title: Lung, isotype, day 2, rep 2

description: Gene expression after two days in isotype treated lungs

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 2, replicate2


title: Lung, isotype, day 3, rep 2

status: Public on Jul 29 2017

type: RNA

city: Phoenix

first: Deepak

middle: K

last: Nayak

state: Arizona

address: 475 N. 5th Street

country: USA

institute: University of Arizona College of Medicine

description: Gene expression after three days in isotype treated lungs

hyb_protocol: Hybridization of the labeled cDNAs was done in Agilent 2x gene expession hybrization buffer, agilent 10x blocking reagent and kreatech Kreablock onto Agilent 4x44K V2 microarrays at 65oC for 20 min

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner.

data_processing: Gridding and analysis of images was performed using Agilent Feature Extraction V11.5.1.1.

molecule: total RNA

organism: Mus musculus

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 3, replicate2

label_protocol: cDNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics) and Cy5-labeled cDNAs were hybridized to Agilent Mouse v2 4x44K microarrays (G4846A-026655).

extract_protocol: Total RNA was extracted by PureLink RNA kit (Ambion), DNase I treated and evaluated by an Agilent 2100 Bioanalyzerfor for RNA integrity number >7 indicating good quality RNA . Full-length mRNA was enriched by MessageAmpII aRNA Amplification kit (Life Technologies) and reverse transcribed into cDNA.

treatment_protocol: Wildtype C57BL/6 (H-2Kb) mice were administered with intrabronchial delivery of Abs (anti-H-2Kb or isotype control) on days 1, 2, 3 and 6. Four hrs post Ab administration, lungs were perfused with phosphate-buffered saline, pH 7.4 to remove circulating leukocytes and lung tissues were harvested and stored in RNALater (Lifetechnologies) at -20ºC.

tag: strain

tag: tissue

value: Whole lungs (perfused)

tag: gender

value: Male

tag: age

value: 8 wk


title: Lung, isotype, day 3, rep 3

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 3, replicate3


title: No prior radiation history, meningioma tumor 19 (NPRM19)

type: genomic

city: PITTSBURGH

first: SAMEER

last: AGNIHOTRI

state: Pennsylvania

address: Rangos Research Center, 7th Floor, ROOM 7126, 530, 45th Street

department: MacFeeters-Hamilton Brain Tumour Centre

institute: University of Pittsburgh

hyb_protocol: Hybridization protocol was performed as prescribed by core illumina hybridizing kit

scan_protocol: Methylation chips were scanned on the HiScan as required by illumina protocols

data_processing: Control probes were assessed to ensure successful bisulfite conversion, labelling and hybridization. The ratio of Unmethylated and methylated probe values were used to calculate beta values.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Resected patient meningioma at Toronto Western Hospital

label_protocol: Labelling protocol was performed as prescribed by core illumina labelling kit

growth_protocol: Resected tumors. Stored as frozen samples prior to gDNA extraction

extract_protocol: gDNA was extracted with a gSYNC kit (Geneaid). gSYNC Protocol was follow.

treatment_protocol: Not applicable

value: female

tag: disease state

value: meningioma tumor

tag: who grade

tag: history

value: No prior radiation history


title: Lung, isotype, day 2, rep 3

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 2, replicate3


title: No prior radiation history, meningioma tumor 13 (NPRM13)


title: No prior radiation history, meningioma tumor 2 (NPRM2)

value: male


title: No prior radiation history, meningioma tumor 17 (NPRM17)


title: No prior radiation history, meningioma tumor 11 (NPRM11)


title: No prior radiation history, meningioma tumor 5 (NPRM5)


title: No prior radiation history, meningioma tumor 3 (NPRM3)


title: Prior radiation history, meningioma tumor 18 (RIM28)

value: prior radiation history


title: No prior radiation history, meningioma tumor 18 (NPRM18)


title: No prior radiation history, meningioma tumor 6 (NPRM6)


title: Lung, isotype, day 1, rep 3

description: Gene expression after one day in isotype treated lungs

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 1, replicate3


title: No prior radiation history, meningioma tumor 14 (NPRM14)


title: No prior radiation history, meningioma tumor 1 (NPRM1)


title: No prior radiation history, meningioma tumor 9 (NPRM9)


title: No prior radiation history, meningioma tumor 7 (NPRM7)


title: No prior radiation history, meningioma tumor 12 (NPRM12)


title: No prior radiation history, meningioma tumor 16 (NPRM16)


title: No prior radiation history, meningioma tumor 4 (NPRM4)


title: Lung, anti-H-2Kb, day 6, rep 3

description: Gene expression after six days in anti-H-2Kb Ab treated lungs

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 6, replicate3


title: No prior radiation history, meningioma tumor 8 (NPRM8)


title: Prior radiation history, meningioma tumor 18 (RIM27)


title: No prior radiation history, meningioma tumor 10 (NPRM10)


title: No prior radiation history, meningioma tumor 15 (NPRM15)


title: Lung, anti-H-2Kb, day 3, rep 2

description: Gene expression after three days in anti-H-2Kb Ab treated lungs

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 3, replicate2


title: Prior radiation history, meningioma tumor 18 (RIM18)


title: Lung, anti-H-2Kb, day 3, rep 1

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 3, replicate1


title: Lung, isotype, day 2, rep 1

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 2, replicate1


title: Lung, anti-H-2Kb, day 6, rep 2

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 6, replicate2


title: Lung, anti-H-2Kb, day 2, rep 2

description: Gene expression after two days in anti-H-2Kb Ab treated lungs

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 2, replicate2


title: Lung, anti-H-2Kb, day 3, rep 3

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 3, replicate3


title: Lung, anti-H-2Kb, day 1, rep 2

description: Gene expression after one day in anti-H-2Kb Ab treated lungs

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 1, replicate2


title: Lung, anti-H-2Kb, day 1, rep 3

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 1, replicate3


title: Lung, anti-H-2Kb, day 2, rep 1

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 2, replicate1


title: Lung, anti-H-2Kb, day 6, rep 1

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 6, replicate1


title: Lung, anti-H-2Kb, day 2, rep 3

source_name: Lung RNA, 4 hr post intrabronchial anti-H-2Kb challenge, day 2, replicate3


title: Lung, isotype, day 1, rep 1

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 1, replicate1


title: Lung, isotype, day 1, rep 2

source_name: Lung RNA, 4 hr post intrabronchial Ab isotype challenge, day 1, replicate2


title: Prior radiation history, meningioma tumor 12 (RIM12)

source_name: Resected patient meningioma at Toronto Western Hospital


title: Prior radiation history, meningioma tumor 7 (RIM07)


title: Prior radiation history, meningioma tumor 17 (RIM17)


title: Prior radiation history, meningioma tumor 14 (RIM14)


title: Prior radiation history, meningioma tumor 2 (RIM02)


title: Prior radiation history, meningioma tumor 10 (RIM10)


title: Prior radiation history, meningioma tumor 15 (RIM15)


title: Prior radiation history, meningioma tumor 11 (RIM11)


title: Prior radiation history, meningioma tumor 3 (RIM03)


title: Prior radiation history, meningioma tumor 9 (RIM09)


title: Prior radiation history, meningioma tumor 13 (RIM13)


title: Prior radiation history, meningioma tumor 5 (RIM05)


title: Prior radiation history, meningioma tumor 8 (RIM08)


title: Prior radiation history, meningioma tumor 1 (RIM01)


title: Prior radiation history, meningioma tumor 6 (RIM06)


title: Prior radiation history, meningioma tumor 4 (RIM04)


title: Healthy HP0006

city: Shanghai

first: Dongyi

last: He

address: Changning District

department: Department of Rheumatology

country: China

institute: Shanghai Guanghua Hospital of Integrated Traditional and Western Medicine

description: Han Population

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

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

data_processing: standard Illumina protocol

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

value: F

tag: sample type

value: Control


title: M-VM3, 48h, tumor 1

city: Buffalo

first: Vadim

last: Mett

state: NY

address: 73 High Street

institute: Buffalo BioLabs, LLC

description:
SAMPLE 11
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quantile normalization and background subtraction was conducted using Illumina Genestudio

source_name: M-VM3, 48h, tumor

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

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

value: TRAMP mice

value: 4-5 months

value: TRAMP mouse prostate tumor

tag: treatment

tag: time


title: Ad-mCherry, 48h, tumor 1

description:
SAMPLE 9
replicate 1

source_name: Ad-mCherry, 48h, tumor

value: Ad-mCherry


title: Healthy HP0009

description: Han Population


title: PBS, 48h, tumor 2

description:
SAMPLE 8
replicate 2

source_name: PBS, 48h, tumor

value: PBS


title: M-VM3, 48h, tumor 2

description:
SAMPLE 12
replicate 2


title: Ad-mCherry, 48h, tumor 2

description:
SAMPLE 10
replicate 2


title: Prior radiation history, meningioma tumor 16 (RIM16)


title: Healthy HP0008

description: Han Population


title: Healthy HP0007

description: Han Population


title: Healthy HP0004

description: Han Population


title: Healthy HP0003

description: Han Population


title: Healthy HP0005

description: Han Population


title: Ad-mCherry, 24h, tumor 2

description:
SAMPLE 4
replicate 2

source_name: Ad-mCherry, 24h, tumor


title: M-VM3, 24h, tumor 2

description:
SAMPLE 6
replicate 2

source_name: M-VM3, 24h, tumor


title: Healthy HP0011

description: Han Population

value: M


title: PBS, 48h, tumor 1

description:
SAMPLE 7
replicate 1


title: M-VM3, 24h, tumor 1

description:
SAMPLE 5
replicate 1


title: PBS, 24h, tumor 2

description:
SAMPLE 2
replicate 2

source_name: PBS, 24h, tumor


title: PBS, 24h, tumor 1

description:
SAMPLE 1
replicate 1


title: Ad-mCherry, 24h, tumor 1

description:
SAMPLE 3
replicate 1


title: Healthy HP0002

description: Han Population


title: Rheumatoid Arthritis RA0008

description: Han Population

value: Case


title: HGSC_JH1075

status: Public on Jul 28 2017

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

hyb_protocol: Total RNA (100 ng) was obtained from 95 of 96 samples, and hybridized to the nCounter Human miRNA sample probes (Seattle, WA).

scan_protocol: Each sample was scanned for 600 FOV on the nCounter Digital Analyzer

data_processing: The nanoStringNorm procedure as implemented in the nanoStringNorm Bioconductor package was used to pre-process the miRNA data, followed by differential expression analysis with Empirical Bayes methods via the limma Bioconductor package.

source_name: primary ovarian tumor tissue

label_protocol: Not applicable

extract_protocol: DNA and RNA were co-isolated from frozen tissue tumor blocks, and RNA was isolated from normal tissues utilizing Ambion’s ToTALLY RNA™ RNA Isolation Kit (Part Number AM1910, ©Ambion, Inc.).  DNA concentration was confirmed using a PicoGreen protocol. RNA quality was confirmed by utilizing an Agilent Bioanalyzer and assigning an RNA Integrity Number (RIN) to each sample.

tag: stic

value: Yes

value: IV

value: Suboptimal

value: Ovarian Ca

tag: platinumstatus

value: Sensitive

tag: recurrence

value: Y

tag: vitalstatus

value: Alive

tag: race

value: WHITE

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JH993

value: No

value: IIIA

value: Optimal

value: N


title: HGSC_JH1085

value: IA


title: HGSC_JH1069

value: IIC

value: OTHER


title: HGSC_JH1048

value: IIIC


title: HGSC_JH1066


title: HGSC_JH1035

value: Yes

value: Unknown

value: Endometrial cancer


title: HGSC_RG953

value: Ovarian Ca


title: HGSC_JH1072

value: IV

value: Sensitive

value: ASIAN


title: HGSC_JB5962

value: Fallopian Tube Ca

value: Resistant

value: Alive

value: WHITE


title: Healthy HP0001

description: Han Population

value: M

value: Control


title: Rheumatoid Arthritis RA0009

description: Han Population

value: F

value: Case


title: HGSC_JB5982

value: Optimal

value: N

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB5861

value: Yes


title: HGSC_JB5893

value: IIIC

value: Fallopian tube Ca


title: Rheumatoid Arthritis RA0007

description: Han Population


title: HGSC_JB5860

value: No

value: Ovarian Ca

value: Y


title: shRNA scramble replication timing 1

city: Paris

first: Jean-Charles

last: Cadoret

address: 15 rue hélène Brion

country: France

institute: CNRS/ Université de Paris

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray (SurePrint G3 Human CGH Microarray Kit, 4x180K, AGILENT Technologies, genome reference Hg18) that covers the whole genome with one probe every 13 Kb (11 KB in RefSeq sequences).

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner using a resolution of 3 µm and the autofocus option.

data_processing: Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.

source_name: neosynthetized DNA in early S phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification was conducted (WGA, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Sigma) and 2mM L-glutamine (ATCC 30-2214) at 37°C, 5% CO2 and 5% O2 (standard culture conditions).

extract_protocol: cells were incubated with BrdU (50µM) for 90 minutes, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 100,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) as described by Hiratani et al 2008. To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

treatment_protocol: cell lines were established by transfection using Lipofectamine2000 followed by Zeocine selection (20µg/ml).

tag: cell line

source_name: neosynthetized DNA in late S phase


title: Healthy HP0012

description: Han Population


title: Healthy HP0010

description: Han Population


title: shRNA SAMHD1 replication timing 1


title: HGSC_JB5615

value: IV

value: Fallopian Tube Ca

value: ASIAN


title: HGSC_JB5617

value: Sensitive

value: Alive

value: WHITE


title: HGSC_JB5588


title: HGSC_JB5841

value: Resistant


title: HGSC_JB5585

value: Dead


title: HGSC_JB5537

value: Suboptimal


title: HGSC_JB5565


title: Rheumatoid Arthritis RA0004

description: Han Population

value: F

value: Case


title: HGSC_JB5523

value: Yes

value: Optimal

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB5516

value: IIIC

value: N


title: HGSC_JB5464

value: Ovarian Ca

value: Y


title: HGSC_JB5471

value: No

value: IV


title: HGSC_JB5439

value: Fallopian Tube Ca

value: Sensitive

value: BLACK


title: Rheumatoid Arthritis RA0006

description: Han Population


title: HGSC_JB5506

value: Alive

value: WHITE


title: HGSC_JB5567


title: Rheumatoid Arthritis RA0012

description: Han Population

value: M


title: HGSC_JB5427


title: HGSC_JB5326


title: Rheumatoid Arthritis RA0002

description: Han Population

value: F


title: HGSC_JB5318


title: HGSC_JB5293


title: HGSC_JB5287


title: HGSC_JB5548


title: HGSC_JB5223


title: HGSC_JB5214

value: Resistant


title: HGSC_JB5234


title: HGSC_JB5276


title: HGSC_JB5268

value: Not available


title: HGSC_JB5143

value: Yes

value: Optimal

value: Dead


title: HGSC_JB5087

value: primary tumor tissue from high grade serous ovarian tumors


title: Rheumatoid Arthritis RA0005

description: Han Population

value: Case


title: Rheumatoid Arthritis RA0003

description: Han Population


title: Rheumatoid Arthritis RA0001

description: Han Population

data_processing: BeadStudio was used to


title: Rheumatoid Arthritis RA0010

description: Han Population


title: Rheumatoid Arthritis RA0011

description: Han Population


title: HGSC_JB5019

value: IIIC

value: Ovarian Ca

value: N


title: HGSC_JB5051

value: Fallopian Tube Ca

value: Y


title: HGSC_JB4960

value: IV

value: Sensitive


title: HGSC_JB4998

value: No

value: Alive

value: WHITE


title: HGSC_JB4952

value: Peritoneum Ca NOS


title: HGSC_JB4976


title: HGSC_JB4912

value: ASIAN


title: HGSC_JB4962

value: Yes


title: HGSC_JB4904

value: Optimal


title: HGSC_JB4900


title: HGSC_JB4887


title: HGSC_JB4886

value: Suboptimal


title: HGSC_JB4878

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB4860


title: HGSC_JB4841

value: IIIB


title: HGSC_JB4853

value: IIC


title: HGSC_JB4833

value: IIIC

value: Ovarian Ca


title: HGSC_JB4752

value: Fallopian Tube Ca


title: HGSC_JB4838

value: Y


title: HGSC_JB4757

value: Dead


title: HGSC_JB4744

value: Sensitive

value: N

value: OTHER


title: HGSC_JB4684

value: IV

value: Alive

value: WHITE


title: HGSC_JB4733

value: Yes

value: Resistant


title: HGSC_JB4675

value: Optimal


title: HGSC_JB4674

value: No

value: Peritoneum Ca NOS

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_JB 5685

description: JB 5685

value: IIIC


title: HGSC_JB4234

value: Ovarian Ca

value: ASIAN


title: HGSC_JB4442

value: Fallopian Tube Ca

value: Y


title: HGSC_JB 5768

description: JB 5768

value: Sensitive


title: HGSC_GL5113


title: HGSC_JB 5705

description: JB 5705

value: N


title: HGSC_GL4490

value: BLACK


title: HGSC_40211

value: III

value: Suboptimal

value: Not available

value: Dead


title: HGSC_222T

value: WHITE


title: HGSC_323T

value: Optimal

value: Alive


title: HGSC_40209

value: No


title: HGSC_914T

value: primary tumor tissue from high grade serous ovarian tumors


title: HGSC_GL4226

value: IIIC


title: HGSC_40208

value: Yes


title: HGSC_40207


title: HGSC_331T

value: Ovarian Ca


title: HGSC_40206


title: HGSC_JB4548

value: IV

value: Fallopian Tube Ca


title: HGSC_40204

value: Y


title: HGSC_JB 5727

description: JB 5727

value: Sensitive

value: N

value: HISPANIC


title: HGSC_40199

value: III

value: Suboptimal


title: HGSC_40200

value: Not available


title: HGSC_40197

value: Dead


title: HGSC_40201

value: Optimal


title: HGSC_40203


title: HGSC_40202


title: HGSC_40190


title: HGSC_40193

value: II

value: Unknown

value: Alive


title: HGSC_40187

value: No

value: primary tumor tissue from high grade serous ovarian tumors


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33; 5 days post treatment (rep c)

city: Hamilton

first: Yonghong

last: Wan

state: ON

address: 1280 Main St W

country: Canada

institute: McMaster University

description:
d5-Tm+VSVc
replicate a-d

data_processing: The obtained values were VST transformed, background corrected, and normalized with quantile normalization

label: biotin

source_name: Mouse tumor

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

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

value: 6-8 weeks

value: tumor

value: gp33-specific Tm + VSV-gp33


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33; 5 days post treatment (rep d)

description:
d5-Tm+VSVd
replicate a-d


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33 + MS-275; 5 days post treatment (rep c)

description:
d5-Tm+VSV+Mc
replicate a-d

value: gp33-specific Tm + VSV-gp33 + MS-275


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33 + MS-275; 5 days post treatment (rep b)

description:
d5-Tm+VSV+Mb
replicate a-d


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33 + MS-275; 5 days post treatment (rep d)

description:
d5-Tm+VSV+Md
replicate a-d


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33; 5 days post treatment (rep b)

description:
d5-Tm+VSVb
replicate a-d


title: mTEC lo_5

city: Heidelberg

first: Benedikt

last: Brors

address: Berliner str. 41

department: Applied Bioinformatics

country: Germany

institute: German Cancer Research Center

data_processing: Quantile normalization (Smyth, 2005) and limma differential gene expression analysis were performed to identify differentially expressed genes between the different TPA-defined mTEC subsets. P value ≤ 0.01 and fold change (Fc) ≥ 2 or ≤ 2 were the criteria used to define genes as differentially expressed. All calculations were performed in R version 13.1

source_name: mTEC lo

label_protocol: The amplified cDNA was labeled and hybridized to microarrays for gene expression profiling using Illumina’s BeadArrays

growth_protocol: Isolation of mTECs: Thymi were removed from embryonic, postnatal and/or adult mice and placed into RPMI-1640 medium (containing 5 % FCS) on ice. The remaining digestion steps for adult and postnatal thymi were performed as described previously (Derbinski et al., 2001; Michel et al., 2016 in preparation). The thymi from embryos were digested using collagenase/dispase for 20-30 min at 37 °C with intermittent agitation using a 1000 or 200 µl pipette.

extract_protocol:
The cells were FACS sorted on BD FACSAriaTM III cell sorter (BD Biosciences, USA), using either propidium iodide (0.2 μg/ml) or Fixable Viability Dye eFluor® 780 or eFluor® 450 (eBiosciences, USA) to exclude dead cells. FACS analysis was performed using a BDTM LSRII flow cytometer (BD Biosciences).
RNA preparation and cDNA synthesis: The RNA from single-cell suspensions was isolated using the High Pure RNA Isolation Kit (Roche, Germany). The isolated RNA was reverse transcribed into cDNA with Oligo(dT)20 Primer and Superscript II Reverse Transcriptase (Invitrogen, Switzerland) followed by RNase H digestion (Fermentas, Germany).

value: female

tag: cell type

value: thymic epithelial cells

tag: mhc-ii

value: low

tag: tpa

value: minus


title: mTEC lo+3

source_name: mTEC lo+

tag: gender

tag: strain

value: plus


title: mTEC lo+5


title: Untreated control tumor

description: Control

tag: age

tag: tissue

value: control


title: mTEC hi_3

source_name: mTEC hi

value: high


title: mTEC hi+4

source_name: mTEC hi+


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33; 5 days post treatment (rep a)

description:
d5-Tm+VSVa
replicate a-d


title: mTEC lo+4


title: Tumors derived from mice treated with gp33-specific Tm + VSV-gp33 + MS-275; 5 days post treatment (rep a)

description:
d5-Tm+VSV+Ma
replicate a-d


title: mTEC hi_5


title: mTEC hi+3


title: mTEC hi_4


title: mTEC hi+5


title: mTEC lo_3


title: mTEC hi_2


title: mTEC hi+2


title: mTEC lo+2


title: ATCC 17616_WT SM, biological rep2

city: Lisboa

first: Leonilde

middle: Morais

last: Moreira

address: A. Rovisco Pais

department: Bioengineering

country: Portugal

institute: Instituto Superior Tecnico

description: wild-type strain

hyb_protocol: Following fragmentation, 2 µg of end-labeled fragmented cDNA were used in a 200-µl hybridization cocktail containing added hybridization controls and hybridized on arrays for 16 hours at 50ºC. Modified post-hybridization wash and double-stain protocols (FLEX450_0005; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Scanned arrays were analyzed with Affymetrix Expression Console software. Subsequent analysis was carried out with DNA-Chip Analyzer 2008. First a digital mask was applied, leaving for analysis only the 9291 probe sets on the array representing Burkholderia multivorans ATCC 17616 transcripts. Then the 6 arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method. Normalized CEL intensities of the arrays were used to obtain model-based gene expression indices based on a Perfect Match (PM)-only model. Replicate data (triplicates) for each bacterial isolate was weighted gene-wise by using inverse squared standard error as weights. All genes compared were considered to be differentially expressed if the 90% lower confidence bound of the fold change between experiment and baseline was above 1.2.

organism: Burkholderia multivorans

source_name: ATCC 17616 wild-type grown in SM medium (20 g/l D-mannitol) for 22 hours

label_protocol: RNA was processed for use on Affymetrix Burkholderia dual species Genome Arrays, according to the manufacturer’s Prokaryotic Target Preparation Assay. Briefly, 10 ug of total RNA containing spiked in Poly-A RNA controls (GeneChip Expression GeneChip Eukaryotic Poly-A RNA Control Kit; Affymetrix, Santa Clara, CA) was used in a reverse transcription reaction with random primers (Invitrogen Life Technologies) to generate first-strand cDNA. After removal of RNA, 2 ug of cDNA were fragmented with DNase and end-labeled with biotin using terminal polynucleotidyl transferase (GeneChip WT Terminal Labeling Kit; Affymetrix). Size distribution of the fragmented and end-labeled cDNA, was assessed using an Agilent 2100 Bioanalyzer.

growth_protocol: Wild-type ATCC 17616 and delta Bmul_2557 mutant  were grown overnight in LB medium and inoculated into 50 ml S medium supplemented with 20 g/l  of D-glucose (with OD600nm 0.1) contained into 100 ml Erlenmyer flasks at 37ºC, 200 r.p.m. for 22 h, followed by RNA extraction. The wild-type B. multivorans ATCC 17616 was also inoculated into 50 ml of S medium supplemented with 20 g/l D-mannitol (SM medium) and incubated under the same condiotions prior to RNA extraction.

extract_protocol: Total RNA extraction was carried out using the RNeasy MiniKit (Qiagen) by following manufacturer’s recommendation

treatment_protocol: Bacterial cells were resuspended in RNAprotect bacteria reagent (Qiagen).

tag: genotype


title: mTEC lo_4


title: ATCC 17616_WT SM, biological rep3

description: wild-type strain


title: delta_Bmul_2557, biological rep2

description: delta Bmul_2557 mutant

source_name: delta Bmul_2557 grown in S medium with 20 g/l D-glucose for 22 hours

value: ATCC 17616 delta Bmul_2557


title: ATCC 17616_WT SM, biological rep1

description: wild-type strain


title: NMP 3_NC

city: Genova

first: simona

last: coco

address: L.go R. Benzi, 10

country: Italy

institute: IRCCS Ospedale Policlinico San Martino

description: miRNA expression of FFPE Nonmalignant pleura from healthy individuals

hyb_protocol: The hybridization and washing steps were performed according to the “miRNA Microarray System with miRNA Complete Labeling and Hyb protocol” (v. 2.4, September 2011) (Agilent Technologies). The flow-thought volume of desalted cy3-labeled miRNA sample (specific activity >6 pmol Cy3 per μg cRNA) was completely dried using a vacuum concentrator (45°C) for approximately one hour. Dried Cy3-labeled miRNA sample was resuspended in 17 ml of nuclease-free water and mixed with: 1 ml of 3rd dilution of Hyb Spike-In solution, 4.5 ml of GE Blocking Agent 10X, and 22.5 ml of Hi-RPM Hybridization Buffer 2X (Agilent Technologies). After the denaturation step (100°C for 5 minutes), 40 ml of samples were hybridized to Human miRNA microarray slide 8x60K (miRBase Release 19.0; 2006 human miRNAs represented) (Agilent Technologies), for 20 hours at 55°C in the rotating hybridization oven (20 rpm) (Agilent Technologies). After hybridization, microarray underwent to two washing steps as follows: 5 minutes at room temperature with GE Wash Buffer 1 plus 0.005% of Triton X-102 (Agilent Technologies) and 5 minutes at 37°C with GE Wash Buffer 2 plus 0.005% of Triton X-102 (Agilent Technologies).

scan_protocol: Slide was scanned immediately after washing on the G2565CA Agilent DNA Microarray Scanner (Agilent Technologies) using setting for AgilentG3_miRNA (Dye Channel: Green; Scan Area 61x21.6 mm; Scan resolution: 3 mm; Tiff file dynamic range: 20bit; Green PMT gain: 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software v.10 (Agilent Technologies) using default parameters (Protocol: miRNA_107_Sept09; Grid: 046064_D_F_20121223) to obtain background software. Finally expression data were normalized using GeneSpring software v.12.6 (Agilent Technologies).

source_name: NMP Tissue

label_protocol: The labeling reaction was performed according to “miRNA Microarray System with miRNA Complete Labeling and Hyb protocol” (v. 2.4, September 2011). Briefly cyanine-3 (Cy3) labeled miRNA was prepared starting from 100 ng total RNA using “miRNA Complete Labeling and Hyb Kit” (Agilent Technologies) according to the manufacturer's instructions. Then each sample underwent to a purification step using Micro Bio-Spin™ P-6 Gel Columns (Bio-Rad; Hercules, CA, USA) and the dye incorporation yield for each desalted cy3-labeled miRNA was checked with the NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

extract_protocol: Each FFPE tumor block was revised by the pathologist to check the tumor cells content (>50%). Total RNA including  the miRNA fraction was isolated starting from two FFPE macro-dissected tissue sections (10 mm) using the Recover All Total Nucleic Acid Isolation Kit for FFPE Tissue (ThermoFisher Scientific, Wilmington, DE, USA), including a RNase-free DNase I treatment. RNA quantity and quality were assessed by NanoDrop ND-1000 (Thermo Scientific, Wilmington, DE, USA) and 2100 Bioanalyzer instrument using RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA). The samples with at least 150 ng of total RNA, were defined suitable for further analyses.

treatment_protocol: This information is not available. The 26 tumor samples and 3 NMP profiled in the present study were all fixed in formalin and embedded in paraffin (FFPE), and the FFPE tissue processing was performed in a large period of time (since 1998 to 2008). Therefore, the reagents such as fixative type changed among the samples and no standard protocol was commonly used in our cohort of tumors and normal tissues.

tag: origin tissue

value: Mesothelium of the lung

tag: Sex

value: not available

tag: age at diagnosis (years)

tag: histology

tag: os (months)

tag: survival

value: Long Survivor (LS):OS >36 months; Short Survivor (SS):OS <12 months):Normal Control

tag: asbestos exposure

tag: smoking habits


title: delta_Bmul_2557, biological rep3

description: delta Bmul_2557 mutant


title: NMP 2_NC


title: NMP 4_NC


title: ATCC 17616_WT, biological rep3

description: wild-type strain

source_name: ATCC 17616 wild-type grown in S medium with 20 g/l D-glucose for 22 hours


title: MPM 8879-04_SS

description: miRNA expression of FFPE MPM tumor tissue obtained from unresected patient at diagnosis

source_name: MPM Tumor Sample

value: Male

value: Epithelioid

value: Long Survivor (LS):OS >36 months; Short Survivor (SS):OS <12 months):SS

value: Unknown

value: Former smoker


title: delta_Bmul_2557, biological rep1

description: delta Bmul_2557 mutant


title: ATCC 17616_WT, biological rep2

description: wild-type strain


title: MPM 6423-08_SS

value: Occupational

value: No smoker


title: MPM 1330-01_SS


title: MPM 6854-02_SS

value: Environmental


title: MPM 5963-07_SS


title: ATCC 17616_WT, biological rep1

description: wild-type strain


title: MPM 2175-05_SS

value: Biphasic


title: MPM 1287-05_SS

value: Female


title: MPM10495-03_SS

value: Smoker


title: MPM 6014-07_SS


title: MPM 9063-05_SS

value: Sarcomatoid


title: MPM 6736-98_SS

value: MPM not otherwise specified


title: mTEC lo_2

value: female

value: thymic epithelial cells

value: low

value: minus


title: MPM 1396-03_SS

value: Mesothelium of the lung

value: Male


title: MPM 8844-05_SS

value: Epithelioid

value: Long Survivor (LS):OS >36 months; Short Survivor (SS):OS <12 months):SS


title: MPM 4939-99_SS

value: Former smoker


title: MPM 6547-06_SS

value: Occupational


title: MPM 5950-07_LS

value: Long Survivor (LS):OS >36 months; Short Survivor (SS):OS <12 months):LS

value: Unknown


title: MPM 7678-00_LS


title: MPM 2707-06_LS

value: No smoker


title: MPM 1311-98_LS


title: MPM 9946-04_LS

value: Female

value: Environmental


title: MPM 641-06_LS


title: MPM 8224-04_LS


title: MPM 407-00_LS

value: Smoker


title: MPM 3386-00_LS


title: MPM 3693-01_LS


title: 526723A01_2014-10-29_46CmES

city: Tallahassee

first: David

middle: M

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

description: Mouse genomic data

hyb_protocol: Standard NimbleGen protocol. Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing oligonucleotide probes across the entire mouse genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: Log ratio is calculated as described in Ryba et al., 2011 (DOI: 10.1038/nprot.2011.328), and scaled with R

source_name: Early-replicating DNA

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as previously described (Ryba, T. et al., 2011. Nat Protoc 6: 870–895). Briefly, replication intermediates were prepared from cells pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba, T. et al [Nat Protoc (2011) 6: 870–895].

treatment_protocol: BrdU labeled

tag: cell line

tag: replication timing

value: early

source_name: Late-replicating DNA

value: late


title: MPM 6246-03_LS


title: BC3/Control IP

status: Public on Jul 27 2017

type: SRA

city: Oakland

first: Ravi

last: Sachidanandam

state: CA

address: 2945 Webster St

institute: Girihlet Inc.

description: Raw fastq data are not available due to computer failure

library_source: transcriptomic

data_processing:
reads were extracted from the fastq files, and each unique read was assigned a count (frequency) and mapped (exact matches) to the pombe genome (from pombase.org, circa 2013)
annotations from pombase as gff3 files were downloaded and used to annotate each mapped read.
These annotations and counts are provided in the processed and tabDelimited files
All the processing was done using custom software
Genome_build: Release 20 (2013)
Supplementary_files_format_and_content: tabDelimited files include all reads for the sample; processed files are mapping/annotation for the sample

organism: Schizosaccharomyces pombe

source_name: Control immunoprecipation representing the background of the experiment

growth_protocol: S. pombe cells were grown in 200 ml yeast extract (YE) supplemented with Adenine at 30℃ and 220 rpm up to OD595=1.2

extract_protocol:
Immunoprecipitated RNA was extracted and purified using the classical phenol-chlofororm extraction and ethanol precipitation
Immunoprecipitated RNA was subjected to 5' RACE experiments (shared RNA ligated to 5'-adapter, reverse transcribed using RT-oligo with random hexamer at the 3'-end, then PCR amplified).

treatment_protocol: No treatment

value: wild type

tag: antibody

value: irrelevant antibody


title: BC4/Mmi1 IP

source_name: Mmi1 immunoprecipitation


title: Slide 345108

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011.

scan_protocol: Scanning was done using the GenePix 4200AL laser scanner.

data_processing: Dual-channel array images were analyzed with GenePix 6. Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: ∆tpxD mutant with H2O2

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe Post-labeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Streptococcus pneumoniae D39∆tpxD were grown in THY medium till OD620=0.25 and then treated with 0mM and 1mM H2O2 for 40mins.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche Diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche Diagnostics). RNA was isolated from three replicate cultures.

treatment_protocol: With or without 1mM H2O2 for 40mins.

tag: strain/background

tag: genotype/variation

value: ∆tpxD

tag: treatment

value: 1mM H2O2

source_name: ∆tpxD mutant without H2O2

value: 0mM H2O2


title: Slide 345107


title: cMSC_3

city: Leiden

first: Danielle

last: Leuning

address: Albinusdreef 2

department: Nephrology

country: Netherlands

institute: LUMC

description:
cMSC3
SAMPLE 6

hyb_protocol: cDNA and cRNA synthesis, labeling and subsequent hybridization on the Human HT12 V4 Gene Expression Beadchips (Illumina Inc., San Diego, USA) were performed according to manufacturer’s protocols. The beadchips, targeting more than 47000 gene transcripts, were scanned using iSCAN system (Illumina Inc., San Diego, USA) and fluorescence intensities were uploaded into GenomeStudio Software (Illumina Inc, San Diego, USA)

data_processing: Genes with a detection p-value of >0.05 for all samples were excluded. Subsequent data was quantile normalized in Genome Studio. Differential expression was analyzed using the gene expression module of Genome Studio (Illumina).

source_name: 10 K18 kapsel P5

growth_protocol: both cell types were grown in 5% platelet lysates

extract_protocol: RNA was isolated from biological triplicates using Trizol reagent (Life Technologies, Bleiswijk, the Netherlands) and the RNeasy kit (Qiagen, Heidelberg, Germany) according to the manufacturer’s protocol. The quality and quantity of RNA was assessed using a Nanodrop

treatment_protocol: Cells were grown untill passage 5-7. No specific treatments were applied.

value: kidney

tag: cell type

value: capsule derived MSCs (cMSC)

tag: passage


title: Slide 345106

source_name: Wild type with H2O2

growth_protocol: Streptococcus pneumoniae D39 wild-type were grown in THY medium till OD620=0.25 and then treated with 0mM or 1mM H2O2 for 40mins.

source_name: Wild type without H2O2


title: BC1/Mmi1 IP

tag: strain

tag: genotype


title: Slide 345109


title: BC2/Control IP


title: Slide 345104


title: Slide 345105


title: kPSC_1

description:
kPSC1
SAMPLE 1

label_protocol: cDNA and cRNA synthesis, labeling and subsequent hybridization on the Human HT12 V4 Gene Expression Beadchips (Illumina Inc., San Diego, USA) were performed according to manufacturer’s protocols. The beadchips, targeting more than 47000 gene transcripts, were scanned using iSCAN system (Illumina Inc., San Diego, USA) and fluorescence intensities were uploaded into GenomeStudio Software (Illumina Inc, San Diego, USA)

tag: tissue

value: perivascular stromal cells  (kPSC)


title: kPSC_3

description:
kPSC3
SAMPLE 3


title: cMSC_2

description:
cMSC2
SAMPLE 5

source_name: 8 K17 kapsel P5


title: cMSC_1

description:
cMSC1
SAMPLE 4

source_name: 7 K16 kapsel P5


title: HUVEC

city: Bunkyo-ku

first: Taketomo

last: Kido

state: Tokyo

address: 1-1-1 Yayoi

department: Institute for Quantitative Biosciences

country: Japan

institute: The University of Tokyo

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: human umbilical vein endothelial cells

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

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen, California, US) according to the manufacturer's protocol. Quantity and quality of RNA were monitored using a NanoDrop and the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: umbilical vein endothelial cells


title: kPSC_2

description:
kPSC2
SAMPLE 2


title: LSEC

source_name: hiPSC-derived liver sinusoidal endothelial cells

value: liver sinusoidal endothelial cells


title: MSC

source_name: human mesenchymal stem cells

value: mesenchymal stem cells


title: HSC

source_name: hiPSC-derived hepatic stellate cells

value: hepatic stellate cells


title: PMBC_CON_POSTEX24_S8

city: Washington

first: Monica

last: Hubal

state: DC

address: 111 Michigan Ave NW

department: Integrative Systems Biology

institute: Children's National Medical Center

hyb_protocol: Illumina DirectHyb assay

scan_protocol: Illumina HiScan

data_processing: BeadStudio quantile normalization

label_protocol: Illumina TotalPrep kit

extract_protocol: Trizol - standard protocol; Qiagen cleanup

treatment_protocol: Ficoll separation

tag: group

value: Prediabetic

tag: age

tag: hrs post exercise


title: PMBC_CON_PRE_S10


title: PMBC_CON_PRE_S7


title: PMBC_CON_POSTEX6_S9


title: PMBC_CON_POSTEX1_S3

value: Healthy


title: PMBC_CON_PRE_S8


title: PMBC_CON_PRE_S5


title: PMBC_CON_POSTEX24_S3


title: PMBC_CON_POSTEX6_S6


title: PMBC_CON_PRE_S6


title: PMBC_CON_POSTEX6_S8


title: PMBC_CON_POSTEX24_S6


title: PMBC_CON_POSTEX1_S7


title: PMBC_CON_POSTEX1_S5


title: PMBC_CON_POSTEX24_S10


title: PMBC_CON_PRE_S4


title: PMBC_CON_POSTEX6_S5


title: PMBC_CON_POSTEX24_S5


title: PMBC_CON_PRE_S9


title: PMBC_CON_POSTEX1_S10


title: PMBC_CON_POSTEX1_S6


title: PMBC_CON_POSTEX24_S9


title: PMBC_CON_PRE_S3


title: PMBC_CON_POSTEX6_S4


title: PMBC_CON_POSTEX1_S8


title: PMBC_CON_POSTEX24_S4


title: PMBC_CON_POSTEX1_S9


title: PMBC_CON_POSTEX6_S3


title: PMBC_CON_POSTEX1_S4


title: PMBC_CON_POSTEX6_S10


title: PMBC_CON_POSTEX24_S2


title: PMBC_CON_POSTEX1_S2


title: PMBC_CON_POSTEX6_S2


title: PMBC_CON_POSTEX6_S1


title: PMBC_CON_POSTEX24_S1


title: PMBC_CON_POSTEX1_S1


title: PMBC_CON_PRE_S2


title: SHR_kidney_2

city: Toledo

first: Bina

last: Joe

state: Ohio

address: Block Health Science Bldg, 3000 Arlington Ave

department: Department of Physiology and Pharmacology

institute: University of Toledo, College of Medicine and Life Sciences

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, heated at 60 °C for 30 min and finally reconstituted with 25 μl of 2 × Hybridization buffer  to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled onto the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization of raw data and subsequent data processing were conducted using the R software limma package. Low intensity filtering was performed after quantile normalization of the raw data and the circRNAs that at least 3 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

organism: Rattus norvegicus

source_name: SHR, kidney, rat 2

label_protocol: Sample labeling was performed according to Arraystar Super RNA Labeling protocol (Arraystar Inc.; http://www.arraystar.com/). Briefly, total RNA was digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and facilitate enrichment of circular RNAs. The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured using a NanoDrop ND-1000.

extract_protocol: RNA was extracted using TRIzol Reagent (Life Technologies) according to the manufacturer's protocol. RNA quantity and quality were determined using the NanoDrop ND-1000. RNA integrity was assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: All the experimental rats were weaned at 28–30 d of age and fed with a low salt (0.3% NaCl) Harlan Teklad diet. At 57 days of age, all the rats were euthanized through carbon dioxide inhalation. The kidney tissues were collected for the microarray study.

value: Spontaneously hypertensive rat (SHR)

tag: gender

value: male

value: 57 days


title: WKY_kidney_3

source_name: WKY, kidney, rat 3

value: Wistar Kyoto rat (WKY)


title: R_kidney_3

source_name: R, kidney, rat 3

value: Dahl salt-resistant rat (R)


title: SHR_kidney_1

source_name: SHR, kidney, rat 1


title: SHR_kidney_3

source_name: SHR, kidney, rat 3


title: Pathological condition, CD31_DMJ1_09012014_bis

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

institute: Université Paris-Saclay

description:
CD31_DMJ1_09012014_bis
Gene expression from human endothelial cells in disease condition (JDM: Juvenile Dermatomyositis).

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed and analyzed using Partek Genomic Suite.

label: Biotin

source_name: deltoid muscle, endothelial cells, JDM

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labelling Assay kit).

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

value: deltoid muscle

value: endothelial cells

tag: cell marker

tag: disease

value: juvenile dermatomyositis (JDM)

value: 9 weeks

tag: Sex

value: F


title: Normal condition, CD31_S5_25032014_bis

description:
CD31_S5_25032014_bis
Gene expression from human endothelial cells in normal condition.

source_name: deltoid muscle, endothelial cells, normal

value: normal

value: 12 weeks


title: WKY_kidney_2

source_name: WKY, kidney, rat 2

value: kidney


title: Normal condition, CD56_Sain_25032014_bis

description:
CD56_Sain_25032014_bis
Gene expression from human satellite cells in normal condition.

source_name: deltoid muscle, satellite cells, normal

value: satellite cells


title: Pathological condition, CD56_DMJ_09012014_bis

description:
CD56_DMJ_09012014_bis
Gene expression from human satellite cells in disease condition (JDM: Juvenile Dermatomyositis).

source_name: deltoid muscle, satellite cells, JDM


title: WKY_kidney_1

source_name: WKY, kidney, rat 1


title: Pathological condition, CD56_DMJ_25012014_bis

description:
CD56_DMJ_25012014_bis
Gene expression from human satellite cells in disease condition (JDM: Juvenile Dermatomyositis).

value: 11 weeks


title: Normal condition, CD56_Sain_03122013_bis

description:
CD56_Sain_03122013_bis
Gene expression from human satellite cells in normal condition.

value: 16 weeks


title: Normal condition, CD31_S1_03122013_bis

description:
CD31_S1_03122013_bis
Gene expression from human endothelial cells in normal condition.


title: Normal condition, CD31_S3_18032014_bis

description:
CD31_S3_18032014_bis
Gene expression from human endothelial cells in normal condition.

value: 14 weeks


title: Normal condition, CD56_Sain_18032014_bis

description:
CD56_Sain_18032014_bis
Gene expression from human satellite cells in normal condition.


title: Pathological condition, CD31_DMJ2_23012014_bis

description:
CD31_DMJ2_23012014_bis
Gene expression from human endothelial cells in disease condition (JDM: Juvenile Dermatomyositis).


title: Pathological condition, CD31_DMJ3_08042014_bis

description:
CD31_DMJ3_08042014_bis
Gene expression from human endothelial cells in disease condition (JDM: Juvenile Dermatomyositis).


title: Pathological condition, CD56_DMJ_08042014_bis

description:
CD56_DMJ_08042014_bis
Gene expression from human satellite cells in disease condition (JDM: Juvenile Dermatomyositis).


title: R_kidney_2

source_name: R, kidney, rat 2


title: R_kidney_1

source_name: R, kidney, rat 1


title: S_kidney_3

source_name: S, kidney, rat 3

value: Dahl salt-sensitive rat (S)


title: 4n_2i_MEFs_2_3

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

institute: University of Tokyo

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99℃ for 5 minutes, then 45℃ for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 80μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 17 hours at 45° at 60rpm• Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data analyses were processed using Genespring software (version13.0). For the analysis of 2i-ESCs and S-ESCs, 2i_ESCs_15_(MoGene-1_0-st-v1).CEL(raw) and S_ESCs_36_(MoGene-1_0-st-v1).CEL(raw) were loaded using Genespring. For the analysis of 2n-2i-MEFs, 4n-2i-MEFs and control MEFs, 2n_MEFs_15_1_(MoGene-1_0-st-v1).CEL(raw), 4n_2i_MEFs_2_3_(MoGene-1_0-st-v1).CEL(raw) and control_MEF_4_(MoGene-1_0-st-v1).CEL(raw) were loaded using Genespring.

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

extract_protocol: RNeasy Plus Mini kit

value: MEFs

tag: background strain

value: F1 of 129X1/SvJ X MSM/Ms


title: control_MEFs_4


title: S_kidney_2

source_name: S, kidney, rat 2

value: male

value: 57 days


title: PMBC_CON_PRE_S1

value: Healthy


title: 2n_2i_MEFs_15_1


title: S_ESCs_36

value: ES cells


title: S_kidney_1

source_name: S, kidney, rat 1


title: 2i_ESCs_15


title: skeletal_muscle_197_control_rep1

status: Public on Jul 26 2017

city: Leicester

first: Karl

middle: Eric

last: Herbert

address: Glenfield Hospital

department: Cardiovascular Sciences

country: United Kingdom

institute: University of Leicester

description: Replicate 1

hyb_protocol: standard Illumina hybridization

scan_protocol: standard Illumina scanning

data_processing: Raw data were log (base 2) transformed followed by quantile normalization without background subtraction. Performed in ArrayTrack.

source_name: thigh skeletal muscle_control 28days

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA amplification kit

extract_protocol: Skeletal muscle was pulverized in liq N2 using mortar and pestle. Total RNA was extracted with an RNeasy fibrous kit (Qiagen) followed by clean-up with DNase I, all in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent 2100 Bioanalyser.

value: Wistar Han

value: femoris skeletal muscle


title: Prostate cancer cell DU145 biotinylated miR-17 pulldown, rep 3

city: Singapore

first: Henry

last: Yang

address: 28 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore

description:
DU145_17_3 PD
Cells (#3)  isolated from DU145 prostate cancer cell line with biotinylated miR-17 mimic

hyb_protocol: Following fragmentation, cRNA were hybridized for 18.5 hr at 58°C on Illumina Human HT-12 version 4 Array. Chips were washed in hybex water bath and stained using Cy3-Streptavidin.

scan_protocol: Chips were scanned using the BeadArray Reader.

data_processing:
The data were extracted with the backround and normalized using the Cross Correlation method.  The trimmed mean target intensity of each array was set to 16 (4 in log2 scale) based on detection p value of 0.05.
log2 intensity for processed data and background subtracted raw intensity for raw data

label_protocol: Biotinylated cRNA were prepared according to the manufacturer's instruction (Epicentre-Illumina nano labeling kit).

growth_protocol: Prostate cancer DU145 cells were cultured in DMEM medium supplemented with 10% FBS in a 37°C incubator with 5% CO2 atmosphere.

treatment_protocol:
Prostate cancer DU145 cells were transfected with biotinylated non-targeting controls (NC1 or NC2) or miRNA-638, or miRNA mimic controls NC1 or NC2, or miRNA-638 mimic.
pulldown protocol; Biotinylated  microRNA pulldown was performed as previously described (Lal et al., 2011, PLoS Genet.).

tag: cell line

value: Human prostate cancer cell line

tag: transfected with

value: biotinylated miR-17 mimic

tag: molecule subtype

value: pulldown RNA


title: skeletal_muscle_150ppm SI compd 177_rep2

description: Replicate 2

source_name: thigh skeletal muscle_SI compound 177 28days


title: Prostate cancer cell DU145 biotinylated NC2 pulldown, rep 3

description:
DU145_NC2_3  PD
Cells (#3)  isolated from DU145 prostate cancer cell line with biotinylated NC2 mimic

value: biotinylated NC2 mimic


title: skeletal_muscle_177_control_rep2

description: Replicate 2


title: skeletal_muscle_177_control_rep3

description: Replicate 3


title: skeletal_muscle_177_control_rep1

description: Replicate 1


title: skeletal_muscle_150ppm SI compd 177_rep1

description: Replicate 1


title: skeletal_muscle_197_control_rep3

description: Replicate 3


title: skeletal_muscle_150ppm SI compd 197_rep2

description: Replicate 2

source_name: thigh skeletal muscle_SI compound 197 28days


title: Prostate cancer cell DU145 biotinylated miR-17 pulldown, rep 1

description:
DU145_17_1 PD
Cells (#1)  isolated from DU145 prostate cancer cell line with biotinylated miR-17 mimic


title: Prostate cancer cell DU145 biotinylated NC2 pulldown, rep 2

description:
DU145_NC2_2  PD
Cells (#2)  isolated from DU145 prostate cancer cell line with biotinylated NC2 mimic


title: skeletal_muscle_150ppm SI compd 177_rep3

description: Replicate 3


title: skeletal_muscle_150ppm SI compd 197_rep1

description: Replicate 1


title: skeletal_muscle_150ppm SI compd 197_rep4

description: Replicate 4


title: Prostate cancer cell DU145 biotinylated miR-638 pulldown, rep 2

description:
DU145_638_2 PD
Cells (#2)  isolated from DU145 prostate cancer cell line with biotinylated miR-638 mimic

value: biotinylated miR-638 mimic


title: Prostate cancer cell DU145 biotinylated miR-638 pulldown, rep 3

description:
DU145_638_3 PD
Cells (#3)  isolated from DU145 prostate cancer cell line with biotinylated miR-638 mimic


title: Prostate cancer cell DU145 biotinylated miR-17 pulldown, rep 2

description:
DU145_17_2 PD
Cells (#2)  isolated from DU145 prostate cancer cell line with biotinylated miR-17 mimic


title: skeletal_muscle_197_control_rep2

description: Replicate 2


title: skeletal_muscle_150ppm SI compd 177_rep4

description: Replicate 4


title: Prostate cancer cell DU145 biotinylated NC2 pulldown, rep 1

description:
DU145_NC2_1  PD
Cells (#1)  isolated from DU145 prostate cancer cell line with biotinylated NC2 mimic


title: Prostate cancer cell DU145 biotinylated NC1 pulldown, rep 2

description:
DU145_NC1_2  PD
Cells (#2)  isolated from DU145 prostate cancer cell line with biotinylated NC1 mimic

value: biotinylated NC1 mimic


title: Prostate cancer cell DU145 biotinylated NC1 pulldown, rep 3

description:
DU145_NC1_3  PD
Cells (#3)  isolated from DU145 prostate cancer cell line with biotinylated NC1 mimic


title: Prostate cancer cell DU145 with miR-638 mimic, rep4

description:
DU145_638_4 OE
Cells (#4)  isolated from DU145 prostate cancer cell line with miRNA mimic miR-638

value: miRNA mimic miR-638

value: total RNA


title: Prostate cancer cell DU145 with miR-638 mimic, rep3

description:
DU145_638_3 OE
Cells (#3)  isolated from DU145 prostate cancer cell line with miRNA mimic miR-638


title: Prostate cancer cell DU145 biotinylated miR-638 pulldown, rep 1

description:
DU145_638_1 PD
Cells (#1)  isolated from DU145 prostate cancer cell line with biotinylated miR-638 mimic


title: Prostate cancer cell DU145 biotinylated NC1 pulldown, rep 1

description:
DU145_NC1_1  PD
Cells (#1)  isolated from DU145 prostate cancer cell line with biotinylated NC1 mimic


title: skeletal_muscle_197_control_rep4

description: Replicate 4


title: Prostate cancer cell DU145 with miR-638 mimic, rep2

description:
DU145_638_2 OE
Cells (#2)  isolated from DU145 prostate cancer cell line with miRNA mimic miR-638


title: Prostate cancer cell DU145 with NC1 mimic, rep4

description:
DU145_NC1_4 OE
Cells (#4)  isolated from DU145 prostate cancer cell line with miRNA mimic NC1

value: miRNA mimic NC1


title: Prostate cancer cell DU145 with NC2 mimic, rep4

description:
DU145_NC2_4 OE
Cells (#4)  isolated from DU145 prostate cancer cell line with miRNA mimic NC2

value: miRNA mimic NC2


title: skeletal_muscle_150ppm SI compd 197_rep3

description: Replicate 3


title: skeletal_muscle_177_control_rep4

description: Replicate 4


title: Prostate cancer cell DU145 with NC2 mimic, rep2

description:
DU145_NC2_2 OE
Cells (#2)  isolated from DU145 prostate cancer cell line with miRNA mimic NC2


title: Prostate cancer cell DU145 with NC1 mimic, rep1

description:
DU145_NC1_1 OE
Cells (#1)  isolated from DU145 prostate cancer cell line with miRNA mimic NC1


title: OLD_CD14posCD16pos_0A9_E45

city: Cleveland

first: Peter

middle: A

last: Wilkinson

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
OLD_CD14posCD16pos
8981245075_F

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Dr. Mark Cameron Genomics core at Collaborative Genomics Center (CGC), of the Vaccine and Gene Therapy Instiutute.

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the quantified output data was conducted using the limma from the R statistical language and other software packages from Bioconductor version 3.4.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

source_name: Sorted Cells from PBMC

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

growth_protocol: Total PBMCs isolated from adults and old subjects were treated with benzonase nuclease (Millipore, Billerica, MA USA) for 30min at 37oC in a 5% CO2-humidified environment. For ex vivo microarray data, monocytes were sorted directly from PBMCs.  For stimulation microarray data, PBMCs were washed and total monocytes were enriched by negative selection using human monocyte enrichment kit without CD16 depletion (Stem cell, Vancouver, DC Canada). Monocytes were counted and resuspended at 50M/ml with sorting buffer (RPMI without phenol red, 2%FBS, and 1M HEPES 1:40 (25mM)) into 5ml polypropylene tubes. Cells were incubated with TruStain FcR block for 5 min at room temperature. The following antibody cocktail CD19 PE Cy7 (Biolegend), CD3 APC Cy7 (BD Biosciences), CD16 Pacific Blue (BD Biosciences) or AlexFluor 700 (Biolegend), and CD14 PerCP (R&D Systems, Minneapolis, MN USA) were added and cells were incubated for 20 min at 37oC in a 5% CO2-humidified environment. Dead cells were identified using LIVE/DEAD Fixable Aqua Dead Cell Stain Kit for flow cytometry (Life Technologies, Carlsbad, CA USA). Cells were washed and resuspended in sorting buffer at 30M/ml and filtered using a 5ml polystyrene tube with cell-strainer cap (BD Biosciences). Cells were sorted at 4oC using BD Sorter into 5ml FACS tubes containing 500ul sorting buffer and 500ul FBS. Cells were kept on ice before and after sorting.

extract_protocol: Individual monocyte subsets were sorted directly into 1.7ml tube with 500ul RLT buffer w/ beta-mercaptoethanol (10ul BME/1ml RLT) and placed on dry ice then transferred to -80oC.  Reverse transcription reactions were performed to obtain cDNAs, which were hybridized to the Illumina Human HT-12 V4 Expression BeadChips according to the manufacturer’s instruction, and quantified using an Illumina iScan System

treatment_protocol: Sorted monocyte subsets were transferred to 5ml polypropylene tubes, spun down and suspended in cultured RPMI medium [RPMI with L-glutamine (Corning Cellgro, Manassas, VA USA) supplemented with 10% FBS and 1X (50U) Penicillin-Streptomycin (Invitrogen, Carlsbad, CA USA)]. Cells were plated at 30,000 cells/well in 96-well U-bottom plates. TLR and RIG-I agonists were added at the following concentrations: LPS-TLR4 (0.5 µg/ml) or CLO97-TLR7/8 (1 µg/ml) or 5’-pppRNA-RIG-I (500 ng/ml). Optimal concentrations of different TLR agonists were selected based on median production of IL-6 and IFNα and a ≥ 85% survival rate of monocytes. All PRR ligands were purchased commercially (InvivoGen, San Diego, CA) except for 5’-pppRNA, which was custom synthesized, as previously described [23]. PBMCs cultured in medium alone were used as a control for LPS and CLO97. Stimulation by 5’-pppRNA required the use of a cationic transfection agent LyoVec (InvivoGen), medium plus Lyovec alone was used as a control. PBMCs were cultured for 24 hrs at 37oC in a 5% CO2-humidified environment.

value: OLD

tag: donor

tag: sourcecells

value: sorted PBMC

tag: celltypesort

tag: celltypeshort

value: PosPos

tag: sampleID


title: OLD_CD14posCD16pos_OA2_E24

description:
OLD_CD14posCD16pos
8981245075_J


title: YNG_CD14posCD16neg_YA7_E47

description:
YNG_CD14posCD16neg
8981245075_K

value: YNG

value: PosNeg


title: Prostate cancer cell DU145 with NC1 mimic, rep3

description:
DU145_NC1_3 OE
Cells (#3)  isolated from DU145 prostate cancer cell line with miRNA mimic NC1

tag: cell type


title: OLD_CD14dimCD16pos_OA3_E25

description:
OLD_CD14dimCD16pos
8981245062_H

value: DimPos


title: Prostate cancer cell DU145 with NC1 mimic, rep2

description:
DU145_NC1_2 OE
Cells (#2)  isolated from DU145 prostate cancer cell line with miRNA mimic NC1


title: YNG_CD14posCD16pos_YA6_E18

description:
YNG_CD14posCD16pos
8981245075_D


title: YNG_CD14dimCD16pos_YA5_E13

description:
YNG_CD14dimCD16pos
8981245075_E


title: OLD_CD14posCD16neg_OA7_E38

description:
OLD_CD14posCD16neg
8981245075_I


title: Prostate cancer cell DU145 with miR-638 mimic, rep1

description:
DU145_638_1 OE
Cells (#1)  isolated from DU145 prostate cancer cell line with miRNA mimic miR-638


title: Prostate cancer cell DU145 with NC2 mimic, rep1

description:
DU145_NC2_1 OE
Cells (#1)  isolated from DU145 prostate cancer cell line with miRNA mimic NC2


title: OLD_CD14posCD16neg_OA5_E32

description:
OLD_CD14posCD16neg
8981245062_L


title: YNG_CD14posCD16neg_YA4_E11

description:
YNG_CD14posCD16neg
8981245075_H


title: YNG_CD14posCD16pos_YA1_E3

description:
YNG_CD14posCD16pos
8981245075_C


title: YNG_CD14posCD16pos_YA7_E48

description:
YNG_CD14posCD16pos
8981245075_G


title: Prostate cancer cell DU145 with NC2 mimic, rep3

description:
DU145_NC2_3 OE
Cells (#3)  isolated from DU145 prostate cancer cell line with miRNA mimic NC2


title: OLD_CD14posCD16pos_OA5_E33

description:
OLD_CD14posCD16pos
8981245062_I


title: YNG_CD14posCD16neg_YA5_E14

description:
YNG_CD14posCD16neg
8981245075_A


title: OLD_CD14posCD16neg_OA3_E26

description:
OLD_CD14posCD16neg
8981245062_G


title: OLD_CD14dimCD16pos_OA5_E31

description:
OLD_CD14dimCD16pos
8981245062_J


title: OLD_CD14dimCD16pos_OA9_E43

description:
OLD_CD14dimCD16pos
8981245062_K


title: YNG_CD14posCD16pos_YA8_E51

description:
YNG_CD14posCD16pos
8981245062_E


title: YNG_CD14posCD16pos_YA9_E54

description:
YNG_CD14posCD16pos
8981245062_F


title: OLD_CD14dimCD16pos_OA6_E34

description:
OLD_CD14dimCD16pos
8981245062_D


title: OLD_CD14posCD16pos_OA3_E27

description:
OLD_CD14posCD16pos
8981245075_B


title: OLD_CD14dimCD16pos_OA4_E28

description:
OLD_CD14dimCD16pos
8981245025_L


title: OLD_CD14posCD16neg_OA9_E44

description:
OLD_CD14posCD16neg
8981245025_K


title: OLD_CD14posCD16neg_OA4_E29

description:
OLD_CD14posCD16neg
8981245062_B


title: YNG_CD14posCD16pos_YA3_E9

description:
YNG_CD14posCD16pos
8981245025_G


title: OLD_CD14posCD16pos_OA7_E39

description:
OLD_CD14posCD16pos
8981245025_D


title: YNG_CD14dimCD16pos_YA9_E52

description:
YNG_CD14dimCD16pos
8659387032_L


title: YNG_CD14posCD16neg_YA9_E53

description:
YNG_CD14posCD16neg
8981245025_C


title: YNG_CD14posCD16pos_YA2_E6

description:
YNG_CD14posCD16pos
8659387032_I


title: OLD_CD14posCD16neg_OA6_E35

description:
OLD_CD14posCD16neg
8659387032_H


title: OLD_CD14posCD16pos_OA4_E30

description:
OLD_CD14posCD16pos
8659387032_J


title: YNG_CD14posCD16neg_YA1_E2

description:
YNG_CD14posCD16neg
8981245025_H


title: YNG_CD14dimCD16pos_YA7_E46

description:
YNG_CD14dimCD16pos
8981245025_F


title: OLD_CD14dimCD16pos_OA8_E40

description:
OLD_CD14dimCD16pos
8981245025_J


title: YNG_CD14posCD16neg_YA8_E50

description:
YNG_CD14posCD16neg
8981245062_A


title: YNG_CD14dimCD16pos_YA2_E4

description:
YNG_CD14dimCD16pos
8981245062_C


title: YNG_CD14dimCD16pos_YA1_E1

description:
YNG_CD14dimCD16pos
8659387032_K


title: YNG_CD14dimCD16pos_YA3_E7

description:
YNG_CD14dimCD16pos
8516095066_L


title: YNG_CD14posCD16pos_YA4_E12

description:
YNG_CD14posCD16pos
8659387032_C


title: OLD_CD14dimCD16pos_OA1_E19

description:
OLD_CD14dimCD16pos
8659387032_D


title: OLD_CD14posCD16neg_OA8_E41

description:
OLD_CD14posCD16neg
8516095066_K


title: OLD_CD14dimCD16pos_OA7_E37

description:
OLD_CD14dimCD16pos
8659387032_F


title: OLD_CD14posCD16pos_OA8_E42

description:
OLD_CD14posCD16pos
8659387032_E


title: OLD_CD14posCD16pos_OA6_E36

description:
OLD_CD14posCD16pos
8981245025_I


title: OLD_CD14posCD16pos_OA1_E21

description:
OLD_CD14posCD16pos
8981245025_B


title: YNG_CD14dimCD16pos_YA6_E16

description:
YNG_CD14dimCD16pos
8659387032_G


title: YNG_CD14dimCD16pos_YA4_E10

description:
YNG_CD14dimCD16pos
8981245025_E


title: OLD_CD14posCD16neg_OA2_E23

description:
OLD_CD14posCD16neg
8659387032_B


title: OLD_CD14posCD16neg_OA1_E20

description:
OLD_CD14posCD16neg
8981245025_A


title: YNG_CD14posCD16neg_YA6_E17

description:
YNG_CD14posCD16neg
8516095066_J


title: YNG_CD14posCD16neg_YA3_E8

description:
YNG_CD14posCD16neg
8516095066_I


title: YNG_CD14posCD16pos_YA5_E15

description:
YNG_CD14posCD16pos
8516095066_F


title: Bios-BC39 Breast Cancer serum sample 15

type: other

city: Stratford

first: Robert

middle: G

last: Nagele

state: NJ

address: 2 Medical Center Drive

department: NJISA

institute: UMDNJ-SOM

hyb_protocol: none provided by submitter

scan_protocol: Protein microarrays were scanned using a Genepix 4000B microarray scanner at 635nm using default parameters, PMT of 600, and a pixel size of 5um.

data_processing:
The GPR files were imported into Invitrogen's Prospector v5.2.1 microarray analysis software.  Individual serum results were characterized into disease and control groups and then linearly normalized for group-to-group analysis of differential expression.  Further Training and Testing set biomarker discovery, assessment, and significance analysis was performed using Random Forest (RF).
Normalized fluorescence intensities are presented in Relative Fluorescent Units (RFUs).

label: Alexa Fluor 647

molecule: other

source_name: Breast Cancer serum

label_protocol: Probing and analysis of microarrays was performed with strict adherence to suggested manufacturer protocols.  (See Invitrogen and Molecular Devices online.)

extract_protocol: All serum samples were purchased from commercial biofluid repositiories, drawn and stored under proper conditions, and collected and used with IRB approval.

value: FEMALE


title: Bios-BC29 Breast Cancer serum sample 10


title: Bios-BC37 Breast Cancer serum sample 14


title: Bios-BC27 Breast Cancer serum sample 9


title: Bios-BC25 Breast Cancer serum sample 8


title: YNG_CD14posCD16neg_LyoVec_E174

data_processing: Analysis of the quantified output data was conducted using the limma from the R statistical language and other software packages from Bioconductor version 3.4.  Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation. Raw data was convertex to log base 2.

growth_protocol: Sorted monocyte subsets were transferred to 5ml polypropylene tubes, spun down and suspended in cultured RPMI medium [RPMI with L-glutamine (Corning Cellgro, Manassas, VA USA) supplemented with 10% FBS and 1X (50U) Penicillin-Streptomycin (Invitrogen, Carlsbad, CA USA)]. Cells were plated at 30,000 cells/well in 96-well U-bottom plates. TLR and RIG-I agonists were added at the following concentrations: LPS-TLR4 (0.5 µg/ml) or CLO97-TLR7/8 (1 µg/ml) or 5’-pppRNA-RIG-I (500 ng/ml). Optimal concentrations of different TLR agonists were selected based on median production of IL-6 and IFNα and a ≥ 85% survival rate of monocytes. All PRR ligands were purchased commercially (InvivoGen, San Diego, CA) except for 5’-pppRNA, which was custom synthesized, as previously described [23]. PBMCs cultured in medium alone were used as a control for LPS and CLO97. Stimulation by 5’-pppRNA required the use of a cationic transfection agent LyoVec (InvivoGen), medium plus Lyovec alone was used as a control. PBMCs were cultured for 24 hrs at 37oC in a 5% CO2-humidified environment.

tag: samplenumber

tag: arrayid

tag: sampleset

value: b

tag: treatment

value: LyoVec

tag: subgroup

tag: sampletype

value: C

tag: agetreatment

tag: celltypesorttx

tag: agecelltypesorttx

tag: celltype

value: PBMCs


title: OLD_CD14posCD16pos_LyoVec_E093

tag: age


title: OLD_CD14posCD16pos_LyoVec_E209

tag: donor


title: YNG_CD14posCD16pos_LyoVec_E350


title: OLD_CD14posCD16pos_LyoVec_E296


title: OLD_CD14posCD16neg_LyoVec_E301


title: YNG_CD14posCD16neg_LyoVec_E063


title: YNG_CD14posCD16neg_YA2_E5

description:
YNG_CD14posCD16neg
8516095066_G

tag: sourcecells


title: YNG_CD14dimCD16pos_YA8_E49

description:
YNG_CD14dimCD16pos
8516095066_H

tag: celltypesort


title: YNG_CD14posCD16pos_RIGI_E348

value: RIGI

value: S


title: OLD_CD14posCD16neg_RIGI_E192


title: Bios-BC23 Breast Cancer serum sample 7

tag: gender


title: Bios-BC35 Breast Cancer serum sample 13


title: Bios-BC21 Breast Cancer serum sample 6


title: Bios-BC31 Breast Cancer serum sample 11


title: OLD_CD14dimCD16pos_RIGI_E086

tag: sampleID


title: YNG_CD14posCD16pos_RIGI_E008


title: Bios-BC19 Breast Cancer serum sample 5


title: OLD_CD14dimCD16pos_LyoVec_E291


title: Bios-BC17 Breast Cancer serum sample 4


title: OLD_CD14posCD16pos_RIGI_E294


title: YNG_CD14posCD16neg_RIGI_E259


title: Bios-BC15 Breast Cancer serum sample 3


title: OLD_CD14posCD16neg_LyoVec_E103


title: OLD_CD14dimCD16pos_RIGI_E182


title: Bios-BC13 Breast Cancer serum sample 2


title: MJFF-PD124 Early-Stage Parkinson's Disease serum sample 15

source_name: Early-Stage Parkinson's Disease serum


title: Bios-BC11 Breast Cancer serum sample 1


title: MJFF-PD115 Early-Stage Parkinson's Disease serum sample 14

value: MALE


title: OLD_CD14posCD16neg_LyoVec_E375


title: MJFF-PD100  Early-Stage Parkinson's Disease serum sample 13


title: MJFF-PD88 Early-Stage Parkinson's Disease serum sample 12


title: MJFF-PD84  Early-Stage Parkinson's Disease serum sample 11


title: MJFF-PD39 Early-Stage Parkinson's Disease serum sample 10


title: MJFF-PD24 Early-Stage Parkinson's Disease serum sample 9


title: MJFF-PD12 Early-Stage Parkinson's Disease serum sample 7


title: YNG_CD14dimCD16pos_RIGI_E269


title: OLD_CD14posCD16pos_RIGI_E111


title: OLD_CD14posCD16pos_RIGI_E028


title: OLD_CD14posCD16neg_LyoVec_E040


title: OLD_CD14dimCD16pos_OA2_E22

description:
OLD_CD14dimCD16pos
8981245075_L

tag: celltypeshort


title: MJFF-PD11 Early-Stage Parkinson's Disease serum sample 6


title: OLD_CD14posCD16neg_RIGI_E038

tag: samplenumber


title: OLD_CD14posCD16neg_RIGI_E319

tag: arrayid


title: OLD_CD14dimCD16pos_LyoVec_E108

tag: sampleset


title: MJFF-PD9 Early-Stage Parkinson's Disease serum sample 5


title: YNG_CD14dimCD16pos_RIGI_E249

tag: treatment


title: MJFF-PD8 Early-Stage Parkinson's Disease serum sample 4


title: MJFF-PD6 Early-Stage Parkinson's Disease serum sample 3


title: MJFF-PD2 Early-Stage Parkinson's Disease serum sample 2


title: MJFF-PD1 Early-Stage Parkinson's Disease serum sample 1


title: YNG_CD14posCD16pos_RIGI_E051

tag: subgroup


title: MJFF-PD15 Early-Stage Parkinson's Disease serum sample 8


title: OLD_CD14posCD16neg_RIGI_E299

tag: sampletype


title: Ast-CT14 Normal Control Donor serum sample 31

source_name: Normal Control Donor serum


title: OLD_CD14posCD16pos_RIGI_E368

tag: agetreatment


title: YNG_CD14dimCD16pos_LyoVec_E251

tag: celltypesorttx


title: YNG_CD14posCD16pos_RIGI_E167

tag: agecelltypesorttx


title: YNG_CD14dimCD16pos_LyoVec_E345

tag: celltype


title: YNG_CD14posCD16neg_LyoVec_E083

tag: age


title: YNG_CD14posCD16pos_LyoVec_E256

tag: donor


title: YNG_CD14dimCD16pos_RIGI_E003


title: CY5 Normal Control Donor serum sample 29


title: YNG_CD14posCD16neg_LyoVec_E281


title: YNG_CD14dimCD16pos_LyoVec_E271


title: CY13 Normal Control Donor serum sample 30


title: YNG_CD14posCD16neg_RIGI_E152


title: BioS-CT62 Normal Control Donor serum sample 27


title: BioS-CT61 Normal Control Donor serum sample 26


title: BioS-CT64 Normal Control Donor serum sample 28


title: BioS-CT44 Normal Control Donor serum sample 25


title: BioS-CT39 Normal Control Donor serum sample 24


title: BioS-CT38 Normal Control Donor serum sample 23


title: BioS-CT36 Normal Control Donor serum sample 21


title: BioS-CT34 Normal Control Donor serum sample 19


title: BioS-CT35 Normal Control Donor serum sample 20


title: OLD_CD14posCD16neg_RIGI_E373


title: OLD_CD14posCD16pos_LyoVec_E189


title: OLD_CD14posCD16pos_RIGI_E314


title: YNG_CD14dimCD16pos_RIGI_E343


title: OLD_CD14posCD16pos_RIGI_E187


title: OLD_CD14dimCD16pos_LyoVec_E365


title: OLD_CD14dimCD16pos_RIGI_E289


title: OLD_CD14posCD16neg_RIGI_E121


title: OLD_CD14posCD16neg_LyoVec_E194


title: BioS-CT33 Normal Control Donor serum sample 18


title: BioS-CT32 Normal Control Donor serum sample 17


title: BioS-CT37 Normal Control Donor serum sample 22


title: BioS-CT29 Normal Control Donor serum sample 14


title: YNG_CD14posCD16neg_RIGI_E353


title: BioS-CT27 Normal Control Donor serum sample 12


title: BioS-CT28 Normal Control Donor serum sample 13


title: OLD_CD14posCD16neg_LyoVec_E214


title: BioS-CT31 Normal Control Donor serum sample 16


title: OLD_CD14posCD16neg_LyoVec_E321


title: BioS-CT26 Normal Control Donor serum sample 11


title: YNG_CD14posCD16neg_RIGI_E279


title: BioS-CT25 Normal Control Donor serum sample 10


title: OLD_CD14posCD16pos_RIGI_E207


title: BioS-CT24 Normal Control Donor serum sample 9


title: OLD_CD14posCD16pos_LyoVec_E316


title: OLD_CD14posCD16neg_LyoVec_E123


title: YNG_CD14posCD16pos_RIGI_E254


title: BioS-CT22 Normal Control Donor serum sample 7


title: YNG_CD14posCD16neg_LyoVec_E261


title: YNG_CD14posCD16pos_RIGI_E071


title: BioS-CT23 Normal Control Donor serum sample 8


title: YNG_CD14posCD16neg_LyoVec_E154


title: BioS-CT21 Normal Control Donor serum sample 6


title: BioS-CT20 Normal Control Donor serum sample 5


title: BioS-CT19 Normal Control Donor serum sample 4


title: YNG_CD14posCD16pos_LyoVec_E276


title: OLD_CD14dimCD16pos_RIGI_E202


title: BioS-CT17 Normal Control Donor serum sample 2


title: YNG_CD14dimCD16pos_LyoVec_E005


title: BioS-CT16 Normal Control Donor serum sample 1


title: YNG_CD14posCD16pos_LyoVec_E053


title: BioS-MS51 Relapsing-Remitting Multiple Sclerosis serum sample 31


title: BioS-MS50 Relapsing-Remitting Multiple Sclerosis serum sample 30


title: YNG_CD14dimCD16pos_LyoVec_E144


title: BioS-MS47 Relapsing-Remitting Multiple Sclerosis serum sample 27


title: BioS-MS45 Relapsing-Remitting Multiple Sclerosis serum sample 25


title: OLD_CD14dimCD16pos_LyoVec_E311


title: YNG_CD14posCD16pos_LyoVec_E149


title: BioS-CT30 Normal Control Donor serum sample 15


title: YNG_CD14posCD16pos_LyoVec_E169


title: BioS-MS44 Relapsing-Remitting Multiple Sclerosis serum sample 24


title: BioS-CT18 Normal Control Donor serum sample 3


title: OLD_CD14dimCD16pos_RIGI_E363


title: BioS-MS42 Relapsing-Remitting Multiple Sclerosis serum sample 22


title: BioS-MS41 Relapsing-Remitting Multiple Sclerosis serum sample 21


title: OLD_CD14posCD16pos_RIGI_E091


title: YNG_CD14posCD16neg_LyoVec_E355


title: YNG_CD14posCD16pos_RIGI_E147


title: YNG_CD14posCD16pos_RIGI_E274


title: BioS-MS40 Relapsing-Remitting Multiple Sclerosis serum sample 20


title: YNG_CD14dimCD16pos_RIGI_E142


title: YNG_CD14posCD16neg_RIGI_E081


title: BioS-MS46 Relapsing-Remitting Multiple Sclerosis serum sample 26


title: BioS-MS39 Relapsing-Remitting Multiple Sclerosis serum sample 19


title: YNG_CD14posCD16pos_LyoVec_E010


title: BioS-MS38 Relapsing-Remitting Multiple Sclerosis serum sample 18


title: OLD_CD14dimCD16pos_RIGI_E309


title: OLD_CD14posCD16pos_LyoVec_E113


title: OLD_CD14posCD16pos_LyoVec_E370


title: OLD_CD14dimCD16pos_LyoVec_E184


title: BioS-MS36 Relapsing-Remitting Multiple Sclerosis serum sample 16


title: BioS-MS37 Relapsing-Remitting Multiple Sclerosis serum sample 17


title: OLD_CD14dimCD16pos_LyoVec_E204


title: BioS-MS35 Relapsing-Remitting Multiple Sclerosis serum sample 15


title: OLD_CD14dimCD16pos_LyoVec_E088


title: BioS-MS32 Relapsing-Remitting Multiple Sclerosis serum sample 12


title: BioS-MS34 Relapsing-Remitting Multiple Sclerosis serum sample 14


title: BioS-MS31 Relapsing-Remitting Multiple Sclerosis serum sample 11


title: OLD_CD14posCD16neg_RIGI_E212


title: BioS-MS33 Relapsing-Remitting Multiple Sclerosis serum sample 13


title: YNG_CD14posCD16neg_RIGI_E172


title: BioS-MS30 Relapsing-Remitting Multiple Sclerosis serum sample 10


title: YNG_CD14posCD16neg_RIGI_E061


title: BioS-MS29 Relapsing-Remitting Multiple Sclerosis serum sample 9


title: YNG_CD14dimCD16pos_NT_E344

value: a

value: NT


title: BioS-MS28 Relapsing-Remitting Multiple Sclerosis serum sample 8


title: YNG_CD14posCD16pos_NT_E052


title: BioS-MS27 Relapsing-Remitting Multiple Sclerosis serum sample 7


title: BioS-MS26 Relapsing-Remitting Multiple Sclerosis serum sample 6


title: YNG_CD14posCD16pos_NT_E168


title: OLD_CD14dimCD16pos_CLO97_E085


title: BioS-MS25 Relapsing-Remitting Multiple Sclerosis serum sample 5


title: OLD_CD14posCD16neg_LPS_E190

value: LPS


title: BioS-MS23 Relapsing-Remitting Multiple Sclerosis serum sample 3


title: BioS-MS22 Relapsing-Remitting Multiple Sclerosis serum sample 2


title: BioS-MS21 Relapsing-Remitting Multiple Sclerosis serum sample 1


title: BioS-MS24 Relapsing-Remitting Multiple Sclerosis serum sample 4


title: BioS-MS20 Secondary Progressive Multiple Sclerosis serum sample 20


title: YNG_CD14posCD16pos_LPS_E346


title: YNG_CD14posCD16pos_LPS_E069


title: BioS-MS19 Secondary Progressive Multiple Sclerosis serum sample 19


title: YNG_CD14dimCD16pos_CLO97_E045


title: YNG_CD14posCD16neg_NT_E082


title: BioS-MS18 Secondary Progressive Multiple Sclerosis serum sample 18


title: YNG_CD14dimCD16pos_CLO97_E141


title: OLD_CD14posCD16pos_CLO97_E367

value: OLD


title: BioS-MS17 Secondary Progressive Multiple Sclerosis serum sample 17


title: BioS-MS15 Secondary Progressive Multiple Sclerosis serum sample 15


title: OLD_CD14posCD16pos_CLO97_E293


title: BioS-MS14 Secondary Progressive Multiple Sclerosis serum sample 14


title: YNG_CD14posCD16pos_LPS_E006


title: OLD_CD14dimCD16pos_CLO97_E181


title: OLD_CD14posCD16neg_CLO97_E372


title: YNG_CD14dimCD16pos_LPS_E267


title: OLD_CD14posCD16pos_LPS_E109


title: YNG_CD14posCD16pos_NT_E255


title: BioS-MS13 Secondary Progressive Multiple Sclerosis serum sample 13


title: BioS-MS16 Secondary Progressive Multiple Sclerosis serum sample 16


title: BioS-MS11 Secondary Progressive Multiple Sclerosis serum sample 11


title: BioS-MS12 Secondary Progressive Multiple Sclerosis serum sample 12


title: OLD_CD14dimCD16pos_NT_E203


title: BioS-MS10 Secondary Progressive Multiple Sclerosis serum sample 10


title: OLD_CD14posCD16neg_NT_E193


title: YNG_CD14posCD16neg_LPS_E257


title: YNG_CD14posCD16neg_LPS_E059


title: YNG_CD14posCD16pos_NT_E072


title: OLD_CD14dimCD16pos_NT_E183


title: OLD_CD14dimCD16pos_RIGI_E106


title: BioS-MS7 Secondary Progressive Multiple Sclerosis serum sample 7


title: BioS-MS5 Secondary Progressive Multiple Sclerosis serum sample 5


title: BioS-MS4 Secondary Progressive Multiple Sclerosis serum sample 4


title: BioS-MS6 Secondary Progressive Multiple Sclerosis serum sample 6


title: YNG_CD14posCD16pos_LPS_E252


title: OLD_CD14posCD16neg_CLO97_E191


title: OLD_CD14dimCD16pos_NT_E024


title: BioS-MS3 Secondary Progressive Multiple Sclerosis serum sample 3


title: Bios-MS2 Secondary Progressive Multiple Sclerosis serum sample 2


title: BioS-MS8 Secondary Progressive Multiple Sclerosis serum sample 8


title: BioS-MS1 Secondary Progressive Multiple Sclerosis serum sample 1


title: OLD_CD14posCD16pos_LPS_E292


title: BioS-MS9 Secondary Progressive Multiple Sclerosis serum sample 9


title: BioS-MS43 Relapsing-Remitting Multiple Sclerosis serum sample 23


title: OLD_CD14posCD16neg_NT_E122


title: OLD_CD14posCD16neg_LPS_E099


title: OLD_CD14posCD16pos_CLO97_E313


title: OLD_CD14posCD16pos_LPS_E205


title: OLD_CD14posCD16neg_LPS_E371


title: OLD_CD14dimCD16pos_NT_E290


title: YNG_CD14dimCD16pos_NT_E270


title: YNG_CD14dimCD16pos_CLO97_E161


title: YNG_CD14dimCD16pos_LPS_E160


title: BioS-MS48 Relapsing-Remitting Multiple Sclerosis serum sample 28


title: YNG_CD14posCD16pos_NT_E009


title: OLD_CD14posCD16pos_NT_E295


title: BioS-MS49 Relapsing-Remitting Multiple Sclerosis serum sample 29


title: YNG_CD14dimCD16pos_LPS_E140


title: OLD_CD14dimCD16pos_NT_E087


title: OLD_CD14posCD16pos_LPS_E366


title: YNG_CD14posCD16pos_LPS_E145


title: YNG_CD14posCD16neg_LPS_E150


title: YNG_CD14posCD16neg_NT_E019


title: Muscle iPS #2

first: Roderick

last: Slieker

address: PO Box 9600

department: Medical Oncology

institute: Leiden University Medical Center

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: DNA methylation data was functional normalized. Probes were discarded if they had a low bead count (< 3), high detection P value  (> 0.01), or  a low success rate (< 95%).

source_name: iPS derived from Muscle

label_protocol: According to Illumina protocol

extract_protocol: Chlorophorm/isoamyl alcohol protocol

tag: tissue

value: Muscle iPS

tag: age (weeks after last menstrual period)

tag: Sex

value: Male


title: OLD_CD14posCD16pos_NT_E092

tag: sampleID

tag: celltypesort


title: Pancreas iPS #1

source_name: iPS derived from Pancreas

value: Pancreas iPS


title: OLD_CD14posCD16pos_NT_E188

tag: samplenumber


title: Kidney iPS #2

source_name: iPS derived from Kidney

value: Kidney iPS


title: OLD_CD14dimCD16pos_CLO97_E201

tag: arrayid


title: YNG_CD14dimCD16pos_CLO97_E248

tag: sampleset

value: YNG


title: YNG_CD14posCD16neg_CLO97_E171

tag: treatment


title: YNG_CD14dimCD16pos_LPS_E247

tag: subgroup


title: YNG_CD14posCD16pos_CLO97_E146

tag: sampletype


title: OLD_CD14posCD16neg_LPS_E210

tag: agetreatment


title: Brain iPS #2

source_name: iPS derived from Brain

value: Brain iPS


title: YNG_CD14posCD16pos_CLO97_E273

tag: celltypesorttx


title: Pancreas iPS #3


title: Skin iPS #1

source_name: iPS derived from Skin

value: Skin iPS


title: Muscle iPS #1


title: OLD_CD14dimCD16pos_LPS_E021

tag: agecelltypesorttx


title: OLD_CD14posCD16neg_LPS_E317

tag: celltype


title: Lung iPS #2

source_name: iPS derived from Lung

value: Lung iPS


title: Skin iPS #2


title: YNG_CD14posCD16neg_LPS_E351

tag: age


title: YNG_CD14dimCD16pos_CLO97_E268

tag: donor


title: Brain iPS #1

tag: tissue


title: OLD_CD14dimCD16pos_NT_E107

value: C


title: BO1 Muscle

source_name: Muscle

value: Muscle

tag: age (weeks after last menstrual period)


title: YNG_CD14posCD16pos_LPS_E165

value: PBMCs


title: Kidney iPS #1

tag: Sex


title: OLD_CD14posCD16neg_NT_E300

tag: sampleID


title: YNG_CD14posCD16pos_CLO97_E070

value: S

tag: celltypesort


title: YNG_CD14posCD16neg_CLO97_E278

tag: samplenumber


title: BO1 Skin

source_name: Skin

value: Skin


title: BO1 Brain

source_name: Brain

value: Brain


title: BO1 Lung

source_name: Lung

value: Lung


title: BO1 Pancreas

source_name: Pancreas

value: Pancreas


title: CR1_Tongue_22

source_name: Tongue

value: Tongue


title: Bios-BC33 Breast Cancer serum sample 12

tag: gender

value: FEMALE


title: CR1_Stomach_22

source_name: Stomach

value: Stomach


title: CR1_Lung_22


title: OLD_CD14posCD16pos_LPS_E026

source_name: Sorted Cells from PBMC

tag: arrayid

tag: sampleset

value: a

value: OLD

value: LPS


title: OLD_CD14posCD16pos_CLO97_E110

tag: treatment

tag: subgroup


title: BO1 Kidney

source_name: Kidney

value: Kidney

value: Male


title: Lung iPS #1

value: Lung iPS


title: CR1_Intestine_22

source_name: Intestine

value: Intestine


title: CR1_Skin_22


title: CR1_Liver_22

source_name: Liver

value: Liver


title: OLD_CD14posCD16pos_NT_E369

value: NT

tag: sampletype

value: C

tag: agetreatment

value: PBMCs


title: YNG_CD14posCD16pos_NT_E275

value: YNG

tag: celltypesorttx

tag: agecelltypesorttx


title: OLD_CD14posCD16neg_NT_E320

tag: age

tag: celltype


title: OLD_CD14posCD16neg_NT_E374

tag: donor


title: CR1_Brain_22

tag: tissue

value: Brain

tag: age (weeks after last menstrual period)


title: CR1_Placenta_22

source_name: Placenta

value: Placenta


title: YNG_CD14posCD16neg_LPS_E277

tag: sampleID

value: S


title: YNG_CD14posCD16pos_CLO97_E050

tag: celltypesort


title: YNG_CD14dimCD16pos_CLO97_E342

tag: samplenumber


title: OLD_CD14dimCD16pos_LPS_E287


title: DF1_Tongue_9

value: Tongue


title: CZ1_Lung_9

value: Lung


title: OLD_CD14dimCD16pos_LPS_E084

value: a


title: YNG_CD14posCD16pos_CLO97_E166


title: DF1_Skin_9

value: Skin


title: DF1_Intestine_9


title: DM2_Spleen_12

source_name: Spleen

value: Spleen


title: YNG_CD14posCD16neg_NT_E173


title: YNG_CD14posCD16neg_CLO97_E352


title: YNG_CD14posCD16pos_LPS_E272

value: LPS


title: CZ1_Liver_9


title: DF1_Brain_9


title: YNG_CD14posCD16neg_NT_E062


title: OLD_CD14posCD16neg_LPS_E119

value: OLD


title: CC3_Heart A_22

source_name: Heart A

value: Heart A


title: CF2_Heart V_22

source_name: Heart V

value: Heart V


title: BO1_Lung_22


title: OLD_CD14posCD16pos_NT_E208


title: OLD_CD14posCD16neg_CLO97_E100


title: YNG_CD14dimCD16pos_LPS_E044


title: BO1_Tongue_22


title: YNG_CD14posCD16neg_NT_E354


title: YNG_CD14posCD16neg_NT_E260


title: BO1_Skin_22


title: YNG_CD14posCD16pos_NT_E349


title: OLD_CD14dimCD16pos_LPS_E361


title: OLD_CD14posCD16pos_CLO97_E090


title: DJ1_Heart V_9


title: OLD_CD14posCD16neg_LPS_E297


title: OLD_CD14dimCD16pos_NT_E364


title: YNG_CD14posCD16neg_LPS_E170


title: OLD_CD14posCD16pos_NT_E029


title: BM1_Gonad_22

source_name: Gonad

value: Gonad


title: DJ1_Kidney_9

value: Kidney


title: CC3_Kidney_22


title: CF2_Heart A_22


title: OLD_CD14posCD16pos_LPS_E089


title: YNG_CD14posCD16pos_CLO97_E347


title: CF2_Spleen_22


title: CZ1_Gonad_9


title: BO1_Eye_22

source_name: Eye

value: Eye


title: OLD_CD14dimCD16pos_NT_E310

value: NT

value: C

value: PBMCs


title: DF1_Stomach_9

value: Stomach


title: CC3_Heart V_22


title: BO1_Liver_22

value: Liver


title: BO1_Placenta_22

value: Placenta


title: CP1_Gonad_22


title: DJ1_Heart A_9


title: DN2_Chorion_18

source_name: Chorion

value: Chorion


title: DN2_Heart A_18


title: OLD_CD14dimCD16pos_CLO97_E362

value: a

value: S


title: YNG_CD14dimCD16pos_NT_E143

value: YNG


title: OLD_CD14posCD16neg_NT_E102


title: OLD_CD14dimCD16pos_LPS_E307

value: LPS


title: BO1_Brain_22

value: Brain


title: DN2_Gonad_18


title: OLD_CD14posCD16pos_NT_E315

value: OLD


title: BO1_Intestine_22

value: Intestine


title: OLD_CD14dimCD16pos_LPS_E180


title: BO1_Stomach_22


title: DJ1_Skin_9

source_name: Skin

value: Skin


title: YNG_CD14posCD16pos_NT_E148


title: YNG_CD14dimCD16pos_NT_E250


title: DF1_Chorion_9


title: YNG_CD14posCD16neg_NT_E280


title: OLD_CD14posCD16neg_NT_E213


title: DJ1_Liver_9


title: OLD_CD14posCD16neg_CLO97_E318


title: YNG_CD14dimCD16pos_NT_E163


title: DJ1_Lung_9

value: Lung


title: YNG_CD14posCD16neg_CLO97_E258


title: DJ1_Brain_9

source_name: Brain


title: BO1_Pancreas_22

value: Pancreas


title: DN2_Eye_18

value: Eye


title: BO1_Kidney_22

value: Kidney


title: OLD_CD14dimCD16pos_CLO97_E022

value: PBMCs


title: YNG_CD14posCD16neg_CLO97_E080


title: YNG_CD14dimCD16pos_LPS_E341


title: OLD_CD14posCD16pos_NT_E112

value: NT

value: C


title: YNG_CD14dimCD16pos_NT_E067


title: YNG_CD14dimCD16pos_CLO97_E065


title: CP1_Chorion_22


title: YNG_CD14dimCD16pos_NT_E047


title: YNG_CD14posCD16neg_LPS_E016


title: YNG_CD14dimCD16pos_LPS_E064


title: OLD_CD14posCD16pos_LPS_E312


title: YNG_CD14posCD16neg_CLO97_E060


title: DN2_Amnion_18

source_name: Amnion

value: Amnion


title: BO1_Muscle_22

source_name: Muscle

value: Muscle


title: DN2_Muscle_18


title: YNG_CD14posCD16neg_NT_E153

value: a


title: OLD_CD14dimCD16pos_CLO97_E308

value: S


title: BO1_Amnion_22


title: BO1_Adrenal_22

source_name: Adrenal

value: Adrenal


title: OLD_CD14dimCD16pos_CLO97_E288


title: DN2_Adrenal_18


title: OLD_CD14dimCD16pos_CLO97_E105


title: DN2_Heart V_18

value: Heart V


title: CF2_Amnion_22


title: BP1_Adrenal_9


title: CL3_Amnion_9


title: DL1_Muscle_9


title: CC2_Lung_18

source_name: Lung


title: CR1_Adrenal_22


title: CR1_Muscle_22


title: DF1_Placenta_9

value: Placenta


title: CF2_Pancreas_22

source_name: Pancreas


title: DN2_Pancreas_18


title: OLD_CD14dimCD16pos_LPS_E104

source_name: Sorted Cells from PBMC

value: OLD

value: LPS


title: YNG_CD14posCD16neg_CLO97_E151

value: YNG


title: CF2_Muscle_22


title: CC2_Intestine_18

source_name: Intestine

value: Intestine


title: CC2_Liver_18

source_name: Liver

value: Liver


title: CC2_Stomach_18

source_name: Stomach

value: Stomach


title: CF2_Adrenal_22


title: CC2_Skin_18

value: Skin


title: CC2_Spleen_18

source_name: Spleen

value: Spleen


title: CC2_Adrenal_18


title: CC2_Kidney_18

source_name: Kidney

value: Kidney


title: CC2_UmbCord_18

source_name: Umb. Cord

value: Umb. Cord


title: CF1_Pancreas_18

value: Pancreas


title: CH1_Muscle_9

value: Muscle


title: CF1_Muscle_18


title: CC2_Tongue_18

source_name: Tongue

value: Tongue


title: MUG-Chor1 LIF

city: IStanbul

first: Sukru

last: Gulluoglu

address: Acibadem Mah. IStek vakfi binasi

country: Turkey

institute: Yeditepe University

description: Gene expression data from monolayer MUG-Chor1 cell line grown with 100 ng /mL LIF for 3 weeks

hyb_protocol: 943 ng of ss-cDNA were hybridized for 20 hr at 48C on Human Gene 2.1 ST Array. Array strpis were washed and stained in the GeneAtlas Fluidics station (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneAtlas Array scanner

data_processing: The resulting data were analyzed with Transcriptome Analysis Console 3 software

source_name: MUG-Chor1 cells grown under 100 ng/mL Leukemia Inhibitory Factor

label_protocol: Fragmented and Labeled ss-cDNA were prepared according to WT PLUS Reagent Kit from 500 ng total RNA

growth_protocol: Cells were cultured in culture flasks or well plates coated with 0.1% gelatin (SIGMA-ALDRICH cat. no. G1890-100G), (IMDM/RPMI (4:1) containing 10% fetal bovine serum and 1% antibiotics)

treatment_protocol: 100 ng/mL human recombinant LIF in medium has been administered to cell lines except control groups for 3 weeks.

tag: cell line


title: CF1_Amnion_18

value: Amnion


title: CC2_Muscle_18


title: CH1_Amnion_9


title: CF1_Adrenal_18

value: Adrenal


title: CC2_Amnion_18


title: CH1_Pancreas_9


title: MUG-Chor1 ctrl

description: Gene expression data from monolayer MUG-Chor1 cell line grown under normal conditions at 3 weeks

source_name: MUG-Chor1 cells grown under normal conditions


title: BP1_Pancreas_9


title: CC2_Pancreas_18


title: CJ1_Kidney_9


title: CJ1_UmbCord_9


title: CC2_Brain_18

value: Brain


title: U-CH1 ctrl

description: Gene expression data from monolayer U-CH1 cell line grown under normal conditions for 3 weeks

source_name: U-CH1 cells grown under normal conditions


title: BP1_Muscle_9


title: lung_JF1_P70_rep5

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description:
JF1_P70_5
Gene expression data from lung_JF1_P70_rep5.

hyb_protocol: According to the Affymetrix expression protocol.

scan_protocol: According to the Affymetrix expression protocol (Scanner 3000 7G).

data_processing:
Expression Console (v.1.3.0.187, Affymetrix) was used to obtain normalized RMA gene-level data (standard settings including sketch-quantile normalisation).
mm9 (MGSCv37) is the genome build upon which transcript assignments are based.
'Extended' is the exon group used in the analysis.
Probe group file: MoEx-1_0-st-v1.r2.pgf
Meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.extended.mps

source_name: Total lung tissue from JF1/MsJ mice at postnatal day 70

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay (Affymetrix) without rRNA depletion.

growth_protocol: Mice were housed in specific pathogen-free conditions. Food and water were available ad libitum.

extract_protocol: RNeasy Mini Kit (#74104; Qiagen, Hilden, Germany).

treatment_protocol: No treatment.

tag: strain/background

value: lung

tag: developmental stage

value: postnatal day 70

tag: gender

value: female


title: lung_JF1_P70_rep2

description:
JF1_P70_2
Gene expression data from lung_JF1_P70_rep2.


title: lung_JF1_P70_rep4

description:
JF1_P70_4
Gene expression data from lung_JF1_P70_rep4.