title: MBS83

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: Patient 30

status: Public on Feb 01 2016

type: RNA

city: Madrid

first: Juan Ángel

last: Fresno Vara

state: Madrid

address: Paseo de la castellana 261

department: INGEMM

country: Spain

institute: Hospital La Paz

description: custom TLDAs were designed such that contained 4 reference genes, 1 mandatory control and 59 genes previously related with prognosis in hormone-receptor negative breast cancer

data_processing: mRNA transcript level of each gene was analyzed by using SDS applied biosystems software by setting thresholds within the phase of the PCR determining the cycle number at which the threshold was reached (Cq).The maximum Cq value was set at 40. For a given gene, the threshold value was kept constant in all 65 samples. Four genes (IPO8, POLR2A, SDHA and UBC) were selected by NorMean (Sánchez-Navarro et al. Biotechniques 2010) as the best reference genes for FFPE samples. The geometric mean of these genes was calculated for each sample as normalization factor. The relative expression level of each target gene was expressed as ΔCq = Cqref - Cqgene. Reference normalized expression measurements were adjusted so that subsequent 1-unit increases reflecting an approximate doubling of the RNA.

label: FAM,NFQ

molecule: total RNA

organism: Homo sapiens

source_name: primary breast cancer

label_protocol: Gene expression was quantified by RT-qPCR using TaqMan technology. We normalized to total RNA input; therefore, first-strand cDNA was synthesized from 1 μg of total RNA using random primers, according to the High Capacity cDNA Reverse Transcription Kit protocol (Applied Biosystems). Reactions were carried out using TaqMan Low Density Arrays (custom TLDAs; Applied Biosystems) containing 50 μL TaqMan Universal PCR Master Mix (Applied Biosystems) and 50 μL cDNA template corresponding to 100 ng total RNA per channel of the microfluidic card.

extract_protocol: On average five 10 μm tissue sections were prepared. Total RNA was extracted with RecoverAll Total Nucleic Isolation Kit from Ambion using manufacturer's instruction

tag: tissue

value: FFPE tumor sample

tag: histology

value: invasive ductal carcinoma

tag: age (years)

tag: Sex

value: female

tag: size

tag: number of nodes

tag: grade

tag: hormone receptor status (both estrogen and progesterone receptor)

value: negative

value: positive

tag: disease metastasis-free survival (months)

tag: recurrence (0=non recurrence; 1=distant metastasis)

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: Patient 34

hyb_protocol: Gene expression was quantified by RT-qPCR using TaqMan technology


title: Patient 29

scan_protocol: Gene expression was quantified by RT-qPCR using TaqMan technology


title: MBS82

type: protein

city: Irvine

first: Elisabeth

last: Baum

state: CA

address: Med Surge II

country: USA

institute: University of California Irvine

hyb_protocol: Serum samples were diluted 1:200 in Protein Array Blocking buffer (Whatman Inc, Sanford, ME) supplemented with 10% (vol/vol) DH5α E. coli lysate (MCLAB, San Francisco, CA) and incubated on arrays over night at 4°C. Microarray slides were incubated in biotin-conjugated anti-IgG Fc fragment secondary antibody (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer, and detected by incubation with streptavidin-conjugated SureLight P-3 (Columbia Biosciences, Columbia, MD). The slides were washed and air-dried by brief centrifugation.

scan_protocol: Probed array slides were scanned in a Perkin Elmer ScanArray Express HT at a wavelength of 670 nm, at 95% laser power and 55% PMT. The output RGB TIFF files generated by the scanner were quantitated using ProScanArray Express software (Perkin Elmer, Waltham, MA) with spot-specific background correction.

data_processing: For analysis of antibody binding to Pf or Pv proteins on the microarray, the following steps were taken: i) the median background signal of antibody binding to 24 spots of IVTT reaction without DNA template (no template control, NTC) was calculated for each individual sample; ii) the raw values of antibody binding to Pf and Pv polypeptides were divided by their corresponding median NTC value, generating fold-over-control (FOC) values; iii) FOC values were log2-transformed for data normalization (data presented in Sample data tables).

molecule: protein

source_name: plasma, exposed, healthy

value: plasma

tag: sample collection time

value: March 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)

value: exposed

value: healthy

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Patient 28


title: Patient 27


title: MBS80

value: January 2014

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: MBS81

tag: tissue

tag: age (years)


title: Patient 26

tag: histology

tag: Sex

tag: size


title: MBS79

value: August 2013


title: MBS120


title: 2R Sample - repeat 8 - mAdbID:105764

city: Baltimore

first: Nevil

middle: John

last: Singh

state: MD

address: 685 W Baltimore Street

department: Microbiology & Immunology

institute: UMB

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105764

hyb_protocol: Agilent Hybridization Protocol According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45103101

data_processing:
Protocol_Name: GE2_105_Dec08 (Read Only)
The samples were analysed using BRBArraytools v.4.2.1. Data was filtered to exclude spots with both intensities below 30. Normalisation was using the lowess smoother

organism: Mus musculus

source_name: Pooled mouse T cell Reference Sample

label_protocol:
Agilent ULS Cy5 Labeling Protocol
Total RNA was labeled with Cy5 using the Agilent ULS protocol.

extract_protocol:
Trizol Extraction Protocol
T cells were suspended in Trizol reagent (Invitrogen/Life Technologies, CA) followed by homogenization by spinning through a Qiashredder column (Qiagen, MD). 0.2 volumes of chloroform was added to the lysate and the aqueous phase separated out after centrifugation. An equal volume of 70% Ethanol was added to this phase and the suspension passed through a RNeasy mini column (Qiagen). Bound RNA was eluted and quantitated. 50ng of total RNA was then amplified using the Ovation RNA amplification system v2 (Nugen, CA) and purified with DNA Clean & Concentrator -25 (Zymo Research).

value: Spleen and Lymph Nodes

tag: cell type

value: T cells

tag: sample type

value: standard reference RNA was derived from pooled mouse T cells

source_name: 2R Sample

label_protocol:
Agilent ULS Cy3 Labeling Protocol
Total RNA was labeled with Cy3 using the Agilent ULS protocol.

treatment_protocol: In-vivo treatment: Naïve 5C.C7 T cells were transferred to B10.A, PCC+,CD3epsilon-/- mouse hosts to generate 1R T cells and retransferred to fresh B10.A, PCC+,CD3epsilon-/- hosts to generate 2R T cells. In re-transfer experiments, 1R T cells were enriched by negative selection using a cocktail of antibodies targeting non T cells (B220, CD11b, NK1.1, CD8a and Class II) and then separated using anti-mouse or anti-rat coated Dynabeads (Life Technologies,CA) and magnetic stands. The enriched T cells were sorted to >99% purity on CD4+TCR+ lineage -ve gates using a flow cytometer (BD ARIA II or BD FACS Vantage)

tag: strain

value: B10.A, 5C.C7 TCR tg, RAG2-/-

tag: genotype/variation

value: 5C.C7 TCR tg, RAG2-/-


title: 2R Sample - repeat 7 - mAdbID:105763

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105763


title: Patient 25

value: FFPE tumor sample

value: invasive ductal carcinoma

tag: number of nodes

tag: grade

tag: hormone receptor status (both estrogen and progesterone receptor)

tag: disease metastasis-free survival (months)

tag: recurrence (0=non recurrence; 1=distant metastasis)

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: 1R Sample - repeat 4 - mAdbID:105475

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105475

source_name: 1R Sample


title: 1R Sample - repeat 5 - mAdbID:105479

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105479


title: 2R Sample - repeat 3 - mAdbID:105474

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105474


title: 2R Sample - repeat 4 - mAdbID:105476

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105476


title: 1R Sample - repeat 3 - mAdbID:105473

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105473


title: 2R Sample - repeat 5 - mAdbID:105478

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105478


title: 4M to 5F4

city: Shanghai

first: Bing

last: Yang

state: Shanghai

country: China

institute: SIBS，CAS

description:
sample8
4th molting compared to 5th instar feeding 4, Biological replicate 4 of 4 4M compared to 5F

hyb_protocol: Array hybridization was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: Raw data were analyzed using BRB-Array Tools (http://linus.nci.nih.gov/BRB-ArrayTools.html). Expression data were normalized by centering each array using the median over the entire array as a reference. Genes with data missing from more than 25% of samples were omitted, and a base-2 logarithmic transformation was applied to the dataset. Differentially expressed genes were selected using SAM  with a false discovery rate of 0.001. Significance was determined with q-values set at 1% and an at least two fold ratio of signal intensity between two developmental stages.

organism: Bombyx mori

source_name: Bombyx 5th feeding stage midgut

label_protocol: Total RNA (5 μg) was used to prepare fluorescent dye-labeled cDNA using a cRNA Amplification and Labeling Kit (CapitalBio) for the following microarray assay.Total RNA (5 μg) was used to prepare fluorescent dye-labeled cDNA using a cRNA Amplification and Labeling Kit (CapitalBio) for the following microarray assay.

growth_protocol: Silkworm larvae (Nistari) were reared on mulberry leaves at 25°C under a 12-h photoperiod.

extract_protocol: Midguts of silkworm larvae from the fourth feeding stage (IV-3) and 3 h after the beginning of molting (IV-M:3 h) were dissected. Isolated midguts were then pulverized in liquid nitrogen and stored at -80°C in TRIzol (Invitrogen, San Diego, USA).

treatment_protocol: Midgut was dissected in PBS and washed several times before being quickly frozen in liquid nitrogen.

tag: develpmental stage

value: 5th feeding stage

value: midgut

source_name: Bombyx 4th molting midgut

value: Bombyx 4th molting


title: 1R Sample - repeat 2 - mAdbID:105471

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105471

tag: tissue


title: 1R Sample - repeat 1 - mAdbID:105468

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105468


title: 2R Sample - repeat 6 - mAdbID:105759

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105759


title: 2R Sample - repeat 1 - mAdbID:105466

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105466


title: Patient 24

tag: age (years)

value: female

value: negative

value: positive


title: MBS78

value: plasma

tag: sample collection time

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed

tag: symptomatic or asymptomatic at sample collection

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: 4M to 5F2

description:
sample6
4th molting compared to 5th instar feeding 2, Biological replicate 2 of 4 4M compared to 5F


title: Patient 23

tag: histology

tag: Sex

tag: size

tag: number of nodes


title: 4L to 5F3

description:
sample3
day 3 of 4th feeding  compared to 5th instar feeding 3, Biological replicate 3 of 4 4L compared to 5F

source_name: Bombyx day 3 of 4th feeding midgut

value: day 3 of 4th feeding


title: 4L to 5F4

description:
sample4
day 3 of 4th feeding  compared to 5th instar feeding 4, Biological replicate 4 of 4 4L compared to 5F


title: 2R Sample - repeat 2 - mAdbID:105467

description:
The sample is RNA from T cells of B10.A, 5C.C7 TCR tg, RAG2-/- which were treated by transferring to B10.A, PCC+,CD3epsilon-/- mouse hosts.
mAdb experiment ID: 105467

value: Spleen and Lymph Nodes

tag: cell type

value: T cells

tag: sample type

tag: strain

tag: genotype/variation


title: MBS77

source_name: plasma, exposed, fever

tag: tissue

value: March 2013

value: fever

value: P. vivax


title: Patient 22

description: custom TLDAs were designed such that contained 4 reference genes, 1 mandatory control and 59 genes previously related with prognosis in hormone-receptor negative breast cancer

value: FFPE tumor sample

value: invasive ductal carcinoma

tag: age (years)

tag: grade

tag: hormone receptor status (both estrogen and progesterone receptor)

tag: disease metastasis-free survival (months)

tag: recurrence (0=non recurrence; 1=distant metastasis)

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: MBS75

source_name: plasma, exposed, asymptomatic

tag: sample collection time

value: January 2014

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

value: asymptomatic

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species

value: P. falciparum, P. vivax


title: MBS74

value: healthy

value: negative


title: Patient 20

tag: histology

tag: Sex

value: female

tag: size

tag: number of nodes

value: positive


title: 4L to 5F2

description:
sample2
day 3 of 4th feeding  compared to 5th instar feeding 2, Biological replicate 2 of 4 4L compared to 5F

tag: develpmental stage

value: 5th feeding stage

tag: tissue

value: midgut


title: 4M to 5F3

description:
sample7
4th molting compared to 5th instar feeding 3, Biological replicate 3 of 4 4M compared to 5F

value: Bombyx 4th molting


title: Patient 21

tag: age (years)

tag: grade

tag: hormone receptor status (both estrogen and progesterone receptor)

tag: disease metastasis-free survival (months)


title: 4L to 5F1

description:
sample1
day 3 of 4th feeding  compared to 5th instar feeding 1, Biological replicate 1 of 4 4L compared to 5F

value: day 3 of 4th feeding


title: 4M to 5F1

description:
sample5
4th molting compared to 5th instar feeding 1, Biological replicate 1 of 4 4M compared to 5F


title: MBS72

value: plasma

tag: sample collection time

value: August 2013

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)

value: exposed


title: MBS73

tag: sample collection site


title: Patient 17

value: FFPE tumor sample

value: invasive ductal carcinoma

tag: recurrence (0=non recurrence; 1=distant metastasis)

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: Patient 18


title: MBS70

value: March 2013

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

value: asymptomatic

tag: qpcr screening for plasmodium genus


title: MBS76

value: healthy

tag: qpcr plasmodium species


title: MBS71

value: negative


title: MBS69


title: MBS68


title: MBS66


title: MBS67


title: Patient 15

tag: histology

tag: Sex

value: female

tag: size

tag: number of nodes


title: Patient 13

tag: tissue

tag: age (years)

tag: grade

value: positive


title: Patient 12

tag: hormone receptor status (both estrogen and progesterone receptor)

tag: disease metastasis-free survival (months)


title: Patient 19

tag: recurrence (0=non recurrence; 1=distant metastasis)


title: MBS65

tag: sample collection time

tag: sample collection site


title: Patient 14

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: MBS63

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: MBS64

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Patient 16

tag: histology

tag: Sex

tag: size


title: MBS61

tag: tissue

tag: age (years)


title: MBS62


title: MCF10A sh529_2

first: Saraswati

last: Sukumar

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

description: replicate 2

hyb_protocol: Manufacturer recommended protocol.

scan_protocol: Manufacturer recommended protocol.

data_processing: Quantile normalized, log2 transformed

label: biotin

label_protocol: Manufacturer recommended protocol.

growth_protocol: DMEM F12

extract_protocol: RNeasy mini kit (#74104, Qiagen)

treatment_protocol: Transduction with scramble or target (HOXA5) shrna

tag: knockdown

value: knockdown

tag: cell line


title: MBS60

value: January 2014


title: MCF10A sh528_2

description: replicate 2


title: Patient 7

tag: number of nodes

tag: grade

tag: hormone receptor status (both estrogen and progesterone receptor)

tag: disease metastasis-free survival (months)

tag: recurrence (0=non recurrence; 1=distant metastasis)


title: Patient 5

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: Patient 10


title: Patient 9


title: Patient 11


title: MBS59

tag: sample collection time

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: Patient 6

tag: histology

tag: Sex

tag: size


title: MBS58

tag: tissue

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: MCF10A scrambled shrna_2

description: replicate 2

source_name: MCF10A scrambled shrna_2

tag: knockdown

value: scrambled

value: scr

tag: cell line


title: Patient 8

tag: number of nodes

tag: grade

tag: hormone receptor status (both estrogen and progesterone receptor)

tag: disease metastasis-free survival (months)

tag: recurrence (0=non recurrence; 1=distant metastasis)


title: MCF10A sh528

description: replicate 1

source_name: MCF10A sh528


title: Patient 4

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: MCF7 CTL FGF10 Rep3

city: Cambridge

first: Kerstin

last: Meyer

address: Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

description: CTL E2.FGF10 3

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol using an Illumina BeadArray reader.

data_processing: Raw image files were processed and analysed using the Beadarray R package. The data was corrected for spatial artifacts, log (base 2) transformed, and quantile normalised. Note: detection p-values are not available.

label: Biotin

source_name: MCF-7 cell line transfected with non-targeting siRNA and treated with estrogen and FGF10

label_protocol: Standard Illumina label protocol.

growth_protocol: MCF-7 human breast cancer cells were cultured in DMEM (Invitrogen) supplemented with 10% FBS and antibiotics. All cells were maintained at 37°C, 5% CO2. Cells were transfected with either ON-TARGETplus SMARTpool siRNA directed against FGFR2 (Dharmacon), or a non-targeting control siRNA (Dharmacon) and left for 24 h. Cell synchronisation via estrogen deprivation was carried out for three consecutive days in the transfected cells in phenol red-free media supplemented with 5% charcoal dextran-treated FBS and antibiotics, with media changed every 24 h.

extract_protocol: RNA was extracted using the miRNeasy spin column kit (QIAGEN) and quality checked using an RNA 6000 Nano chip on a 2100 Bioanalyser (Agilent). 250ng RNA (RIN>7) was used for cRNA amplification and labelling using the Illumina TotalPrep-96 kit (Ambion 4397949).

treatment_protocol: Estrogen deprived cells that had been transfected with siRNA directed againsy FGFR2 or a non-targeting control siRNA were stimulated with 1 nM estradiol (Sigma); 100ng/mL FGF10 (Invitrogen) for a period of 6 h.

tag: cell type

value: breast cancer


title: MBS57

value: plasma

tag: sample collection time

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: MCF7 siFGFR2 E2 Rep3

description: siRNA E2 3

source_name: MCF-7 cell line transfected with FGFR2 siRNA and treated with estrogen


title: MCF10A scrambled shrna

description: replicate 1

source_name: MCF10A scrambled shrna


title: Patient 3

tag: tissue

tag: histology

tag: age (years)

tag: Sex

tag: size


title: MCF7 CTL FGF10 Rep1

description: CTL E2.FGF10 1

tag: cell line


title: Patient 2

tag: number of nodes

tag: grade

tag: hormone receptor status (both estrogen and progesterone receptor)


title: MBS56

value: Mae Salid Noi, Tak, Thailand

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: MCF10A sh529

description: replicate 1

source_name: MCF10A sh529

tag: knockdown


title: MCF7 siFGFR2 FGF10 Rep2

description: siRNA E2.FGF10 2

source_name: MCF-7 cell line transfected with FGFR2 siRNA and treated with estrogen and FGF10

tag: cell type


title: MBS55

tag: sample collection time

value: August 2013

tag: sample collection site

value: community mass blood survey (ACD)


title: MBS54

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed


title: MBS53

tag: tissue

tag: symptomatic or asymptomatic at sample collection


title: MCF7 CTL Starved Rep2

description: CTL starved 2

source_name: MCF-7 cell line transfected with non-targeting siRNA and treated with vehicle


title: MCF7 siFGFR2 Starved Rep1

description: siRNA starved 1

source_name: MCF-7 cell line transfected with FGFR2 siRNA and treated with vehicle


title: MCF7 CTL E2 Rep4

description: CTL E2 4

source_name: MCF-7 cell line transfected with non-targeting siRNA and treated with estrogen


title: Patient 1

source_name: primary breast cancer

value: FFPE tumor sample

tag: histology

value: invasive ductal carcinoma

tag: age (years)

tag: disease metastasis-free survival (months)

tag: recurrence (0=non recurrence; 1=distant metastasis)

tag: overall survival (months)

tag: status at last date of follow-up (0=alive; 1=dead)


title: MBS52

source_name: plasma, exposed, healthy

value: March 2013


title: MBS51

value: healthy


title: MCF7 CTL E2 Rep1

description: CTL E2 1

tag: cell line


title: Genomic DNA from CD4 T cells of Healthy Subject 6

type: genomic

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

description:
Sample 12
CD4+ T cells from healthy subjects.

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina HiScanSQ platform using standard recommended Illumina scanner setting.

data_processing: GenomeStudio v20111.1 software.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: CD4+ T cells, healthy subject

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from samples using DNA/RNA/miRNA Universal kit (Qiagen) according to standard instructions.

tag: gender

value: male

value: CD4+ T cells

tag: disease state

value: normal


title: MBS50

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: MCF7 CTL Starved Rep1

description: CTL starved 1

tag: cell type


title: 246742_Ctx

city: Chapel HIll

first: Ryan

last: Miller

state: North Carolina

department: Pathology

institute: University of North Carolina

hyb_protocol: Labeled sample RNA and Stratagen Universal Mouse Reference RNA (Agilent, #740100)  as a reference were cohybridized at 65 C for 17 hours in a rotating hybridization oven.

scan_protocol: Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology (Part no. G2565CA)

data_processing: Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD).  Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels.  Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapsed by averaging. Samples from  different batches  were combined using the parametric settings in combatR, a module in the R statistical programming language (R Development Core Team, 2006 http://www.R-project.org) with no covariates included.  Normalized data provided is the filtered, batch combined,  non-median centered data used to draw conclusions in the study.

source_name: tumor

label_protocol: Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent.  1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes.  Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes.  Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.

extract_protocol: Total RNA was extracted s with Qiagen RNeasy kit according to manufacturer's instructions

treatment_protocol: Tumors were harvested from bains of mice and immediately flash-frozen in liquid nitrogen.

value: high-grade astrocytoma (HGA) tumor

tag: ID

tag: genotype

value: TR

tag: brain location

value: Ctx

tag: batch

tag: subtype

tag: survival (mo)

tag: diagnosis

value: GBM

source_name: Stratagene whole mouse reference RNA

tag: sample type

value: Stratagene whole mouse reference RNA


title: Genomic DNA from CD4 T cells of Healthy Subject 1

description:
Sample 7
CD4+ T cells from healthy subjects.


title: Genomic DNA from CD4 T cells of Healthy Subject 4

description:
Sample 10
CD4+ T cells from healthy subjects.

value: female


title: MCF7 CTL E2 Rep2

description: CTL E2 2

value: breast cancer


title: 246302_BS

tag: tissue

value: TRPhet

value: BS


title: MBS49

value: plasma

tag: sample collection time

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed

tag: symptomatic or asymptomatic at sample collection

tag: age (years)


title: MCF7 siFGFR2 Starved Rep2

description: siRNA starved 2

tag: cell line


title: 246300_BS


title: MCF7 siFGFR2 Starved Rep3

description: siRNA starved 3

tag: cell type


title: Genomic DNA from CD4 T cells of Healthy Subject 2

description:
Sample 8
CD4+ T cells from healthy subjects.

tag: gender

value: male

tag: disease state


title: Genomic DNA from CD4 T cells of Healthy Subject 3

description:
Sample 9
CD4+ T cells from healthy subjects.

value: CD4+ T cells


title: MBS48

value: March 2013

value: healthy

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Genomic DNA from CD4 T cells of Healthy Subject 5

description:
Sample 11
CD4+ T cells from healthy subjects.

value: normal


title: MCF7 CTL Starved Rep3

description: CTL starved 3


title: MCF7 siFGFR2 E2 Rep2

description: siRNA E2 2


title: 246270_2_OFB

value: high-grade astrocytoma (HGA) tumor

tag: ID

tag: genotype

value: TRPnull

tag: brain location

value: OFB

tag: batch

tag: subtype


title: MCF7 siFGFR2 FGF10 Rep4

description: siRNA E2.FGF10 4


title: Genomic DNA from CD4 T cells of IgAN Patient 2

description:
Sample 2
CD4+ T cells from IgA nephropathy (IgAN) patients.

source_name: CD4+ T cells, IgAN patient

value: affected


title: 245660_2_OFB

tag: tissue

tag: survival (mo)

tag: diagnosis

value: GBM

tag: sample type

value: Stratagene whole mouse reference RNA


title: MBS46

tag: sample collection time

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

value: negative


title: MCF7 CTL FGF10 Rep4

description: CTL E2.FGF10 4

tag: cell line

tag: cell type

value: breast cancer


title: Genomic DNA from CD4 T cells of IgAN Patient 3

description:
Sample 3
CD4+ T cells from IgA nephropathy (IgAN) patients.

tag: gender

tag: disease state


title: 245861_Di

tag: ID

tag: genotype

value: TR

value: Di


title: 245660_1_BS

value: TRPhet

tag: brain location

value: BS

tag: batch


title: Genomic DNA from CD4 T cells of IgAN Patient 5

description:
Sample 5
CD4+ T cells from IgA nephropathy (IgAN) patients.

value: female


title: Genomic DNA from CD4 T cells of IgAN Patient 6

description:
Sample 6
CD4+ T cells from IgA nephropathy (IgAN) patients.

value: male

value: CD4+ T cells


title: MBS47

source_name: plasma, exposed, asymptomatic

tag: tissue

value: plasma

value: March 2013

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)

value: exposed

value: asymptomatic

tag: age (years)

tag: qpcr screening for plasmodium genus

value: positive

tag: qpcr plasmodium species

value: P. falciparum


title: MBS44

tag: sample collection time

value: healthy

value: negative


title: MBS45

tag: sample collection site


title: Genomic DNA from CD4 T cells of IgAN Patient 4

description:
Sample 4
CD4+ T cells from IgA nephropathy (IgAN) patients.

value: affected


title: 245304_BS

value: high-grade astrocytoma (HGA) tumor

tag: subtype

tag: survival (mo)

tag: diagnosis

tag: sample type

value: Stratagene whole mouse reference RNA


title: LM16R_rep4

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

description: resistant cell line obtained after repeated exposure to PLX4032

hyb_protocol: Standard Illumina DASL hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were log2 transformed and normalized with robust spline normalization using the lumi package from Bioconductor.

source_name: melanoma cell line derived from nodal metastasis

label_protocol: According to whole genome DASL assay (Illumina)

growth_protocol: The parental melanoma cell line LM16 and the resistant variant LM16-R were cultured in RPMI medium supplemented with 10% FCS, HEPES buffer, glutamine and antibiotics. Cells were grown for 72 hours before recovery for RNA extraction.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with Ambion miRVANA kit according to the protocol provided by the manufacturer.

treatment_protocol: The PLX4032-resistant cell line variant LM16-R was generated by repeated exposures to PLX4032 (3 µM) until the onset of resistance.

tag: plx4032 sensitivity

value: Resistant

tag: cell type


title: MCF7 CTL E2 Rep3

description: CTL E2 3

tag: cell line

value: breast cancer


title: 244939_2_OFB

tag: ID

value: TRPhet

value: OFB


title: 245237_Di

tag: genotype

value: TRPnull

value: Di

value: GBM


title: MCF7 CTL Starved Rep4

description: CTL starved 4


title: MBS42

value: plasma

value: January 2014

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: LM16R_rep3

value: resistant cell line obtained after repeated exposure to PLX4032


title: Genomic DNA from CD4 T cells of IgAN Patient 1

description:
Sample 1
CD4+ T cells from IgA nephropathy (IgAN) patients.

tag: gender

value: male

value: CD4+ T cells

tag: disease state


title: Molar tissue_3

city: L´Hospitalet de Llobregat

first: David

last: Monk

state: Barcelona

address: 199-203 Av. Gran Via de L' Hospitalet

department: PEBC

institute: IDIBELL

description:
Sample name: NLRP7_3
tissue

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

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

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

source_name: Placenta

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

value: female

tag: tissue

value: Biparental hydatidiform mole


title: Molar tissue_4

description:
Sample name: NLRP7_4
tissue


title: MCF7 CTL FGF10 Rep2

description: CTL E2.FGF10 2

source_name: MCF-7 cell line transfected with non-targeting siRNA and treated with estrogen and FGF10


title: MBS41

tag: sample collection time

value: August 2013

value: exposed

value: healthy

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: 236024_2_OFB

value: high-grade astrocytoma (HGA) tumor

value: TRPhet

tag: brain location

value: OFB

tag: batch

tag: subtype

tag: survival (mo)

tag: diagnosis

value: Stratagene whole mouse reference RNA


title: 244190_BS

tag: ID

value: BS

tag: sample type


title: MCF7 siFGFR2 Starved Rep4

description: siRNA starved 4

tag: cell line

tag: cell type

value: breast cancer


title: LM16R_rep2

tag: plx4032 sensitivity

value: Resistant


title: LM16R_rep1


title: Molar tissue_2

description:
Sample name: NLRP7_2
tissue

tag: gender


title: 243852_OFB

tag: genotype

value: GBM


title: MCF7 siFGFR2 E2 Rep1

description: siRNA E2 1

source_name: MCF-7 cell line transfected with FGFR2 siRNA and treated with estrogen


title: Molar tissue_1

description:
Sample name: NLRP7_1
tissue

tag: tissue


title: LM16_rep3

description: parental melanoma cell line derived from nodal metastasis and sensitive to PLX4032. Its genetic characterization has been reported in Vergani et al., Neoplasia 2011; 13(12):1132-42

value: Sensitive


title: 235344_2_Di

value: TR

value: Di


title: MBS39

source_name: plasma, exposed, fever at 1mo

value: plasma

tag: sample collection time

value: March 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

value: fever at 1mo

value: positive

value: P. falciparum


title: MBS36

value: January 2014

value: exposed

value: healthy

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: Blood_4

description:
Sample name: Mum_4
tissue

source_name: Blood

value: female

value: Blood


title: 246270_1_Ctx

value: high-grade astrocytoma (HGA) tumor

value: TRPnull

tag: brain location

value: Ctx

tag: batch

tag: subtype

tag: survival (mo)

tag: diagnosis

value: GBM

value: Stratagene whole mouse reference RNA


title: Blood_2

description:
Sample name: Mum_2
tissue


title: MCF7 siFGFR2 E2 Rep4

description: siRNA E2 4

tag: cell line

tag: cell type

value: breast cancer


title: MCF7 siFGFR2 FGF10 Rep1

description: siRNA E2.FGF10 1

source_name: MCF-7 cell line transfected with FGFR2 siRNA and treated with estrogen and FGF10


title: LM16_rep1

tag: plx4032 sensitivity

value: Sensitive

value: parental melanoma cell line derived from nodal metastasis and sensitive to PLX4032. Its genetic characterization has been reported in Vergani et al., Neoplasia 2011; 13(12):1132-42


title: MBS38

tag: tissue

value: plasma

value: March 2013

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)


title: 245936_BS

tag: ID

tag: genotype

value: TRPhet

value: BS

tag: sample type


title: MBS35

tag: sample collection time

value: January 2014

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed

value: healthy

value: negative


title: 245665_OFB

value: high-grade astrocytoma (HGA) tumor

value: TRPnull

value: OFB


title: 245586_BS

value: Stratagene whole mouse reference RNA


title: 245662_BS

value: GBM


title: LM16_rep2

value: Sensitive


title: Blood_1

description:
Sample name: Mum_1
tissue

tag: gender

value: female

value: Blood


title: MBS34

value: plasma

tag: symptomatic or asymptomatic at sample collection

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Blood_3

description:
Sample name: Mum_3
tissue


title: Donor 5 - Influenza treated - 8h

city: Dallas

first: Michelle

middle: Ann

last: Gill

address: 5323 Harry Hines Blvd

department: Pediatrics

institute: University of Texas Southwestern Medical Center

description: Donor 5 - Influenza treated - 8h

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using quantile normalization with Illumina Genome Studio

source_name: Blood pDCs

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

growth_protocol: Primary human pDCs were cultured in complete RPMI media (10% FBS, 1% penicillin-streptomycin, 1% sodium pyruvate, 1% HEPES buffer solution, 1% non-essential amino acids, 1% glutamate) and IL-3.

extract_protocol: RNA was extracted using Arcturus® PicoPure® RNA isolation kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: pDCs were cultured with or without influenza A virus for 8 h.

tag: donor

value: Donor 5

tag: agent

value: Influenza A

value: Primary human pDCs


title: Donor 5 - No virus control   - 8h

description: Donor 5 - No virus control   - 8h

value: No virus control

tag: cell type


title: Donor 4 - Influenza treated - 8h

description: Donor 4 - Influenza treated - 8h

value: Donor 4


title: MBS33

value: August 2013

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)

value: exposed


title: MBS32

value: healthy

value: negative


title: MBS31


title: 245116_1_Ctx

value: high-grade astrocytoma (HGA) tumor

value: TRPhet

tag: brain location

value: Ctx

tag: batch

tag: subtype

tag: survival (mo)

tag: diagnosis

value: Stratagene whole mouse reference RNA


title: MBS30

tag: tissue

tag: sample collection time

value: March 2013


title: 245116_2_Di

tag: ID

tag: genotype

value: Di

value: GBM

tag: sample type


title: MBS43

value: plasma

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: Donor 4 - No virus control   - 8h

description: Donor 4 - No virus control   - 8h

tag: donor

value: Primary human pDCs


title: Donor 3 - Influenza treated - 8h

description: Donor 3 - Influenza treated - 8h

value: Donor 3

tag: agent

value: Influenza A


title: MBS27

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Donor 3 - No virus control   - 8h

description: Donor 3 - No virus control   - 8h

value: No virus control

tag: cell type


title: MCF7 siFGFR2 FGF10 Rep3

description: siRNA E2.FGF10 3

tag: cell line

value: breast cancer


title: MBS28

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)


title: MBS29

value: exposed

value: healthy


title: MBS40

value: August 2013

value: negative


title: 244939_1_Ctx

value: high-grade astrocytoma (HGA) tumor

value: TRPhet

tag: brain location

value: Ctx

tag: batch

tag: subtype

tag: survival (mo)

tag: diagnosis


title: Donor 2 - Influenza treated - 8h

description: Donor 2 - Influenza treated - 8h

value: Donor 2


title: 244189_Di

tag: tissue

tag: ID

tag: genotype

value: Di

tag: sample type

value: Stratagene whole mouse reference RNA


title: 244706_2_BS

value: BS

value: GBM


title: Donor 1 - Influenza treated - 8h

description: Donor 1 - Influenza treated - 8h

value: Donor 1

value: Influenza A

value: Primary human pDCs


title: 244706_1_OFB

value: OFB


title: BPA 100mg/ml

city: Ferrara

first: Annalaura

last: Mancia

address: via L.Borsari, 46

department: Life Sciences and Biotechnology

institute: University of Ferrara

description:
TT_SKIN_BPA_100
Gene expression wild dolphin skin

hyb_protocol: 500ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to custom Tursiops truncatus Microarray (Agilent) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately with a wash in acetonitrile (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 4x44k array slides (Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software A8.5.3 (Agilent) using default parameters (protocol GE1) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Tursiops truncatus

source_name: Skin biopsy

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Amplification  kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and the Agilent 2100 Bioanalyzer.

growth_protocol: Slices (about 2 mm-thick) spanning the epidermis and dermis  were  cut from skin samples of the stranded specimen immediately after collection, to set up the organotypic cultures

extract_protocol: RNA was extracted using the Aurum TM Total Fatty and Fibrous Tissue kit (Bio-Rad) following the manufacturer’s instructions.

treatment_protocol: Distinct slices were separately incubated for 24 h at room temperature (ranging from 24 to 28 °C) in cell culture media containing BPA (0.1 µg/ml or 1 µg/ml), or PFOA (0.1 µg/ml or 1 µg/ml), or the vehicle (ethanol for BPA and methanol for PFOA).

tag: location

value: Tuscany shore, Italy

tag: gender

value: female

value: Skin

tag: cultured in the media containing

value: BPA 100mg/ml


title: 245016_BS


title: Donor 1 - No virus control   - 8h

description: Donor 1 - No virus control   - 8h

tag: donor

tag: agent

value: No virus control


title: 242486_Di

value: high-grade astrocytoma (HGA) tumor

value: TRPnull


title: BPA 1mg/ml

description:
TT_SKIN_BPA_1
Gene expression wild dolphin skin

value: BPA 1mg/ml


title: TSCM product D5 S011

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
TSCM product
9447848053_K

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 Genomics core at Collaborative Genomics Center (CGC).

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 various software packages from Bioconductor.  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

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

growth_protocol: From PBMCs, CD4+ T cells as well as CD4+ T cell subsets were sorted with the FACSAria (Becton Dickinson)

extract_protocol: Cells were washed twice with cold PBS and lysed with 100 µl of cold RLT buffer (QIAGEN, Germany) supplemented with 1% beta-mercaptoethanol (BM) (Sigma, St. Louis, MO USA), and transferred to 1.7 ml tubes with 250 µl of cold RLT/BM buffer and quickly stored at -80oC. The samples underwent nucleic acid isolation in a designated Pre-PCR room using Qiagen’s RNeasy Micro Kit and underwent DNase I treatment.  Total RNA concentrations were quantified using a NanoDrop 2000c spectrophotometer and quality was assessed using BioRad’s Experion automated electrophoresis system.  With each batch of samples a 500 ng HeLa RNA control and two water non-template negative controls were included.

treatment_protocol: For gene array analysis of immune subsets, 10,000 sorted CD4+ T cells were collected directly into RNAse-free 1.5mL eppendorf tubes containing 500µL of RLT buffer with 1% β-mercaptoethanol and stored at -80°C until analysis.

tag: cell subset

value: TSCM

tag: time point

value: product

tag: sampleID


title: 244605_Ctx

value: TRPhet

tag: brain location

value: Ctx

value: Stratagene whole mouse reference RNA


title: BPA 0.1mg/ml

description:
TT_SKIN_BPA_0.1
Gene expression wild dolphin skin

value: BPA 0.1mg/ml


title: CD8_mem product D7 S007

description:
CD8_mem product
9447848053_L

tag: batch


title: Donor 2 - No virus control   - 8h

description: Donor 2 - No virus control   - 8h

value: Donor 2

tag: cell type


title: MBS25

value: plasma

tag: sample collection time

value: March 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed

tag: symptomatic or asymptomatic at sample collection

value: healthy

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: MBS24

tag: tissue


title: Ethanol (BPA Carrier)

description:
TT_SKIN_BPA_CNT
Gene expression wild dolphin skin

tag: location

value: Tuscany shore, Italy

tag: gender

value: female

value: Skin

tag: cultured in the media containing

value: Ethanol (BPA Carrier)


title: MBS26


title: MBS37

value: January 2014


title: MBS23

source_name: plasma, exposed, fever

value: fever

value: positive

value: P. falciparum, P. vivax


title: MBS20

source_name: plasma, exposed, healthy


title: MBS18

value: August 2013

value: asymptomatic

value: P. vivax


title: MBS21

value: plasma

value: March 2013


title: MBS22

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)


title: MBS19

value: exposed


title: 242092_BS

value: high-grade astrocytoma (HGA) tumor

tag: ID

tag: genotype

value: TR

value: BS

tag: subtype

tag: survival (mo)

tag: diagnosis

tag: sample type

value: Stratagene whole mouse reference RNA


title: Innate secondTP D5 S027

description:
Innate secondTP
9447848053_I

tag: donor

tag: cell subset

value: Innate

tag: time point

value: secondTP

tag: batch

tag: sampleID


title: 241102_Di

value: TRPnull

tag: brain location

value: Di

value: GBM


title: PFOA 1mg/ml

description:
TT_SKIN_PFOA_0.1
Gene expression wild dolphin skin

value: Tuscany shore, Italy

value: female

value: Skin

value: PFOA 1mg/ml


title: CD8_mem product D5 S005

description:
CD8_mem product
9447848053_H

value: product


title: 235791_BS


title: PFOA 0.1mg/ml

description:
TT_SKIN_PFOA_1
Gene expression wild dolphin skin

value: PFOA 0.1mg/ml


title: 236024_1_Ctx

value: TRPhet

value: Ctx


title: 241898_BS

value: high-grade astrocytoma (HGA) tumor


title: CD8_mem product D8 S008

description:
CD8_mem product
9447848053_F


title: MBS17

value: plasma

tag: sample collection time

value: August 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed

tag: symptomatic or asymptomatic at sample collection

value: healthy

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: control (culture media)

description:
TT_SKIN_CNT
Gene expression wild dolphin skin

tag: location

tag: gender

tag: tissue

tag: cultured in

value: control media


title: CD8_mem product D9 S009

description:
CD8_mem product
9447848053_J

tag: donor

tag: cell subset


title: Methanol (PFOA vehicole)

description:
TT_SKIN_PFOA_CNT
Gene expression wild dolphin skin

value: Tuscany shore, Italy

tag: cultured in the media containing

value: Methanol (PFOA vehicle)


title: 235344_1_BS

tag: ID

tag: genotype

value: TR

value: BS

tag: batch

tag: subtype

tag: survival (mo)

tag: diagnosis

value: GBM

tag: sample type

value: Stratagene whole mouse reference RNA


title: 236070_Ctx

value: TRPnull

tag: brain location


title: TSCM product D3 S016

description:
TSCM product
9447848053_E

value: TSCM

tag: time point

value: product

tag: sampleID


title: TSCM product D1 S014

description:
TSCM product
9447848053_C


title: Innate secondTP D2 S024

description:
Innate secondTP
9447848053_D

value: Innate

value: secondTP


title: 235316_BS

value: high-grade astrocytoma (HGA) tumor


title: 234750_BS


title: TSCM product D2 S015

description:
TSCM product
9447848053_B


title: CD8_mem product D10 S006

description:
CD8_mem product
9447848053_G


title: Innate secondTP D6 S022

description:
Innate secondTP
9447848053_A


title: MBS15

value: plasma

tag: sample collection time

value: March 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Innate firstTP D10 S019

description:
Innate firstTP
9447848040_K

tag: donor

tag: cell subset

value: firstTP


title: MBS12

tag: tissue

value: exposed

value: healthy

value: negative


title: MBS13


title: MBS11


title: MBS14


title: MBS16


title: MBS10


title: MBS9

value: asymptomatic

value: positive

value: P. vivax


title: 233352_OFB

tag: ID

tag: genotype

value: TRPhet

value: OFB

tag: batch

tag: subtype

tag: survival (mo)

value: GBM

value: Stratagene whole mouse reference RNA


title: 233106_BS

tag: brain location

value: BS

tag: diagnosis

tag: sample type


title: TSCM product D8 S018

description:
TSCM product
9447848040_J

value: TSCM

tag: time point

value: product

tag: sampleID


title: 233117_OFB

value: high-grade astrocytoma (HGA) tumor

value: Ctx


title: Innate secondTP D8 S025

description:
Innate secondTP
9446908077_I

value: Innate

value: secondTP


title: 234458_Di

value: Di


title: MBS8

value: plasma

tag: sample collection time

value: March 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed

tag: symptomatic or asymptomatic at sample collection

value: healthy


title: 232366_BS

value: TR


title: Innate secondTP D9 S026

description:
Innate secondTP
9446908077_J

tag: donor

tag: cell subset


title: 234451_OFB

tag: tissue

tag: ID

value: TRPhet

value: OFB

value: GBM


title: TSCM product D10 S012

description:
TSCM product
9446908077_H

value: TSCM

tag: batch


title: CD8_mem product D2 S001

description:
CD8_mem product
9446908077_L

value: product


title: TSCM product D4 S010

description:
TSCM product
9446908077_G


title: 06-026A primary PCa tumor

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: 06-026A primary PCa tumor

hyb_protocol: Hybridizations to Agilent 44K whole human genome expression oligonucleotide microarray slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer’s suggested protocols.

scan_protocol: Fluorescence array images were collected for Cy3 and Cy5 using the Agilent DNA microarray scanner G2505C (Agilent Technologies, Inc., Santa Clara, CA).

data_processing: Agilent Feature Extraction software versions 10.7.3.1 were used to grid and extract the data using the GE2_105_Jan09 protocols with default settings. Data was loess normalized within arrays (normexp background correction with offset 50) and quantile normalized between arrays in R using the Limma Bioconductor package by batch. Control probes were removed, duplicate probes averaged, and spots flagged by Agilent Feature Extraction software as being foreground feature nonuniformity or population outliers were assigned a value of NA. Data was normalized separately for LuCaP xenografts and CRPC metastases. CRPC metastases were subject to an additional normalization step  to remove systematic batch effects due to date of RNA-amplification by application of the ComBat function within the sva Bioconductor package to the log2 Cy3 signal intensities. Batches are indicated in the ch2: characteristics: batch field and indicates RNA-amplification batch. Batch normalization was applied to a larger set of CRPC samples than those that appear in this study.

label_protocol: amplified amino-allyl aRNA from each experimental sample was labeled with Cy3 fluorescent dye (reference amino-allyl aRNA was labeled with Cy5) following the manufacturer’s suggested protocols.

extract_protocol: To provide a reference standard RNA for use on two-color oligo microarrays, we pooled equal amounts of total RNA isolated from LNCaP, DU145, PC3, and CWR22 cell lines (American Type Culture Collection, Manassas, VA) growing at log phase in dye-free RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA).  Reference RNA was purified using TRIzol (Invitrogen, Carlsbad, CA) following the manufacturer’s protocol. Reference RNA was then further purified by RNeasy maxi kit and treated with DNAse using the RNase-Free DNase Set (Qiagen Inc, Valencia, CA) followed by two rounds of mRNA amplification with amino-allyl incorporation in the second round using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

tag: gender

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

extract_protocol: Eight-micron thick sections from radical prostatectomy tissue frozen in Optimal Cutting Temperature compound (OCT; Tissue-Tek) were cut using a Leica CM3050S cryostat, collected on PEN Membrane Frame Slides (Life Technologies) and immediately fixed in 95% ethanol. Sections were briefly stained with hematoxylin then dehydrated in 100% ethanol. 5,000-10,000 tumor cells per sample were laser capture microdissected with an Arcturus Veritas instrument and collected on CapSure® Macro LCM Caps (Life Technologies). Digital photographs were taken of tissue sections before, during, and after LCM and assessed by a pathologist to confirm the tumor content. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit and the samples were DNAse treated using the Qiagen RNase-Free DNase Set. Total RNA was amplified two rounds with amino-allyl incorporation using the Ambion MessageAmp aRNA Kit (Ambion Inc, Austin, TX), according to the manufacturer’s specifications.

value: second round aRNA

value: All samples were obtained from patients who signed written informed consent under the aegis of the Prostate Cancer Donor Program at the University of Washington, and approved by the Institutional Review Board. Primary PCa radical prostatectomy specimens were obtained from the University of Washington Medical Center (UWMC).

value: no batch normalization applied

tag: ne group

tag: erg group

value: ERG negative group


title: MBS7

value: plasma

value: March 2013

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: 05-131B primary PCa tumor

description: 05-131B primary PCa tumor

tag: sample type

value: ERG positive group


title: MBS6

tag: sample collection time

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)

value: exposed

value: healthy


title: siG9a 3

city: Paris

first: PONTIS

last: Julien

address: 35, rue Hélène BRION

country: France

institute: UMR7216 CNRS

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene from Affymetrix 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 RMA normalized and analysed with Partek Genomic Suite.

source_name: C2C12 cells

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: C2C12 cells were grown in DMEM media supplemented with 15 % of fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin, and sodium pyruvate (PAA, Les Mureaux, France)

extract_protocol: Total RNA was extracted using Rneasy mini-kit (Qiagen) following manufacturer’s procedures.

treatment_protocol: siRNAs were purchased from Sigma and transfected using Hi-Perfect reagent (Qiagen) (Table 1). We transfect 0.2 μmol of siRNA per 100 mm cell culture dish.

tag: sirna


title: 05-199B primary PCa tumor

description: 05-199B primary PCa tumor


title: siGLP 1

value: siGLP


title: TSCM product D7 S013

description:
TSCM product
9446908077_F

value: TSCM

tag: time point

tag: sampleID


title: MBS5

value: January 2014

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection


title: 05-056C primary PCa tumor

description: 05-056C primary PCa tumor

value: male

tag: tissue


title: 04-025B primary PCa tumor

description: 04-025B primary PCa tumor

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: batch


title: MBS4


title: siGLP 2


title: CD8_mem product D1 S004

description:
CD8_mem product
9446908077_E

tag: donor

tag: cell subset

value: product


title: Innate firstTP D9 S021

description:
Innate firstTP
9446908077_D

value: Innate

value: firstTP


title: Control 2

value: Control


title: 03-191D primary PCa tumor

description: 03-191D primary PCa tumor

tag: gender

value: second round aRNA

value: All samples were obtained from patients who signed written informed consent under the aegis of the Prostate Cancer Donor Program at the University of Washington, and approved by the Institutional Review Board. Primary PCa radical prostatectomy specimens were obtained from the University of Washington Medical Center (UWMC).

value: no batch normalization applied

tag: ne group

tag: erg group

value: ERG negative group


title: siG9a 1


title: MBS3

value: plasma

value: August 2013

value: Mae Salid Noi, Tak, Thailand

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: LZ_PN_Liver

city: Piscataway

first: Le

last: Zhan

state: NJ

address: 170 Frelinghuysen Rd

department: Pharmacology and Toxicology

institute: Rutgers University

description: Gene expression data from liver tissues collected from 8 days PN infused mice

hyb_protocol: Following labeling, 3ug of the labeled product was loaded onto the Mouse Gene 2.0ST arrays. The arrays were loaded and placed in the hybridization oven at 45°C at 60RPM for 17hours. GeneChips were washed and stained in the Affymetric Fluidics Stations 450 according to the array protocol.

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

data_processing:
Affymetrix Expression Console (v.1.4.0.38) was used for data processing.
RMA normalization followed by pair-wise expression analysis and by 1.5 fold cutoff-filtering
Please note that sample data table contains the data filtered by 1.5-fold cutoff

source_name: liver_PN infused control mice

label_protocol: 3.75ug of cDNA was fragmented and labeled using the NuGEN Encore Biotin Kit.

growth_protocol: Wild-type (WT) C57BL/6J mice used in this study were obtained from the Jackson Laboratory (Bar Harbor, ME). Mice were maintained in the pathogen-free animal facilities in the Comparative Medicine Resources at the Nelson Animal Facility at Rutgers University, under a standard 12-hr light/dark cycle (6 AM/6 PM) with temperature-, humidity-controlled conditions. Mice were fed at ad libitum with standard mouse chow and autoclaved tap water before surgical experiments.

extract_protocol: Total RNA was isolated using TRI reagent (Sigma, St. Louis, MO) according to the manufacturer’s instructions.

treatment_protocol: On day 1, jugular vein catheterization survival surgery was performed on mouse (age 6-10 weeks).On day 2, the catheter was connected to an infusion line and the mouse was transferred to a metabolic cage. Surgical mice then started to receive saline infusion. On day 3, surgical mice started receiving either parenteral nutrion (PN), or saline infusion as control. Food was removed from the cage for mice in the PN group. Mice in saline group continue to have access to food. On day 11, PN and saline control mice were sacrificed and liver tissues were collected for RNA isolation.

tag: strain

tag: mouse group

value: parenteral nutrition (PN),

value: Liver


title: LZ_Saline_Liver

description: Gene expression data from liver tissues collected from 8 days saline infused mice

data_processing:
Affymetrix Expression Console (v.1.4.0.38) was used for data processing.
RMA normalization followed by pair-wise expression analysis and by 1.5-fold cutoff-filtering
Please note that sample data table contains the data filtered by 1.5-fold cutoff

source_name: liver_saline infused control mice

value: saline control


title: 03-148E primary PCa tumor

description: 03-148E primary PCa tumor

value: male

tag: sample type


title: siG9a 2

tag: sirna


title: CD8_mem product D4 S003

description:
CD8_mem product
9446908077_K

tag: time point

tag: sampleID


title: TSCM product D9 S017

description:
TSCM product
9446908077_C

value: TSCM


title: MBS2

tag: sample collection time

tag: sample collection site

tag: sample source

value: community mass blood survey (ACD)

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed

tag: symptomatic or asymptomatic at sample collection

value: healthy


title: 02-061A primary PCa tumor

description: 02-061A primary PCa tumor

tag: gender

tag: tissue

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: batch


title: MBS1

value: March 2013

value: asymptomatic

tag: age (years)

value: positive

value: P. falciparum, P. vivax, P. ovale, P. malariae


title: 02-088C primary PCa tumor

description: 02-088C primary PCa tumor

value: second round aRNA

value: All samples were obtained from patients who signed written informed consent under the aegis of the Prostate Cancer Donor Program at the University of Washington, and approved by the Institutional Review Board. Primary PCa radical prostatectomy specimens were obtained from the University of Washington Medical Center (UWMC).

value: no batch normalization applied

tag: ne group

tag: erg group

value: ERG positive group


title: CD8_mem product D3 S002

description:
CD8_mem product
9446908077_B

tag: donor

tag: cell subset

value: product


title: Innate firstTP D8 S020

description:
Innate firstTP
9443362082_L

value: Innate

value: firstTP


title: PBT003 gliblastoma stem cells, TET3 shRNA 2 replicate 2

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing shTET3-2 replicate 2
Brain tumor PBT003 gliblastoma stem cells

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45ºC on Human PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Partek® Genomics SuiteTM.  Expression values were RMA normalized, and fold-change values were then calculated using least-squares mean between samples.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (wt_sensetarget_label_manual).

growth_protocol: Cells were cultured in DMEM-F12 medium supplemented with B27 and growth factors EGF and FGF.

extract_protocol: Total RNA was extracted by Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were treated with lentivurs expressing constrol shRNA or target (TLX or TET3) shRNA for 24 hours and were cultured for another 48 hours before RNA extraction.

tag: cell line


title: CD4_EM thirdTP D9 S017

description:
CD4_EM thirdTP
9377358074_I

value: thirdTP


title: CD8_TEMRA thirdTP D10 S031

description:
CD8_TEMRA thirdTP
9377358074_D


title: CD8_CM thirdTP D10 S030

description:
CD8_CM thirdTP
9377358074_G


title: PBT003 gliblastoma stem cells, TET3 shRNA 2 replicate 1

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing shTET3-2 replicate 1
Brain tumor PBT003 gliblastoma stem cells


title: PBT003 gliblastoma stem cells, TET3 shRNA 1 replicate 2

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing shTET3-1 replicate 2
Brain tumor PBT003 gliblastoma stem cells


title: CD8_EM thirdTP D9 S020

description:
CD8_EM thirdTP
9377358070_J


title: CD8_CM secondTP D8 S014

description:
CD8_CM secondTP
9377358074_H

value: secondTP


title: FALS iPS derived MPC6

city: Niigata

first: Masato

last: Yano

address: 757, Ichibancho, Asahimachidori, Chuo-ku, Niigata-shi,

department: Division of Neurobiology and Anatomy

country: Japan

institute: Niigata University

scan_protocol: GeneChip® Scanner 3000 7G/GeneChip® Command Console® Software (AGCC)

data_processing: GEneSpring GX Version12.5

label: TdT (Affymetrix WT Sense Target Labeling Assay)

source_name: FALS iPS derived MPC6

extract_protocol: Trizol Extraction

tag: cell type

value: FALS motor neuron precursor cells


title: Control 1

tag: sirna

value: Control


title: FALS iPS derived MPC5

hyb_protocol: Affymetrix WT Sense Target Labeling Assay

source_name: FALS iPS derived MPC5


title: PBT003 gliblastoma stem cells, TET3 shRNA 1 replicate 1

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing shTET3-1 replicate 1
Brain tumor PBT003 gliblastoma stem cells


title: CD4_EM Baseline D7 S001

description:
CD4_EM Baseline
9377358070_I

tag: time point

value: Baseline

tag: sampleID


title: PBT003 gliblastoma stem cells, control shRNA replicate 1

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing control shRNA replicate 1
Brain tumor PBT003 gliblastoma stem cells


title: 02-178C primary PCa tumor

description: 02-178C primary PCa tumor

value: male

value: reference pool of LNCaP, DU145, PC3, and CWR22 cell lines

tag: sample type


title: 00-005D primary PCa tumor

description: 00-005D primary PCa tumor

value: ERG negative group


title: Innate secondTP D7 S023

description:
Innate secondTP
9446908077_A


title: PBT003 gliblastoma stem cells, control shRNA replicate 2

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing control shRNA replicate 2
Brain tumor PBT003 gliblastoma stem cells


title: FALS iPS derived MPC4

source_name: FALS iPS derived MPC4

label_protocol: Affymetrix WT Sense Target Labeling Assay


title: FALS iPS derived MPC2

source_name: FALS iPS derived MPC2


title: FALS iPS derived MPC3

source_name: FALS iPS derived MPC3


title: PBT003 gliblastoma stem cells, TLX shRNA 1

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing TLX shRNA 1
Brain tumor PBT003 gliblastoma stem cells


title: PBT003 gliblastoma stem cells, control shRNA 2

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing control shRNA 2
Brain tumor PBT003 gliblastoma stem cells


title: E4 chick embryonic midbrain CA*/GFP -ve cells biological rep 3

city: Edinburgh

first: Katherine

last: Long

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

description: E4 midbrain neuroepithelial cells neighbouring those expressing CA* itgb1

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

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

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

organism: Gallus gallus

source_name: Electroporated region of E4 chick midbrain, CA*b1/GFP negative FACS sorted

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

growth_protocol: Chick embryos were cultured up to E2

extract_protocol: Electroporated areas were dissected, disociated and FACS sorted to obtain the nieghbouring CA*/GFP positive and negative cells

treatment_protocol: At E2, midbrains were electroporated with CA*itgb1 and GFP, then eggs were resealed and embryos incubated for a further 48 hours

tag: developmental stage

value: E4 embryo

value: midbrain

tag: electroporated with

value: CA*itgb1 (constitutively active itgb1) and GFP

value: FACS sorted midbrain neuroepithelial cells

tag: cell subgroup

value: GFP negative


title: CD4_CM thirdTP D9 S019

description:
CD4_CM thirdTP
9377358070_F


title: FALS iPS derived MPC1

source_name: FALS iPS derived MPC1


title: Innate thirdTP D9 S024

description:
Innate thirdTP
9377358070_D


title: PBT003 gliblastoma stem cells, TLX shRNA 2

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing TLX shRNA 2
Brain tumor PBT003 gliblastoma stem cells


title: CD8_TM Baseline D7 S005

description:
CD8_TM Baseline
9377358070_C

value: pent


title: CD8_TEMRA Baseline D7 S007

description:
CD8_TEMRA Baseline
9377358070_E


title: PBT003 gliblastoma stem cells, control shRNA 1

description:
Gene expression data from PBT003 gliblastoma stem cells treated with virus expressing control shRNA 1
Brain tumor PBT003 gliblastoma stem cells


title: CD4_EM secondTP D8 S009

description:
CD4_EM secondTP
9377358070_H


title: Control iPS derived MPC3

source_name: Control iPS derived MPC3

value: control motor neuron precursor cells


title: BT474_1day_AICAR_rep2

city: Québec City

first: Etienne

last: Audet-Walsh

state: QC

address: 2705 boulevard Laurier

department: Molecular Medicine

country: Canada

institute: Université Laval

hyb_protocol: RNA was hybridized to GeneChip® Human Genome U133 Plus 2.0 (Affymetrix) and quantified at Génome Québec Innovation Centre (McGill University)

scan_protocol: Scan of the microarrays was performed by the Génome Québec Innovation Centre (McGill University)

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.3.1.187
The expression data were analyzed using FlexArray10 software.

source_name: BT474 cells treated for 24h with AICAR

label_protocol: Labeling was performed using standard Affymetrix protocol at Génome Québec Innovation Centre (McGill University)

growth_protocol: Cells were cultured in regular DMEM. 24h after seeding, media was changed and fresh media with vehicle or AICAR 0.5mM

extract_protocol: After 24h with vehicle or AICAR, RNA was purified with Aurum Total RNA Mini-Kit (Bio-Rad).

treatment_protocol: Reagents were simply added to the media for cell treatment in regular 6cm culture dish.

value: breast cancer cell line BT474

tag: agent

value: AICAR


title: E4 chick embryonic midbrain CA*/GFP +ve cells biological rep 3

description: E4 midbrain neuroepithelial cells expressing CA* itgb1

source_name: Electroporated region of E4 chick midbrain, CA*b1/GFP positive FACS sorted

tag: tissue

value: GFP positive; expressing CA* itgb1


title: E4 chick embryonic midbrain CA*/GFP -ve cells biological rep 2


title: Syriaca Bee Thorax_Cy5

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: The labeled samples were cleaned up using Amicon Ultra columns 30kDa ( Catlog No.UFC503096)  size exclusion filter. The labeled Cy5-dUTP and Cy3-dUTPsample was combined and Salmon Sperm DNA (Catlog No: 1632-011), Agilent aCGH/CoC Blocking agent(Part No: 5188-6416) and Hybridization Buffer (part No: 5188-2460) was added to it. The labeled samples in above hybridization mix were denatured at 95oC for 3 minutes and the microfuge tubes were incubated at 37oC for 30 minutes.

scan_protocol: The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and scanned using the Agilent Microarray Scanner G2505C

data_processing: Channel spit analysis was performed  by splitting the cy3 and cy5 channels and data was analyzed using background substracted signal intensities . 75th percentile shift normalization and baseline transformation with resepect to control sample.( 1L,2L,3L,4L,5L vs. Thorax) was done using  Genespring GX Software  and Agilent DNA Analytics  Software was used to identify theSignificant abberations in Jordan Bee conmpared to Syriaca Bee.

organism: Apis mellifera

source_name: Bee thorax tissue

label_protocol: The  genomic DNA quality control test was performed using Nanodrop-1000 (JH Bio, USA) and Agarose Gel QC to determine the quality, purity and quantity.0.5 to 3ug of DNA in 20.2ul was taken into a microfuge tube and digestion master mix containing Restriction enzymes namely Alu I 5U (R0137S) and Rsa I 5U (R0167S) was added to it. The samples were incubated at 37oC for 2 hours followed by heat inactivation of enzymes at 65oC for 20 minutes. Samples were labeled using Agilent gDNA Labeling Kit ( Part  No: 5190-0449 )

extract_protocol: DNA was extracted for honey bee legs by standard phenol chloroform method. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.

tag: strain

value: Syriaca Bee

value: thorax


title: Algerian Bee 1L

data_processing: Channel split analysis was performed by splitting the cy3 and cy5 channels and data was analyzed using background substracted signal intensities. 75th percentile shift normalization and baseline transformation was done using Genespring GX Software and Agilent DNA Analytics Software was used to identify the Significant abberations in Algerian bee compared to Jordan Bee.

organism: Apis mellifera intermissa

source_name: Algerian Bee

value: Bee leg


title: E4 chick embryonic midbrain CA*/GFP -ve cells biological rep 1


title: Control iPS derived MPC2

source_name: Control iPS derived MPC2


title: E4 chick embryonic midbrain CA*/GFP +ve cells biological rep 2


title: CD8_TM secondTP D8 S013

description:
CD8_TM secondTP
9377358070_B

source_name: Sorted Cells

value: secondTP

tag: batch


title: CD3_CD63_stimulated-control_24h

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

hyb_protocol: Affymetrix EukGE-WS2v5

scan_protocol: Affymetrix cel analysis

data_processing: Bioconductor/R RMA

source_name: CD3+ T-cells

label_protocol: Affymetrix in vitro transcription

extract_protocol: Total RNA was isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA), but with subsequent RNA clean-up of the water phase using the RNeasy Qiagen MinElute kit (Qiagen, Germantown, MD). The quality of the RNA was confirmed on the Agilent Bioanalyzer using RNA Nano chips (Agilent Technologies, Santa Clara, CA).

tag: time

value: 24 hours

tag: stimulant

tag: supplement

value: Control


title: BT474_1day_vehicle_rep2

source_name: BT474 cells treated for 24h with vehicle

value: control


title: Control iPS derived MPC1

source_name: Control iPS derived MPC1


title: CD8_EM thirdTP D10 S028

description:
CD8_EM thirdTP
9377358064_J

tag: donor

tag: cell subset

value: thirdTP


title: CD3_CD63_stimulated_in_presence_of_D2-domain-construct_24h


title: Innate secondTP D8 S016

description:
Innate secondTP
9377358064_K

value: Innate


title: BT474_1day_vehicle_rep1

tag: cell line


title: E4 chick embryonic midbrain CA*/GFP +ve cells biological rep 1

value: E4 embryo

value: midbrain

value: CA*itgb1 (constitutively active itgb1) and GFP

tag: cell type


title: C3 frontal cortex

city: London

first: Christos

last: Proukakis

address: Rowland Hill Street

department: Clinical Neuroscience

institute: UCL Institute of Neurology

hyb_protocol: RA1 resuspended DNA was loaded onto a BeadChip array. After overnight incubation at 48C, wash was performed with PB1, and single-base extension and allele-specific staining was performed with standard reagents (RA1, PB1, XC1-4, TEM, STM, ATM).

scan_protocol: Beadhcip was scanned on a iScan (Illumina).

data_processing: Data processing was done using BlueFuse (Illumina); Genotype: AA,AB,BB,or NC (no call)

label: biotin (C,G), dinitrophenyl (A,T)

source_name: human control frontal cortex C4

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (MSM) and primer/neutralization mix (MA1-MA2-0.1N NaOH). The amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol / PM1, and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from fresh frozen human brain tissue was performed using the Qiagen Dneasy blood & tissue kit

tag: brain region

value: frontal cortex


title: CD4_TM thirdTP D9 S018

description:
CD4_TM thirdTP
9377358064_I

tag: time point

tag: sampleID


title: Algerian Bee 2L


title: CD3_CD28_stimulated_in_presence_of_D2-domain-construct_24h


title: C1 frontal cortex

source_name: human control frontal cortex C2


title: CD4_CM secondTP D8 S011

description:
CD4_CM secondTP
9377358064_H


title: C4 cerebellum

source_name: human control cerebellum C4

value: cerebellum


title: Jordan Bee 5L_Cy3

source_name: Bee leg tissue

value: Jordan Bee

value: leg


title: C3 cerebellum

source_name: human control cerebellum C3


title: CD4_TM secondTP D8 S010

description:
CD4_TM secondTP
9377358070_G


title: C2 frontal cortex

source_name: human control frontal cortex C3


title: C2 cerebellum

source_name: human control cerebellum C2


title: Jordan Bee 3L_Cy3


title: C1 cerebellum

source_name: human control cerebellum C1


title: Jordan Bee 3L_Cy5


title: Jordan Bee 2L_Cy5


title: Jordan Bee 4L_Cy3


title: CD8_TEMRA secondTP D8 S015

description:
CD8_TEMRA secondTP
9377358064_G


title: Jordan Bee 5L_Cy5


title: CD3_CD63_stimulated-control_12h

value: 12 hours


title: CD3_CD28_stimulated-control_24h


title: T-Rex293 cells, 6 d dox treatment, biological repl 3

city: Boston

first: Xiaoyan

middle: Robert

last: Bao

state: Massachusetts

address: 185 Cambridge St. CPZN 6400

department: Molecular Biology

institute: Massachusetts General Hospital

description: Gene expression in the parent T-Rex293 cell line treated with doxycycline to control for effects of doxycycline treatment independent of PolGdn expression

hyb_protocol: cRNA was fragmented and hybridized overnight to microarrays at 45 C and 60 rpm. Microarrays were then washed and stained on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Microarrays were scanned on an Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were processed using RMAexpress with the standard Affymetrix CDF, using quantile normalization and the median Polish signal estimation algorithm

source_name: T-Rex293 cells

label_protocol: RNA samples were processed and biotinylated according to manufacturer's recommendations

growth_protocol: Cells were grown in 10 cm tissue culture polystyrene plates with DMEM (high glucose, high glutamine) plus 10% FBS. They were split at 3 d intervals

extract_protocol: Total RNA was extracted using Qiagen RNeasy columns with DNase treatment according to manufacturer's recommendations

treatment_protocol: Cells were treated with doxyxycline at 1 ug/ml for 6 d to induce expression of dominant negative PolG

tag: protein overexpression

value: constitutive tet repressor


title: T-Rex293 cells, 6 d dox treatment, biological repl 2


title: CD8_CM Baseline D7 S006

description:
CD8_CM Baseline
9377358064_B

value: Baseline


title: BT474_1day_AICAR_rep1

source_name: BT474 cells treated for 24h with AICAR

value: breast cancer cell line BT474

value: AICAR


title: Innate Baseline D7 S008

description:
Innate Baseline
9377358064_F


title: Innate thirdTP D10 S032

description:
Innate thirdTP
9377358064_D


title: CD3_CD63_stimulated_in_presence_of_D2-domain-construct_12h


title: CD4_TM thirdTP D10 S026

description:
CD4_TM thirdTP
9377358064_E


title: CD4_TM Baseline D7 S002

description:
CD4_TM Baseline
9377358064_C


title: CD3_CD28_stimulated_in_presence_of_D2-domain-construct_12h


title: CD3_CD28_stimulated-control_12h


title: CD4_CM thirdTP D10 S027

description:
CD4_CM thirdTP
9372535065_I


title: 214828_Forebrain_TRPhet

city: Chapel HIll

first: Ryan

last: Miller

institute: University of North Carolina

hyb_protocol: Labeled sample RNA and Stratagen Universal Mouse Reference RNA (Agilent, #740100)  as a reference were cohybridized at 65 C for 17 hours in a rotating hybridization oven.

data_processing: Image analyzed using Agilent Feature Extraction Software. Data was uploaded to the UNC microarray database (UMD).  Data was normalized in UMD using Lowess normalization on the Cy3 and Cy5 channels.  Data extraction was performed by selecting genes with an absolute signal intensity of at least 10 units in both dye channels and data present in at least 70% of experimental samples, afterwhich replicate probe IDs were collapse by averaging. Sampless from  different batches  were combined using the parametric settings in combatR, a module in the R statistical programming language (R Development Core Team, 2006 http://www.R-project.org) with brain location and genotype as covariates.  Normalized data provided is the filtered, batch combined,  non-median centered data used to draw conclusions in the study.

label_protocol: Labeling was performed according to the Low RNA Input Linear Amplification kit from Agilent.  1µg of RNA was primed with 1.2 µl of provided T7 promoter primer at 65 °C for 10 minutes.  Reverse transcription was performed with provided Moloney Murine Leukemia Virus Reverse Transcriptase at 40 °C for 2 hours, 65 °C for 15 minutes, and 4 °C for 5 minutes.  Laeled RNA was made by adding 1µl of 10mM Cy3 or Cy5 added to trancription cocktail and incubated at 40 °C for 2 hours, 4 °C for 1 minute.

extract_protocol: Total RNA was extracted from brain regions with Qiagen RNeasy kit according to manufacturer's instructions

treatment_protocol: Brains were harvested from mice.  Brain regions were separated during gross dissection and immediately flash-frozen in liquid nitrogen.

tag: ID

tag: genotype

value: TRPhet

value: Forebrain

source_name: Stratagene whole mouse reference RNA

tag: sample type

value: Stratagene whole mouse reference RNA


title: 221184_Forebrain_T

value: T

tag: tissue


title: 215214_Forebrain_RPnull

value: RPnull


title: T-Rex293 cells, untreated control, biological repl 2

description: Gene expression in the parent T-Rex293 cell line


title: 216175_Forebrain_TRPhet


title: T-Rex293 cells, 6 d dox treatment, biological repl 1


title: CD8_TM thirdTP D9 S021

description:
CD8_TM thirdTP
9372535065_F

value: thirdTP


title: T-Rex293 cells, untreated control, biological repl 3


title: CD8_CM thirdTP D9 S022

description:
CD8_CM thirdTP
9372535065_G


title: CD8_EM secondTP D8 S012

description:
CD8_EM secondTP
9372535065_E

value: secondTP


title: CD4_EM thirdTP D10 S025

description:
CD4_EM thirdTP
9372535065_H


title: 220727_Forebrain_T


title: PolGdn cells after 6 d of dox treatment and 19 d of washout

description: Gene expression in T-Rex293 cells recovering from 6 d of induced mtDNA depletion

source_name: T-Rex293 cells stably expressing dominant negative PolG under tet repressor control

value: constitutive tet repressor; PolGdn under tet repressor control


title: T-Rex293 cells, untreated control, biological repl 1


title: CD8_TM thirdTP D10 S029

description:
CD8_TM thirdTP
9372535065_J


title: 222912_Forebrain_TR

value: TR


title: 215216_Forebrain_RPhet

value: RPhet


title: CD8_EM Baseline D7 S004

description:
CD8_EM Baseline
9372535065_D


title: PolGdn cells after 6 d of dox treatment and 17 d of washout


title: 225569_Forebrain_TR


title: CD8_mem Baseline D2 S025

description:
CD8_mem Baseline
9231092117_L


title: PolGdn cells after 6 d of dox treatment and 15 d of washout


title: PolGdn cells after 6 d of dox treatment and 12 d of washout


title: 243054_Forebrain_TRPnull

value: TRPnull


title: Innate Baseline D4 S033

description:
Innate Baseline
9231092117_J

value: Innate


title: CD4_Naiive thirdTP D5 S109

description:
CD4_Naiive thirdTP
9231092117_K


title: PolGdn cells after 6 d of dox treatment and 10 d of washout


title: PolGdn cells after 6 d of dox treatment and 6 d of washout


title: 220724_OB_P_het

value: Phet

value: OFB


title: CD4_EM secondTP D5 S071

description:
CD4_EM secondTP
9231092117_H


title: CD4_EM thirdTP D5 S111

description:
CD4_EM thirdTP
9231092117_E


title: PolGdn cells after 6 d of dox treatment and 3 d of washout


title: 243054_OB_TRPnull


title: 219918_OB_RP_null


title: PolGdn cells after 6 d of dox treatment and 8 d of washout


title: CD4_CM secondTP D7 S079

description:
CD4_CM secondTP
9231092117_G


title: 219973_OB_TPhet

value: TPhet


title: CD4_Naiive secondTP D7 S078

description:
CD4_Naiive secondTP
9231092117_D


title: PolGdn cells with 6 d of dox treatment

description: Gene expression in T-Rex293 cells after 6 d of induced mtDNA depletion


title: PolGdn cells after 6 d of dox treatment and 4 d of washout


title: CD4_Naiive Baseline D7 S040

description:
CD4_Naiive Baseline
9231092117_C

value: Baseline


title: 219913_OB_TRP_het


title: PolGdn cells after 6 d of dox treatment and 1 d of washout


title: CD4_EM Baseline D4 S031

description:
CD4_EM Baseline
9231092117_I


title: PolGdn cells with 5 d of dox treatment

description: Gene expression in T-Rex293 cells after 5 d of induced mtDNA depletion


title: 219591_OB_TP_het


title: CD4_TM Baseline D7 S136

description:
CD4_TM Baseline
9231092117_F


title: PolGdn cells after 6 d of dox treatment and 2 d of washout


title: CD4_EM Baseline D8 S129

description:
CD4_EM Baseline
9231092117_B


title: 215216_OB_RP_het


title: PolGdn cells with 2 d of dox treatment

description: Gene expression in T-Rex293 cells after 2 d of induced mtDNA depletion


title: 216175_OB_TRP_het


title: PolGdn cells with 3 d of dox treatment

description: Gene expression in T-Rex293 cells after 3 d of induced mtDNA depletion


title: PolGdn cells with 1 d of dox treatment

description: Gene expression in T-Rex293 cells after 1 d of induced mtDNA depletion


title: 219595_OB_TP_null

value: TPnull


title: 215214_OB_RP_null


title: CD8_mem thirdTP D5 S112

description:
CD8_mem thirdTP
9231092117_A


title: 221928_OB_P_null

value: Pnull


title: CD4_TM secondTP D5 S070

description:
CD4_TM secondTP
9231092108_L


title: CD4_EM Baseline D2 S024

description:
CD4_EM Baseline
9231092108_I


title: CD4_EM secondTP D2 S062

description:
CD4_EM secondTP
9231092108_H


title: CD4_Naiive secondTP D5 S068

description:
CD4_Naiive secondTP
9231092108_K


title: PolGdn cells just prior to dox treatment

description: Gene expression in baseline T-Rex293 cells with repressed PolGdn


title: 219973_Forebrain_TPhet

value: Forebrain


title: CD8_mem thirdTP D9 S124

description:
CD8_mem thirdTP
9231092108_E


title: CD8_mem Baseline D5 S036

description:
CD8_mem Baseline
9231092108_F


title: 214828_OB_TRP_het

value: TRPhet

value: Stratagene whole mouse reference RNA


title: CD4_EM firstTP D7 S054

description:
CD4_EM firstTP
9231092108_G

value: firstTP


title: F070

city: La Jolla

first: Sunil

last: Kurian

address: 10550 N Torrey Pines Road

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

hyb_protocol: The Gene Titan Hybridization, Wash and Stain Kit for WT Array Plates (Affymetrix) is used to hybridize 3ug of the labeled cDNA to a multi peg Gene 1.1 ST Array Plate. The hybridization cocktail also contains Control Oligo B2 and 20X Eukaryotic Hybridization Controls as recommended by Affymetrix. Hybridization is carried out for 17 hours at 48C in the Gene Titan MC (Multichannel) Instrument ( Affymetrix). After hybridization the peg array plate is automatically washed and stained and moved to the scanner.

scan_protocol: The peg array plate is automatically moved to the Xenon laser scanner of the Titan MC instrument and scanned at default settings recommended for the peg array.

data_processing: Probes to Import: Interrogating Probes and Control Probes, Probe filtering: skip, Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish

label: SAPE

source_name: Peripheral Blood_Fibromyalgia Patient

label_protocol: The cDNA generated from the WT Expression Kit is fragmented and biotin labeled with the Affymetrix GeneChip WT Terminal Labeling Kit ( Affymetrix). The cDNA is fragmented with a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonucleaseI (APE I). The fragmented cDNA is then labeled with terminal deoxynucleotidyl transferase (TdT) and a biotin reagent.

extract_protocol: RNA Extraction from PAXgene Blood Tubes: Total RNA including small and miRNA is extracted with the PreAnalytiX  PAXgene Blood miRNA kit ( QIAGEN). A semi automated method using the QIAcube (QIAGEN) is used following manufacturer’s instructions. The quantity and quality of the RNA is assessed on a nanodrop and Agilent Bioanalyzer. miRNAeasy kit PN 217004 (Qiagen)

tag: diagnosis

value: fibromyalgia

value: peripheral blood

tag: fiqr score

tag: bmi

tag: migraine

value: No

tag: irritable bowel syndrome

value: Yes

tag: major depression

tag: bipolar disorder

tag: chronic fatigue syndrome


title: 214987_OB_RP_het

scan_protocol: Microarrays were scanned on an Agilent Technologies DNA Microarray Scanner with Surescan High-Resolution Technology (Part no. G2565CA)

value: RPhet

tag: batch


title: Jordan Bee 1L_Cy3

tag: strain

value: Jordan Bee

value: leg


title: N-RE10(Fr)

city: Tokyo

first: Toyoki

last: Yoshimoto

address: Minato-ku, Toranomon 2-2-2

institute: Toranomon Hospital

description:
normal rectal mucosa, sample2, rep1
microRNA expression

hyb_protocol: Labelled samples were incubated with diluted hybridization Spike-In, 10x Gene Expression Blocking Agent and 2xHi-RPM Hybridization Buffer(Agilent), at 100°C for 5min, and immediately cooled with ice. Next, samples were hybridized to the 8 x 60K format SurePrint G3 Agilent human miRNA array for 20 hours at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Array slides were scanned immediately after washing on the Agilent DNA Microarray Scanner(4000B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and R/G PMT is set to 100%, no XDR).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1. (Agilent) using default parameters (miRNA_1010_Sep10 and Grid: 031181_D_F_20101116).

source_name: rectum, normal tissue

label_protocol: Samples were labelled with pCp-Cy3 by incubation with T4 ligase at 16°C for two hours according to the manufacturer's instructions. followed by purification by MicroBioSpin6(BioRad) and concentration.

extract_protocol: Total RNA was isolated using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) for fresh frozen samples and a miRNeasy FFPE Kit (Qiagen) for FFPE samples. RNA concentrations were measured with the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), while RNA quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) using the RNA 6000 Nano kit (Agilent Technologies).

treatment_protocol: Fresh tissues obtained during surgery were frozen in liquid nitrogen, typically 15 min after removal, and stored at -80°C until further use. Simultaneously, resected specimens were formalin-fixed and paraffin-embedded (FFPE) for standard histopathological examinations.

value: rectum

tag: disease state

value: normal tissue

tag: tissue preparation

value: fresh frozen tissue

tag: gender

value: M

tag: age


title: CD4_EM Baseline D10 S038

description:
CD4_EM Baseline
9231092108_C

data_processing: Analysis of the quantified output data was conducted using the limma from the R statistical language and various software packages from Bioconductor.  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

tag: donor

tag: cell subset

tag: time point

value: Baseline

tag: sampleID


title: CD8_mem secondTP D2 S063

description:
CD8_mem secondTP
9231092108_D

value: secondTP


title: 214254_OB_P_het

tag: ID

tag: genotype

value: Phet

tag: tissue

value: OFB

tag: sample type


title: F069

tag: diagnosis

tag: fiqr score

tag: bmi

tag: migraine

tag: irritable bowel syndrome

tag: major depression


title: 214252_OB_TR

value: TR

tag: batch

value: Stratagene whole mouse reference RNA


title: 221180_OB_TP_null

value: TPnull


title: PolGdn cells at 1 d prior to dox treatment

tag: cell line

tag: protein overexpression

value: constitutive tet repressor; PolGdn under tet repressor control


title: F067_2

value: fibromyalgia

value: peripheral blood

tag: bipolar disorder

tag: chronic fatigue syndrome


title: 219159_OB_RP_null

value: RPnull


title: F068

value: Yes

value: No


title: 221927_OB_P_null

value: Pnull


title: CD4_TM secondTP D2 S061

description:
CD4_TM secondTP
9231092108_B

tag: donor

tag: cell subset

tag: time point


title: 221181_OB_RP_het

tag: ID

tag: genotype

value: RPhet


title: CD4_Naiive thirdTP D1 S093

description:
CD4_Naiive thirdTP
9231092100_G

value: thirdTP

tag: sampleID


title: F066

tag: diagnosis

tag: tissue


title: 217871_OB_P_het

tag: sample type


title: F067

tag: fiqr score

tag: bmi

tag: migraine


title: N-TC19(Fr)

description:
normal lung tissue, sample6, rep1
microRNA expression

source_name: lung, normal tissue

value: lung

tag: disease state

value: normal tissue

tag: tissue preparation

value: fresh frozen tissue

tag: gender

value: M

tag: age


title: N-TC14(Fr)

description:
normal lung tissue, sample5, rep1
microRNA expression


title: N-RE11(Fr)

description:
normal rectal mucosa, sample3, rep1
microRNA expression

value: rectum

value: F


title: N-TC10(Fr)

description:
normal lung tissue, sample4, rep1
microRNA expression


title: N-TC9(Fr)

description:
normal lung tissue, sample3, rep1
microRNA expression


title: CD4_Naiive firstTP D9 S055

description:
CD4_Naiive firstTP
9231092100_E

value: firstTP

tag: batch


title: N-TC8(Fr)

description:
normal lung tissue, sample2, rep1
microRNA expression


title: 217463_OB_P_het

value: Phet

value: OFB

value: Stratagene whole mouse reference RNA