title: Cultured fibroblasts from orangutan KB10460

description: Gene expression data of orangutan fibroblasts

source_name: dermal fibroblast from Sumatran orangutan KB10460

value: dermal fibroblasts


title: Cultured fibroblasts from orangutan KB10973

status: Public on Jun 10 2015

type: RNA

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

country: USA

institute: University of Southern California

hyb_protocol: followed affymetrix protocol

scan_protocol: followed affymetrix protocol

data_processing: WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

label: biotin

molecule: total RNA

organism: Pongo abelii

source_name: dermal fibroblast from Sumatran orangutan KB10973

label_protocol: followed affymetrix protocol

growth_protocol: Fibroblasts were maintained in Dulbecco’s modified eagle medium (DMEM) containing 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 µM nonessential amino acids and 0.5% penicillin and streptomycin. iPSCs were cultured in 1:1 ratio of DMEM:F12 medium supplemented with 20% KSR at 37°C, 5% CO2.

extract_protocol: RNA was isolated  using the RNA Stat-60 reagent according to the manusfacturer's suggested protocol (Tel-Test, Inc.).

treatment_protocol: Fibroblasts were dissociated with 0.05% trypsin at 37°C, 5% CO2 for 5minutes and collected by centrifugation; iPSCs were dissociated with 1mg/ml collagenase IV at 37°C, 5% CO2 for 5 minutes, manually detached and collected by centrifugation

tag: tissue

tag: genotype

value: healthy control

tag: age

value: 29 year old

tag: Sex

value: male


title: CAL51-MCF7_SNP6

status: Public on Jun 09 2015

type: genomic

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
Genotypes were derived from the CEL files using custom Reference Supported Genotyper software after calibration with 270 Hapmap samples and allowable genotyping distance of 1.5 standard deviations from the mean of the allele cluster.
CEL files were processed using custom RSG genotyper with 270 HapMap samples as reference. Further analysis was performed using scripts described in [Maruyama et al] primary data description: Genotype Call (SNP call): AA, AB, BB, and NoCall; 'Confidence' = Confidence call from RSG algorithm. Values left blank represent NA, not available.
Customized algorithm used to generate the data. We processed three SNP data (three CEL files: luminal parent, basal parent and their heterofusion) at the same time to generate ONE processed data (TableS4-SNP-updated_121114.xlsx).

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: breast cancer cell line heterofusion CAL51-MCF7

label_protocol: Affymetrix standard procedure

extract_protocol: Genomic DNA was extracted from breast cancer cell lines and the fusion cell lines with a standard method using proteinase K digestion, phenol-chloroform extraction and ethanol precipitation. The DNA was subjected to genotyping.

tag: cell line

value: heterofusion CAL51-MCF7


title: SUM159-MDA453_SNP6

source_name: breast cancer cell line heterofusion SUM159PT-MDA-MB-453

value: heterofusion SUM159PT-MDA-MB-453


title: SUM159-ZR75_SNP6

source_name: breast cancer cell line heterofusion SUM159PT-ZR75-1

value: heterofusion SUM159PT-ZR75-1


title: spleen_Cip2a_rep2

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description:
SAMPLE 6
replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalized using cubic spline normalization with Illumina Genomestudio 2011.1

organism: Mus musculus

source_name: spleen

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

tag: strain

value: C57BL/6Jx 129Ola

tag: genotype/variation

value: mutant

value: 18 weeks

tag: gender

tag: mouse id


title: ZR75_SNP6

source_name: breast cancer cell line ZR75-1


title: MDAMB453_SNP6

source_name: breast cancer cell line MDA-MB-453


title: SUM159-21NT_SNP6

source_name: breast cancer cell line heterofusion SUM159PT-21NT

value: heterofusion SUM159PT-21NT


title: 21NT_SNP6

source_name: breast cancer cell line 21NT


title: CAL51_SNP6

source_name: breast cancer cell line CAL51


title: spleen_wt_rep2

description:
SAMPLE 2
replicate 2

value: wild type


title: CSES22p16_T12_Teratoma

city: Jerusalem

first: Yishai

last: Avior

state: Israel

address: Edmond J. Safra Campus, Givat Ram

department: Genetics

country: Israel

institute: Hebrew University of Jeursalem

hyb_protocol: Affymetrix protocol, 11ug cRNA

scan_protocol: GeneChip scanner 3000 7G, GeneChip Operating Software v1.4

data_processing: Affymetrix Expression Console RMA

source_name: Teratroma from aneuploid hESC (trisomy 12)

label_protocol: 200ng total RNA, Affymetrix protocol

extract_protocol: According to the manufacture instruction. RNA was subjected to Human Genome U133 Plus 2.0 microarray platform (Affymetrix); washing and scanning were performed according to the manufacturer’s protocol


title: Os_root_WT_treatment N+, biological rep 1

city: Capital Federal

first: Mariana

last: Obertello

address: Vuelta de Obligado 2490

department: Department of Biology

country: Argentina

institute: INGEBI-CONICET

hyb_protocol: We used 15 µg of labeled cRNA to hybridize the Arabidopsis ATH1 Affymetrix and Rice Affymetrix gene chip for 16 h at 42°C. Washing, staining and scanning were performed as recommended by Affymetrix.

scan_protocol: Scanning were performed as recommended by Affymetrix.

data_processing: All microarray data was processed with Robust Microarray Analysis (RMA) normalization and summarization were done using the R Bioconductor package.

organism: Oryza sativa

label_protocol: Biotin-labeled cRNA was synthesized using the Enzo BioArray HighYield RNA Transcript Labeling Kit (Enzo, New York, NY).

growth_protocol: Seeds were surface-sterilized in 70% ethanol for 3 minutes followed by commercial H2O2 for 30 minutes with gently agitation, and washed with distilled water. Seeds were sown onto basal MS salts (custom-made; GIBCO) with 0.5 mM ammonium succinate and 3 mM sucrose, 0.8% BactoAgar at pH 5.5 for 3 days in dark conditions at 27°C. Following germination, embryos with developed root system and aerial tissue were dissected from the rest of the seed using a sterile blade and transferred to a hydroponic system (Phytatray II, Sigma Aldrich) containing basal MS salts (custom-made; GIBCO) with 0.5 mM ammonium succinate and 3 mM sucrose at pH 5.5 at light intensity of 180 μE.s-1.m-2 and at 27°C.  Fresh media was exchanged every 3 days. Arabidopsis seeds were placed for 2 days in the dark at 4°C to synchronize germination. Seeds were surface-sterilized and then transferred to a hydroponic system (Phytatray I, Sigma Aldrich) containing the same media previously described for rice (pH 5.7). Growth conditions were the same as in rice, except that plants were under 50 μE.s-1.m-2 light intensity at 22°C.

extract_protocol: RNA was isolated from whole plants using Trizol reagent according to the intructions of the manufacturer (15596; Invitrogen).

treatment_protocol: On day 13,  plants were transiently treated for 2 h at the start of their light cycle by adding N at a final concentration of 20 mM KNO3 and 20 mM NH4NO3. Control plants were treated with KCl at a final concentration of 20 mM. After treatment, whole seedlings were harvest and immediately frozen in liquid nitrogen.

value: 13 days

value: root

tag: treated with

value: 20 mM KNO3 and 20 mM NH4NO3 (final conc) for 2hr


title: spleen_wt_rep3

description:
SAMPLE 3
replicate 3


title: spleen_wt_rep1

description:
SAMPLE 1
replicate 1


title: Knockdown MAF1

city: Taipei

first: Ming-Ta

last: Hsu

address: No.155, Sec.2, Linong Street

country: Taiwan

institute: National Yang Ming University

hyb_protocol: Affymetrix Eukaryotic Target Hybridization

scan_protocol: Affymetrix  GeneChip  Scanner 3000

data_processing: GeneChip  Operating Software (GCOS). The absolute results (*.chp) from different experiments (probe arrays of the same type) that are scaled to the same target signal using the All Probe Sets scaling portion may be directly compared. parameter: Alpha1=0.05, Alpha2=0.065, Tau=0.015

source_name: MCF-7 cell line

label_protocol: Biotin-labeled cRNA. One-Cycle Target Labeling &IVT Amplification of cRNA with T7 RNA Polymerase.

growth_protocol: MCF-7 cell lines were originally obtained from ATCC (Manassas, VA). MCF-7 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, and incubated in a humidified 37 oC incubator with 5% CO2.

extract_protocol: Cells were grown to 85 % confluence in 6 cm tissue culture dish. Each 6 cm dish was washed with 1 X PBS for three times. Total RNA was extracted using TRIreagent (Invitrogen) protocol. The integrity of the RNA extract was checked by 1.2 % (w/v) agarose gel electrophoresis and the concentration of RNA was estimated by ultraviolet spectrophotometry.

treatment_protocol: Knockdown assay was performed using siRNA obtained from MISSION®RNA (Sigma). Inhibition of expression of Pol III (SASI_Hs01_00046568) and MAF1 (SASI_Hs01_00135954) was achieved by transfection with LipofectamineTM RNAiMax (Invitrogen) according to the manufacturer’s protocol. MISSION® siRNA Universal Negative Control (Sigma) was used as knockdown control. Cells were transfected in serum-free medium. After 8 h, the siRNA containing medium was replaced with complete medium.

tag: treatment

value: knockdown with 50 nM of MAF1 (SASI_Hs01_00135954, Sigma)


title: CSES45p30_T12_Teratoma


title: Os_shoot_WT_treatment N-, biological rep 2

value: shoot

value: 20mM KCl (final conc.) for 2hr


title: spleen_Cip2a_rep1

description:
SAMPLE 5
replicate 1


title: CSES12_WT_Teratoma

source_name: Teratroma from diploid hESC


title: Os_root_WT_treatment N-, biological rep 1


title: Knockdown POLR3A

value: knockdown with 50 nM of POLR3A (SASI_Hs01_00046568, Sigma)


title: spleen_wt_rep4

description:
SAMPLE 4
replicate 4


title: Knockdown Control

value: knockdown with 50 nM of universal negative control (Sigma)


title: Os_root_WT_treatment N-, biological rep 2


title: Os_shoot_WT_treatment N-, biological rep 1


title: Os_root_WT_treatment N+, biological rep 2


title: fresh PBMC 3

city: Würzburg

first: Claus

middle: Juergen

last: Scholz

address: Josef-Schneider-Str. 2

department: Core Unit SysMed

institute: University Hospital Würzburg

description: Donor 3, CD8+ memory T-cells from fresh PBMC.

hyb_protocol: 130µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C and 60 rpm to GeneChip PrimeView arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0002.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data were preprocessed in the R v3.1.2 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

source_name: PBMC from a healthy donor

label_protocol: Total RNAs were subjected to three amplification rounds using the C&E TRinucleotide Nano Kit (AmpTec, Hamburg, Germany); RNA labeling was performed with the IVT PLUS kit (Affymetrix).

growth_protocol: Human PBMC were in-vitro cultured at a high cell density (10^7 cells/mL) at 37C and 5% CO2 for 2 days.

extract_protocol: Total RNA was extracted from isolated CD8+CD45R0+ T-cells from either fresh or precultured PBMC using TRIzol (Life Technologies).

treatment_protocol: CD8+CD45R0+ T-cells were isolated from fresh PBMC and high cell density cultured PBMC using a FACSAria III (BD Biosciences) cell sorter.

tag: donor

value: Donor 3

tag: cell type

value: CD8+ memory T-cells

tag: cell density

value: fresh PBMC


title: 293T_shERRalpha_0h

city: beijing

first: Xiang

last: He

address: taiping road

country: China

institute: Beijing Institute of Biotechnology

description: Gene expression in 293T with ERRalpha knockdown at 0h

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: 293T with ERRalpha knockdown at 0h

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

growth_protocol: The cells grew at 37 ºC in a humidified incubator with 5% CO2.

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

treatment_protocol: The cells were cultured with DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.


title: precultured PBMC 2

description: Donor 2, CD8+ memory T-cells from high density cultured PBMC.

value: Donor 2

value: high density cultured


title: precultured PBMC 3

description: Donor 3, CD8+ memory T-cells from high density cultured PBMC.


title: precultured PBMC 1

description: Donor 1, CD8+ memory T-cells from high density cultured PBMC.

value: Donor 1


title: fresh PBMC 1

description: Donor 1, CD8+ memory T-cells from fresh PBMC.


title: 5-Fluoro-uracil_1

description: HT29 xenograft with 5-Fluoro-uracil treatment, biological replicate 1

data_processing: Data were preprocessed in the R v3.0.1 environment with Bioconductor packages affy and vsn; VSN normalization and RMA probeset summary were performed with the vsnrma command using default parameter settings.

source_name: ATCC

label_protocol: 100ng of total RNA were amplified and labeled with the IVT Express Kit (Affymetrix); all steps were performed according to the manufacturers' protocols.

growth_protocol: Tumor cells from HT29 cell line were subcutaneously injected in NOD/SCID mice, and tumors grew for 14 days.

extract_protocol: RNA was extracted according to manufactures' guidelines for QiaCube device (Qiagen).

treatment_protocol: Mice were treated for 3 days and sacrificed 24h after treatments end.

value: Colon adenocarcinoma

tag: sample type

value: HT29 xenograft


title: Control_2

description: HT29 xenograft with vehicle treatment, biological replicate 2

value: vehicle


title: Control_1

description: HT29 xenograft with vehicle treatment, biological replicate 1


title: Fluoxetine_3

description: HT29 xenograft with Fluoxetine treatment, biological replicate 3

value: Fluoxetine


title: fresh PBMC 2

description: Donor 2, CD8+ memory T-cells from fresh PBMC.


title: 293T_shERRalpha_12h

description: Gene expression in 293T with ERRalpha knockdown at 12h

source_name: 293T with ERRalpha knockdown at 12h


title: 293T_shControl_0h

description: Gene expression in 293T with Control knockdown at 0h

source_name: 293T with Control knockdown at 0h


title: 5-Fluoro-uracil_2

description: HT29 xenograft with 5-Fluoro-uracil treatment, biological replicate 2


title: 5-Fluoro-uracil_3

description: HT29 xenograft with 5-Fluoro-uracil treatment, biological replicate 3


title: 293T_shControl_12h

description: Gene expression in 293T with Control knockdown at 12h

source_name: 293T with Control knockdown at 12h


title: Control_3

description: HT29 xenograft with vehicle treatment, biological replicate 3


title: Fluoxetine_2

description: HT29 xenograft with Fluoxetine treatment, biological replicate 2


title: Fluoxetine_1

description: HT29 xenograft with Fluoxetine treatment, biological replicate 1


title: HK-2 cell control, biological rep2

city: Suwon

first: Sangdun

last: Choi

address: Woncheon-dong, Yeongtong-gu

department: Department of Molecular Science and Technology

country: South Korea

institute: Ajou University

hyb_protocol: 7.5µg fragmented and labeled RNA were hybridized for 16h at 45℃ on Human Genome U219 Array Strip. Array Strip was washed and stained in the GeneAtlasTM fluidics station.

scan_protocol: Array Strips were scanned in the GeneAtlasTM imaging station.

data_processing: The data were normalized using the robust multi-array average analysis via the Affymetrix Expression Console software (ver. 1.1)

source_name: HK-2 cells, non treated

label_protocol: 10ng of total RNA was labeled using a GeneAtlasTM 3'IVT Express Kit Assay (Affymetrix) according to the manufacturer's instructions.

growth_protocol: HK-2 cells were grown in keratinocyte-serum-free medium supplemented with L-glutamine, epidermal growth factor, and bovine pituitary extract and maintained at 37°C under 5% CO2.

extract_protocol: Total RNA was extracted using an RNeasy mini kit (QIAGEN) and it was performed according to the manufacturer's instructions.

treatment_protocol: HK-2 cells were treated with cisplatin (50μM) for 6h or 24h

value: renal proximal tubule cells

value: control


title: 6h after cisplatin treatment, biological rep2

source_name: HK-2 cells treated by cisplatin for 6h

value: cisplatin for 6h


title: 24h after cisplatin treatment, biological rep1

source_name: HK-2 cells treated by cisplatin for 24h

value: cisplatin for 24h


title: 6h after cisplatin treatment, biological rep1


title: 24h after cisplatin treatment, biological rep2


title: HK-2 cell control, biological rep1


title: SUM159-MCF7_SNP6

data_processing:
Genotypes were derived from the CEL files using custom Reference Supported Genotyper software after calibration with 270 Hapmap samples and allowable genotyping distance of 1.5 standard deviations from the mean of the allele cluster.
CEL files were processed using custom RSG genotyper with 270 HapMap samples as reference. Further analysis was performed using scripts described in [Maruyama et al] primary data description: Genotype Call (SNP call): AA, AB, BB, and NoCall; 'Confidence' = Confidence call from RSG algorithm.  Values left blank represent NA, not available.
Customized algorithm used to generate the data. We processed three SNP data (three CEL files: luminal parent, basal parent and their heterofusion) at the same time to generate ONE processed data (TableS4-SNP-updated_121114.xlsx).

source_name: breast cancer cell line heterofusion SUM159PT_MCF7

value: heterofusion SUM159PT_MCF7


title: mcf7puro_SNP6

source_name: breast cancer cell line MCF7


title: SUM159PN627_SNP6

source_name: breast cancer cell line SUM159PT


title: SUM159-474_SNP6

source_name: breast cancer cell line heterofusion SUM159PT_BT-474

value: heterofusion SUM159PT_BT-474


title: genomic DNA from blood sample 81

first: Steve

last: Horvath

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description:
genomic DNA from blood sample 81
Human blood from EDTA blood tube
Sample81

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

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

data_processing: BeadStudio software v3.2. The unmethylated and methylated signal intensities can be found in the file datSignal_blood.csv available on the series record.  Data were processed as follows: Background corrected, average beta values (no special processing)

label: cy3 and cy5

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from whole blood. Qiagen DNeasy Kit according to standard instructions.

value: blood

tag: hivstatus

value: Positive

value: male

tag: dnamage

tag: ageaccelerationvscontrols

tag: ageaccelerationresidual

tag: exhausted cd8t cells

tag: naïve cd8 t cells

tag: naïve cd4 t cells

tag: cd8 t cells

tag: cd4 t cells

tag: natural killer

tag: b cells

tag: monocytes

tag: granulocytes


title: MDA231-MCF783_SNP6

source_name: breast cancer cell line heterofusion MDA-MB-231_MCF7

tag: cell line

value: heterofusion MDA-MB-231_MCF7


title: T47Dpuro_SNP6

source_name: breast cancer cell line T-47D


title: genomic DNA from blood sample 89

description:
genomic DNA from blood sample 89
Human blood from EDTA blood tube
Sample89

tag: tissue

tag: age

tag: gender


title: genomic DNA from blood sample 83

description:
genomic DNA from blood sample 83
Human blood from EDTA blood tube
Sample83

tag: hivstatus


title: genomic DNA from blood sample 76

description:
genomic DNA from blood sample 76
Human blood from EDTA blood tube
Sample76

value: Negative

tag: dnamage


title: MCF7PN_SNP6


title: genomic DNA from blood sample 91

description:
genomic DNA from blood sample 91
Human blood from EDTA blood tube
Sample91

value: female

tag: ageaccelerationvscontrols


title: genomic DNA from blood sample 92

description:
genomic DNA from blood sample 92
Human blood from EDTA blood tube
Sample92

tag: ageaccelerationresidual


title: genomic DNA from blood sample 87

description:
genomic DNA from blood sample 87
Human blood from EDTA blood tube
Sample87

tag: exhausted cd8t cells


title: genomic DNA from blood sample 85

description:
genomic DNA from blood sample 85
Human blood from EDTA blood tube
Sample85

tag: naïve cd8 t cells


title: genomic DNA from blood sample 88

description:
genomic DNA from blood sample 88
Human blood from EDTA blood tube
Sample88

tag: naïve cd4 t cells


title: MDA231neo_SNP6

source_name: breast cancer cell line MDA-MB-231


title: SUM159neo_SNP6


title: BT474_SNP6

source_name: breast cancer cell line BT-474


title: SUM159-T47D_SNP6

source_name: breast cancer cell line heterofusion SUM159PT_T-47D

value: heterofusion SUM159PT_T-47D


title: genomic DNA from blood sample 90

description:
genomic DNA from blood sample 90
Human blood from EDTA blood tube
Sample90

tag: cd8 t cells


title: genomic DNA from blood sample 86

description:
genomic DNA from blood sample 86
Human blood from EDTA blood tube
Sample86

tag: cd4 t cells


title: genomic DNA from blood sample 82

description:
genomic DNA from blood sample 82
Human blood from EDTA blood tube
Sample82

tag: natural killer


title: genomic DNA from blood sample 77

description:
genomic DNA from blood sample 77
Human blood from EDTA blood tube
Sample77

tag: b cells


title: genomic DNA from blood sample 80

description:
genomic DNA from blood sample 80
Human blood from EDTA blood tube
Sample80

tag: monocytes


title: genomic DNA from blood sample 78

description:
genomic DNA from blood sample 78
Human blood from EDTA blood tube
Sample78

tag: granulocytes


title: genomic DNA from blood sample 79

description:
genomic DNA from blood sample 79
Human blood from EDTA blood tube
Sample79


title: genomic DNA from blood sample 84

description:
genomic DNA from blood sample 84
Human blood from EDTA blood tube
Sample84


title: genomic DNA from blood sample 73

description:
genomic DNA from blood sample 73
Human blood from EDTA blood tube
Sample73


title: genomic DNA from blood sample 75

description:
genomic DNA from blood sample 75
Human blood from EDTA blood tube
Sample75


title: genomic DNA from blood sample 70

description:
genomic DNA from blood sample 70
Human blood from EDTA blood tube
Sample70


title: genomic DNA from blood sample 71

description:
genomic DNA from blood sample 71
Human blood from EDTA blood tube
Sample71


title: genomic DNA from blood sample 69

description:
genomic DNA from blood sample 69
Human blood from EDTA blood tube
Sample69


title: genomic DNA from blood sample 74

description:
genomic DNA from blood sample 74
Human blood from EDTA blood tube
Sample74


title: genomic DNA from blood sample 67

description:
genomic DNA from blood sample 67
Human blood from EDTA blood tube
Sample67


title: genomic DNA from blood sample 61

description:
genomic DNA from blood sample 61
Human blood from EDTA blood tube
Sample61


title: genomic DNA from blood sample 62

description:
genomic DNA from blood sample 62
Human blood from EDTA blood tube
Sample62


title: genomic DNA from blood sample 54

description:
genomic DNA from blood sample 54
Human blood from EDTA blood tube
Sample54


title: genomic DNA from blood sample 55

description:
genomic DNA from blood sample 55
Human blood from EDTA blood tube
Sample55


title: genomic DNA from blood sample 64

description:
genomic DNA from blood sample 64
Human blood from EDTA blood tube
Sample64


title: genomic DNA from blood sample 56

description:
genomic DNA from blood sample 56
Human blood from EDTA blood tube
Sample56


title: genomic DNA from blood sample 66

description:
genomic DNA from blood sample 66
Human blood from EDTA blood tube
Sample66


title: genomic DNA from blood sample 58

description:
genomic DNA from blood sample 58
Human blood from EDTA blood tube
Sample58


title: genomic DNA from blood sample 50

description:
genomic DNA from blood sample 50
Human blood from EDTA blood tube
Sample50


title: genomic DNA from blood sample 59

description:
genomic DNA from blood sample 59
Human blood from EDTA blood tube
Sample59


title: genomic DNA from blood sample 63

description:
genomic DNA from blood sample 63
Human blood from EDTA blood tube
Sample63


title: genomic DNA from blood sample 53

description:
genomic DNA from blood sample 53
Human blood from EDTA blood tube
Sample53


title: genomic DNA from blood sample 60

description:
genomic DNA from blood sample 60
Human blood from EDTA blood tube
Sample60


title: genomic DNA from blood sample 46

description:
genomic DNA from blood sample 46
Human blood from EDTA blood tube
Sample46


title: genomic DNA from blood sample 57

description:
genomic DNA from blood sample 57
Human blood from EDTA blood tube
Sample57


title: genomic DNA from blood sample 49

description:
genomic DNA from blood sample 49
Human blood from EDTA blood tube
Sample49


title: genomic DNA from blood sample 51

description:
genomic DNA from blood sample 51
Human blood from EDTA blood tube
Sample51


title: genomic DNA from blood sample 45

description:
genomic DNA from blood sample 45
Human blood from EDTA blood tube
Sample45


title: genomic DNA from blood sample 52

description:
genomic DNA from blood sample 52
Human blood from EDTA blood tube
Sample52


title: genomic DNA from blood sample 48

description:
genomic DNA from blood sample 48
Human blood from EDTA blood tube
Sample48


title: genomic DNA from blood sample 44

description:
genomic DNA from blood sample 44
Human blood from EDTA blood tube
Sample44


title: genomic DNA from blood sample 68

description:
genomic DNA from blood sample 68
Human blood from EDTA blood tube
Sample68


title: genomic DNA from blood sample 43

description:
genomic DNA from blood sample 43
Human blood from EDTA blood tube
Sample43


title: genomic DNA from blood sample 72

description:
genomic DNA from blood sample 72
Human blood from EDTA blood tube
Sample72


title: genomic DNA from blood sample 65

description:
genomic DNA from blood sample 65
Human blood from EDTA blood tube
Sample65


title: genomic DNA from blood sample 47

description:
genomic DNA from blood sample 47
Human blood from EDTA blood tube
Sample47


title: genomic DNA from blood sample 42

description:
genomic DNA from blood sample 42
Human blood from EDTA blood tube
Sample42


title: genomic DNA from blood sample 41

description:
genomic DNA from blood sample 41
Human blood from EDTA blood tube
Sample41


title: genomic DNA from blood sample 40

description:
genomic DNA from blood sample 40
Human blood from EDTA blood tube
Sample40


title: genomic DNA from blood sample 39

description:
genomic DNA from blood sample 39
Human blood from EDTA blood tube
Sample39


title: genomic DNA from blood sample 32

description:
genomic DNA from blood sample 32
Human blood from EDTA blood tube
Sample32


title: genomic DNA from blood sample 19

description:
genomic DNA from blood sample 19
Human blood from EDTA blood tube
Sample19


title: genomic DNA from blood sample 38

description:
genomic DNA from blood sample 38
Human blood from EDTA blood tube
Sample38


title: genomic DNA from blood sample 37

description:
genomic DNA from blood sample 37
Human blood from EDTA blood tube
Sample37


title: genomic DNA from blood sample 36

description:
genomic DNA from blood sample 36
Human blood from EDTA blood tube
Sample36


title: genomic DNA from blood sample 33

description:
genomic DNA from blood sample 33
Human blood from EDTA blood tube
Sample33


title: genomic DNA from blood sample 31

description:
genomic DNA from blood sample 31
Human blood from EDTA blood tube
Sample31


title: genomic DNA from blood sample 27

description:
genomic DNA from blood sample 27
Human blood from EDTA blood tube
Sample27


title: genomic DNA from blood sample 35

description:
genomic DNA from blood sample 35
Human blood from EDTA blood tube
Sample35


title: genomic DNA from blood sample 25

description:
genomic DNA from blood sample 25
Human blood from EDTA blood tube
Sample25


title: genomic DNA from blood sample 21

description:
genomic DNA from blood sample 21
Human blood from EDTA blood tube
Sample21


title: genomic DNA from blood sample 29

description:
genomic DNA from blood sample 29
Human blood from EDTA blood tube
Sample29


title: genomic DNA from blood sample 28

description:
genomic DNA from blood sample 28
Human blood from EDTA blood tube
Sample28


title: genomic DNA from blood sample 30

description:
genomic DNA from blood sample 30
Human blood from EDTA blood tube
Sample30


title: genomic DNA from blood sample 24

description:
genomic DNA from blood sample 24
Human blood from EDTA blood tube
Sample24


title: genomic DNA from blood sample 20

description:
genomic DNA from blood sample 20
Human blood from EDTA blood tube
Sample20


title: genomic DNA from blood sample 14

description:
genomic DNA from blood sample 14
Human blood from EDTA blood tube
Sample14


title: genomic DNA from blood sample 12

description:
genomic DNA from blood sample 12
Human blood from EDTA blood tube
Sample12


title: genomic DNA from blood sample 22

description:
genomic DNA from blood sample 22
Human blood from EDTA blood tube
Sample22


title: genomic DNA from blood sample 26

description:
genomic DNA from blood sample 26
Human blood from EDTA blood tube
Sample26


title: genomic DNA from blood sample 18

description:
genomic DNA from blood sample 18
Human blood from EDTA blood tube
Sample18


title: genomic DNA from blood sample 13

description:
genomic DNA from blood sample 13
Human blood from EDTA blood tube
Sample13


title: genomic DNA from blood sample 17

description:
genomic DNA from blood sample 17
Human blood from EDTA blood tube
Sample17


title: genomic DNA from blood sample 34

description:
genomic DNA from blood sample 34
Human blood from EDTA blood tube
Sample34


title: genomic DNA from blood sample 16

description:
genomic DNA from blood sample 16
Human blood from EDTA blood tube
Sample16


title: genomic DNA from blood sample 15

description:
genomic DNA from blood sample 15
Human blood from EDTA blood tube
Sample15


title: genomic DNA from blood sample 10

description:
genomic DNA from blood sample 10
Human blood from EDTA blood tube
Sample10


title: genomic DNA from blood sample 11

description:
genomic DNA from blood sample 11
Human blood from EDTA blood tube
Sample11


title: genomic DNA from blood sample 5

description:
genomic DNA from blood sample 5
Human blood from EDTA blood tube
Sample5


title: genomic DNA from blood sample 23

description:
genomic DNA from blood sample 23
Human blood from EDTA blood tube
Sample23


title: genomic DNA from blood sample 2

description:
genomic DNA from blood sample 2
Human blood from EDTA blood tube
Sample2


title: genomic DNA from blood sample 7

description:
genomic DNA from blood sample 7
Human blood from EDTA blood tube
Sample7


title: genomic DNA from blood sample 8

description:
genomic DNA from blood sample 8
Human blood from EDTA blood tube
Sample8


description:
genomic DNA from human frontal lobe sample 32
Fresh frozen human frontal lobe (brain)
Sample32

data_processing:
BeadStudio software v3.2.  The unmethylated and methylated signal intensities can be found in the file datSignal_frontal_lobe.csv available on the series record.  Data were processed as follows: Background corrected, average beta values (no special processing)
The data matrix with normalized beta values differs from the file with raw signal intensities with respect to 65 CpG probes that are labelled by Refseq ID such as rs10033147 rs1019916. Unfortunately, the raw signal intensities are not available for these 65 SNPs because our pre-processing pipeline automatically removes these probes. In contrast, we used GenomeStudio to generate the normalized beta values. Therefore, these data are complete.

label: Cy3 and Cy5

source_name: frontal lobe

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using AllPrep DNA/RNA Minikit from Qiagen

value: brain

tag: brain region

value: frontal lobe


description:
genomic DNA from human frontal lobe sample 33
Fresh frozen human frontal lobe (brain)
Sample33

tag: tissue


description:
genomic DNA from human frontal lobe sample 27
Fresh frozen human frontal lobe (brain)
Sample27

tag: age


title: genomic DNA from blood sample 1

description:
genomic DNA from blood sample 1
Human blood from EDTA blood tube
Sample1

tag: gender


title: genomic DNA from blood sample 3

description:
genomic DNA from blood sample 3
Human blood from EDTA blood tube
Sample3

tag: hivstatus


description:
genomic DNA from human frontal lobe sample 29
Fresh frozen human frontal lobe (brain)
Sample29

tag: dnamage


description:
genomic DNA from human frontal lobe sample 25
Fresh frozen human frontal lobe (brain)
Sample25

tag: ageaccelerationvscontrols


description:
genomic DNA from human frontal lobe sample 30
Fresh frozen human frontal lobe (brain)
Sample30

tag: ageaccelerationresidual


description:
genomic DNA from human frontal lobe sample 31
Fresh frozen human frontal lobe (brain)
Sample31


description:
genomic DNA from human frontal lobe sample 23
Fresh frozen human frontal lobe (brain)
Sample23


description:
genomic DNA from human frontal lobe sample 22
Fresh frozen human frontal lobe (brain)
Sample22


description:
genomic DNA from human frontal lobe sample 20
Fresh frozen human frontal lobe (brain)
Sample20


title: genomic DNA from blood sample 9

description:
genomic DNA from blood sample 9
Human blood from EDTA blood tube
Sample9

tag: exhausted cd8t cells


description:
genomic DNA from human frontal lobe sample 19
Fresh frozen human frontal lobe (brain)
Sample19


description:
genomic DNA from human frontal lobe sample 18
Fresh frozen human frontal lobe (brain)
Sample18


description:
genomic DNA from human frontal lobe sample 16
Fresh frozen human frontal lobe (brain)
Sample16


title: genomic DNA from blood sample 6

description:
genomic DNA from blood sample 6
Human blood from EDTA blood tube
Sample6

tag: naïve cd8 t cells


description:
genomic DNA from human frontal lobe sample 24
Fresh frozen human frontal lobe (brain)
Sample24


title: genomic DNA from blood sample 4

description:
genomic DNA from blood sample 4
Human blood from EDTA blood tube
Sample4

tag: naïve cd4 t cells


description:
genomic DNA from human frontal lobe sample 12
Fresh frozen human frontal lobe (brain)
Sample12


description:
genomic DNA from human frontal lobe sample 13
Fresh frozen human frontal lobe (brain)
Sample13


description:
genomic DNA from human frontal lobe sample 21
Fresh frozen human frontal lobe (brain)
Sample21


description:
genomic DNA from human frontal lobe sample 15
Fresh frozen human frontal lobe (brain)
Sample15


description:
genomic DNA from human frontal lobe sample 26
Fresh frozen human frontal lobe (brain)
Sample26


description:
genomic DNA from human frontal lobe sample 28
Fresh frozen human frontal lobe (brain)
Sample28


description:
genomic DNA from human frontal lobe sample 4
Fresh frozen human frontal lobe (brain)
Sample4


description:
genomic DNA from human cerebellum sample 20
Fresh frozen human cerebellum
Sample20

data_processing:
BeadStudio software v3.2.  The unmethylated and methylated signal intensities can be found in the file datSignal_cerebellum.csv available on the series record.  Data were processed as follows: Background corrected, average beta values (no special processing)
The data matrix with normalized beta values differs from the file with raw signal intensities with respect to 65 CpG probes that are labelled by Refseq ID such as rs10033147 rs1019916. Unfortunately, the raw signal intensities are not available for these 65 SNPs because our pre-processing pipeline automatically removes these probes. In contrast, we used GenomeStudio to generate the normalized beta values. Therefore, these data are complete.

source_name: Cerebellum

value: Cerebellum


description:
genomic DNA from human frontal lobe sample 17
Fresh frozen human frontal lobe (brain)
Sample17


description:
genomic DNA from human frontal lobe sample 8
Fresh frozen human frontal lobe (brain)
Sample8


description:
genomic DNA from human frontal lobe sample 5
Fresh frozen human frontal lobe (brain)
Sample5


description:
genomic DNA from human cerebellum sample 18
Fresh frozen human cerebellum
Sample18


description:
genomic DNA from human frontal lobe sample 9
Fresh frozen human frontal lobe (brain)
Sample9


description:
genomic DNA from human frontal lobe sample 10
Fresh frozen human frontal lobe (brain)
Sample10


description:
genomic DNA from human cerebellum sample 13
Fresh frozen human cerebellum
Sample13


description:
genomic DNA from human cerebellum sample 16
Fresh frozen human cerebellum
Sample16


description:
genomic DNA from human cerebellum sample 9
Fresh frozen human cerebellum
Sample9


description:
genomic DNA from human cerebellum sample 14
Fresh frozen human cerebellum
Sample14


description:
genomic DNA from human cerebellum sample 6
Fresh frozen human cerebellum
Sample6


description:
genomic DNA from human frontal lobe sample 3
Fresh frozen human frontal lobe (brain)
Sample3


description:
genomic DNA from human cerebellum sample 8
Fresh frozen human cerebellum
Sample8


description:
genomic DNA from human cerebellum sample 12
Fresh frozen human cerebellum
Sample12


description:
genomic DNA from human cerebellum sample 10
Fresh frozen human cerebellum
Sample10


description:
genomic DNA from human cerebellum sample 17
Fresh frozen human cerebellum
Sample17


description:
genomic DNA from human cerebellum sample 11
Fresh frozen human cerebellum
Sample11


description:
genomic DNA from human cerebellum sample 7
Fresh frozen human cerebellum
Sample7


description:
genomic DNA from human cerebellum sample 5
Fresh frozen human cerebellum
Sample5


description:
genomic DNA from human frontal lobe sample 1
Fresh frozen human frontal lobe (brain)
Sample1


description:
genomic DNA from human frontal lobe sample 6
Fresh frozen human frontal lobe (brain)
Sample6


description:
genomic DNA from human cerebellum sample 4
Fresh frozen human cerebellum
Sample4


description:
genomic DNA from human frontal lobe sample 2
Fresh frozen human frontal lobe (brain)
Sample2


description:
genomic DNA from human cerebellum sample 1
Fresh frozen human cerebellum
Sample1


description:
genomic DNA from human cerebellum sample 19
Fresh frozen human cerebellum
Sample19


description:
genomic DNA from human frontal lobe sample 14
Fresh frozen human frontal lobe (brain)
Sample14


description:
genomic DNA from human frontal lobe sample 11
Fresh frozen human frontal lobe (brain)
Sample11


description:
genomic DNA from human cerebellum sample 15
Fresh frozen human cerebellum
Sample15


description:
genomic DNA from human cerebellum sample 2
Fresh frozen human cerebellum
Sample2


description:
genomic DNA from human frontal lobe sample 7
Fresh frozen human frontal lobe (brain)
Sample7


description:
genomic DNA from human cerebellum sample 3
Fresh frozen human cerebellum
Sample3


title: MDAMB231-MCF7_AVG_Beta

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

data_processing: BeadStudio software

label: Cy5 and Cy3

source_name: breast cancer cell lines

extract_protocol: Genomic DNA was extracted from breast cancer cell lines and the fusion cell lines with a standard method using proteinase K digestion, phenol-chloroform extraction and ethanol precipitation.

tag: cell line

tag: cell type

value: Heterofusion


title: SUM159-CAL51_AVG_Beta


title: MDAMB231_AVG_Beta

value: Basal-like cells


title: CAL51_AVG_Beta


title: SUM159-MDA231_AVG_Beta


title: SUM159-MCF7_AVG_Beta


title: CAL51-MCF7_AVG_Beta


title: MCF7_AVG_Beta

value: Luminal cells


title: MDAMB453_AVG_Beta


title: HS578_AVG_Beta


title: genomic DNA from Brain Occipital of subject 82

description:
Sample123
genomic DNA from Brain Occipital of Control subject

data_processing: BeadStudio software v3.2.

source_name: Brain Occipital

growth_protocol: DNA extracted from fresh frozen brain tissue

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using AllPrep DNA/RNA mini kit according to standard instructions

treatment_protocol: Standard Illumina Protocol

tag: subjectid

value: Brain Occipital

tag: Sex

value: M

tag: sexpredictedusingdnamethdata

value: AllPrep

tag: dnamethylationage

tag: postmorteminterval

value: Control

tag: hivstatusdetectableviralloadinblood


title: genomic DNA from Brain MedialFrontalCortex of subject 44

description:
Sample128
genomic DNA from Brain MedialFrontalCortex of HIV subject

source_name: Brain MedialFrontalCortex

tag: tissue

value: Brain MedialFrontalCortex

tag: age

value: HIV

value: HIV+VLoad+


title: ZR75-1_AVG_Beta


title: 21NT_AVG_Beta


title: SUM159-MDAMB453_AVG_Beta


title: genomic DNA from Brain Frontal of subject 30

description:
Sample129
genomic DNA from Brain Frontal of Control subject

source_name: Brain Frontal

value: Brain Frontal

value: F

tag: hivstatus


title: SUM159_AVG_Beta


title: T47D_AVG_Beta


title: genomic DNA from Brain MedialFrontalCortex of subject 49

description:
Sample127
genomic DNA from Brain MedialFrontalCortex of HIV subject

value: male


title: BT474_AVG_Beta


title: genomic DNA from Brain Frontal of subject 32

description:
Sample124
genomic DNA from Brain Frontal of Control subject

value: female


title: genomic DNA from Brain MedialFrontalCortex of subject 43

description:
Sample122
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 48

description:
Sample126
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: SUM159-BT474_AVG_Beta


title: SUM159-ZR75-1_AVG_Beta


title: genomic DNA from Brain CRBM of subject 68

description:
Sample119
genomic DNA from Brain CRBM of HIV subject

source_name: Brain CRBM

value: Brain CRBM


title: genomic DNA from Brain Occipital of subject 83

description:
Sample130
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain Frontal of subject 28

description:
Sample121
genomic DNA from Brain Frontal of HIV subject


title: genomic DNA from Brain CRBM of subject 53

description:
Sample125
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Frontal of subject 31

description:
Sample120
genomic DNA from Brain Frontal of Control subject


title: SUM159-21NT_AVG_Beta


title: genomic DNA from Brain MedialFrontalCortex of subject 52

description:
Sample116
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 69

description:
Sample118
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: SUM159-T47D_AVG_Beta


title: genomic DNA from Brain CRBM of subject 43

description:
Sample117
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 37

description:
Sample114
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 38

description:
Sample115
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 9

description:
Sample110
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 69

description:
Sample113
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 11

description:
Sample106
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 72

description:
Sample105
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 56

description:
Sample108
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Occipital of subject 8

description:
Sample92
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 31

description:
Sample103
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain Occipital of subject 1

description:
Sample102
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 22

description:
Sample90
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 29

description:
Sample84
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 50

description:
Sample89
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 36

description:
Sample109
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Occipital of subject 44

description:
Sample93
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 30

description:
Sample104
genomic DNA from Brain CRBM of Control subject


title: genomic DNA from Brain Occipital of subject 68

description:
Sample97
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 69

description:
Sample91
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 72

description:
Sample107
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Occipital of subject 66

description:
Sample96
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 64

description:
Sample95
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 61

description:
Sample99
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 62

description:
Sample94
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 67

description:
Sample100
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Occipital of subject 20

description:
Sample87
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 47

description:
Sample81
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 56

description:
Sample88
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 48

description:
Sample86
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Frontal of subject 29

description:
Sample85
genomic DNA from Brain Frontal of HIV subject


title: genomic DNA from Brain CRBM of subject 74

description:
Sample71
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 57

description:
Sample83
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 24

description:
Sample80
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 19

description:
Sample77
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 35

description:
Sample111
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 31

description:
Sample61
genomic DNA from Brain CRBM of Control subject


title: genomic DNA from Brain Occipital of subject 4

description:
Sample78
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 67

description:
Sample68
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 80

description:
Sample67
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain MedialFrontalCortex of subject 46

description:
Sample73
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Occipital of subject 67

description:
Sample76
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 15

description:
Sample79
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 63

description:
Sample75
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 78

description:
Sample70
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain CRBM of subject 71

description:
Sample66
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 32

description:
Sample69
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain Hippocampus of subject 31

description:
Sample64
genomic DNA from Brain Hippocampus of Control subject

source_name: Brain Hippocampus

value: Brain Hippocampus


title: genomic DNA from Brain CRBM of subject 35

description:
Sample63
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain CRBM of subject 70

description:
Sample72
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 55

description:
Sample98
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 33

description:
Sample65
genomic DNA from Brain CRBM of Control subject


title: genomic DNA from Brain Temporal of subject 30

description:
Sample112
genomic DNA from Brain Temporal of Control subject

source_name: Brain Temporal

value: Brain Temporal


title: genomic DNA from Brain Hippocampus of subject 33

description:
Sample58
genomic DNA from Brain Hippocampus of Control subject


title: genomic DNA from Brain MedialFrontalCortex of subject 71

description:
Sample101
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Occipital of subject 12

description:
Sample57
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 7

description:
Sample59
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 39

description:
Sample62
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 16

description:
Sample82
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 26

description:
Sample60
genomic DNA from Brain Occipital of HIV subject


title: Xpc_KO_rep3

city: Kobe

first: Hitoshi

last: Niwa

state: Hyogo

address: 2-2-3 Minatojima-minamimachi,Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

description: Gene expression in subcloned Xpc-null ES cells

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hours at 65°C in a rotating 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 air dried.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505C) at the resolution of 3um.

data_processing: The scanned images were quantified with Feature Extraction Software 10.7.3.1 (Agilent).

source_name: Embryonic stem cells, Xpc KO, replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ng RNA using the Low RNA Input Quick Amplification Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini column purification (QIAGEN, Valencia, CA).

extract_protocol: RNA was prepared using the QuickGene RNA cultured cell HC kit (KURABO) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Embryonic stem cells


title: genomic DNA from Brain Occipital of subject 25

description:
Sample55
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 45

description:
Sample53
genomic DNA from Brain Occipital of HIV subject


title: Xpc_KO_rep2

source_name: Embryonic stem cells, Xpc KO, replicate2


title: genomic DNA from Brain Occipital of subject 23

description:
Sample51
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 6

description:
Sample52
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 84

description:
Sample50
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain Occipital of subject 60

description:
Sample46
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 59

description:
Sample44
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 10

description:
Sample45
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 40

description:
Sample47
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 2

description:
Sample48
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 3

description:
Sample49
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 51

description:
Sample43
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 79

description:
Sample37
genomic DNA from Brain Occipital of Control subject


title: Xpc_KO_rep1

source_name: Embryonic stem cells, Xpc KO, replicate1


title: Xpc_f/f+Tx_day4_rep2

description: Gene expression after 4days of Xpc deletion

source_name: Embryonic stem cells, Xpc induced KO, 4days, replicate2


title: Xpc_f/f+Tx_day4_rep3

source_name: Embryonic stem cells, Xpc induced KO, 4days, replicate3


title: genomic DNA from Brain Hippocampus of subject 32

description:
Sample36
genomic DNA from Brain Hippocampus of Control subject


title: genomic DNA from Brain Occipital of subject 30

description:
Sample33
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain MidBrain  of subject 33

description:
Sample41
genomic DNA from Brain MidBrain  of Control subject

source_name: Brain MidBrain

value: Brain MidBrain


title: genomic DNA from Brain MidBrain  of subject 32

description:
Sample35
genomic DNA from Brain MidBrain  of Control subject


title: genomic DNA from Brain Occipital of subject 33

description:
Sample42
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain MedialFrontalCortex of subject 35

description:
Sample74
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Hippocampus of subject 30

description:
Sample40
genomic DNA from Brain Hippocampus of Control subject


title: genomic DNA from Brain Occipital of subject 65

description:
Sample54
genomic DNA from Brain Occipital of HIV subject


title: Xpc_f/f+Tx_day4_rep1

source_name: Embryonic stem cells, Xpc induced KO, 4days, replicate1


title: Xpc_f/f-Tx_rep1

description: Gene expression without Xpc deletion

source_name: Embryonic stem cells, Xpc floxed, replicate1


title: genomic DNA from Brain CRBM of subject 28

description:
Sample39
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain CRBM of subject 46

description:
Sample26
genomic DNA from Brain CRBM of HIV subject


title: Xpc_f/f-Tx_rep2

description: Gene expression without Xpc deletion

source_name: Embryonic stem cells, Xpc floxed, replicate2


title: Xpc_f/f-Tx_rep3

description: Gene expression without Xpc deletion

source_name: Embryonic stem cells, Xpc floxed, replicate3


title: genomic DNA from Brain MedialFrontalCortex of subject 74

description:
Sample38
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain CRBM of subject 32

description:
Sample24
genomic DNA from Brain CRBM of Control subject


title: genomic DNA from Brain Occipital of subject 18

description:
Sample56
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain Occipital of subject 77

description:
Sample29
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain Temporal of subject 31

description:
Sample31
genomic DNA from Brain Temporal of Control subject


title: genomic DNA from Brain MedialFrontalCortex of subject 75

description:
Sample27
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain Temporal of subject 33

description:
Sample30
genomic DNA from Brain Temporal of Control subject


title: genomic DNA from Brain Frontal of subject 33

description:
Sample34
genomic DNA from Brain Frontal of Control subject


title: genomic DNA from Brain Occipital of subject 76

description:
Sample32
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain Occipital of subject 17

description:
Sample21
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 36

description:
Sample18
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 73

description:
Sample22
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain CRBM of subject 56

description:
Sample15
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 81

description:
Sample25
genomic DNA from Brain Occipital of Control subject


title: genomic DNA from Brain Temporal of subject 32

description:
Sample28
genomic DNA from Brain Temporal of Control subject


title: genomic DNA from Brain CRBM of subject 44

description:
Sample14
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 54

description:
Sample19
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 70

description:
Sample13
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 68

description:
Sample16
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: genomic DNA from Brain MedialFrontalCortex of subject 53

description:
Sample17
genomic DNA from Brain MedialFrontalCortex of HIV subject


title: CD4+T-cells_HDC_PBMC

description: Gene expression data from CD4 T-cells isolated from human PBMC cultured at a high cell density of a healthy blood donor

hyb_protocol: 200µl hybridization mix prepared from labeled cRNA fragments was hybridized for 16h at 45°C to GeneChip Human Genome U133 Plus 2.0 arrays. Microarrays were washed and stained in the Affymetrix Fluidics Station 450 using script FS450_0001.

source_name: blood of a healthy donor

growth_protocol: Human PBMC were in-vitro cultured at a low cell density (10^6 cells/mL) or at a high cell density (10^7 cells/mL) at 37C and 5% CO2 for 2 days.

extract_protocol: Total RNA extraction was performed with the RNeasy Mini Kit (50) from QIAGEN according to the manufacturer's instructions.

treatment_protocol: CD4+ or CD8+ T-cells were untouched isolated from PBMC after in-vitro culture by using the CD4 or CD8 T-cell isolation kit from Miltenyi biotec GmbH (purity of separation >95%).

value: T-cells from peripheral blood mononuclear cells (PBMC)


title: genomic DNA from Brain Occipital of subject 42

description:
Sample10
genomic DNA from Brain Occipital of HIV subject

source_name: Brain Occipital

value: Brain Occipital


title: CD4+T-cells_LDC_PBMC

description: Gene expression data from CD4 T-cells isolated from human PBMC cultured at a low cell density of a healthy blood donor


title: genomic DNA from Brain Occipital of subject 21

description:
Sample12
genomic DNA from Brain Occipital of HIV subject


title: Clofibrate

city: suzhou

first: Shuyu

last: Zhang

state: jiangsu

address: No.199 Ren’ai Rd

department: Medical  College

institute: Soochow  University

description: The sample is the total RNA of the Panc1 cell which is pretreated with Clofibrate and seted to be the experiment group.

hyb_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. The 2 gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.
Genes that have values greater than or equal to lower cut-off: 100.0 in at least 1 out of 2 samples (“All Targets Value”) were chosen for data analysis. Differentially expressed genes were identified through Fold Change filtering.

source_name: Human pancreatic cancer cell line Panc1

growth_protocol: The human pancreatic cancer cell line Panc1 was maintained in DMEM supplemented with 10% FBS and antibiotics (100 units/ml penicillin G, 100 units/ml streptomycin sulfate;Gibco, Grand Island, NY). Cells were grown in a 37°C incubator with 5% CO2.

extract_protocol: Total RNA was extracted from cells with Trizol reagent (Invitrogen, Carlsbad, CA ).Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.Results were provided in the RNA_QC.pdf file.

treatment_protocol: Panc1 cells were pretreated with DMSO and Clofibrate for 24 h , RNA was extracted and subjected to microarray analysis.

value: human pancreatic cancer cell line

tag: pretreated with

value: Clofibrate for 24hrs


title: genomic DNA from Brain Occipital of subject 58

description:
Sample6
genomic DNA from Brain Occipital of HIV subject

value: AllPrep


title: genomic DNA from Brain Occipital of subject 36

description:
Sample11
genomic DNA from Brain Occipital of HIV subject


title: DMSO

description: The sample is the total RNA of the Panc1 cell which is pretreated with DMSO and seted to be the control group.

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

value: DMSO for 24 hrs


title: genomic DNA from Brain CRBM of subject 52

description:
Sample23
genomic DNA from Brain CRBM of HIV subject

value: HIV


title: genomic DNA from Brain Occipital of subject 70

description:
Sample20
genomic DNA from Brain Occipital of HIV subject

value: HIV+VLoad+


title: genomic DNA from Brain Occipital of subject 5

description:
Sample9
genomic DNA from Brain Occipital of HIV subject


title: CD8+T-cells_LDC-PBMC

description: Gene expression data from CD8 T-cells isolated from human PBMC cultured at a low cell density of a healthy blood donor


title: genomic DNA from Brain CRBM of subject 75

description:
Sample1
genomic DNA from Brain CRBM of HIV subject


title: genomic DNA from Brain Occipital of subject 27

description:
Sample3
genomic DNA from Brain Occipital of HIV subject


title: BT474_AVG_Beta

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

data_processing: BeadStudio software (version 2011.1)

source_name: breast cancer cell lines

extract_protocol: standard procedure

value: Luminal cells


title: SUM159PT_BT474_AVG_Beta

value: Heterofusion


title: MCF7_H3K27me3_AVG_Beta


title: MDAMB231_AVG_Beta

value: Basal-like cells


title: T47D_H3K27me3_AVG_Beta


title: CD8+T-cells_HDC-PBMC

description: Gene expression data from CD8 T-cells isolated from human PBMC cultured at a high cell density of a healthy blood donor


title: MDAMB231_MCF7_AVG_Beta


title: genomic DNA from Brain Occipital of subject 14

description:
Sample8
genomic DNA from Brain Occipital of HIV subject

value: male


title: genomic DNA from Brain CRBM of subject 49

description:
Sample2
genomic DNA from Brain CRBM of HIV subject

source_name: Brain CRBM

value: Brain CRBM


title: genomic DNA from Brain Occipital of subject 41

description:
Sample5
genomic DNA from Brain Occipital of HIV subject


title: SUM159PT_MCF7_AVG_Beta


title: SUM159PT_T47D_AVG_Beta


title: genomic DNA from whole blood of HIV+ man 21 [2012]

description: Sample 21

data_processing: BeadStudio software v3.2. The non_normalized.txt contains unmethylated and methylated signal intensities.

source_name: whole blood

growth_protocol: Fresh frozen blood

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: whole blood

tag: dnamage

tag: chipid

value: positive

tag: age (yrs)

tag: bmi


title: genomic DNA from whole blood of HIV+ man 22 [2012]

description: Sample 22


title: genomic DNA from Brain Occipital of subject 34

description:
Sample4
genomic DNA from Brain Occipital of HIV subject


title: genomic DNA from whole blood of HIV+ man 14 [2012]

description: Sample 14


title: genomic DNA from whole blood of HIV+ man 20 [2012]

description: Sample 20


title: genomic DNA from whole blood of HIV+ man 24 [2012]

description: Sample 24


title: controls pool, technical replicate 1

description: gene expression data from T2DM control group

hyb_protocol: 100µl hyb-cocktail prepared from labeled low molecular weight RNA was hybridized for 16h at 48°C to GeneChip miRNA array. Microarrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using a GeneChip Scanner 3000 7G.

data_processing: Data were preprocessed in the R/Bioconductor environment using the affy package; background correction, normalization and probeset summary were performed with the „rma“ function using default parameter settings.

source_name: T2DM controls pool 1

label_protocol: 80µl of pooled total RNA from 17-20 individuals were preprocessed with the Flash-Tag HSR kit (Genisphere, Hatfield, PA, USA) following the manufacturer's protocol, thereby labeling the low molecular weight RNA with biotin.

extract_protocol: total RNA was isolated from plasma using miRNeasy kit and 10ul from individual 30µl miRNA rich elutes was pooled.

treatment_protocol: clinical samples from patients

tag: sample type

value: plasma

tag: disease state

value: 4 females, 16 males


title: controls pool, technical replicate 2

source_name: T2DM controls pool 2


title: genomic DNA from whole blood of HIV+ man 17 [2012]

description: Sample 17


title: patients pool, technical replicate 1

description: gene expression data from T2DM+PAD+W group

source_name: T2DM+PAD+Wound patients pool 1

value: T2DM + PAD + Wound

value: 3 females, 14 males


title: genomic DNA from whole blood of HIV+ man 18 [2012]

description: Sample 18


title: genomic DNA from whole blood of HIV+ man 15 [2012]

description: Sample 15


title: patients pool, technical replicate 2

source_name: T2DM+PAD+Wound patients pool 2


title: genomic DNA from whole blood of HIV+ man 11 [2012]

description: Sample 11


title: HCT116 Colon Cancer Cells transduced by TRCN 0000231589

city: Columbia

first: Sharad

last: Khare

state: Missouri

address: CE447 Clinical and Educational Support Building

department: Division of Gastroenterology and Hepatology

institute: University of Missouri

description: medium Sprouty2 suppression

hyb_protocol: Labeled samples were hybridized to miRCURY LNATM microRNA Array (7th Gen).The hybridization was performed according to the miRCURY LNATM microRNA array instruction manual using Tecan hybridization station.

scan_protocol: The microRNA slides were scanned using the Agilent G2565BA Microarray scanner system.

data_processing: The image analysis was carried out using the ImaGeneR9 (miRCURY LNATM microRNA Array analysis software, Exiqon). The quantified signals were background corrected and normalized using the global Lowess (Locally Weighted Scatterplot Smoothing, LOWESS) regression algorithm.

source_name: HCT116 Colon Cancer Cells transduced with Sprouty2 MISSION shRNA Lentiviral Transduction Particle TRCN 0000231589

label_protocol: 750 ng total RNA from both sample and reference was labeled with Hy3TM and Hy5TM fluorescent label, respectively, using the miRCURY LNATM microRNA labeling kit Hy3TM/Hy5TM (Exiqon).

extract_protocol: Total RNA was extracted with a RNA isolation kit (Exiqon, USA) according to the manufacturer's instructions and further purified using Turbo Kit (Ambion, USA). RNA purity was assessed by measuring absorptions at 260 and 280 nm and samples that had A260/A280 ratio of 1.9–2.1 were considered acceptable.

tag: cell line

tag: tranduction

source_name: HCT116 Colon Cancer Cells (reference pool of all samples)


title: genomic DNA from whole blood of HIV+ man 13 [2012]

description: Sample 13


title: HCT116 Colon Cancer Cells transduced by TRCN 0000231588

description: minimum Sprouty2 suppression

source_name: HCT116 Colon Cancer Cells transduced with Sprouty2 MISSION shRNA Lentiviral Transduction Particle TRCN 0000231588


title: SUM159PT_AVG_Beta

tag: cell type


title: genomic DNA from whole blood of HIV+ man 16 [2012]

description: Sample 16


title: 5hmCIP_450k (MCS_Pb_p38_32hmc)

status: Public on Jun 08 2015

city: Detroit

first: Douglas

last: Ruden

state: Michigan

address: 275 E. Hancock Ave., Room  291.1

department: Department of Obstetrics and Gynecology

institute: Wayne State University

hyb_protocol: As defined by Illumina

scan_protocol: As defined by Illumina

data_processing:
ChAMP pipeline for data diltering, Beta mixed interquantile normalisation (BMIQ) for probe bias correction, SNP filtering, A-Clustering for differential methylation analysis
processed beta value provided as .txt file; processed_betas_Pb_hESC_HMeDIP450K.txt

label: Cy3, Cy5

source_name: H9- hESCs

label_protocol: As defined by Illumina

growth_protocol: The human ESC line WA09 (H9) (Thomson et al. 1998) was obtained from the WiCell Research Institute (Madison, WI, USA) and maintained in a humidified incubator at 37oC with 5% CO2, as previously described (Senut et al., 2014). Briefly, undifferentiated hESCs (passages 26-39) were cultured in DMEM/F12 supplemented with knockout serum replacement, nonessential amino acids, penicillin/streptomycin, L-Glutamine, 2-mercaptoethanol, and human basic fibroblast growth factor (Life Technologies) on a feeder layer of irradiated mouse embryonic fibroblasts (Globalstem).

extract_protocol: DNA was isolated from hESCs by using QiagenDNA Easy Kit™.  The “Purification of DNA from Cells” protocol, the EZ1 DNA Cell Card, and the EZ1 DNA Cell 350-μl Kit were used for this study. DNA was isolated from ~1 million cells with Qiagen EZ1 Advanced® using the DNA Investigator® reagents and protocol card. DNA concentrations were quantified by UV spectrophotometry using the DropSense96® Microplate Spectrophotometer (Trinean), and the purity was assessed based on the A260/A280 and A260/A230 ratios.Approximately 3µg genomic DNA was diluted in 130µl of buffer TE (10mM Tris (pH 8.0), and 1mM EDTA (pH 8.0)) and sheared into ~200-600bp fragment using microcavitation (Covaris, Inc, setting: Duty Cycle = 5%, Intensity = 3, Cycles/burst = 200, Time = 75 seconds run at 6-8°C). 125µl of the sheared DNA samples were mixed with 330µl of buffer TE. The sheared DNA was denatured by boiling it in the Thermomixer at 95°C and 700rpm for ten minutes and left on ice for 10min. 51 µl of 10x immunoprecipitation buffers and 3µl of  5hmC specific antibodies(Active Motif) at a concentration of 1µg/µl was added to the denatured DNA sample and incubated for ≥ 2hours at 4°C with tipping. Then, 25µl protein G beads was added to the samples and incubated overnight at 4°C with tipping. The residual beads were collected with a magnetic rack and washed 3 times with 700µl 1xIP buffer. The bead were then re-suspended in 20mg/ml Proteinase K solution and incubated for 3hours at 50°C and 800rpm. The residual beads where pelleted using a magnetic rack. The supernatant was collected for phenol/chloroform extraction. For extraction, the supernatant was treated with 250µl phenol: chloroform: isoamyl at a ratio of 25:24:1, vortexed and then spun down for 2 minutes at 14,000rpm. Then, the supernatant was treated with 250µl chloroform, vortexed and spun down for 2 minutes. Finally, DNA was precipitated by adding 20µl 5M NaCl, 1µl glycogen and 500µl 100% ethanol and incubated at -20°C for 30 minutes. The samples were then pelleted at 4°C and 14,000rpm for 20 minutes and allowed to dry at room temperature for 10 minutes. The dried out samples are re-suspended in 25-50µl water and readied for the HM450K bead chip array for methylation analysis.

treatment_protocol: Stock solutions (100-fold concentrated) of Pb acetate (Pb(C2H3O2)2) (Sigma-Aldrich) were prepared in sterile distilled water. Two physiologically relevant concentrations of Pb acetate chosen on the basis of our previous work 24 were tested in this study: 0.8μM (16 μg/dL) and 1.5μM (32 μg/dL). Distilled water was used as a vehicle control. Undifferentiated hESCs were acutely exposed to the different concentrations of Pb or vehicle for 24 hours, at which time the hESC colonies were dissected and their DNA was isolated.

value: ESC line WA09 (H9)

tag: agent

value: Pb

tag: dose

tag: ip antibody

value: 5hmC-specific antibodies (Active Motif)


title: 5hmCIP_450k (MCS_Pb_p26_32hmc)


title: genomic DNA from Brain Occipital of subject 13

description:
Sample7
genomic DNA from Brain Occipital of HIV subject

tag: subjectid

tag: tissue

value: Brain Occipital

tag: Sex

tag: sexpredictedusingdnamethdata

value: AllPrep

tag: dnamethylationage

tag: postmorteminterval

tag: hivstatusdetectableviralloadinblood


title: SNU484 G9a-ΔSET

city: Daegu

first: You Mie

last: Lee

address: 80, Daehak-ro

institute: Kyungpook National University

description:
Gene expression from SNU484 cells expressing GFP-G9a-ΔSET vector under normoxic condition
The SET domain of G9a is the catalytic domain and is responsible for methyltransferase activity.

hyb_protocol: Complementary RNA was hybridized using the Agilent's Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for array slides.

data_processing: The scanned images were analyzed Agilent's GeneSpring Software.

source_name: Gastric cancer cell line, G9a-ΔSET overexpression

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: microenvironment

value: G9a-delta-SET overexpression


title: genomic DNA from whole blood of HIV+ man 19 [2012]

description: Sample 19

tag: gender

tag: dnamage

tag: chipid

tag: hivstatus

tag: age (yrs)

tag: bmi


title: HCT116 Colon Cancer Cells transduced by TRCN 0000007522

description: maximum Sprouty2 suppression

source_name: HCT116 Colon Cancer Cells transduced with Sprouty2 MISSION shRNA Lentiviral Transduction Particle TRCN 0000007522

tag: cell line

tag: tranduction


title: 5hmCIP_450k (MCS_Pb_p39_32hmc)

tag: agent

tag: dose

tag: sample type

tag: ip antibody


title: Control HCT116 colon cancer cells transduced with non-targeted shRNA

description: Control

source_name: HCT116 Colon Cancer Cells transduced with non-targeted shRNA control from Sigma

value: non-targeted shRNA control from Sigma


title: genomic DNA from whole blood of HIV+ man 10 [2012]

description: Sample 10

tag: tissue


title: 5hmCIP_450k (MCS_Pb_p26_16hmc)


title: genomic DNA from whole blood of HIV+ man 9 [2012]

description: Sample 9


title: genomic DNA from whole blood of HIV+ man 12 [2012]

description: Sample 12


title: 5hmCIP_450k (MCS_Pb_p38_16hmc)


title: genomic DNA from whole blood of HIV+ man 8 [2012]

description: Sample 8


title: 5hmCIP_450k (H9 p34(2)- 16-HMC)


title: 5hmCIP_450k (MCS_Pb_p38_0hmc)

value: control


title: 5hmCIP_450k (MCS_Pb_p39_0hmc)


title: 5hmCIP_450k (MCS_Pb_p26_0hmc)


title: 5hmCIP_450k (H9 p34(2)-0-HMC)


title: 5hmCIP_450k (H9 p34(2) -32-HMC)


title: noIP_450K (0202-C)

data_processing:
ChAMP pipeline for data filtering, Beta mixed interquantile normalisation (BMIQ) for probe bias correction, SNP filtering, A-Clustering for differential methylation analysis
Processed beta matrix for HM450K and HMeDIP-450K is provided as .txt files; processed_betas_UCB_HM450K.txt and processed_betas_UCB_HMeDIP450K.txt

source_name: Umbilical cord blood (ELEMENT cohort)

growth_protocol: Human Cohort, not applicable

extract_protocol: DNA was isolated from hESCs by using QiagenDNA Easy Kit™.  The “Purification of DNA from Cells” protocol, the EZ1 DNA Cell Card, and the EZ1 DNA Cell 350-μl Kit were used for this study. Approximately 3µg genomic DNA was diluted in 130µl of buffer TE (10mM Tris (pH 8.0), and 1mM EDTA (pH 8.0)) and sheared into ~200-600bp fragment using microcavitation (Covaris, Inc, setting: Duty Cycle = 5%, Intensity = 3, Cycles/burst = 200, Time = 75 seconds run at 6-8°C). 125µl of the sheared DNA samples were mixed with 330µl of buffer TE. The sheared DNA was denatured by boiling it in the Thermomixer at 95°C and 700rpm for ten minutes and left on ice for 10min. 51 µl of 10x immunoprecipitation buffers and 3µl of 5hmC specific antibodies (Active Motif) at a concentration of 1µg/µl was added to the denatured DNA sample and incubated for ≥ 2hours at 4°C with tipping. Then, 25µl protein G beads was added to the samples and incubated overnight at 4°C with tipping. The residual beads were collected with a magnetic rack and washed 3 times with 700µl 1xIP buffer. The bead were then re-suspended in 20mg/ml Proteinase K solution and incubated for 3hours at 50°C and 800rpm. The residual beads where pelleted using a magnetic rack. The supernatant was collected for phenol/chloroform extraction. For extraction, the supernatant was treated with 250µl phenol: chloroform: isoamyl at a ratio of 25:24:1, vortexed and then spun down for 2 minutes at 14,000rpm. Then, the supernatant was treated with 250µl chloroform, vortexed and spun down for 2 minutes. Finally, DNA was precipitated by adding 20µl 5M NaCl, 1µl glycogen and 500µl 100% ethanol and incubated at -20°C for 30 minutes. The samples were then pelleted at 4°C and 14,000rpm for 20 minutes and allowed to dry at room temperature for 10 minutes. The dried out samples are re-suspended in 25-50µl water and readied for the HM450K bead chip array for methylation analysis.

treatment_protocol: The Early Life Exposure in Mexico to Environmental Toxicants (ELEMENT) cohort consists of over 4000 mother-infant pairs, belonging to a low income population recruited from 1994 onwards from three hospitals in Mexico City (Mexican Social Security Institute, Manuel Gea Gonzalez Hospital, and National Institute of Perinatology).We used umbilical cord blood (UCB) from the fourth wave of the ELEMENT study (Each of the four waves had approximately 1000 children participants). The blood lead concentrations of umbilical cord blood were determined using atomic absorption spectroscopy (Model 3000; PerkinElmer, Chelmsford, MA, USA) at the metals laboratory of the American British Cowdray Hospital in Mexico City .For our study, we randomly selected UCB from 24 male and 24 female children from the 1st and 4th quartiles of Pb levels. The UCB for male children had a minimum blood lead level (BLL) of 0.59 µg/dl and highest BLL of 7.21µg/dl. The UCB for female children had a minimum BLL of 0.68µg/dl and highest BLL of 10.53 µg/dl. Five male children and seven female children had BLL in UCB ≥ 5µg/dl and classified as high BLL group.

value: umbilical cord blood

value: Female

tag: socioeconomic score

tag: gestational age

tag: smoke ever

value: No

tag: birth weight

tag: pbconc (ng/dl)

value: no IP


title: genomic DNA from whole blood of HIV+ man 23 [2012]

description: Sample 23

tag: gender

value: male

value: whole blood

tag: dnamage

value: positive


title: genomic DNA from whole blood of HIV+ man 5 [2012]

description: Sample 5

tag: chipid

tag: hivstatus


title: 5hmCIP_450K (0202-C-HMC)


title: genomic DNA from whole blood of HIV+ man 7 [2012]

description: Sample 7

tag: age (yrs)

tag: bmi


title: 5hmCIP_450K (0088-C-HMC)

value: Male

value: Yes


title: noIP_450K (0283-C)


title: noIP_450K (0185-C)


title: genomic DNA from whole blood of HIV+ man 4 [2012]

description: Sample 4


title: 5hmCIP_450K (0070-C-HMC)


title: noIP_450K (0070-C)


title: noIP_450K (0041-C)


title: 5hmCIP_450K (0283-C-HMC)


title: noIP_450K (0162-C)


title: 5hmCIP_450K (0269-C-HMC)


title: noIP_450K (0230-C)


title: genomic DNA from whole blood of HIV+ man 6 [2012]

description: Sample 6


title: 5hmCIP_450K (0041-C-HMC)


title: 5hmCIP_450K (0162-C-HMC)


title: genomic DNA from whole blood of HIV+ man 1 [2012]

description: Sample 1


title: 5hmCIP_450K (0305-C-HMC)


title: noIP_450K (0305-C)


title: genomic DNA from whole blood of HIV+ man 2 [2012]

description: Sample 2


title: 5hmCIP_450K (0185-C-HMC)


title: 5hmCIP_450K (0230-C-HMC)


title: noIP_450K (0092-C)


title: genomic DNA from whole blood of HIV+ man 3 [2012]

description: Sample 3


title: noIP_450K (0062-C)


title: noIP_450K (0088-C)


title: 5hmCIP_450K (0092-C-HMC)


title: PK_in-vivo_Aa_time_point6

city: Singapore

first: Zbynek

last: Bozdech

state: Select if applicable

department: Molecular Genetics&Cell Biology

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 65°C in a rotating hybridization oven at 10rpm.

scan_protocol: Microarray scanning was done using PowerScanner (Tecan, Austria) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments, USA) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Features with flag>0 and with median foreground intensity greater than 2 fold median background intensity for either channel passed quality control and were accepted. Local  background correction using substraction, followed by lowess normalization across all features were carried out to generate the normalized Log2 gene expression ratios.

organism: Plasmodium knowlesi

source_name: P. knowlesi field isolate

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol:
For ex-vivo samples, a rhesus monkey was infected with P. knowlesi to obtain ring iRBCs to establish a short-term culture to immediately collect ex vivo derived time points every 4 hours in the course of the parasite’s 24-hour life cycle
For in-vivo samples, the same clone of P. knowlesi grown in the ex-vivo cultrue of the rhesus macaque host were adapted to long-term in vitro culture.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: culture

value: In vitro culture

tag: Stage

value: blood stage

tag: time

source_name: P. knowlesi RNA reference pool

value: asexual blood stage

tag: composition

value: mixture of equal amounts of RNA harvested every 4 hours over the 24-hour parasite's intraerythrocytic life cycle


title: PK_in-vivo_Aa_time_point5


title: 5hmCIP_450K (0062-C-HMC)

tag: sample type

tag: ip antibody

value: 5hmC-specific antibodies (Active Motif)


title: noIP_450K (0082-C)

tag: tissue

tag: socioeconomic score


title: noIP_450K (0076-C)

tag: gestational age

tag: smoke ever


title: PK_in-vivo_Aa_time_point8


title: PK_in-vivo_Aa_time_point4


title: PK_in-vivo_Aa_time_point3


title: PK_in-vivo_Aa_time_point1


title: 5hmCIP_450K (0082-C-HMC)

tag: birth weight

tag: pbconc (ng/dl)


title: 5hmCIP_450K (0076-C-HMC)

tag: gender


title: noIP_450K (0196-C)


title: PK_in-vivo_Aa_time_point2


title: noIP_450K (0105-C)


title: noIP_450K (0101-C)


title: 5hmCIP_450K (0276-C-HMC)


title: noIP_450K (0276-C)


title: PK_in-vivo_Ha_time_point7


title: PK_in-vivo_Ha_time_point6


title: PK_in-vivo_Ha_time_point4


title: 5hmCIP_450K (0196-C-HMC)


title: 5hmCIP_450K (0105-C-HMC)


title: PK_in-vivo_Ha_time_point3


title: PK_in-vivo_Ha_time_point1


title: PK_in-vivo_Ha_time_point2


title: 5hmCIP_450K (0101-C-HMC)


title: PK_Ex-vivo_schizont_stage2

value: Ex vitro culture

tag: life cycle stage

value: schizont


title: PK_Ex-vivo_schizont_stage1


title: PK_Ex-vivo_mid_trophozoite_stage2

value: middle trophozoite


title: noIP_450K (0150-C)

value: umbilical cord blood


title: noIP_450K (0207-C)


title: 5hmCIP_450K (0235-C-HMC)

value: Female


title: noIP_450K (0184-C)


title: noIP_450K (0083-C)

value: No


title: noIP_450K (0017-C)

value: no IP


title: 5hmCIP_450K (0207-C-HMC)


title: noIP_450K (0203-C)


title: 5hmCIP_450K (0150-C-HMC)


title: PK_in-vivo_Ha_time_point5


title: noIP_450K (0235-C)


title: PK_Ex-vivo_ring_stage

value: early rings


title: PK_Ex-vivo_mid_trophozoite_stage1


title: 5hmCIP_450K (0184-C-HMC)


title: noIP_450K (0189-C)


title: PK_Ex-vivo_late_ring_stage

value: late rings


title: UGent11-7_2

city: Gent

first: Pieter

last: mestdagh

address: De Pintelaan 185

country: Belgium

institute: Center for Medical Genetics

hyb_protocol: Labeled RNA was hybridized to a custom gene expression microarray containing probes for all protein coding genes and 15902 lncRNA genes (AMADID# 041648).

scan_protocol: Arrays were scanned using the Agilent G2565CA Microarray Scanner and Scan Control Software 8.5 according to the manufacturer's instructions.

data_processing: Probe intensities were extracted using Feature Extraction software (Agilent).

source_name: cell culture

label_protocol: Total RNA (100ng) was labeled using the low input Quick Amp WT labeling kit (Agilent Technologies) according to the manufacturer’s instructions.

extract_protocol: Cell pellets were lysed in TRIzol (Invitrogen), total RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

tag: cell line

tag: cell type

value: embryonic stem cell

tag: pluripotency state

value: primed


title: n-UGent11-7_2

value: naive


title: n-H1 OCT4:GFP hESC_1

value: H1 OCT4:GFP


title: H1 OCT4:GFP hESC_2


title: n-UGent10-1_2


title: 5hmCIP_450K (0203-C-HMC)

value: Yes


title: 5hmCIP_450K (0083-C-HMC)

value: Male


title: 5hmCIP_450K (0189-C-HMC)


title: n-H1 OCT4:GFP hESC_2


title: noIP_450K (0269-C)


title: 5hmCIP_450K (0017-C-HMC)


title: n-UGent10-1_1


title: noIP_450K (0168-C)


title: noIP_450K (0199-C)


title: UGent10-1 hESC_2


title: UGent10-1 hESC_1


title: noIP_450K (0264-C)


title: noIP_450K (0278-C)


title: 5hmCIP_450K (0278-C-HMC)


title: 5hmCIP_450K (0264-C-HMC)


title: 5hmCIP_450K (0199-C-HMC)


title: 5hmCIP_450K (0168-C-HMC)


title: noIP_450K (0120-C)


title: UGent11-7_1


title: noIP_450K (0012-C)


title: noIP_450K (0099-C)


title: H1 OCT4:GFP hESC_1


title: noIP_450K (0164-C)


title: n-UGent11-7_1


title: 5hmCIP_450K (0099-C-HMC)


title: 5hmCIP_450K (0012-C-HMC)


title: 5hmCIP_450K (0164-C-HMC)


title: Pre-CD4-1

city: St Louis

first: Gary

middle: E

last: Grajales-Reyes

state: Mo

address: Room 7766, CSRB

department: Immunology

institute: Washington University in St. Louis

hyb_protocol: Hybridized onto Mouse Gene 2.0 ST Arrays (Affymetrix)

scan_protocol: stardard Affymetrix protocol

data_processing: Data was analyzed using DNASTAR Arraystar software.

source_name: N8 Zbtb46GFP/+

label_protocol: amplified using NuGen Ovation Pico WTA amplification system. Fragmentation was performed with the NuGen encore biotin module

growth_protocol: Bone marrow was harvested with mortar and pestle, primary splenocytes were harvested by digestion with Collagenase B and DNAse1

extract_protocol: ZbtbGFP/+ progenitor and CD24 DC sort: CDPs sorted as Lin– CD117int CD135+ CD115+ CD11c– MHC II– BM cells; pre-CD8 DCs as Lin– CD135+ CD117int Siglec H– CD11c+ MHC IIint BM cells; pre-CD4 DCs as Lin– CD135+ CD117low CD115+ CD11c+ MHC II– BM cells; CD24 DCs as CD11c+ MHC II– CD24+ CD172a-; CD172a DCs were sorted as CD11c+ MHCII + CD172a+

treatment_protocol: Mice were analyzed at steady-state.

tag: strain


title: Pre-CD4-2


title: Pre-CD8-2


title: CDP-3

value: CDP


title: PK_in-vivo_Aa_time_point7

tag: culture

value: In vitro culture

tag: Stage

value: blood stage

value: asexual blood stage

value: mixture of equal amounts of RNA harvested every 4 hours over the 24-hour parasite's intraerythrocytic life cycle


title: CDP-1


title: Pre-CD8-1


title: CDP-2


title: noIP_450K (0222-C)

value: umbilical cord blood


title: noIP_450K (0141-C)

value: Female


title: CD24-3


title: CD24-1


title: noIP_450K (0091-C)


title: CD24-2


title: noIP_450K (0239-C)


title: CD172a-1


title: L540 Ixazomib Replicate 3

city: Mountain View

first: Afshin

last: Beheshti

address: Moffett Blvd

institute: NASA Ames Research Center

description: Gene expression data from L540 Cells with 25nM of Ixazomib treatment for 24 hours

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

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

data_processing: The data were analyzed with RMAExpress which performs background adjustments and quantile normalization

source_name: L540 Cells with Ixazomib Treatment

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: L540 and Jurkat cell lines were grown in RPMI 1640 consisting of 10% heat inactivated fetal bovine serum and 200U of penicillin/streptomycin (Mediatech, Manassas, VA) under 5% CO2 and 37C. Ixazomib was kindly provided by Takeda Pharmaceuticals, Inc. Cells were treated with ixazomib for 24 hours at 25nM.

extract_protocol: RNA was isolated using RNeasy Minikit (Qiagen)

value: Hodgkin Lymphoma

tag: treatment

value: 25nM of Ixazomib for 24 Hours


title: L540 Ixazomib Replicate 2

treatment_protocol: Cells were treated with ixazomib for 24 hours at 25nM.


title: 5hmCIP_450K (0239-C-HMC)

tag: sample type

value: 5hmC-specific antibodies (Active Motif)


title: 5hmCIP_450K (0222-C-HMC)

value: No

tag: ip antibody


title: L540 Control Replicate 1

description: Gene expression data from L540 Cells as Controls

source_name: L540 Cells

value: Control


title: L540 Control Replicate 2


title: 5hmCIP_450K (0141-C-HMC)

tag: tissue


title: 5hmCIP_450K (0120-C-HMC)

tag: socioeconomic score


title: CD172a-2


title: Jurkat Ixazomib Replicate 3

description: Gene expression data from Jurkat Cells with 25nM of Ixazomib treatment for 24 hours

source_name: Jurkat Cells with Ixazomib Treatment

value: T-Cell Lymphoma


title: Jurkat Ixazomib Replicate 2


title: HES20

city: Guangzhou

first: Wenyin

last: HE

state: Guangdong

address: No.63, Duobao road

institute: The third affiliated hospital of Guangzhou medical university

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Data processing was performed in Chromosome Analysis Suite 2.0 (CHAS2.0) software (Affymetrix), via the standard reference library provided by the manufacturer based on the Hidden Markov Model

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

value: Embryonic stem cells


title: Jurkat Ixazomib Replicate 1


title: 5hmCIP_450K (0091-C-HMC)

tag: gestational age


title: noIP_450K (0247-C)

tag: smoke ever

value: no IP


title: noIP_450K (0032-C)

tag: birth weight


title: L540 Control Replicate 3


title: noIP_450K (0215-C)

value: Yes

tag: pbconc (ng/dl)


title: Jurkat Control Replicate 3

description: Gene expression data from Jurkat Cells as Controls

source_name: Jurkat Cells


title: Jurkat Control Replicate 2


title: 5hmCIP_450K (0247-C-HMC)

tag: gender


title: Jurkat Control Replicate 1


title: noIP_450K (0135-C)


title: 5hmCIP_450K (0135-C-HMC)


title: 5hmCIP_450K (0032-C-HMC)

value: Male


title: 5hmCIP_450K (0215-C-HMC)


title: iPS-FF-g

source_name: iPS-FF-g

value: induced pluripotent stemm cell line

value: iPS-FF-g


title: iPS-FF-h

source_name: iPS-FF-h

value: iPS-FF-h


title: iPS-AF-11


title: L428 Cells resistant to Ixazomib Replicate 3

description: Gene expression data from L428 Cells resistant to Ixazomib treatment for 24 hours

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were corrected with normalization to housekeeping genes and then quantile normalisation with GenePattern Illumina Normalizer Module

source_name: L428 Cells resistant to Ixazomib

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

growth_protocol: L428 cell lines were grown in RPMI 1640 consisting of 10% heat inactivated fetal bovine serum and 200U of penicillin/streptomycin (Mediatech, Manassas, VA) under 5% CO2 and 37C. Ixazomib was kindly provided by Takeda Pharmaceuticals, Inc. Cells were treated with ixazomib for 24 hours at 25nM.

treatment_protocol: Cells were treated with ixazomib for 24 hours at 25nM and 71.25nM

value: Cells resistant to Ixazomib treatment


title: iPS-AF-411


title: L428 Cells resistant to Ixazomib Replicate 2


title: noIP_450K (0015-C)


title: L428 Cells resistant to Ixazomib Replicate 1


title: iPS-AF-3


title: L540 Ixazomib Replicate 1


title: iPS-AF-2


title: L428 71.25nM Ixazomib Replicate 3

description: Gene expression data from L428 Cells with 71.25nM of Ixazomib treatment for 24 hours

source_name: L428 Cells with 71.25nM Ixazomib Treatment

value: 71.25nM of Ixazomib for 24 Hours


title: noIP_450K (0129-C)

value: umbilical cord blood


title: L428 71.25nM Ixazomib Replicate 1

description: Gene expression data from L428 Cells with 25nM of Ixazomib treatment for 24 hours


title: noIP_450K (0212-C)

value: Female


title: 5hmCIP_450K (0212-C-HMC)


title: L428 71.25nM Ixazomib Replicate 2

value: Hodgkin Lymphoma


title: noIP_450K (0144-C)


title: iPS-AF-9


title: iPS-AF-6