title: FK18Bp143

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Vrije Universiteit Medical Center

hyb_protocol: Hybridisation was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)

scan_protocol: Scanning was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)

data_processing: Data was processed and normalised using the pipeline described by Touleimat and Tost, which takes into account the different chemistry of class I and class II probes and returns Beta values representing the percentage of methylation for that particular CpG dinucleotide (Touleimat and Tost, Epigenomics 2012)

label: Cy3 and Cy5

source_name: HPV-18-transfected human foreskin keratinocytes_line B

label_protocol: Labelling was done as described in the automated protocol of the Infinium HD assay methylation protocol guide (version: December 2010)

growth_protocol: Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines and isolation and culture of primary human foreskin keratinocytes (HFKs) were described previously (Steenbergen et al, Oncogene 1996). The human cervical carcinoma cell lines SiHa, HeLa and CaSki were obtained from the American Type Culture Collection (Manassas, VA, USA) and cultured as described previously (Steenbergen et al, J Natl Cancer Inst 2001).

extract_protocol: Genomic DNA was isolated using the PurelinkTM Genomic DNA Minikit (Life Technologies) following the manufacturer's instructions. 500ng double stranded DNA was bisulfite converted using the EZ DNA Methylation kit (D5002, Zymo Research) according to the manufacturer's instructions.

treatment_protocol: No treatment was performed

tag: cell type

value: primary human foreskin keratinocytes transfected with HPV18

tag: transformation stage

value: anchorage independent


title: AAB-M-060-AU-L

status: Public on Feb 09 2017

type: RNA

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

country: USA

institute: University of Iowa

hyb_protocol: Following fragmentation, 5 ug of cDNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G3000.

data_processing: The data were analyzed with Bioconductor/R and were GCRMA normalized and MAS5 normalized.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: skin biopsy

label_protocol: NuGen Ovation Amplification System 2 and Encore Biotin Module

extract_protocol: PAXgene tissue miRNA kit

tag: patient id

tag: disease status

value: AU

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

tag: gender

value: F

tag: age

tag: registry site

value: Minnesota

tag: microarray batch

tag: dataset

value: Discovery Dataset


title: AAB-HT050-AT-L

value: AT

value: Houston


title: AAB-C048-AT-L

value: Columbia


title: FK16Bp142

type: genomic

molecule: genomic DNA

source_name: HPV-16-transfected human foreskin keratinocytes_line B

value: primary human foreskin keratinocytes transfected with HPV16


title: FK18Ap162

source_name: HPV-18-transfected human foreskin keratinocytes_line A


title: PBMC from Stable  11.2 at T0

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

country: France

institute: Institut national de la santé et de la recherche médicale-INSERM

description: STA, Biological replicate  11 of 190, Technical replicate 2 of 2

hyb_protocol: 1 mg of Cy5-labeled reference aRNA and 1 mg of Cy3-labeled sample aRNA were hybridized on the array for 16 h at 428C in a sealed chamber (Telechem Int., Sunnyval, CA).

scan_protocol: Hybridized slides were scanned by fluorescence confocal microscopy (ScanArray 3000,GSI-Lumonics) using independent laser excitation of the two fluorescent dyes at 532 and 633 nm at a 10 mm/pixel resolution. Fluorescence values and ratios were extracted with the GenePix Pro 5.1 software.

data_processing: The data were normalized using a lowest fit approach independently applied to each log ratio distributions.

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

label_protocol: All aRNA samples were fragmented using RNA fragmentation Reagents (Ambion) according to the manufacturer’s protocols. Fragmented aRNA  were labeled with Cyanine 3 (Cy3; Amersham Biosciences, Buckinghamshire, UK). As the reference for the hybridization, aRNA were prepared as described from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment. This referential aRNA was pooled and labeled with Cyanine 5 (Cy5). Cyanine incorporation and aRNA quantities were confirmed using a Nanodrop ND1000 spectrometer.

extract_protocol: Ten milliliters of peripheral blood were collected in EDTA tubes. Peripheral Blood Mononuclear Cells (PBMC) were separated on a Ficoll layer (Eurobio, Les Ulis, France) and frozen in Trizol1 reagent (Invitrogen, Life Technologies, CA). One microgram of total RNA (tRNA) of each sample was subjected to amplification using the Amino Allyl MessageAmp TM II aRNA Amplification Kit (Ambion, Austin, TX) according to the manufacturer’s protocols. Quality and quantity of tRNA and amplified RNA (aRNA) was tested by an Agilent 2100 Bioanalyser.

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA011.2

tag: tissue

value: PBMC from STA011

tag: individual replicate

value: STA 11 of 190

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: PBMC from Stable  11.1 at T0

description: STA, Biological replicate  11 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA011.1

value: Replicate 1 of 2


title: FK16Ap220

source_name: HPV16-transfected human foreskin keratinocytes_line A


title: AABM046-AAP-NL

value: AAP

value: NL


title: PBMC from Stable  10.2 at T0

description: STA, Biological replicate  10 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA010.2

value: PBMC from STA010

value: STA 10 of 190


title: genomic DNA from 9741950032_R05C01

city: New Haven

first: Ke

last: Xu

address: 300 George St.

department: department of psychiatry

institute: Yale University

description: 9741950032_R05C01: Sample 271

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

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

data_processing: GenomeStudio V2011.1

label: Cy5 and Cy3

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: DNAs were extracted from whole blood using the standard protocol.

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9701417085_R04C01

description: 9701417085_R04C01: Sample 270


title: AAB-C020-AAP.T-NL

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: gender

value: M

tag: age


title: AAB-C038-AAP-L

value: L

tag: registry site

tag: microarray batch

tag: dataset


title: genomic DNA from 9701417107_R04C02

description: 9701417107_R04C02: Sample 268

value: Other


title: AABM046-AAP-L

value: F

value: Minnesota

value: Discovery Dataset


title: EK942RS

source_name: primary human foreskin keratinocytes donor 2

tag: cell type

value: primary human foreskin keratinocytes

tag: transformation stage

value: normal


title: PC3 rep1

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

country: Canada

institute: McGill

description: replicate 1

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing: Genome Studio (Illumina; version 2011.1, Methylation module (Version 1.9.0)

source_name: PC3 cell line

label_protocol: Standard Illumina Protocol (Cy5 and Cy3)

growth_protocol: HepG2, SKHep1 and MCF-7 cells were maintained in MEM medium (Gibco, Invitrogen, Life Technologies). MCF7 cells were cultured with 0.01 mg/ml of insulin (Invitrogen, Carlsbad, California). MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle’s medium (Invitrogen). PC3 and LNCaP were cultured in RPMI1640 media (Gibco, Invitrogen, Life Technologies). All media were supplemented with 2 mmol/L glutamine (Sigma-Aldrich), 10% FBS (Gibco), 1 U/mL penicillin and 1 mg/mL streptomycin (Gibco).

extract_protocol: Cell were resuspended first in cell lysis buffer lysate and incubated with RNAase A (50 U/mg; 30 min; Roche) followed by incubation with proteinase K (20 μl; 20 mg/ml; Roche, Basel, Switzerland) at 55 C for 12 h. Samples were treated  and phenol-chloroform (1:1). To precipitate DNA, ethanol [95% (vol/vol)] was added. The pellet was washed and redissolved in buffer DNAse free double distillued water.

value: male

tag: sample type

value: cell line

tag: disease state

value: cancer

tag: cell line

value: PC3 cell line


title: genomic DNA from 9407201144_R01C01

description: 9407201144_R01C01: Sample 267

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex

tag: gran


title: EK074p5

source_name: primary human foreskin keratinocytes donor 1


title: genomic DNA from 9741950016_R03C02

description: 9741950016_R03C02: Sample 266

tag: nk

tag: bcell

tag: mono


title: PBMC from Stable  10.1 at T0

description: STA, Biological replicate  10 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA010.1

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PC3 rep3

description: replicate 3

tag: gender


title: PC3 rep2

description: replicate 2


title: PBMC from Stable  9.1 at T0

description: STA, Biological replicate  9 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA009.1

value: PBMC from STA009

value: STA 9 of 190


title: PBMC from Stable  8.2 at T0

description: STA, Biological replicate  8 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA008.2

value: PBMC from STA008

value: STA 8 of 190

value: Replicate 2 of 2


title: genomic DNA from 9407210065_R02C01

description: 9407210065_R02C01: Sample 265

value: Other


title: genomic DNA from 9701417139_R06C02

description: 9701417139_R06C02: Sample 264


title: AAB-N-C032-Normal-NC

tag: patient id

tag: disease status

value: Normal

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NC

value: M

tag: age

tag: registry site

value: Columbia

tag: microarray batch

tag: dataset


title: SKHep1 rep2

description: replicate 2

source_name: SKHep1 cell line

value: male

tag: sample type

tag: disease state

tag: cell line

value: SKHep1 cell line


title: SKHep1 rep3

description: replicate 3

value: cell line

value: cancer


title: AAB-C020-AAP.T-L

value: L

value: Discovery Dataset


title: AAB-N-C034-Normal-NC


title: genomic DNA from 9701417107_R03C02

description: 9701417107_R03C02: Sample 263

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell


title: PBMC from Stable  8.1 at T0

description: STA, Biological replicate  8 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA008.1

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PBMC from Stable  7.2 at T0

description: STA, Biological replicate  7 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA007.2

value: PBMC from STA007

value: STA 7 of 190


title: AAB-C047-AT-L

source_name: skin biopsy

tag: patient id

tag: disease status

value: AT

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: gender

tag: age

tag: registry site


title: AAB-N-C030-Normal-NC

value: F

tag: microarray batch

tag: dataset


title: AAB-M044-AU-L

value: AU

value: Minnesota


title: genomic DNA from 9701417139_R04C01

description: 9701417139_R04C01: Sample 262

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: mono


title: LNCaP rep1

description: replicate 1

source_name: LNCaP cell line

tag: sample type

tag: disease state

tag: cell line

value: LNCaP cell line


title: AAB-HT017-AAP.T-NL

value: NL

value: M

value: Houston


title: genomic DNA from 9701417086_R01C02

description: 9701417086_R01C02: Sample 261

tag: dmgsex

tag: gran

tag: nk

tag: bcell


title: genomic DNA from 9701417107_R02C01

description: 9701417107_R02C01: Sample 260


title: PBMC from Stable  6.1 at T0

description: STA, Biological replicate  6 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA006.1

tag: tissue

value: PBMC from STA006

tag: individual replicate

value: STA 6 of 190

tag: techical replicate

tag: time point


title: PBMC from Stable  6.2 at T0

description: STA, Biological replicate  6 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA006.2

value: Replicate 2 of 2


title: SKHep1 rep1

description: replicate 1

tag: gender

value: male

value: cell line

value: cancer

value: SKHep1 cell line


title: HepG2 rep1

description: replicate 1

source_name: HepG2 cell line

value: HepG2 cell line


title: AAB-HT018-AAP-NL

tag: patient id

tag: disease status

value: AAP

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

tag: microarray batch

tag: dataset

value: Discovery Dataset


title: genomic DNA from 9407201144_R02C01

description: 9407201144_R02C01: Sample 269

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: mono


title: genomic DNA from 9701417107_R01C01

description: 9701417107_R01C01: Sample 259

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell


title: PBMC from Stable  4.2 at T0

description: STA, Biological replicate  4 of 190, Technical replicate 2 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA004.2

tag: tissue

value: PBMC from STA004

tag: individual replicate

value: STA 4 of 190

tag: techical replicate

tag: time point


title: HepG2 rep2

description: replicate 2

tag: gender

tag: disease state

tag: cell line


title: MDA-MB-231 rep1

description: replicate 1

source_name: MDA-MB-231 cell line

value: female

value: MDA-MB-231 cell line


title: genomic DNA from 9701417081_R02C02

description: 9701417081_R02C02: Sample 258

source_name: whole blood


title: genomic DNA from 9701417141_R06C01

description: 9701417141_R06C01: Sample 257


title: PBMC from Stable  5.2 at T0

description: STA, Biological replicate  5 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA005.2

value: PBMC from STA005

value: STA 5 of 190


title: HepG2 rep3

description: replicate 3


title: MDA-MB-231 rep3

description: replicate 3


title: AAB-C014-AAP-NL

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NL

value: F

tag: age

tag: registry site

value: Columbia

tag: microarray batch

tag: dataset


title: PBMC from Stable  3.2 at T0

description: STA, Biological replicate  3 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA003.2

value: PBMC from STA003

value: STA 3 of 190

value: Replicate 2 of 2


title: PBMC from Stable  5.1 at T0

description: STA, Biological replicate  5 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA005.1

value: Replicate 1 of 2


title: MCF7 rep3

description: replicate 3

source_name: MCF7 cell line

value: cell line

value: cancer

value: MCF7 cell line


title: genomic DNA from 9407201144_R05C02

description: 9407201144_R05C02: Sample 255

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: mono


title: genomic DNA from 9701417086_R05C01

description: 9701417086_R05C01: Sample 256

tag: bcell


title: AAB-HT018-AAP-L

value: AAP

value: L

tag: gender

value: Houston

value: Discovery Dataset


title: PBMC from Stable  4.1 at T0

description: STA, Biological replicate  4 of 190, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA004.1

tag: tissue

value: PBMC from STA004

tag: individual replicate

value: STA 4 of 190

tag: techical replicate

tag: time point


title: MCF7 rep2

description: replicate 2

value: female

tag: disease state

tag: cell line


title: AAB-HT017-AAP.T-L

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: M

tag: age

tag: registry site

tag: microarray batch

tag: dataset


title: AAB-N-C028-Normal-NC

value: Normal

value: NC

value: F

value: Columbia


title: AAB-C014-AAP-L


title: PBMC from Stable  3.1 at T0

description: STA, Biological replicate  3 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA003.1

value: PBMC from STA003

value: STA 3 of 190

value: Replicate 1 of 2


title: PBMC from Stable  7.1 at T0

description: STA, Biological replicate  7 of 190, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA007.1

value: PBMC from STA007

value: STA 7 of 190


title: genomic DNA from 9701417141_R05C01

description: 9701417141_R05C01: Sample 253

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex

tag: gran

tag: nk

tag: mono


title: AAB-N-C035-Normal-NC

tag: gender


title: PBMC from Stable  2.2 at T0

description: STA, Biological replicate  2 of 190, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA002.2

tag: tissue

value: PBMC from STA002

tag: individual replicate

value: STA 2 of 190

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: genomic DNA from 9701417086_R06C01

description: 9701417086_R06C01: Sample 254

value: Black

tag: bcell


title: PBMC from Stable  2.1 at T0

description: STA, Biological replicate  2 of 190, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA002.1


title: AAB-N-C029-Normal-NC

source_name: skin biopsy

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: Discovery Dataset


title: LNCaP rep2

description: replicate 2

source_name: LNCaP cell line

value: male

value: cell line

tag: disease state

value: cancer

tag: cell line

value: LNCaP cell line


title: genomic DNA from 9741950016_R01C01

description: 9741950016_R01C01: Sample 252

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC from Stable  1.1 at T0

description: STA, Biological replicate  1 of 190, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA001.1

tag: tissue

value: PBMC from STA001

value: STA 1 of 190


title: MCF7 rep1

description: replicate 1

tag: gender

value: female

value: MCF7 cell line


title: PBMC from Stable  1.2 at T0

description: STA, Biological replicate  1 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA001.2

tag: individual replicate

tag: techical replicate

tag: time point


title: PBMC from Tolerant 17.2 at T0

description: TOL, Biological replicate  21 of 21, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL017.2

value: PBMC from TOL017

value: TOL 21 of 21


title: genomic DNA from 9407201144_R03C01

description: 9407201144_R03C01: Sample 250

tag: nk

tag: bcell

tag: mono


title: PBMC from Stable  9.2 at T0

description: STA, Biological replicate  9 of 190, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), STA009.2

value: PBMC from STA009

value: STA 9 of 190


title: AAB-N-C026-Normal-NC

tag: patient id

tag: disease status

value: Normal

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NC

value: M

tag: age

tag: registry site

value: Columbia

tag: microarray batch

tag: dataset


title: AAB-HT041-AU-L

value: AU

value: L

value: F

value: Houston

value: Discovery Dataset


title: PBMC from Tolerant 17.1 at T0

description: TOL, Biological replicate  21 of 21, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL017.1

value: Replicate 1 of 2


title: genomic DNA from 9701417085_R05C02

description: 9701417085_R05C02: Sample 249

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran


title: AAB-C043-AU-L

tag: gender


title: AAB-N-C027-Normal-NC


title: Methylation of uterine leiomyosarcoma tissue from case8

city: Fukuoka

first: Tomoko

last: Miyata

state: Fukuoka

address: 3-1-1 Maedashi, Higashi-ku

department: Gynecology and Obstetrics

country: Japan

institute: Kyushu University

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

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Genome Studio V2011.2
The methylation level of each of the > 480,000 CpG sites was calculated using the GenomeStudio Methylation Module 1.9.0 (Illumina). Normalization was performed using Normalization to Internal Controls and Background Subtraction options implemented in the Methylation Module 1.9.0.

label: Cy3, Cy5

source_name: uterine leiomyosarcoma

label_protocol: Standard Illumina labelling protocol

growth_protocol: All specimens were isolated during the primary uterus surgery at the Department of Obstetrics and Gynecology in the Kyushu University Hospital, immediately frozen in liquid nigrogen, and stored at -80C˚. SKN (RBRC-RCB0513) obtained from RIKEN BRC, and SK-UT1 (HTB-114TM) and SK-UT1B (HTB-115TM) obtained from American Type Culture Collection. All cells were cultured under standard culture conditions (at 37°C, 5% CO2 in air) in a medium supplemented with 15% fetal bovine serum and Penicillin-Streptomycin-Glutamine Liquid (final 1x, GIBCO 10378-016). HamF12 medium was used for SKN cells, and Eagle medium was used for SK-UT1 and SK-UT1B cells.

extract_protocol: Genomic DNA was isolated using All Prep DNA/RNA Midi kit (Qiagen, Valencia, CA) according to the manufacturer’s instruction.

tag: tissue

value: uterine leiomyosarcoma

value: female


title: Methylation of cell line of human uterine leiomyosarcoma SK-UT1B

source_name: cell line

tag: cell line


title: Methylation of cell line of human uterine leiomyosarcoma SK-UT1


title: Methylation of cell line of human uterine leiomyosarcoma SKN

value: SKN


title: Methylation of uterine leiomyosarcoma tissue from case9


title: AAB-C037-AT-L

value: AT


title: genomic DNA from 9701417085_R03C02

description: 9701417085_R03C02: Sample 248

tag: nk

tag: bcell


title: AAB-C013-AU-L

tag: patient id


title: PBMC from Tolerant 16.2 at T0

description: TOL, Biological replicate  20 of 21, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL016.2

value: PBMC from TOL016

tag: individual replicate

value: TOL 20 of 21

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: PBMC from Tolerant 16.1 at T0

description: TOL, Biological replicate  20 of 21, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL016.1


title: genomic DNA from 9407210093_R01C01

description: 9407210093_R01C01: Sample 247

tag: mono


title: AAB-C033-AU-L

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

tag: microarray batch

tag: dataset


title: Methylation of uterine leiomyosarcoma tissue from case7

tag: gender


title: MDA-MB-231 rep2

description: replicate 2

source_name: MDA-MB-231 cell line

value: cell line

tag: disease state

value: cancer

value: MDA-MB-231 cell line


title: PBMC_sample40

city: University of Tampere

first: Laura

middle: Eeva Marketta

last: Kananen

state: Pirkanmaa

address: Biokatu 6

department: Department of Microbiology and immunology

country: Finland

institute: University of Tampere/School of Medicine

description: no cell type characterization data available

hyb_protocol: bisulphite-converted DNA was subjected to whole-genome amplification after which the DNA was enzymatically fragmented and hybridised to the Infinium HumanMethylation450 BeadChip

scan_protocol: The BeadChips were scanned with the Illumina iScan reader

data_processing: 1st) The data (N=122) was preprocessed as methylumiset object by using R package wateRmelon(normalization&background correction with dasen; pfilter with default settings). Unspecific probes were excluded.  The batch effect of the Infinium chemistries was adjusted with BMIQ algorithm and the batch effect of two different run series was adjusted with EB-based algorithm by using R package Combat.    2nd) The preprosessed beta values were regressed in the variable dispersion beta regression model (implemented in R package betareg) with gender and cell type proportions as predictors after which the standardized weighted residuals were extracted and used in all statistical analyses --> There were 7 samples without information about cell type characterization and thus the total number of samples after residual extraction was 115. (The final statistical analysis was made with N=111 samples because there were 4 samples without information about BMI or MMSE)

source_name: PBMC from fresh blood

label_protocol: Standard Illumina protocol using Cy5 and Cy3

growth_protocol: Fresh blood sampleswere collected to EDTA-tubes. The peripheral blood mononuclear cells (PBMCs) were separated with Ficoll-Paque density gradient

extract_protocol: DNA was extracted from PBMCs using the QIAamp DNA Mini kit (Qiagen, CA, USA)

tag: cell type

value: PBMC


title: AAB-HT012-AAP-NL

value: AAP

value: NL

value: M


title: PBMC_sample22


title: genomic DNA from 9701417141_R01C02

description: 9701417141_R01C02: Sample 245

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk


title: PBMC from Tolerant 15.2 at T0

description: TOL, Biological replicate  19 of 21, Technical replicate 2 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL015.2

tag: tissue

value: PBMC from TOL015

tag: individual replicate

value: TOL 19 of 21

tag: techical replicate

tag: time point


title: genomic DNA from 9407201127_R02C02

description: 9407201127_R02C02: Sample 246

value: Other

tag: bcell

tag: mono


title: PBMC_sample20


title: AAB-HT011-AAP-NL

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: Houston

tag: microarray batch

tag: dataset

value: Discovery Dataset


title: genomic DNA from 9701417085_R03C01

description: 9701417085_R03C01: Sample 244

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex


title: PBMC_sample16

tag: cell type


title: Methylation of uterine leiomyoma tissue from case5

source_name: uterine leiomyoma

tag: tissue

value: uterine leiomyoma

tag: gender

value: female


title: genomic DNA from 9407210065_R04C01

description: 9407210065_R04C01: Sample 243

tag: gran

tag: nk


title: PBMC_sample6


title: PBMC_sample74


title: PBMC_sample12


title: Methylatiom of uterine leiomyoma tissue from case6


title: Methylation of uterine normal myometrium tissue from case3

source_name: normal uterine myometrium

value: normal uterine myometrium


title: genomic DNA from 9701417139_R03C02

description: 9701417139_R03C02: Sample 242

value: Black

tag: bcell

tag: mono


title: genomic DNA from 9407210107_R05C01

description: 9407210107_R05C01: Sample 251


title: genomic DNA from 9701417085_R01C01

description: 9701417085_R01C01: Sample 241


title: PBMC from Tolerant 15.1 at T0

description: TOL, Biological replicate  19 of 21, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL015.1

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: Methylation of uterine leiomyoma tissue from case4

tag: age


title: PBMC from Tolerant 13.2 at T0

description: TOL, Biological replicate  17 of 21, Technical replicate 2 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL013.2

value: PBMC from TOL013

value: TOL 17 of 21

value: Replicate 2 of 2


title: Methylation of uterine normal myometrium tissue from case2


title: PBMC from Tolerant 14.2 at T0

description: TOL, Biological replicate  18 of 21, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL014.2

value: PBMC from TOL014

value: TOL 18 of 21


title: PBMC from Tolerant 14.1 at T0

description: TOL, Biological replicate  18 of 21, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL014.1


title: PBMC from Tolerant 13.1 at T0

description: TOL, Biological replicate  17 of 21, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL013.1


title: genomic DNA from 9407201144_R06C02

description: 9407201144_R06C02: Sample 240


title: PBMC from Tolerant 12.2 at T0

description: TOL, Biological replicate  16 of 21, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL012.2

value: PBMC from TOL012

value: TOL 16 of 21


title: AAB-HT012-AAP-L

source_name: skin biopsy

tag: patient id

tag: disease status

value: AAP

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

value: M

tag: registry site

tag: microarray batch

tag: dataset


title: AAB-HT011-AAP-L

value: Houston

value: Discovery Dataset


title: AAB-N-C025-Normal-NC

value: Normal

value: NC

value: Columbia


title: Methylation of uterine normal myometrium tissue from case1

tag: tissue

value: normal uterine myometrium

value: female


title: genomic DNA from 9701417139_R05C02

description: 9701417139_R05C02: Sample 238

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex


title: PBMC from Tolerant 12.1 at T0

description: TOL, Biological replicate  16 of 21, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL012.1

value: Replicate 1 of 2


title: AAB-C024-Normal-NC

tag: gender


title: genomic DNA from 9701417107_R06C02

description: 9701417107_R06C02: Sample 239

value: Black

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Tolerant 11.2 at T0

description: TOL, Biological replicate  15 of 21, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL011.2

value: PBMC from TOL011

tag: individual replicate

value: TOL 15 of 21

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: AAB-HT010-AAP.T-NL

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: NL

value: F

tag: age

tag: registry site


title: genomic DNA from 9701417139_R04C02

description: 9701417139_R04C02: Sample 237

tag: hiv

tag: agebl


title: PBMC from Tolerant 11.1 at T0

description: TOL, Biological replicate  15 of 21, Technical replicate 1 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL011.1

tag: tissue


title: genomic DNA from 9701417081_R05C01

description: 9701417081_R05C01: Sample 236

tag: racecomg

tag: dmgsex


title: genomic DNA from 9407201144_R04C01

description: 9407201144_R04C01: Sample 235

tag: gran

tag: nk


title: AAB-HT010-AAP.T-L

value: L

tag: gender

tag: microarray batch

tag: dataset


title: AAB-N-C022-Normal-NC


title: genomic DNA from 9701417139_R03C01

description: 9701417139_R03C01: Sample 234

tag: bcell

tag: mono


title: AAB-N-C021-Normal-NC

tag: patient id


title: PBMC from Tolerant 10.2 at T0

description: TOL, Biological replicate  14 of 21, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL010.2

value: PBMC from TOL010

tag: individual replicate

value: TOL 14 of 21

tag: techical replicate

tag: time point


title: genomic DNA from 9701417085_R02C01

description: 9701417085_R02C01: Sample 233

tag: hiv


title: genomic DNA from 9701417139_R01C01

description: 9701417139_R01C01: Sample 232

tag: agebl


title: AAB-HT001-AT-L

tag: disease status

value: AT

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site

value: Houston

value: Discovery Dataset


title: PBMC from Tolerant 9.1 at T0

description: TOL, Biological replicate  13 of 21, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL009.1

tag: tissue

value: PBMC from TOL009

value: TOL 13 of 21


title: PBMC_sample99

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted

source_name: PBMC from fresh blood

tag: cell type

value: PBMC

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: AAB-HT006-AAP-NL

tag: patient id

value: AAP

tag: gender

tag: microarray batch

tag: dataset


title: AAB-HT002-AAP-NL

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

tag: age

tag: registry site


title: AAB-HT003-AAP-NL

value: M


title: AAB-C007-AU-L

value: AU

value: Columbia


title: PBMC from Tolerant 8.1 at T0

description: TOL, Biological replicate  12 of 21, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL008.1

tag: tissue

value: PBMC from TOL008

tag: individual replicate

value: TOL 12 of 21

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: PBMC from Tolerant 9.2 at T0

description: TOL, Biological replicate  13 of 21, Technical replicate 2 of 2

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL009.2

value: Replicate 2 of 2


title: genomic DNA from 9407201144_R02C02

description: 9407201144_R02C02: Sample 231

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Tolerant 8.2 at T0

description: TOL, Biological replicate  12 of 21, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL008.2


title: PBMC_sample98

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC from Tolerant 10.1 at T0

description: TOL, Biological replicate  14 of 21, Technical replicate 1 of 2

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL010.1

tag: tissue

value: PBMC from TOL010

tag: individual replicate

value: TOL 14 of 21

tag: techical replicate

tag: time point


title: PBMC from Tolerant 7.2 at T0

description: TOL, Biological replicate  11 of 21, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL007.2

value: PBMC from TOL007

value: TOL 11 of 21


title: PBMC from Tolerant 7.1 at T0

description: TOL, Biological replicate  11 of 21, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL007.1


title: genomic DNA from 9407201127_R01C02

description: 9407201127_R01C02: Sample 229

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9701417107_R04C01

description: 9701417107_R04C01: Sample 230


title: AAB-HT003-AAP-L

tag: patient id

tag: disease status

tag: skintype (l=lesional, nl=nonlesional, nc=normal control)

value: L

tag: gender

tag: age

tag: registry site

value: Houston

tag: microarray batch

tag: dataset

value: Discovery Dataset


title: AAB-HT002-AAP-L

value: AAP

value: F


title: AAB-HT006-AAP-L


title: genomic DNA from 9701417081_R01C02

description: 9701417081_R01C02: Sample 228

value: White


title: genomic DNA from 9701417139_R02C01

description: 9701417139_R02C01: Sample 227


title: PBMC_sample96

tag: cell type

value: PBMC

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: genomic DNA from 9701417081_R06C01

description: 9701417081_R06C01: Sample 226

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9407201127_R05C01

description: 9407201127_R05C01: Sample 225


title: PBMC_sample91

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion


title: PBMC_sample93

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch


title: PBMC from Tolerant 6.2 at T1

description: TOL, Biological replicate  10 of 21, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL006t.2

tag: tissue

value: PBMC from TOL006

tag: individual replicate

value: TOL 10 of 21

tag: techical replicate

tag: time point


title: PBMC_sample97

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample92


title: PBMC from Tolerant 6.1 at T1

description: TOL, Biological replicate  10 of 21, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL006t.1

value: Replicate 1 of 2


title: genomic DNA from 9407201108_R01C02

description: 9407201108_R01C02: Sample 224

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Tolerant 6.1 at T0

description: TOL, Biological replicate  9 of 21, Technical replicate 1 of 4

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL006.1

tag: tissue

value: TOL 9 of 21

value: Replicate 1 of 4


title: BRB8

city: Taichung

first: Tzu-Hung

last: Hsiao

address: 1650 Taiwan Boulevard Sect. 4

department: Department of Medical Research

country: Taiwan

institute: Taichung Veterans General Hospital

description: Gene expression data from BRB8

hyb_protocol: The biotinylated cRNA targets were then cleaned up, fragmented, and hybridized to GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA). After 16 hours of hybridization at 45 °C, the arrays were washed by Fluidics Station 450

scan_protocol: Chips were scanned using the GeneChip Scanner 3000

data_processing: Background-adjusted signals were normalized by Robust Multichip Analysis (RMA) and quantile normalization algorithm.

source_name: pre-treatment liver biopsy specimen of interferon alpha-2b thearpy

label_protocol: The IVT reaction was carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

extract_protocol: Total RNA from the tissue specimens were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA)  according to the manufacturer's instructions.

tag: response

value: responder

tag: pre or post treatment

value: pre

tag: age

tag: gender

tag: alt

tag: viral titer in serum

value: liver


title: PBMC from Tolerant 6.3 at T0

description: TOL, Biological replicate  9 of 21, Technical replicate 3 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL006.3

tag: individual replicate

tag: techical replicate

value: Replicate 3 of 4

tag: time point


title: PBMC from Tolerant 6.4 at T0

description: TOL, Biological replicate  9 of 21, Technical replicate 4 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL006.4

value: Replicate 4 of 4


title: BRA5

description: Gene expression data from BRA5

source_name: post-treatment liver biopsy specimen of interferon alpha-2b thearpy

value: post

value: M


title: BRB9

description: Gene expression data from BRB9


title: PBMC_sample95

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: BRA6

description: Gene expression data from BRA6

tag: response

tag: pre or post treatment

tag: age

tag: gender

tag: tissue


title: BRB10

description: Gene expression data from BRB10

tag: alt

tag: viral titer in serum


title: BRA7

description: Gene expression data from BRA7


title: PBMC_sample94

tag: cell type

tag: cd4+/cd8+ cell ratio


title: genomic DNA from 9701417141_R06C02

description: 9701417141_R06C02: Sample 223

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC_sample90

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted; sample missing information about BMI

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: mini mental state examination (mmse)


title: BRA4

description: Gene expression data from BRA4

tag: response

tag: pre or post treatment

tag: age

tag: gender

tag: alt

tag: viral titer in serum

tag: tissue


title: genomic DNA from 9701417086_R02C02

description: 9701417086_R02C02: Sample 222

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: dmgsex

tag: gran

tag: nk

tag: bcell


title: PBMC from Tolerant 5.2 at T1

description: TOL, Biological replicate  8 of 21, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL005t.2

value: PBMC from TOL005

tag: individual replicate

value: TOL 8 of 21

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: PBMC from Tolerant 6.2 at T0

description: TOL, Biological replicate  9 of 21, Technical replicate 2 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL006.2

value: PBMC from TOL006

value: Replicate 2 of 4


title: PBMC_sample89

source_name: PBMC from fresh blood

tag: cell type

value: PBMC

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: genomic DNA from 9407210061_R03C01

description: 9407210061_R03C01: Sample 220

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex

tag: gran

tag: nk

tag: mono


title: PBMC_sample9

tag: cell type

tag: cd4+/cd8+ cell ratio


title: genomic DNA from 9407201127_R06C01

description: 9407201127_R06C01: Sample 221

tag: bcell


title: BRA3

description: Gene expression data from BRA3

tag: response

tag: pre or post treatment

tag: age

tag: gender

value: F

tag: alt

tag: viral titer in serum

tag: tissue


title: genomic DNA from 9701417141_R02C02

description: 9701417141_R02C02: Sample 219

tag: hiv


title: PBMC from Tolerant 5.1 at T1

description: TOL, Biological replicate  8 of 21, Technical replicate 1 of 2

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL005t.1

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 2

tag: time point


title: genomic DNA from 9701417085_R06C02

description: 9701417085_R06C02: Sample 218

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk


title: PBMC_sample88

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC from Tolerant 5.3 at T0

description: TOL, Biological replicate  7 of 21, Technical replicate 3 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL005.3

tag: tissue

tag: individual replicate

value: TOL 7 of 21

tag: techical replicate

tag: time point


title: BRA1

description: Gene expression data from BRA1

tag: response

value: responder

tag: pre or post treatment

value: pre

tag: age

tag: gender

tag: alt

tag: viral titer in serum

value: liver


title: PBMC from Tolerant 5.4 at T0

description: TOL, Biological replicate  7 of 21, Technical replicate 4 of 4

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL005.4

value: Replicate 4 of 4


title: genomic DNA from 9701417107_R05C02

description: 9701417107_R05C02: Sample 217

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: BRA2

description: Gene expression data from BRA2

value: post

value: M

tag: tissue


title: PBMC from Tolerant 5.2 at T0

description: TOL, Biological replicate  7 of 21, Technical replicate 2 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL005.2

value: PBMC from TOL005

tag: individual replicate

tag: techical replicate


title: BRB7

description: Gene expression data from BRB7

tag: response

tag: pre or post treatment


title: PBMC_sample87

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: BRB6

description: Gene expression data from BRB6

tag: age

tag: gender

tag: alt

tag: viral titer in serum

tag: tissue


title: genomic DNA from 9407201144_R04C02

description: 9407201144_R04C02: Sample 216

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: BRB5

description: Gene expression data from BRB5

tag: response

tag: pre or post treatment


title: PBMC from Tolerant 4.2 at T1

description: TOL, Biological replicate  6 of 21, Technical replicate 2 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL004t.2

value: PBMC from TOL004

tag: individual replicate

value: TOL 6 of 21

tag: techical replicate

value: Replicate 2 of 2

tag: time point


title: PBMC_sample83

tag: cell type

value: PBMC

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample82


title: genomic DNA from 9407201144_R03C02

description: 9407201144_R03C02: Sample 215

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Tolerant 4.1 at T1

description: TOL, Biological replicate  6 of 21, Technical replicate 1 of 2

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL004t.1

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: genomic DNA from 9701417141_R04C01

description: 9701417141_R04C01: Sample 214


title: PBMC_sample86

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)


title: PBMC_sample84

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample85


title: BRB3

description: Gene expression data from BRB3

tag: response

tag: pre or post treatment

tag: age

tag: gender

value: F

tag: alt

tag: viral titer in serum


title: genomic DNA from 9701417086_R04C01

description: 9701417086_R04C01: Sample 213

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9701417139_R02C02

description: 9701417139_R02C02: Sample 212


title: PBMC from Tolerant 5.1 at T0

description: TOL, Biological replicate  7 of 21, Technical replicate 1 of 4

tag: sample type

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL005.1

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 1 of 4

tag: time point


title: PBMC from Tolerant 4.4 at T0

description: TOL, Biological replicate  5 of 21, Technical replicate 4 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL004.4

value: TOL 5 of 21


title: PBMC from Tolerant 4.1 at T0

description: TOL, Biological replicate  5 of 21, Technical replicate 1 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL004.1


title: PBMC from Tolerant 4.3 at T0

description: TOL, Biological replicate  5 of 21, Technical replicate 3 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL004.3

value: Replicate 3 of 4


title: PBMC_sample80

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: genomic DNA from 9407210063_R06C01

description: 9407210063_R06C01: Sample 211

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: BRB2

description: Gene expression data from BRB2

source_name: pre-treatment liver biopsy specimen of interferon alpha-2b thearpy

tag: response

value: responder

tag: pre or post treatment

value: pre

tag: age

tag: gender

tag: alt

tag: viral titer in serum

tag: tissue

value: liver


title: genomic DNA from 9407210074_R02C01

description: 9407210074_R02C01: Sample 210


title: PBMC_sample81

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: genomic DNA from 9407210061_R03C02

description: 9407210061_R03C02: Sample 209

tag: hiv

tag: agebl

tag: racecomg

value: Black

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Tolerant 4.2 at T0

description: TOL, Biological replicate  5 of 21, Technical replicate 2 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL004.2

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 2 of 4

tag: time point


title: genomic DNA from 9701417086_R02C01

description: 9701417086_R02C01: Sample 208

source_name: whole blood


title: PBMC from Tolerant 3.2 at T1

description: TOL, Biological replicate  4 of 21, Technical replicate 2 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL003t.2

value: PBMC from TOL003

value: TOL 4 of 21


title: BRB4

description: Gene expression data from BRB4

tag: response

tag: pre or post treatment

tag: age

tag: gender

value: M

tag: alt

tag: viral titer in serum


title: BRB1

description: Gene expression data from BRB1


title: genomic DNA from 9407210074_R05C01

description: 9407210074_R05C01: Sample 207

tag: hiv

tag: agebl

tag: racecomg


title: PBMC from Tolerant 3.1 at T1

description: TOL, Biological replicate  4 of 21, Technical replicate 1 of 2

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL003t.1

value: Replicate 1 of 2


title: PBMC_sample8

source_name: PBMC from fresh blood

tag: cell type

value: PBMC

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC from Tolerant 3.2 at T0

description: TOL, Biological replicate  3 of 21, Technical replicate 2 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL003.2

tag: tissue

tag: individual replicate

value: TOL 3 of 21

tag: techical replicate

tag: time point


title: genomic DNA from 9407210063_R02C02

description: 9407210063_R02C02: Sample 206

tag: hiv

tag: agebl

tag: racecomg

value: White

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Tolerant 3.3 at T0

description: TOL, Biological replicate  3 of 21, Technical replicate 3 of 4

value: pool of 169 PBMC samples from Stable patients (STA)

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL003.3


title: PBMC_sample78

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)


title: PBMC_sample79

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC from Tolerant 3.4 at T0

description: TOL, Biological replicate  3 of 21, Technical replicate 4 of 4

source_name: Total RNA from PBMC of 169 kidney graft recipients with stable graft function and under standard immunosuppressive treatment

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL003.4

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 4 of 4

tag: time point


title: genomic DNA from 9701417085_R02C02

description: 9701417085_R02C02: Sample 205

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: L3MBTL1-KD iPS cells 2

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: 10 ug of cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: Affymetrix GeneArray scanner 7G

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

label: Biotin

source_name: GFP+ iPS cells

label_protocol: 200 ng total RNA converted to cRNA using Affymetrix GeneChip®3' IVT Kit and in vitro transcription resulting into biotin-labeled cRNA, fragmented prior to hybridization (Affymetrix Expression Analysis Technical Manual, as described).

growth_protocol: hES cell medium

extract_protocol: RNA extraction plus kit was used to isolate RNA, and cDNA was made with invitrogen superscriptase.

treatment_protocol: Two independent clones of undifferentiated iPS were utilized for microarray. Samples are lentivirally infected to express shRNA (targeting l3mbtl1 or luciferase) and GFP.

tag: cell line

value: iCB 1.9 iPS

tag: lentivirus

value: shRNAs targeting L3MBTL1


title: PBMC_sample77

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: PBMC from Tolerant 2.4 at T0

description: TOL, Biological replicate  2 of 21, Technical replicate 4 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL002.4

tag: tissue

value: PBMC from TOL002

tag: individual replicate

value: TOL 2 of 21

tag: techical replicate

tag: time point


title: PBMC from Tolerant 3.1 at T0

description: TOL, Biological replicate  3 of 21, Technical replicate 1 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL003.1

value: Replicate 1 of 4


title: genomic DNA from 9407210093_R01C02

description: 9407210093_R01C02: Sample 204

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: control iPS cells 2

tag: cell line

tag: lentivirus

value: shRNAs targeting luciferase


title: genomic DNA from 9407210061_R04C02

description: 9407210061_R04C02: Sample 203

value: Black


title: PBMC_sample76

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: mini mental state examination (mmse)


title: PBMC_sample75

tag: body mass index (bmi)


title: L3MBTL1-KD iPS cells 1


title: nasopharyngeal carcinoma, specimen T12

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

country: China

institute: Central South University

description: nasopharyngeal carcinoma

hyb_protocol: Fragmented, biotinylated aRNA was hybridized to Affymetrix HG U133 Plus 2.0 microarrays, as per Affymetrix-recommended procedures.

scan_protocol: Microarray scanning and data acquisition was carried out at the Gene Company (Shanghai, China) using Affymetrix-recommended equipment and procedures.

data_processing: The scanned images were analyzed with Affymetrix GeneChip Operating Software (GCOS) using default parameters to obtain Processed Signal intensities as the raw data. Raw data were normalized with Genespring (Agilent).

source_name: nasopharynx

label_protocol: Polyadenylated RNA was amplified twice using Affymetrix Small Sample Labeling Protocol VII. One-twentieth of second round cDNA was used to assay efficiency of amplification by measuring beta-actin using the Quantitect SYBR Green real time PCR kit (Qiagen, Valencia, CA). Using the BioArray High Yield RNA Labeling Kit (ENZO Life Sciences, Farmingdale, NY), half of the second round cDNA was used to synthesize biotinylated antisense RNA (aRNA).

growth_protocol: Tumor and healthy nasopharyngeal tissue from areas macroscopically not involved in the tumor, was collected with informed consent under approval of the Human Subjects Institutional Review Boards of Central South University, China. After resection, specimens were immediately flash frozen and stored in liquid nitrogen.

extract_protocol: RNA was extracted using Trizol (Invitrogen, Carlsbad, CA), and DNaseI treated.

treatment_protocol: Frozen biopsies were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA) for serial 6 um cryosectioning. Step-sections were stained with hematoxylin and eosin (H&E) and intervening unstained sections were evaluated for cytokeratins using monoclonal mouse anti-human cytokeratin antibody (AE1/AE3, 1:20 dilution) and Envision+ System Peroxidase (DAB) (DAKO Corporation, Carpinteria, CA). Laser capture microdissection (LCM) was performed on tumor samples containing < 70% tumor cells, and to dissect epithelial cells from normal healthy nasopharyngeal specimens. Typically, from one to a few thousand cells per sample were captured.

tag: disease state

value: nasopharyngeal carcinoma


title: PBMC_sample73


title: genomic DNA from 9407201127_R05C02

description: 9407201127_R05C02: Sample 202

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: dmgsex

tag: gran

tag: nk


title: PBMC from Tolerant 2.3 at T0

description: TOL, Biological replicate  2 of 21, Technical replicate 3 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL002.3

tag: tissue

tag: individual replicate

tag: techical replicate

value: Replicate 3 of 4

tag: time point


title: control iPS cells 1

tag: cell line

tag: lentivirus


title: PBMC_sample72

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days


title: PBMC from Tolerant 2.2 at T0

description: TOL, Biological replicate  2 of 21, Technical replicate 2 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL002.2

value: Replicate 2 of 4


title: nasopharyngeal carcinoma, specimen T10

description: nasopharyngeal carcinoma

tag: disease state


title: genomic DNA from 9701417085_R01C02

description: 9701417085_R01C02: Sample 201

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: nasopharyngeal carcinoma, specimen T11

description: nasopharyngeal carcinoma


title: genomic DNA from 9407201127_R06C02

description: 9407201127_R06C02: Sample 200


title: nasopharyngeal carcinoma, specimen T9

description: nasopharyngeal carcinoma


title: genomic DNA from 9701417081_R06C02

description: 9701417081_R06C02: Sample 199


title: PBMC_sample68

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample70

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch


title: genomic DNA from 9407201127_R03C01

description: 9407201127_R03C01: Sample 198


title: PBMC from Tolerant 1.4 at T0

description: TOL, Biological replicate  1 of 21, Technical replicate 4 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL001.4

tag: tissue

value: PBMC from TOL001

tag: individual replicate

value: TOL 1 of 21

tag: techical replicate

tag: time point


title: genomic DNA from 9701417081_R05C02

description: 9701417081_R05C02: Sample 197

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC from Tolerant 1.2 at T0

description: TOL, Biological replicate  1 of 21, Technical replicate 2 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL001.2


title: PBMC_sample71

tag: cell type

value: PBMC

tag: cd4+/cd8+ cell ratio

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days


title: PBMC_sample7

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample66

tag: methylation batch


title: nasopharyngeal carcinoma, specimen T6

description: nasopharyngeal carcinoma

tag: disease state


title: PBMC from Tolerant 1.3 at T0

description: TOL, Biological replicate  1 of 21, Technical replicate 3 of 4

tag: sample type

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL001.3

tag: tissue

tag: individual replicate

tag: techical replicate

tag: time point


title: nasopharyngeal carcinoma, specimen T8

description: nasopharyngeal carcinoma


title: PBMC_sample69

tag: cell type


title: PBMC from Tolerant 1.1 at T0

description: TOL, Biological replicate  1 of 21, Technical replicate 1 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL001.1


title: genomic DNA from 9701417141_R02C01

description: 9701417141_R02C01: Sample 196

source_name: whole blood

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC from Tolerant 2.1 at T0

description: TOL, Biological replicate  2 of 21, Technical replicate 1 of 4

source_name: Total RNA from Peripheral Blood Mononuclear Cells (PBMC), TOL002.1


title: PBMC_sample67

source_name: PBMC from fresh blood

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample65

tag: cell type

tag: methylation batch


title: nasopharyngeal carcinoma, specimen T7

description: nasopharyngeal carcinoma

tag: disease state


title: nasopharyngeal carcinoma, specimen T4

description: nasopharyngeal carcinoma


title: genomic DNA from 9701417085_R06C01

description: 9701417085_R06C01: Sample 194

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex


title: nasopharyngeal carcinoma, specimen T5

description: nasopharyngeal carcinoma


title: genomic DNA from 9407210073_R03C02

description: 9407210073_R03C02: Sample 195

tag: gran

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9701417081_R04C01

description: 9701417081_R04C01: Sample 193


title: genomic DNA from 9701417139_R06C01

description: 9701417139_R06C01: Sample 191


title: genomic DNA from 9407210107_R05C02

description: 9407210107_R05C02: Sample 190


title: PBMC_sample64

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion


title: nasopharyngeal carcinoma, specimen T3

description: nasopharyngeal carcinoma


title: nasopharyngeal carcinoma, specimen T1

description: nasopharyngeal carcinoma


title: nasopharyngeal carcinoma, specimen T2

description: nasopharyngeal carcinoma


title: genomic DNA from 9701417081_R04C02

description: 9701417081_R04C02: Sample 189


title: PBMC_sample63

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: normal nasopharyngeal tissue, specimen N3

description: normal nasopharyngeal epithelia

tag: disease state

value: normal


title: PBMC_sample61

tag: cell type

tag: methylation batch

tag: mini mental state examination (mmse)


title: PBMC_sample62


title: genomic DNA from 9407210074_R05C02

description: 9407210074_R05C02: Sample 188

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex


title: normal nasopharyngeal tissue, specimen N2

description: normal nasopharyngeal epithelia


title: normal nasopharyngeal tissue, specimen N1

description: normal nasopharyngeal epithelia


title: genomic DNA from 9407201127_R04C01

description: 9407201127_R04C01: Sample 187

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC_sample59

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion


title: PBMC_sample60

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: PBMC_sample56

tag: cell type

tag: methylation batch

tag: mini mental state examination (mmse)


title: PBMC_sample57


title: genomic DNA from 9407201108_R05C01

description: 9407201108_R05C01: Sample 185

tag: hiv

tag: agebl

tag: racecomg


title: genomic DNA from 9407201144_R01C02

description: 9407201144_R01C02: Sample 186

tag: dmgsex

tag: gran

tag: nk


title: PBMC_sample55

tag: cd4+/cd8+ cell ratio


title: genomic DNA from 9407201127_R04C02

description: 9407201127_R04C02: Sample 184

value: White

tag: bcell

tag: mono


title: Control_19

city: Roskilde

first: Vibe

last: Skov

address: Koegevej 7-13

department: Hematology

country: Denmark

institute: Roskilde Hospital

description: Gene expression data from control subjects

hyb_protocol: Fragmented aRNA was hybridized to Affymetrix HG-U133 Plus 2.0 chips

scan_protocol: The micorarrays were scanned with the Affymetrix GeneChip Scanner 3000-7G

data_processing: Data were analyzed in R using rma. The regularized t-test limma was used to calculate differences in gene expression between patients and control subjects.

source_name: Whole blood

label_protocol: total RNA was converted to amplified RNA (aRNA) and fragmented using the MessageAmpTM III RNA amplification kit

extract_protocol: Total RNA was extracted from whole-blood using the Paxgene Blood RNA Kit

tag: disease state

value: control

tag: tissue

value: blood


title: Control_20


title: normal nasopharyngeal tissue, specimen N4

description: normal nasopharyngeal epithelia


title: genomic DNA from 9701417107_R02C02

description: 9701417107_R02C02: Sample 182


title: Control_18


title: genomic DNA from 9701417086_R05C02

description: 9701417086_R05C02: Sample 181


title: Control_16


title: Control_15


title: Control_21


title: PBMC_sample54

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)


title: PBMC_sample52

tag: cell type

tag: methylation batch

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: Control_17


title: genomic DNA from 9701417081_R02C01

description: 9701417081_R02C01: Sample 179

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC_sample49

tag: cd4+/cd8+ cell ratio


title: PBMC_sample5


title: Control_13

tag: disease state

tag: tissue


title: PBMC_sample53

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion


title: Control_12


title: Control_14


title: genomic DNA from 9701417139_R05C01

description: 9701417139_R05C01: Sample 178

tag: nk

tag: bcell

tag: mono


title: PBMC_sample48

tag: cell type

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)


title: genomic DNA from 9701417086_R06C02

description: 9701417086_R06C02: Sample 177

tag: hiv

tag: agebl


title: Control_11


title: PBMC_sample58

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: genomic DNA from 9701417141_R05C02

description: 9701417141_R05C02: Sample 176

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC_sample50

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion


title: genomic DNA from 9407210061_R06C02

description: 9407210061_R06C02: Sample 192

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9407201127_R02C01

description: 9407201127_R02C01: Sample 180


title: Control_10

tag: disease state

tag: tissue


title: genomic DNA from 9701417086_R03C01

description: 9701417086_R03C01: Sample 175


title: genomic DNA from 9701417081_R03C01

description: 9701417081_R03C01: Sample 174


title: Control_9


title: PBMC_sample46

tag: cell type

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)


title: genomic DNA from 9701417107_R06C01

description: 9701417107_R06C01: Sample 173

tag: hiv

tag: agebl


title: Control_8


title: genomic DNA from 9407201144_R05C01

description: 9407201144_R05C01: Sample 172

tag: racecomg

tag: dmgsex


title: PBMC_sample45

tag: cd4+/cd8+ cell ratio

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: genomic DNA from 9701417141_R03C01

description: 9701417141_R03C01: Sample 171

tag: gran

tag: nk

tag: bcell


title: PBMC_sample51

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion


title: Control_5

tag: disease state

tag: tissue


title: genomic DNA from 9701417107_R01C02

description: 9701417107_R01C02: Sample 183

tag: mono


title: PBMC_sample42

tag: cell type

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: status (0=alive; 1=died)


title: PBMC_sample44

tag: cd4+/cd8+ cell ratio


title: PBMC_sample47

tag: follow-up time in days


title: Control_6


title: PBMC_sample41

tag: body mass index (bmi)


title: Control_4


title: Control_7


title: genomic DNA from 9407201144_R06C01

description: 9407201144_R06C01: Sample 170

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex


title: PBMC_sample43

tag: cd14+ cell proportion

tag: mini mental state examination (mmse)


title: genomic DNA from 9701417141_R03C02

description: 9701417141_R03C02: Sample 169

tag: gran

tag: nk

tag: bcell


title: genomic DNA from 9407201108_R02C02

description: 9407201108_R02C02: Sample 168

tag: mono


title: genomic DNA from 9701417139_R01C02

description: 9701417139_R01C02: Sample 167


title: Control_3

tag: disease state

tag: tissue


title: PBMC_sample39

tag: cell type

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)


title: genomic DNA from 9701417141_R04C02

description: 9701417141_R04C02: Sample 166

tag: hiv


title: genomic DNA from 9701417086_R04C02

description: 9701417086_R04C02: Sample 165

tag: agebl


title: PBMC_sample38

tag: cd4+/cd8+ cell ratio

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: genomic DNA from 9701417141_R01C01

description: 9701417141_R01C01: Sample 164

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC_sample4

tag: cd14+ cell proportion

tag: mini mental state examination (mmse)


title: Control_1

tag: disease state

tag: tissue


title: genomic DNA from 9701417057_R04C01

description: 9701417057_R04C01: Sample 163

tag: nk

tag: bcell

tag: mono


title: PV_446_AH1

description: Gene expression data from patients with Polycythemia Vera (PV)

data_processing: Data were analyzed in R using rma. The regularized t-test limma for pairwise data was used to calculate differences in gene expression between patients before and after treatment with IFN-alpha2.

value: PV

tag: treatment

value: untreated

value: Whole blood


title: Control_2


title: PV_434_AG1


title: PBMC_sample35

tag: cell type

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)


title: PV_348_AD1


title: genomic DNA from 9407210029_R05C02

description: 9407210029_R05C02: Sample 161

tag: hiv

tag: agebl


title: PV_303_I1


title: genomic DNA from 9407210107_R03C01

description: 9407210107_R03C01: Sample 160

tag: racecomg

tag: dmgsex


title: PV_332_AC1


title: PV_304_Y1


title: PV_302_X1


title: genomic DNA from 9701417057_R05C02

description: 9701417057_R05C02: Sample 162

tag: gran


title: PBMC_sample34

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample30


title: PBMC_sample36


title: genomic DNA from 9407210074_R03C01

description: 9407210074_R03C01: Sample 158

tag: nk

tag: bcell

tag: mono


title: genomic DNA from 9407210061_R02C01

description: 9407210061_R02C01: Sample 157


title: genomic DNA from 9701417048_R04C02

description: 9701417048_R04C02: Sample 159


title: PBMC_sample32

tag: cell type

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion


title: genomic DNA from 9701417086_R03C02

description: 9701417086_R03C02: Sample 156

tag: hiv


title: PBMC_sample33

tag: methylation batch

tag: sex (1=woman; 0=man)


title: PBMC_sample31


title: PBMC_sample3


title: PBMC_sample29


title: PBMC_sample37


title: genomic DNA from 9407210029_R03C01

description: 9407210029_R03C01: Sample 152

tag: agebl

tag: racecomg

tag: dmgsex


title: PV_280_Z1

tag: disease state

tag: treatment

tag: tissue


title: genomic DNA from 9701417053_R02C02

description: 9701417053_R02C02: Sample 155

tag: gran


title: PV_283_U1


title: genomic DNA from 9701417031_R02C02

description: 9701417031_R02C02: Sample 154


title: PV_258_F1


title: genomic DNA from 9701417035_R05C02

description: 9701417035_R05C02: Sample 153


title: PBMC_sample25

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: genomic DNA from 9407210107_R03C02

description: 9407210107_R03C02: Sample 151

tag: nk

tag: bcell

tag: mono


title: PV_262_R1


title: PV_285_T1


title: PV_269_S1


title: PBMC_sample26

tag: cell type

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)


title: PV_260_Q1

tag: disease state

tag: treatment


title: genomic DNA from 9701417048_R06C02

description: 9701417048_R06C02: Sample 149

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: genomic DNA from 9407201127_R01C01

description: 9407201127_R01C01: Sample 150


title: PV_238_O1

tag: tissue


title: PV_242_P1


title: PBMC_sample27

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: PBMC_sample23

tag: cell type

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion


title: PBMC_sample24

tag: methylation batch

tag: sex (1=woman; 0=man)


title: genomic DNA from 9407210029_R06C02

description: 9407210029_R06C02: Sample 148

tag: hiv

tag: nk

tag: bcell

tag: mono


title: PV_233_L1

tag: disease state

tag: treatment


title: genomic DNA from 9407210016_R01C02

description: 9407210016_R01C02: Sample 147

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: PBMC_sample28

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: genomic DNA from 9701417085_R05C01

description: 9701417085_R05C01: Sample 146


title: PV_234_M1

tag: tissue


title: genomic DNA from 9407210061_R01C01

description: 9407210061_R01C01: Sample 145


title: PV_202_D1


title: genomic DNA from 9701417048_R04C01

description: 9701417048_R04C01: Sample 144


title: PBMC_sample122

tag: cell type

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: genomic DNA from 9701417057_R03C01

description: 9701417057_R03C01: Sample 143

tag: hiv

tag: nk

tag: bcell

tag: mono


title: PBMC_sample18


title: PBMC_sample19


title: PBMC_sample2


title: PBMC_sample17


title: genomic DNA from 9701417035_R03C01

description: 9701417035_R03C01: Sample 142

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran


title: PV_228_K1

tag: disease state

tag: treatment


title: genomic DNA from 9701417081_R03C02

description: 9701417081_R03C02: Sample 141


title: PV_230_B1

tag: tissue


title: PMF_306_AA1

description: Gene expression data from patients with Primary Myelofibrosis (PMF)

value: PMF


title: PBMC_sample15

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: PBMC_sample13

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: PMF_227_J1


title: genomic DNA from 9701417047_R02C02

description: 9701417047_R02C02: Sample 140

tag: hiv

tag: agebl

tag: racecomg

tag: nk

tag: bcell

tag: mono


title: PMF_301_V1

tag: disease state

tag: treatment

tag: tissue


title: genomic DNA from 9701417057_R04C02

description: 9701417057_R04C02: Sample 139

tag: dmgsex

tag: gran


title: PBMC_sample21

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: PBMC_sample121

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: PBMC_sample119


title: PBMC_sample14


title: genomic DNA from 9701417048_R02C01

description: 9701417048_R02C01: Sample 138

tag: hiv

tag: agebl

tag: racecomg

tag: nk

tag: bcell

tag: mono


title: ET_337_AB1

description: Gene expression data from patients with Essentiel Thrombocythemia

tag: disease state

value: ET

tag: treatment

tag: tissue


title: genomic DNA from 9701417081_R01C01

description: 9701417081_R01C01: Sample 137

value: Black

tag: dmgsex

tag: gran


title: ET_235_N1


title: genomic DNA from 9701417035_R06C02

description: 9701417035_R06C02: Sample 136


title: PBMC_sample120

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: genomic DNA from 9701417053_R01C02

description: 9701417053_R01C02: Sample 135

tag: hiv


title: genomic DNA from 9407210107_R06C02

description: 9407210107_R06C02: Sample 134

tag: agebl


title: ET_212_H1


title: ET_211_G1


title: genomic DNA from 9701417048_R05C02

description: 9701417048_R05C02: Sample 133

tag: racecomg


title: genomic DNA from 9407210061_R04C01

description: 9407210061_R04C01: Sample 132

tag: nk


title: PBMC_sample118

tag: cd4+cd28- cell proportion

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: ET_205_E1

tag: disease state

tag: treatment

tag: tissue


title: ET_203_C1


title: genomic DNA from 9407210029_R04C01

description: 9407210029_R04C01: Sample 131

tag: dmgsex

tag: gran

tag: bcell

tag: mono


title: genomic DNA from 9407210073_R01C02

description: 9407210073_R01C02: Sample 130


title: ET_197_A1


title: PBMC_sample115

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted; sample missing information about BMI

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days


title: PBMC_sample114

tag: cd4+cd28- cell proportion

tag: body mass index (bmi)


title: genomic DNA from 9701417057_R02C01

description: 9701417057_R02C01: Sample 129

tag: hiv

tag: agebl

tag: racecomg

tag: nk


title: genomic DNA from 9407210107_R01C01

description: 9407210107_R01C01: Sample 128


title: genomic DNA from 9407210093_R05C01

description: 9407210093_R05C01: Sample 127


title: PBMC_sample112

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: PBMC_sample113


title: TNFa 15ng 48h_3

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

description: TNFa 15ng 48h

hyb_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) and cohybridized to Agilent Chip Whole Human genome, 4x44k slides according to the protocol provided by Agilent.

scan_protocol: The slides were incubated for 17h at 65°C and then the scanned using the Agilent B Scanner.

data_processing: Raw images were obtained by scanning the slides with an Agilent Scan G2505B and Agilent Scan Control software (version 9.5). The images were extracted using the Feature Extraction Software (Agilent Technologies). Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) was used for data visualization, identification of differentially expressed transcripts and hierarchical cluster analysis. We transformed the fluorescence intensity data to log2 ratios of each sample versus the universal human RNA reference (Stratagene, Santa Clara, CA, USA).

source_name: TNFa 15ng 48h

growth_protocol: BMSCs were isolated at Department of Transfusion Medicine, Clinical Center, NIH, Bethesda, Maryland. These cells were expanded and characterized as described in our previous work27. Briefly, cells from the bone marrow aspirates were seeded in complete media (α-minimal essential medium [α-MEM], 2mM glutamine, 10µg/ml gentamicin and 20% fetal bovine serum) for 24 hours, and the non-adherent cells were removed. The adherent cells were expanded until 70-80% confluence was reached. Cells were sub-cultured and kept in complete media. These BMSCs were >70% viable and expressed CD73, CD90, CD105 and CD146 but not CD11b, CD14, CD19, CD34 or CD45.

extract_protocol: Total RNA from stimulated and control BMSC samples were isolated and purified by using miRNeasyKit (Qiagen, Germantown, MD, USA). The RNA concentration was determined using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: BMSCs (passage 4) were stimulated with 6.5 or 65 ng/ml of IFN-g (R&D System Minneapolis, MN, USA), and with 1.5 or 15 ng/ml of TNF-a (R&D System Minneapolis, MN, USA), or the combination of IFN-g and TNF-a   (1.5 ng/ml of TNF-a + 6.5 ng/ml of IFN-g or 15 ng/ml of TNF-a + 65 ng/ml of IFN-g).  After the adherent BMSCs were incubated with the cytokines for 48 hours, the BMSCs were harvested using trypsin and they were then evaluated by gene expression profiling. Prior to harvesting the BMSCs, the supernatant was collected, frozen and stored at -80oC for protein analysis.

value: BMSC cell line

source_name: universal human reference RNA

tag: reference type

value: pooled whole human RNA


title: genomic DNA from 9407210073_R01C01

description: 9407210073_R01C01: Sample 126

tag: dmgsex

tag: gran

tag: bcell

tag: mono


title: PBMC_sample111

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: status (0=alive; 1=died)


title: PBMC_sample117

tag: cd4+cd28- cell proportion

tag: follow-up time in days

tag: body mass index (bmi)


title: TNFa 15ng 48h_2

description: TNFa 15ng 48h

label_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA)


title: genomic DNA from 9407210107_R04C01

description: 9407210107_R04C01: Sample 125

tag: hiv

tag: agebl

tag: racecomg

tag: nk


title: ET_399_AF1

tag: disease state

tag: treatment

tag: tissue


title: TNFa 1.5ng 48h_2

description: TNFa 1.5ng 48h

source_name: TNFa 1.5ng 48h

tag: reference type


title: TNFa 1.5ng 48h_3

description: TNFa 1.5ng 48h


title: PBMC_sample109

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: genomic DNA from 9701417047_R06C01

description: 9701417047_R06C01: Sample 124

tag: dmgsex

tag: gran

tag: bcell

tag: mono


title: PMF_381_AE1


title: PBMC_sample104

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: genomic DNA from 9701417107_R05C01

description: 9701417107_R05C01: Sample 123

tag: hiv

tag: agebl

tag: racecomg

value: Other

tag: nk


title: wild type embryo, 25 degrees, rep 3

city: Bethesda

first: Katherine

last: McJunkin

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

description:
N2_25_rep3
Gene expression data from embryos in slow phase of cellularisation.

hyb_protocol: Hybridization was carried out according to GeneChip instructions in a GeneChip Hybridization Oven 640.

scan_protocol: GeneChips were scanned using a GeneChip Scanner.

data_processing: Linear and log2 signals were generated as pivot files in Expression Console from Affymetrix. Further analysis was conducted in GeneSpring from Agilent.

organism: Caenorhabditis elegans

source_name: whole mixed-stage embryos, wild type, 25C

label_protocol: Biotinylated aRNA was generated using the Enzo Single-Round RNA Amplification and Biotin Labeling System, according to instructions.

growth_protocol: Cultures were grown on NGM supplemented with chicken egg yolk, and upshifted from 20 to 25 degrees Celsius 24h before harvest.

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

treatment_protocol: Mixed-stage embryos samples were obtained by hypochlorite treatment of mixed-stage C. elegans cultures.

tag: strain/background

tag: genotype/variation

value: wild type

tag: developmental stage

value: mixed-stage embryos

tag: tissue

value: whole body

tag: temperature


title: wild type embryo, 25 degrees, rep 1

description:
N2_25_rep1
Gene expression data from embryos in slow phase of cellularisation.


title: PBMC_sample110

value: PBMC

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: mir-35-41(nDf50) embryo, 25 degrees, rep 3

description:
mir-35-41_25_rep3
Gene expression data from embryos in slow phase of cellularisation.

source_name: whole mixed-stage embryos, mir-35-41(nDf50) mutant, 25C

value: VT2935 lacking nEx1187

value: mir-35-41(nDf50) mutant


title: genomic DNA from 9407210016_R02C02

description: 9407210016_R02C02: Sample 122

value: White

tag: dmgsex

tag: gran

tag: bcell

tag: mono


title: wild type embryo, 25 degrees, rep 2

description:
N2_25_rep2
Gene expression data from embryos in slow phase of cellularisation.


title: PBMC_sample108

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: status (0=alive; 1=died)

tag: follow-up time in days

tag: body mass index (bmi)


title: genomic DNA from 9701417035_R04C02

description: 9701417035_R04C02: Sample 121

tag: hiv

tag: agebl

tag: racecomg

tag: nk


title: TNFa 1.5ng 48h_1

description: TNFa 1.5ng 48h

tag: reference type


title: PBMC_sample102

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: mini mental state examination (mmse)


title: mir-35-41(nDf50) embryo, 25 degrees, rep 2

description:
mir-35-41_25_rep2
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

tag: strain/background

tag: genotype/variation

tag: developmental stage

tag: tissue

tag: temperature


title: PBMC_sample101

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: status (0=alive; 1=died)


title: genomic DNA from 9701417057_R06C02

description: 9701417057_R06C02: Sample 120

tag: hiv

tag: agebl

tag: racecomg

tag: dmgsex

tag: gran

tag: bcell

tag: mono


title: genomic DNA from 9701417035_R04C01

description: 9701417035_R04C01: Sample 119

tag: nk


title: PBMC_sample107

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: mir-35-41(nDf50) embryo, 25 degrees, rep 1

description:
mir-35-41_25_rep1
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.
Embryos younger than nuclear cycle 9, i.e. before pole cells budding.

tag: strain/background

tag: genotype/variation

tag: developmental stage

tag: tissue

tag: temperature


title: genomic DNA from 9407210065_R05C02

description: 9407210065_R05C02: Sample 117

tag: hiv

tag: agebl

tag: racecomg


title: PBMC_sample11

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted

tag: cell type

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: status (0=alive; 1=died)


title: genomic DNA from 9701417048_R03C01

description: 9701417048_R03C01: Sample 118

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC_sample105

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: follow-up time in days

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: IFNg+TNFa 6.5+1.5ng 48h_3

description: IFNg+TNFa 6.5+1.5ng 48h

source_name: IFNg+TNFa 6.5+1.5ng 48h

tag: reference type


title: IFNg+TNFa 65+15ng 48h_3

description: IFNg+TNFa 65+15ng 48h

source_name: IFNg+TNFa 65+15ng 48h

tag: cell type


title: genomic DNA from 9701417053_R06C01

description: 9701417053_R06C01: Sample 116

tag: hiv

tag: agebl

tag: racecomg


title: PBMC_sample100

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: status (0=alive; 1=died)


title: PBMC_sample106


title: TNFa 15ng 48h_1

description: TNFa 15ng 48h


title: wild type embryo, 20 degrees, rep 3

description:
N2_20_rep3
Gene expression data from embryos in slow phase of cellularisation.

source_name: whole mixed-stage embryos, wild type, 20C

growth_protocol: Cultures were grown on NGM supplemented with chicken egg yolk at 20 degrees Celsius.

tag: strain/background

tag: genotype/variation

tag: developmental stage

tag: tissue

tag: temperature


title: IFNg+TNFa 65+15ng 48h_2

description: IFNg+TNFa 65+15ng 48h


title: PBMC_sample1

description: sample used in the stage of residual extraction where the effects of cell types and gender were adjusted; sample missing information about MMSE

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: follow-up time in days


title: IFNg+TNFa 65+15ng 48h_1

description: IFNg+TNFa 65+15ng 48h

tag: cell type

tag: reference type


title: IFNg+TNFa 6.5+1.5ng 48h_2

description: IFNg+TNFa 6.5+1.5ng 48h


title: genomic DNA from 9407210107_R04C02

description: 9407210107_R04C02: Sample 115

tag: hiv

tag: agebl

tag: dmgsex

tag: gran

tag: nk

tag: bcell

tag: mono


title: PBMC_sample10

tag: cd4+/cd8+ cell ratio

tag: cd14+ cell proportion

tag: cd4+cd28- cell proportion

tag: status (0=alive; 1=died)

tag: body mass index (bmi)

tag: mini mental state examination (mmse)


title: genomic DNA from 9701417047_R01C02

description: 9701417047_R01C02: Sample 114

tag: racecomg


title: mir-35-41(nDf50) embryo, 20 degrees, rep 3

description:
mir-35-41_20_rep3
Gene expression data from embryos in slow phase of cellularisation.

source_name: whole mixed-stage embryos, mir-35-41(nDf50) mutant, 20C

tag: strain/background

tag: genotype/variation

tag: developmental stage

tag: tissue

tag: temperature


title: genomic DNA from 9701417031_R01C02

description: 9701417031_R01C02: Sample 113

tag: hiv

tag: agebl

tag: dmgsex


title: wild type embryo, 20 degrees, rep 2

description:
N2_20_rep2
Gene expression data from embryos in slow phase of cellularisation.


title: PBMC_sample103

tag: cell type

tag: cd8+cd28- cell proportion

tag: methylation batch

tag: sex (1=woman; 0=man)

tag: follow-up time in days


title: genomic DNA from 9701417035_R02C01

description: 9701417035_R02C01: Sample 112

tag: gran

tag: nk

tag: bcell

tag: mono


title: mir-35-41(nDf50) embryo, 20 degrees, rep 2

description:
mir-35-41_20_rep2
Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

tag: strain/background


title: wild type embryo, 20 degrees, rep 1

description:
N2_20_rep1
Gene expression data from embryos in slow phase of cellularisation.

tag: genotype/variation


title: genomic DNA from 9701417053_R05C02

description: 9701417053_R05C02: Sample 110

tag: racecomg