaction was employed using 500 ng of genomic DNA according to the manufacturer’s protocol for the Zymo EZ DNA Methylation kit (Zymo Research). DNA was added to Zymo M-Dilution buffer and incubated for 15 min at 37°C. CT-conversion reagent was then added and the mixture was denatured by heating to 95°C for 30 s followed by incubation for 1 h at 50°C.  This denature/incubation cycle was repeated for a total of 16 h. After bisulfite conversion, the DNA was bound to a Zymo spin column and desulfonated on the column using desulfonation reagent per manufacturer’s protocol. The bisulfite-converted DNA was eluted from the column in 10 µl of elution buffer. Infinium Methylation Assay: 4 µl of bisulfite converted product was transferred to a new plate with an equal amount of 0.1N NaOH and 20 ul of MA1 reagent (Illumina) then allowed to incubate at RT for 10 min.  Immediately following incubation, 68 ul of MA2 reagent and 75 ul of MSM reagent (both Illumina) were added and the plate was incubated at 37°C overnight for amplification. After amplification, the DNA was fragmented enzymatically, precipitated and resuspended in RA1 hybridization buffer.

value: Liver


title: Adenoma_15


title: Adenoma_13


title: Normal_colon_adjacent to carcinoma_05 [methylation]

source_name: Normal colon adjacent to  carcinoma

value: Normal colon adjacent to  carcinoma

value: Colon


title: Adenoma_12


title: Normal_liver_09 [methylation]

value: Normal liver adjacent to liver metastasis


title: Adenoma_11


title: Normal_colon_adjacent to carcinoma_06 [methylation]


title: Carcinoma_06


title: Normal_colon_adjacent to carcinoma_04 [methylation]


title: Carcinoma_07


title: Adenoma_09


title: Adenoma_06


title: Adenoma_08


title: Adenoma_05


title: Normal_colon_adjacent to adenoma_05 [methylation]

source_name: Normal colon adjacent to  adenoma

value: Normal colon adjacent to  adenoma


title: Normal_colon_adjacent to adenoma_08 [methylation]


title: Normal_liver_05 [methylation]


title: Normal_colon_adjacent to carcinoma_02 [methylation]


title: Adenoma_04


title: Normal_colon_adjacent to adenoma_06 [methylation]


title: Adenoma_10


title: Normal_colon_adjacent to adenoma_09 [methylation]


title: Normal_colon_adjacent to adenoma_12 [methylation]


title: Metastasis_06 [methylation]

value: Metastasis


title: Adenoma_02


title: Normal_colon_adjacent to adenoma_14 [methylation]


title: TS_Th17_rep2

city: Saint Louis

first: Eugene

middle: M

last: Oltz

state: Missouri

address: 660 Euclid Ave, Campus Box 8118

department: Pathology & Immumonolgy

description: Gene expression data

hyb_protocol: Products were hybridized to Affymetrix Human Gene 1.0 ST arrays according to the manufacturer’s protocol

data_processing: Gene expression levels were determined using the Affymetrix Expression Console software (v1.2.0.20) with gene-level RMA analysis and default settings

source_name: Tonsils

label_protocol: Purified RNA was amplified using Nugen Ovation Pico SL or Ovation Pico kits and labeled using Nugen Encore Biotin kit.

extract_protocol: RNA was purified using Qiagen RNeasy Kits according to the manufacturer’s protocol.

tag: markers


title: Metastasis_10 [methylation]


title: TS_Th17_rep1

description: Gene expression data


title: Adenoma_01


title: Normal_colon_adjacent to adenoma_03 [methylation]


title: Adenoma_03


title: Metastasis_08 [methylation]


title: TS_Th1_rep2

description: Gene expression data


title: TS_Th1_rep1

description: Gene expression data


title: Carcinoma_18 [methylation]

value: Carcinoma


title: Metastasis_09 [methylation]


title: ILC3_rep4

description: Gene expression data


title: Carcinoma_08 [methylation]


title: Carcinoma_15 [methylation]

value: Colon Transverse


title: Metastasis_01 [methylation]


title: Metastasis_03 [methylation]


title: Metastasis_04 [methylation]


title: Metastasis_02 [methylation]


title: ILC3_rep3

description: Gene expression data


title: Carcinoma_17 [methylation]

value: Rectum


title: Carcinoma_14 [methylation]

value: Colon Sigmoid


title: Carcinoma_13 [methylation]

value: Male


title: ILC3_rep1

description: Gene expression data


title: ILC1_rep4

description: Gene expression data


title: ILC1_rep3

description: Gene expression data


title: ILC1_rep2

description: Gene expression data


title: ILC3_rep5

description: Gene expression data


title: Metastasis_05 [methylation]


title: Carcinoma_06 [methylation]


title: Carcinoma_04 [methylation]

value: Cecum


title: ILC1_rep1

description: Gene expression data


title: Carcinoma_07 [methylation]


title: Adenoma_13 [methylation]


title: FFPE_liver_18hr_PMI

city: Kasugai

first: Masatoshi

last: Ichihara

state: Aichi

address: 1200 Matsumoto-cho

institute: Chubu University

hyb_protocol: The biotin-labeled aRNAs from FF tissues and fragmented DNA from FFPE tissues were hybridized with the array strips at 45°C for 16 h. After hybridization, the strips were washed and stained in the GeneAtlas Fluidics Station using the GeneAtlas Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: The intensity of each hybridized probe was measured using the GeneAtlas Imaging Station.

data_processing: The obtained CEL files were normalized and summarized using the robust multiarray average (RMA) method with Expression Console software (Affymetrix).

source_name: FFPE mouse liver at 18hr in the postmortem interval

label_protocol: Comparative analysis of gene expression profiles was performed using the MG-430 PM Array Strips and the Affymetrix GeneAtlas microarray system (Affymetrix, Santa Clara, CA, USA), according to the manufacturer's instructions. For RNA samples from FF tissues, the corresponding amplified and biotin-labeled antisense RNA (aRNA) was synthesized using a GeneChip 3'IVT Express kit (Affymetrix). The resulting aRNA was fragmented as described by the manufacturer. On the other hand, for RNA samples from FFPE tissues, the corresponding amplified and biotin-labeled DNA fragments were generated using the WT-Ovation FFPE RNA Amplification System V2 (NuGEN, San Carlos, CA, USA) followed by the Encore Biotin Module (NuGEN) according to the manufacturers’ protocols.

extract_protocol: Excised livers and brains were first immersed in RNAlater (Ambion, Austin, TX, USA) and cryopreserved (FF samples). Total RNA was isolated with the RNeasy Mini Kit (Qiagen, Hilden, Germany) from these FF samples. In addition to FF samples, we fixed excised livers and brains with 10% formalin for 24 h and then embedded in paraffin (FFPE samples). FFPE samples were stored at room temperature for 7 d and were then cut into 10-μm wide slices, followed by extraction of RNA using RNeasy FFPE Kit (Qiagen).

value: male

tag: age

value: 10 weeks

tag: strain

value: BALB/c

tag: tissue

value: liver

tag: preservation

value: FFPE


title: BJELM_replicate_2

description: Gene expression data from transformed fibroblast cells

hyb_protocol: Following fragmentation and end-labeling, 1.9 μg of cDNAs were hybridized for 16 hours at 45 C on GeneChip® Human Gene 1.0 ST arrays (Affymetrix). The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix)

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing:
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0.
CEL files were further processed with Affymetrix Expression Console software version 1.3.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

source_name: Transformed BJELM fibroblast cells (cancer cells)

label_protocol: Biotinylated single strand cDNA targets were prepared, starting from 150 ng of total RNA, using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

extract_protocol: Total RNA was extracted from cells using the GENEEluteTM RNA extraction kit (Sigma)

value: BJELM

value: foreskin fibroblast cells


title: FFPE_liver_3hr_PMI

source_name: FFPE mouse liver at 3hr in the postmortem interval


title: BJELM_replicate_1


title: FFPE_liver_0hr_PMI

source_name: FFPE mouse liver at 0hr in the postmortem interval


title: Carcinoma_02 [methylation]


title: FFPE_brain_0hr_PMI

source_name: FFPE mouse brain at 0hr in the postmortem interval

value: brain


title: FFPE_brain_18hr_PMI

source_name: FFPE mouse brain at 18hr in the postmortem interval


title: FF_liver_18hr_PMI

source_name: FF mouse liver at 18hr in the postmortem interval

value: FF


title: ILC3_rep2

description: Gene expression data


title: FFPE_brain_3hr_PMI

source_name: FFPE mouse brain at 3hr in the postmortem interval


title: BJ_replicate_1

description: Gene expression data from normal fibroblast cells

source_name: Primary human BJ foreskin fibroblasts (normal cells)

value: BJ


title: BJ_replicate_2


title: Adenoma_09 [methylation]

value: Adenoma


title: FF_brain_18hr_PMI

source_name: FF mouse brain at 18hr in the postmortem interval


title: Adenoma_20 [methylation]

value: Female


title: Carcinoma_03 [methylation]

value: Carcinoma

value: Colon


title: FF_brain_3hr_PMI

source_name: FF mouse brain at 3hr in the postmortem interval


title: Adenoma_14 [methylation]


title: Adenoma_06 [methylation]


title: FF_liver_0hr_PMI

source_name: FF mouse liver at 0hr in the postmortem interval


title: Carcinoma_09 [methylation]

source_name: Carcinoma


title: FF_brain_0hr_PMI

source_name: FF mouse brain at 0hr in the postmortem interval


title: Adenoma_08 [methylation]

source_name: Adenoma


title: Adenoma_02 [methylation]


title: prostate_cancer_primary_353 (GBX.PCA353)

status: Public on May 12 2016

city: Vancouver

first: Elai

last: Davicioni

state: BC

address: 1152 Mainland St #430

country: Canada

institute: GenomeDx

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data was normalized using SCAN (SCAN.UPC package from Bioconductor)

source_name: FFPE prostate cancer

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer’s recommendations with minor modifications

growth_protocol: Not Applicable

extract_protocol: After histopathologic review of formalin-fixed, paraffin-embedded (FFPE) tumor blocks from each case by 2 expert genitourinary pathologists, the tumor block with the index lesion was selected for specimen processing. The index lesion was identified as the prostatectomy FFPE block with the highest pathologic Gleason grade, regardless of its volume. Two [x] 0.6-mm diameter tissue biopsy punch tool cores were sampled to enrich for tumor cells from the highest Gleason grade in the index lesion and placed in a microfuge tube for RNA extraction.

treatment_protocol: Not Applicable

tag: pathologic gleason score

tag: pathologic stage

tag: preoperative psa

value: prostate cancer


title: prostate_cancer_primary_351 (GBX.PCA351)


title: Adenoma_16 [methylation]


title: Adenoma_12 [methylation]

value: Male


title: prostate_cancer_primary_345 (GBX.PCA345)


title: RAW264.7 cells transfected with a ABHD5 shRNA (ABHD5-KD) D3

city: Chongqing

first: Hongming

last: Miao

state: Chongqing

address: Gaotanyan Street NO.30

department: Department of Biochemistry and Molecular Biology

institute: Third Military Medical University (Army Medical University)

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

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: RAW264.7 cells

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

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

treatment_protocol: The control and ABHD5-silenced Raw264.7 macrophages were subjected to gene expression microarray analysis.

tag: cell line

tag: transfection

value: ABHD5 shRNA (ABHD5-KD)


title: RAW264.7 cells transfected with PLKO C3

value: PLKO


title: Gene expression after 24hr-coculture with CT-26 cells E2

source_name: peritoneal macropahges

treatment_protocol: Murine peritoneal macrophages were treated with regular culture medium (Ctrl) or co-cultured with CRC cells CT-26 (Tumor) for 24 h.

value: peritoneal macropahges

tag: gender

value: male

tag: treatment


title: Adenoma_03 [methylation]


title: RAW264.7 cells transfected with a ABHD5 shRNA (ABHD5-KD) D1


title: Gene expression after 24hr in regular medium A3

value: control


title: RAW264.7 cells transfected with a ABHD5 shRNA (ABHD5-KD) D2


title: prostate_cancer_primary_340 (GBX.PCA340)


title: prostate_cancer_primary_341 (GBX.PCA341)


title: Gene expression after 24hr in regular medium A1


title: prostate_cancer_primary_342 (GBX.PCA342)


title: RAW264.7 cells transfected with PLKO C1


title: Gene expression after 24hr-coculture with CT-26 cells E1

value: co-cultured with CRC cells CT-26 (Tumor)


title: RAW264.7 cells transfected with PLKO C2


title: Gene expression after 24hr-coculture with CT-26 cells E3


title: Carcinoma_05 [methylation]


title: prostate_cancer_primary_335 (GBX.PCA335)


title: prostate_cancer_primary_329 (GBX.PCA329)


title: prostate_cancer_primary_328 (GBX.PCA328)


title: prostate_cancer_primary_325 (GBX.PCA325)


title: prostate_cancer_primary_322 (GBX.PCA322)


title: prostate_cancer_primary_318 (GBX.PCA318)


title: prostate_cancer_primary_316 (GBX.PCA316)


title: prostate_cancer_primary_308 (GBX.PCA308)


title: BJEL_replicate_1

description: Gene expression data from pretransformed fibroblast cells

source_name: Immortalized BJEL fibroblast cells (pretransformed)

value: BJEL

tag: cell type


title: prostate_cancer_primary_315 (GBX.PCA315)


title: Gene expression after 24hr in regular medium A2


title: prostate_cancer_primary_298 (GBX.PCA298)


title: Adenoma_01 [methylation]

tag: tissue type


title: prostate_cancer_primary_284 (GBX.PCA284)


title: prostate_cancer_primary_278 (GBX.PCA278)


title: prostate_cancer_primary_293 (GBX.PCA293)


title: prostate_cancer_primary_262 (GBX.PCA262)


title: prostate_cancer_primary_267 (GBX.PCA267)


title: prostate_cancer_primary_266 (GBX.PCA266)


title: prostate_cancer_primary_260 (GBX.PCA260)


title: prostate_cancer_primary_257 (GBX.PCA257)


title: prostate_cancer_primary_256 (GBX.PCA256)


title: prostate_cancer_primary_288 (GBX.PCA288)


title: prostate_cancer_primary_258 (GBX.PCA258)


title: prostate_cancer_primary_248 (GBX.PCA248)


title: prostate_cancer_primary_259 (GBX.PCA259)


title: prostate_cancer_primary_236 (GBX.PCA236)


title: prostate_cancer_primary_237 (GBX.PCA237)


title: prostate_cancer_primary_232 (GBX.PCA232)


title: prostate_cancer_primary_229 (GBX.PCA229)


title: prostate_cancer_primary_228 (GBX.PCA228)


title: prostate_cancer_primary_220 (GBX.PCA220)


title: prostate_cancer_primary_214 (GBX.PCA214)


title: Adenoma_05 [methylation]

tag: tumor stage


title: prostate_cancer_primary_218 (GBX.PCA218)


title: prostate_cancer_primary_209 (GBX.PCA209)


title: prostate_cancer_primary_213 (GBX.PCA213)


title: prostate_cancer_primary_208 (GBX.PCA208)


title: prostate_cancer_primary_205 (GBX.PCA205)


title: prostate_cancer_primary_246 (GBX.PCA246)


title: prostate_cancer_primary_178 (GBX.PCA178)


title: prostate_cancer_primary_174 (GBX.PCA174)


title: prostate_cancer_primary_182 (GBX.PCA182)


title: prostate_cancer_primary_191 (GBX.PCA191)


title: prostate_cancer_primary_167 (GBX.PCA167)


title: prostate_cancer_primary_164 (GBX.PCA164)


title: prostate_cancer_primary_158 (GBX.PCA158)


title: prostate_cancer_primary_156 (GBX.PCA156)


title: prostate_cancer_primary_155 (GBX.PCA155)


title: prostate_cancer_primary_150 (GBX.PCA150)


title: prostate_cancer_primary_157 (GBX.PCA157)


title: prostate_cancer_primary_224 (GBX.PCA224)


title: prostate_cancer_primary_149 (GBX.PCA149)


title: prostate_cancer_primary_142 (GBX.PCA142)


title: prostate_cancer_primary_153 (GBX.PCA153)


title: prostate_cancer_primary_219 (GBX.PCA219)


title: prostate_cancer_primary_130 (GBX.PCA130)


title: BJEL_replicate_2

value: foreskin fibroblast cells


title: prostate_cancer_primary_106 (GBX.PCA106)


title: prostate_cancer_primary_119 (GBX.PCA119)


title: prostate_cancer_primary_192 (GBX.PCA192)


title: prostate_cancer_primary_103 (GBX.PCA103)


title: prostate_cancer_primary_101 (GBX.PCA101)


title: prostate_cancer_primary_102 (GBX.PCA102)


title: prostate_cancer_primary_133 (GBX.PCA133)


title: prostate_cancer_primary_93 (GBX.PCA93)


title: prostate_cancer_primary_143 (GBX.PCA143)


title: prostate_cancer_primary_80 (GBX.PCA80)


title: prostate_cancer_primary_90 (GBX.PCA90)


title: prostate_cancer_primary_124 (GBX.PCA124)


title: prostate_cancer_primary_83 (GBX.PCA83)


title: prostate_cancer_primary_77 (GBX.PCA77)


title: prostate_cancer_primary_75 (GBX.PCA75)


title: Bxpc-3_5-HT treated_24 hr_rep1

city: Shanghai

first: Shuheng

last: Jiang

address: #800, Dongchuan Road

institute: Shanghai Cancer Institute

description: Gene expression data from 5-HT treated Bxpc-3 pancreatic cancer cell lines

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 on the Agilent Scanner G2505C using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5μm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Expression signals were calculated using the Agilent Feature Extraction software (version 10.7.3.1 Agilent Technologies, Santa Clara, CA).

source_name: Bxpc-3 Pancreatic Cancer Cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, 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: Bxpc-3 cells were maintained in RPMI-1640 medium with 2 mM glutamine, 5 mM glucose supplemented with 1%  penicillin, and streptomycin and tested for mycoplasma contamination.

extract_protocol: Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity 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: Cells were serum-starved for 24 hr and then stimulated with 10 μM 5-HT (Sigma) for another 24 hr.

value: Bxpc-3 treatment group, 5-HT treated 24 hr


title: prostate_cancer_primary_98 (GBX.PCA98)


title: Bxpc-3_5-HT treated_24 hr_rep2


title: prostate_cancer_primary_73 (GBX.PCA73)


title: Bxpc-3_untreated control_24 hr_rep1

description: Gene expression data from  untreated Bxpc-3 pancreatic cancer cell lines

value: Bxpc-3 treatment group, untreated control


title: prostate_cancer_primary_97 (GBX.PCA97)


title: prostate_cancer_primary_74 (GBX.PCA74)