title: PT470_H3K27ac

type: SRA

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

description:
antibody: H3K27ac (Abcam, ab4729)
Raw files have  been deposited at the European Genome-phenome Archive (EGA), which is hosted by the EBI, under accession number EGAS00001001457

library_source: genomic

data_processing:
Reads were aligned to hg19 using BWA.
The resulting alignment files were then filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq density tracks were generated with ‘igvtools count’ and visualized with IGV.
Peaks were called with HOMER 4.6 (Hypergeometric Optimization of Motif EnRichment). Peaks in Duke excluded regions list (wgEncodeDukeMapabilityRegionsExcludable table from UCSC genome browser) were removed.
Genome_build: hg19
Supplementary_files_format_and_content: TDF density files were generate by igvtools

source_name: ACC Primary tumor

growth_protocol: The HPV-transformed ACC cell line ACC112 was cultured in RPMI supplemented with 10% fetal bovine serum, Epidermal Growth Factor, Hydrocortisone and Insulin (all from R&D).

extract_protocol:
Frozen tissue was chopped up using a scalpel before fixation and then further dissociated after fixation by shearing with an 18G needle. Chromatin from formaldehyde-fixed cells (1–5 × 106 cells per histone mark, 107 cells for MYB binding) was fragmented to a size range of 200–700 bases with a Branson 250 Sonifier. Solubilized chromatin was immunoprecipitated with antibody against H3K4me3 (2.5 μl; Millipore, 07-473CA), H3K27ac (2.5 μl; Abcam, ab4729), MYB (10 μl; Bethyl, A304-136A) and TP63 (5 μl; ActiveMotif, #39739). Each of these antibodies was validated by protein blot or dot blot as described45. Antibody-chromatin complexes were pulled down with protein G magnetic beads (Dynabead, 10003D), washed and then eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was treated with RNase and purified with Agencourt AMPure XP (Beckman Coulter A63880).
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

tag: tissue type

value: adenoid cystic carcinoma (ACC)


title: MBS258

status: Public on Feb 01 2016

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

organism: Homo sapiens

source_name: plasma, exposed, healthy

tag: tissue

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: MBS236


title: MBS237


title: MBS234


title: MBS233


title: MBS235


title: patient 74

type: RNA

city: Toronto

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

country: Canada

institute: Univerity of Toronto

description:
mature strand micro RNA
unique oligonucleotide barcode tag combined with color-coded probe pair per miRNA

hyb_protocol: color coded probe pairs were hybridized overnight in large excess to target miRNAs, after hybridization exess probes are washed away using a 2 step magnetic bead based purificaiton, according to Nanostring Technologies standard protocols

scan_protocol: data collection was carried out using the nCounter digital analyzer, digitial images were processed and barcode counts tabulated in a CSV file format, according to Nanostring Technologies standard protocols

data_processing: Normalized signal intensity for miRNAs were computed by normalizing raw counts data to the spike-in positive and negative controls using the nSolver software from Nanostring Technologies

label: biotin

molecule: total RNA

source_name: primary AML

label_protocol: sample preparation involves multiplexed annealing of unique oligonucleotide tags onto target miRNAs, ligation reaction and enzymatic purification to remove non-ligated tags, according to Nanostring Technologies standard protocols

extract_protocol: Standard Trizol RNA purification protocol

tag: Sex

value: M

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

value: diagnosis

tag: sample material

value: BM

tag: fab

value: unclassified

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: nd

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

tag: remission obtained

value: yes

tag: allo-bmt

value: no

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: rfs (days)

tag: rfs event

value: bone marrow


title: patient 73

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

value: positive

value: alive

tag: disease status at last follow-up

value: remission

tag: tissue


title: patient 72

value: F

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: negative

tag: initial treatment

tag: ind1 protocol


title: MBS232

value: plasma

tag: sample collection time

value: January 2014

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

tag: qpcr plasmodium species


title: TRAIL REPLICATE 3

city: RENNES

first: Nathalie

last: THERET

address: 2 avenue Pr Leon Bernard

department: INSERM U1085

country: France

institute: University of Rennes 1

description: Sample name: 253949410823_2_3

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 600 ng Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolverâ gene expression data analysis system (Rosetta Biosoftware).
the signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.

source_name: Cell treated with TRAIL

label_protocol: To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. Yields of cRNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer (NanoDrop Technologies).

growth_protocol: The HT29 human colon adenocarcinoma cell line was obtained from ATCC (American Type Culture Collection, Rockville, MD, USA) and cultured at 37°C under a humidified atmosphere of 5 % CO2 in DMEM medium (GlutaMAXTM, high glucose, Life Technologies, St Aubin, France) supplemented with 10 % heat inactivated-fetal calf serum (FCS)

extract_protocol: standard RNA extraction protocols (NucleoSpin® RNA II).

treatment_protocol: 6 h treatment combining TRAIL (100 ng/ml + 2 µg/ml anti-Flag M2 antibody) with propionibacterial culture supernatant (SN diluted to 1/2) or a mixture of propionate (30 mM) and acetate (15 mM) (C3/C2, the major metabolites used in the amounts present in the diluted SN).

value: colon adenocarcinoma

tag: cell line

tag: agent

value: TRAIL


title: patient 71

tag: Sex

value: M

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

value: diagnosis

tag: sample material

value: PB

tag: fab

value: nd

tag: pb blast count at diagnosis

value: induction

tag: ind1 response

value: CR

tag: remission obtained

value: yes

tag: allo-bmt

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue

value: peripheral blood


title: patient 69

tag: Sex

value: BM

value: mixed lineage leukemia (2 populations on flow - myeloid and B)

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: negative

tag: initial treatment

tag: ind1 protocol

value: NR-PD

value: no

value: alive

tag: disease status at last follow-up

value: active disease

value: failure of induction

value: bone marrow


title: patient 70

value: M

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

tag: fab

tag: pb blast count at diagnosis

value: positive

tag: ind1 response

tag: ind2 protocol

value: NOVE-HIDAC

tag: ind2 response

tag: remission obtained

value: dead

value: relapse


title: patient 68

tag: Sex

value: F

value: diagnosis

tag: wbc at diagnosis

value: induction

value: CR

value: yes

tag: allo-bmt

tag: status at last follow-up

value: remission

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue


title: MBS231

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: MBS230


title: patient 67

tag: Sex

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

value: alive

tag: disease status at last follow-up

value: remission, post-transplant

value: bone marrow


title: patient 66

value: M

value: diagnosis

value: PB

tag: allo-bmt

value: no

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue


title: patient 65

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

tag: fab

tag: wbc at diagnosis

tag: pb blast count at diagnosis

value: induction

value: CR

value: yes

value: dead

value: relapse


title: MBS228

value: plasma

tag: sample collection time

value: January 2014

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

tag: qpcr plasmodium species


title: patient 64

value: de novo

value: BM

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: negative

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue

value: bone marrow


title: patient 63

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

tag: fab

value: unclassified

tag: wbc at diagnosis

value: no


title: patient 61

value: M

value: PB

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

value: alive

tag: disease status at last follow-up

value: remission

value: peripheral blood


title: MBS227

value: plasma

tag: sample collection time

value: January 2014

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)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: patient 59

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

tag: fab

tag: pb blast count at diagnosis

value: negative

tag: remission obtained

value: yes

tag: allo-bmt

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: rfs (days)

tag: rfs event

tag: tissue


title: patient 60

value: M

value: diagnosis

value: PB

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: bone marrow


title: patient 58

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

value: BM

tag: fab

tag: pb blast count at diagnosis

value: induction

value: CR

value: no

value: alive

tag: disease status at last follow-up

value: remission


title: MBS225

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

tag: qpcr plasmodium species


title: patient 54

value: F

value: de novo

value: unclassified

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: negative

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

value: yes

tag: allo-bmt

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: rfs (days)

tag: rfs event

tag: tissue

value: peripheral blood


title: patient 56

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

value: PB

tag: fab

value: induction

value: NR-PD

tag: ind2 protocol

tag: ind2 response

value: CR

value: no

value: failure of induction

value: bone marrow


title: patient 55

value: BM

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

value: alive

tag: disease status at last follow-up

value: remission


title: patient 57

tag: Sex

value: M

value: de novo

value: negative

tag: allo-bmt

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue


title: MBS226

value: plasma

tag: sample collection time

value: January 2014

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

tag: qpcr plasmodium species


title: patient 53

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

value: PB

tag: fab

value: unclassified

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

tag: remission obtained

value: yes

tag: disease status at last follow-up

value: relapse


title: MBS224

tag: tissue

tag: sample collection time

value: August 2013

tag: sample collection site

tag: sample source

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: patient 52

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: allo-bmt

value: no

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

value: bone marrow


title: patient 51

value: de novo

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

value: negative

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

value: alive

tag: disease status at last follow-up

value: remission

tag: tissue


title: MBS223

source_name: plasma, exposed, asymptomatic

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: asymptomatic

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species

value: P. vivax


title: patient 62

tag: Sex

value: M

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

tag: fab

value: unclassified

tag: wbc at diagnosis

tag: bm blast % at diagnosis

value: induction

value: CR

value: yes

tag: allo-bmt

tag: status at last follow-up

value: remission, moved to Calgary, lost to follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event


title: MBS229

tag: tissue

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: healthy

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative


title: patient 49

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

tag: initial treatment

tag: ind1 protocol

value: 3+7 + Mylotarg

tag: ind1 response

tag: remission obtained

value: no

value: alive

tag: disease status at last follow-up

value: CR2 awaiting transplant

value: relapse

value: bone marrow


title: patient 50

value: diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: allo-bmt

tag: status at last follow-up

value: remission, post transplant

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue


title: MBS222

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

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: MBS221

value: August 2013

value: healthy

value: negative


title: patient 46

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

tag: remission obtained

value: yes

tag: disease status at last follow-up

value: remission


title: patient 45

value: M

value: diagnosis

value: nd

tag: allo-bmt

value: no

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: rfs (days)

tag: rfs event

tag: tissue

value: bone marrow


title: patient 48

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

tag: fab

value: unclassified

tag: wbc at diagnosis


title: patient 44

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: negative

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained


title: MBS219

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

tag: qpcr plasmodium species


title: patient 42

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

value: induction

value: CR

value: yes

tag: allo-bmt

tag: status at last follow-up

value: alive

tag: disease status at last follow-up

value: remission post-BMT

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue


title: MBS218

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: asymptomatic

tag: age (years)

tag: qpcr screening for plasmodium genus

value: positive

tag: qpcr plasmodium species

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


title: MBS216

value: plasma

value: January 2014

value: negative


title: patient 39

tag: Sex

value: M

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

tag: fab

value: nd

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: NR-PD

tag: ind2 protocol

tag: ind2 response

tag: remission obtained

value: no

tag: allo-bmt

value: dead

value: failure of induction

value: bone marrow


title: MBS220

tag: tissue

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

tag: qpcr plasmodium species


title: patient 37

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

value: PB

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: induction

value: CR

value: yes

tag: status at last follow-up

value: alive

tag: disease status at last follow-up

value: remission

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event


title: MBS215

tag: tissue

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

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: patient 38

tag: Sex

value: M

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: NR-PD

tag: ind2 protocol

tag: ind2 response

tag: remission obtained

tag: allo-bmt

value: no

value: dead

value: failure of induction

value: relapse


title: patient 33

tag: Sex

value: F

value: de novo

value: NOVE-HIDAC

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: tissue

value: bone marrow


title: MBS214

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

tag: qpcr plasmodium species


title: MBS213

value: plasma

value: negative


title: patient 36

value: M

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

value: PB

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

value: yes

tag: rfs (days)

tag: rfs event


title: patient 35

tag: Sex

value: F

value: de novo

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

value: alive

tag: disease status at last follow-up

value: remission, post-transplant

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: tissue

value: peripheral blood


title: patient 34

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

value: bone marrow


title: patient 32

tag: Sex

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: no

value: remission

tag: rfs (days)

tag: rfs event


title: patient 43

value: M

value: negative

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

tag: tissue


title: patient 47

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

value: PB

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

value: positive

tag: disease status at last follow-up


title: MBS212

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

tag: qpcr plasmodium species


title: patient 31

tag: Sex

value: F

value: de novo

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

tag: remission obtained

value: yes

tag: allo-bmt

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: rfs (days)

tag: rfs event

tag: tissue


title: patient 30

value: M

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

value: BM

tag: fab

value: unclassified

tag: wbc at diagnosis

tag: bm blast % at diagnosis

value: negative

value: no

value: bone marrow


title: patient 40

tag: Sex

value: diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: alive

tag: disease status at last follow-up

value: remission


title: patient 41

value: PB

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

value: peripheral blood


title: patient 28

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

value: induction

tag: tissue


title: patient 29

tag: Sex

value: F

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: CR

value: yes


title: MBS211

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

tag: qpcr plasmodium species


title: patient 27

value: M

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

value: negative

value: nd

tag: remission obtained

tag: allo-bmt

value: no

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: rfs (days)

tag: rfs event

value: bone marrow


title: MBS217

source_name: plasma, exposed, fever at 3mo

tag: tissue

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: fever at 3mo

tag: age (years)

tag: qpcr screening for plasmodium genus

value: positive

value: P. falciparum


title: MBS210

value: plasma

value: August 2013

tag: qpcr plasmodium species

value: P. vivax


title: patient 24

tag: Sex

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

tag: sample material

value: PB

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

tag: remission obtained

value: yes

value: dead

value: peripheral blood


title: patient 25

value: F

value: diagnosis

value: nd

value: negative

tag: allo-bmt

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue


title: patient 26

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

tag: fab

value: unclassified

tag: wbc at diagnosis

value: NR-PD

tag: ind2 protocol

tag: ind2 response

value: failure of induction

value: relapse


title: MBS209

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: asymptomatic

tag: age (years)

tag: qpcr screening for plasmodium genus

value: positive

tag: qpcr plasmodium species


title: patient 23

tag: Sex

value: de novo

value: BM

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: CR

tag: remission obtained

value: yes

tag: allo-bmt

value: no

tag: status at last follow-up

value: alive

tag: disease status at last follow-up

value: remission

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue

value: bone marrow


title: MBS205

tag: sample collection time

value: March 2013

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

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: patient 22

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

tag: sample type

value: diagnosis

tag: sample material

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: nd

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

tag: allo-bmt

value: dead

value: relapse


title: patient 21

value: de novo

value: PB

value: positive

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue

value: peripheral blood


title: patient 18

tag: Sex

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

tag: fab

tag: wbc at diagnosis

value: induction

value: NR-PD

tag: ind2 protocol

tag: ind2 response

value: failure of induction


title: MBS208

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)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: patient 19

tag: Sex

value: M

value: BM

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: CR

tag: remission obtained

value: yes

tag: allo-bmt

value: no

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue

value: bone marrow


title: patient 17

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

value: diagnosis

tag: sample material

tag: fab

tag: wbc at diagnosis

value: negative

value: alive

tag: disease status at last follow-up

value: remission, post-transplant


title: MBS207

tag: sample collection time

value: March 2013

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

value: healthy

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: MBS202

tag: tissue

value: plasma

value: Mae Salid Noi, Tak, Thailand


title: patient 12

tag: Sex

value: PB

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

value: positive

value: nd

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

value: relapse

tag: rfs (days)

tag: rfs event

value: peripheral blood


title: patient 10

value: M

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

tag: fab

tag: wbc at diagnosis

value: CR

value: yes

value: dead


title: MBS204

tag: tissue

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

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: patient 14

tag: Sex

value: F

value: de novo

value: diagnosis

value: BM

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

tag: allo-bmt

value: no

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

value: bone marrow


title: patient 16

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

value: PB

tag: fab

tag: wbc at diagnosis

tag: pb blast count at diagnosis

value: positive

tag: rfs event

tag: tissue


title: patient 13

tag: Sex

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

value: relapse


title: patient 15

value: nd

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)


title: patient 11

tag: age at aml diagnosis

tag: aml onset

tag: sample type

tag: sample material

tag: fab

tag: wbc at diagnosis

tag: pb blast count at diagnosis

value: CR

value: alive

tag: disease status at last follow-up

value: active disease


title: MBS206

tag: tissue

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: healthy

tag: age (years)

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: MBS201

value: exposed

value: negative


title: patient 8

tag: Sex

value: M

tag: age at aml diagnosis

value: de novo

value: diagnosis

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

value: yes

tag: allo-bmt

value: no

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

value: peripheral blood


title: patient 9

value: F

tag: aml onset

tag: sample type

tag: sample material

value: PB

tag: fab

tag: wbc at diagnosis

tag: pb blast count at diagnosis

value: induction

value: CR

tag: disease status at last follow-up

value: remission

tag: tissue

value: bone marrow


title: patient 6

tag: Sex

tag: age at aml diagnosis

value: BM

tag: bm blast % at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

value: auto-transplant

value: relapse


title: patient 7

value: positive

value: negative

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

value: alive

value: remission, lost to follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event


title: MBS203

tag: tissue

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

tag: qpcr plasmodium species


title: patient 5

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

value: diagnosis

tag: sample material

value: PB

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

tag: npm1 mutation

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

value: yes

value: no

tag: disease status at last follow-up

value: peripheral blood


title: patient 20

value: M

value: BM

value: negative

value: nd

value: NR-PD

tag: ind2 protocol

value: SWOG S0106

tag: ind2 response

value: CR

tag: allo-bmt

tag: status at last follow-up

value: dead

tag: os (days)

tag: efs (days)

tag: efs event

value: failure of induction

tag: rfs (days)

tag: rfs event

value: relapse

tag: tissue

value: bone marrow


title: patient 4

tag: Sex

tag: age at aml diagnosis

tag: aml onset

value: de novo

tag: sample type

value: diagnosis

tag: sample material

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

value: alive

value: remission


title: MBS200

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

tag: qpcr plasmodium species


title: patient 3

tag: Sex

value: F

tag: age at aml diagnosis

value: PB

tag: npm1 mutation

value: positive

value: negative

tag: initial treatment

value: induction

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

value: yes

tag: allo-bmt

value: no

tag: status at last follow-up

tag: disease status at last follow-up

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event

tag: tissue


title: patient 2

tag: aml onset

value: de novo

tag: sample type

tag: sample material

value: BM

tag: fab

tag: wbc at diagnosis

tag: bm blast % at diagnosis

tag: pb blast count at diagnosis

tag: cytogenetics at aml diagnosis

value: CR

value: dead

value: relapse

value: bone marrow


title: MBS198

value: plasma

tag: sample collection time

value: March 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

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: MBS197

tag: tissue

value: community mass blood survey (ACD)

value: exposed

value: healthy


title: MBS199


title: patient 1

tag: Sex

value: F

tag: age at aml diagnosis

tag: aml onset

value: diagnosis

tag: npm1 mutation

tag: initial treatment

tag: ind1 protocol

tag: ind1 response

tag: remission obtained

tag: allo-bmt

tag: status at last follow-up

value: alive

tag: disease status at last follow-up

value: remission, post-transplant

tag: os (days)

tag: efs (days)

tag: efs event

tag: rfs (days)

tag: rfs event


title: MBS196

tag: tissue

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

tag: age (years)

tag: qpcr screening for plasmodium genus

value: negative

tag: qpcr plasmodium species


title: MBS195


title: MBS194


title: MBS192

value: August 2013


title: MBS191


title: MBS193

value: January 2014


title: MBS190


title: LP231MemoryD2

city: Manhasset

first: Tam

middle: D

last: Quach

state: NY - New York

address: 350 Community Drive

institute: The Feinstein Medical Research Institute

description: SAMPLE 13

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing:
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: adult peripheral blood memory B cells after 2 days activated in vitro with CpG, anti-Ig, and IL2 cocktail

label_protocol: Affymetrix standard protocol

extract_protocol: QIAGEN RNeasy Plus Kit

treatment_protocol: CpG, anti-Ig, and IL-2 stimulation cocktail was used for Sample12-16 only.

tag: age

value: adult

value: peripheral Blood

tag: cell type

value: Memory cells

tag: activated with

value: CpG, anti-Ig, and IL2 cocktail


title: 395073PB

description: SAMPLE 12

source_name: ex vivo adult peripheral blood plasmablasts

value: Plasmablasts


title: 395072PrePB

description: SAMPLE 8

source_name: ex vivo adult peripheral blood 20+38hi B cells

value: 20+38hi B cells


title: 395073PrePB

description: SAMPLE 9


title: LP234MemoryD2

description: SAMPLE 16


title: 395019PB

description: SAMPLE 10


title: 395019PrePB

description: SAMPLE 7


title: 395072PB

description: SAMPLE 11


title: 395073Mem

description: SAMPLE 6

source_name: ex vivo adult peripheral blood Memory B cells

value: Memory B cells


title: LP232MemoryD2

description: SAMPLE 14


title: 395019Mem

description: SAMPLE 4


title: MBS187

value: plasma

value: March 2013

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)


title: MBS185

value: exposed

value: healthy


title: MBS184


title: MBS183


title: 395073B1

description: SAMPLE 3

source_name: ex vivo adult peripheral blood B-1 cells

value: B1 cells


title: MBS189

value: negative


title: 395019B1

description: SAMPLE 1


title: MBS188


title: MBS186


title: MBS182

value: August 2013


title: MBS181

value: asymptomatic

value: positive

value: P. falciparum


title: MBS178


title: MBS179


title: MBS180


title: WT-DSS 7 days-Colon

city: Tokyo

first: Yoshitaka

last: Taketomi

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

department: CDBIM, Graduate School of Medicine,

country: Japan

institute: The University of Tokyo

description: mixed 3 colon samples

hyb_protocol: 1.65 µg of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit protocol. Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

organism: Mus musculus

source_name: Colon

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: 8-wk-old WT and X-KO mice were housed in climate-controlled (23 oC) pathogen-free facilities with a 12 h light-dark cycle, with free access to standard diet (CE2; CLEA Japan) and water.

extract_protocol: Total RNA was purified using the RNeasy Mini Kit (Qiagen), and the quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: DSS of average molecular weight 36,000–50,000 (MP Biomedicals) was orally applied to mice at a concentration of 1% (w/v) in drinking water, and then the large intestines was removed.

value: colon

tag: genotype

value: wildtype

tag: strain

tag: Sex

value: 9 weeks

value: Male

tag: colitis status

value: DSS


title: 395072Mem

description: SAMPLE 5

value: adult

value: peripheral Blood

value: Memory B cells


title: day3_rep2

city: Chicago

first: NOZOMU

last: TAKATA

state: Illinois

address: 303 East Superior Street, 10-220

department: Center for Vascular and Developmental Biology

institute: Northwestern University Feinberg School of Medicine

description: Day3 sample (epiblast-like tissue) from differentiated mouse ES cells with SFEBq, duplicate2

hyb_protocol: RNA was subsequently fragmented and hybridized to the GeneChip according to manufacturer’s instructions. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: The microarray image data were processed with the GeneChip Scanner 3000 (Affymetrix).

data_processing: The raw data were summarized with the RMA algorithm (R 2.13.0, Bioconductor 2.8).

source_name: mouse ES cells with SFEBq

label_protocol: Biotinylated cRNAs were prepared according to the Affymetrix standard labeling protocol.

extract_protocol: Total RNA was extracted using QIAcubu’s RNA micro extraction mode (Qiagen), and  cDNA was synthesized using SuperScript II Reverse Transcriptase  (invitrogen).

value: differentiated mouse embryonic stem cells


title: 395072B1

description: SAMPLE 2


title: day0_rep2

description: Day0 sample (ES cells) from differentiated mouse ES cells with SFEBq, duplicate2


title: X-KO-DSS 7 days-Colon

description: mixed 3 colon samples

value: X-KO


title: MBS176

value: plasma

value: March 2013

value: Mae Salid Noi, Tak, Thailand

value: community mass blood survey (ACD)

value: exposed


title: C2-fed mouse 1 kidney

city: West Lafayette

first: Chang

last: Kim

state: IN

address: 725 Harrison St

department: Comparative Pathobiology

institute: Purdue

hyb_protocol: Sample_hyb_protocol:    Following fragmentation, 10 ug of cRNA were hybridized with a GeneChip Hybridization Oven 640 for 16 hr at 45C on GeneChip Mouse 430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 400 with fludics protocol EukGE_WS2v5 and user prepared solutions, as per protocols provided by Affymetrix in the GeneChip Expression Analysis Technical Manual, 2004. This included Enzo Life Sciences' BioArray Eukaryotic Hybridization Controls.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G enabled for High-Resolution Scanning. The instruments were controlled using GCOS version1.4 software.

data_processing: The data were condensed with MAS 5.0 using the GeneChip Operation

label: Biotin

source_name: kidney tissue

label_protocol: Biotinylated cRNA were prepared from 2 ug total RNA according to Single Round RNA Amplification and Biotin Labeling System (Enzo Life Sciences Intl. Plymouth Meeting, PA)

growth_protocol: Conventional hosuing of  mice

extract_protocol: Trizol and Qiagen Total RNA isolation

treatment_protocol: Mice were treated with C2 at 200 mM in drinking water

tag: agent

value: acetate

value: kidney


title: Control mouse kidney

value: control

tag: tissue


title: WT-Naïve-Colon

description: mixed 3 colon samples

value: colon

value: wildtype

value: Naïve


title: day3_rep1

description: Day3 sample (epiblast-like tissue) from differentiated mouse ES cells with SFEBq, duplicate1


title: C2-fed mouse 2 kidney


title: day0_rep1

description: Day0 sample (ES cells) from differentiated mouse ES cells with SFEBq, duplicate1


title: MBS173

tag: sample collection time

value: healthy

value: negative


title: X-KO-Naïve-Colon

description: mixed 3 colon samples

value: 9 weeks

value: Male


title: MBS172

tag: sample collection site


title: LP233MemoryD2

description: SAMPLE 15

value: adult

value: peripheral Blood

value: Memory cells

value: CpG, anti-Ig, and IL2 cocktail


title: MBS175

value: plasma

value: March 2013

value: Mae Salid Noi, Tak, Thailand

tag: sample source


title: shTR1 and shSEP15 - repeat 3 - mAdbID:110516

city: Towson

first: Petra

last: Tsuji

state: MD

address: 8000 York Rd

department: Biological Sciences

institute: Towson University

description: mAdb experiment ID: 110516

hyb_protocol: Affymetrix Hybridization Protocol Other: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.

scan_protocol: Affymetrix Scanning Protocol Other: The Scanner 3000 was used to scan the microarrays.

data_processing:
Affymetrix RMA Data Processing
Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).

source_name: shTR1 and shSEP15

label_protocol:
Affymetrix Labeling Protocol
Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol:
Trizol Extraction Protocol
Other: Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).

value: BALB/c

tag: cell line

value: murine colon carcinoma

tag: other

value: The pU6-m3 vector was used for generating shRNA targets. To knockdown TR1 expression, 22-nt sequence 5'-atcgctctgacaagcttattag-3' was chosen from the mouse TR1 cDNA, which was unique to this gene. To knockdown Sep15 expression, 19-nt sequence 5'-acagaagagttccatttaa-3' was chosen from the mouse Sep15 cDNA, which was unique to this gene. These sequences were annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3.

tag: genotype/variation

value: TR1/Sep15 knockdown


title: MBS177

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)

tag: qpcr screening for plasmodium genus


title: MBS171

value: healthy

tag: qpcr plasmodium species


title: MBS174

value: negative


title: shTR1 and shSEP15 - repeat 1 - mAdbID:110514

description: mAdb experiment ID: 110514

value: colon

tag: cell type


title: shTR1 and shSEP15 - repeat 2 - mAdbID:110515

description: mAdb experiment ID: 110515

tag: strain


title: shTR1 - repeat 1 - mAdbID:110510

description: mAdb experiment ID: 110510

value: The pU6-m3 vector was used for generating shRNA targets. To knockdown TR1 expression, 22-nt sequence 5'-atcgctctgacaagcttattag-3' was chosen from the mouse TR1 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3.

value: TR1 knockdown


title: shTR1 - repeat 2 - mAdbID:110511

description: mAdb experiment ID: 110511


title: shTR1 and shSEP15 - repeat 4 - mAdbID:110517

description: mAdb experiment ID: 110517


title: MBS169


title: shTR1 - repeat 4 - mAdbID:110513

description: mAdb experiment ID: 110513


title: MBS167


title: MBS165


title: MBS166


title: MBS164


title: MBS163


title: shTR1 - repeat 3 - mAdbID:110512

description: mAdb experiment ID: 110512


title: MBS168


title: sh Sep15 - repeat 4 - mAdbID:110509

description: mAdb experiment ID: 110509

source_name: sh Sep15

value: The pU6-m3 vector was used for generating shRNA targets. To knockdown Sep15 expression, 19-nt sequence 5'-acagaagagttccatttaa-3' was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3.

value: Sep15 knockdown


title: MBS160


title: MBS159

value: January 2014


title: sh Sep15 - repeat 2 - mAdbID:110507

description: mAdb experiment ID: 110507


title: MBS158

value: plasma


title: sh Sep15 - repeat 3 - mAdbID:110508

description: mAdb experiment ID: 110508


title: Empty Vector Control - repeat 3 - mAdbID:110504

description: mAdb experiment ID: 110504

source_name: Empty Vector Control

value: The empty pU6-m3 vector was transfected into the cells.

value: control


title: MBS170

value: March 2013

value: Mae Salid Noi, Tak, Thailand


title: MBS157

value: asymptomatic

value: positive

value: P. vivax


title: sh Sep15 - repeat 1 - mAdbID:110506

description: mAdb experiment ID: 110506

value: BALB/c

value: murine colon carcinoma


title: MBS162

value: community mass blood survey (ACD)

value: exposed

value: healthy

value: negative


title: Empty Vector Control - repeat 1 - mAdbID:110502

description: mAdb experiment ID: 110502

value: colon


title: MBS156

value: August 2013


title: Empty Vector Control - repeat 4 - mAdbID:110505

description: mAdb experiment ID: 110505


title: Empty Vector Control - repeat 2 - mAdbID:110503

description: mAdb experiment ID: 110503


title: MBS155


title: MBS154


title: MBS153


title: striatum-Wild Type REP2

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

hyb_protocol: Labeled cRNAs were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100 mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20 mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix)

scan_protocol: GeneChips were scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: striatum-Wild Type

label_protocol: cDNA was synthesized from 4 µg of total RNA using one-cycle target labeling and control reagents (Affymetrix) to produce biotin labeled cRNA. The cRNA preparation (15 µg) was fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol: Preparation of transgenic mice expressing a dominant active mutant of DREAM has been reported before (Gomez-Villafuertes et al., 2005; Wu et al., 2010). DREAM knockout mice {Cheng, 2002 #95} were crossed with R6/2 mice to generate R6/2xDREAM+/- mice. The R6 mice were originally from Jackson laboratories.

extract_protocol: RNA from whole striatum from wild type and transgenic mice was prepared using TRIzol (Invitrogen) and the RNAeasy Mini Kit (Qiagen). RNA was quantified and the quality was assessed with a 2100 Bioanalyzer (Agilent technologies).

value: Wild Type

value: striatal neurons


title: MBS152

source_name: plasma, exposed, healthy

value: plasma


title: striatum-Wild Type REP1


title: striatum-Wild Type REP3


title: MBS150

value: January 2014


title: MBS151

value: March 2013


title: MBS148

value: Mae Salid Noi, Tak, Thailand


title: MBS149


title: striatum-Wild Type REP4


title: striatum-R6/2 REP2


title: MBS146


title: striatum-DREAM +/- REP3

source_name: striatum-DREAM +/-

value: DREAM +/-


title: MBS147


title: striatum-R6/2 REP1


title: striatum-R6/2 REP3


title: striatum-R6/2 REP4


title: striatum-DREAM +/- REP2


title: striatum-DREAM +/- REP4


title: striatum-R6/2 x DREAM +/- REP3

source_name: striatum-R6/2 x DREAM +/-

value: R6/2 x DREAM +/-


title: MBS144


title: MBS145


title: MBS143


title: MBS140


title: MBS142


title: striatum-DREAM +/- REP1


title: MBS141

source_name: plasma, exposed, asymptomatic

value: asymptomatic

value: positive

value: P. vivax


title: striatum-R6/2 x DREAM +/- REP1


title: MBS137

value: community mass blood survey (ACD)


title: MBS138

value: exposed


title: striatum-R6/2 x DREAM +/- REP4


title: Flow-v-Static D12 30 min Rep 3 dye-swap

city: Newark

first: Eleftherios

middle: T

last: Papoutsakis

state: DE

address: 15 Innovation Way

department: Chemical and Biomolecular Engineering

institute: University of Delaware

description:
Biological replicate 3 of 3. mRNA from static control or shear-treated d12 stem cell-derived megakaryocytes.
d12-mk-30min-F3-v-S5-rep2

hyb_protocol: RNA was hybridized to Agilent Human GE 4x44K v2 Microarray slides (Cat. 427 #G2519F-026652) and washing was completed following manufacturer’s instructions (Cat. #5188-5327)

scan_protocol: Slides were scanned on an Agilent Microarray scanner (G2565BA) and its Feature Extraction Software was used to extract the data.

data_processing: Please note that sample data tables contain non-normalized log2 ratio of (Cy5/Cy3). Lowess normalization between dye-swap experiments was performed in R software using the limma package and the SNN-LERM (segmental nearest neighbor of logarithmic expression ratio method) algorithm, resulting normalized data (merged) across two technical dye-swap arrays (d*-normalized-matrixtable.txt files)

source_name: d12 megakaryocyte

label_protocol: The Agilent Low Input Quick Amp Labeling Kit was used to generate cDNA and labeled cRNA, along with the Agilent Spike-In Kit to detect an amplification bias.

growth_protocol: Human CD34+ cells were cultured for five days with 100 ng/ml TPO and SCF, 10 ng/ml IL-6 and IL-11, 2.5 ng/ml IL-3, 1 μg/ml hLDL, 20% BIT 9500, in a 5% oxygen atmosphere. On day 5, cytokine conditions were altered to 100 ng/ml TPO and SCF, 10 ng/ml IL-3, IL-9, and IL-11, 1 μg/ml hLDL, 20% BIT, and 20% oxygen atmosphere. CD61+ cells were enriched using magnetic separation. Culture conditions were then altered to 100 ng/ml TPO and SCF, 6.25 mM nicotinamide, and 20% oxygen.

extract_protocol: Total RNA from unstressed (static) and shear-stressed (flow) Mks was isolated using the ReliaPrep RNA Cell Miniprep System (Promega)

treatment_protocol: On day 8, Mks were then seeded into vWF-coated rectangular flow slides (Ibidi μ-Slide I0.6 Luer) at 300,000 cells per slide. On day 9, cells were subjected to shear flow that results in shear stress levels of either 1.0 dyn/cm2 for 2 hours or 2.5 dyn/cm2 for 30 min using a syringe pump system. The remaining Mks were cultured to day 12 using the current condition at day 9.

value: megakaryocyte

tag: time point

value: 30 min

tag: condition

value: Static

value: Flow


title: Flow-v-Static D12 30 min Rep 3

description:
Biological replicate 3 of 3. mRNA from static control or shear-treated d12 stem cell-derived megakaryocytes.
d12-mk-30min-S3-v-F5-rep2


title: MBS136

value: healthy

value: negative


title: Flow-v-Static D12 30 min Rep 1 dye-swap

description:
Biological replicate 1 of 3. mRNA from static control or shear-treated d12 stem cell-derived megakaryocytes.
d12-mk-30min-F3-v-S5-rep1


title: Flow-v-Static D12 30 min Rep 1

description:
Biological replicate 1 of 3. mRNA from static control or shear-treated d12 stem cell-derived megakaryocytes.
d12-mk-30min-S3-v-F5-rep1


title: MBS135

value: plasma


title: Flow-v-Static D12 30 min Rep 2

description:
Biological replicate 2 of 3. mRNA from static control or shear-treated d12 stem cell-derived megakaryocytes.
d12-mk-30min-S3-v-F5-rep2


title: Flow-v-Static D12 30 min Rep 2 dye-swap

description:
Biological replicate 2 of 3. mRNA from static control or shear-treated d12 stem cell-derived megakaryocytes.
d12-mk-30min-F3-v-S5-rep2


title: MBS134


title: striatum-R6/2 x DREAM +/- REP2

value: striatal neurons


title: MBS139

value: March 2013


title: MBS132

value: Mae Salid Noi, Tak, Thailand


title: Flow-v-Static D9 60 min Rep 3 dye-swap

description:
Biological replicate 3 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-60min-F3-v-S5-rep3

source_name: d9 megakaryocyte

value: 60 min


title: Flow-v-Static D9 30 min Rep 3

description:
Biological replicate 3 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-30min-S3-v-F5-rep3


title: Flow-v-Static D9 30 min Rep 2 dye-swap

description:
Biological replicate 2 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-30min-F3-v-S5-rep2


title: Flow-v-Static D9 30 min Rep 3 dye-swap

description:
Biological replicate 3 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-30min-F3-v-S5-rep3


title: MBS131


title: 321_Plb1

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

description: Placebo

hyb_protocol: Fragmentation Buffer and Hybridization Buffer (Agilent Gene Expression Hybridization Kit) were added, and samples applied to Whole Human Genome microarrays

scan_protocol: Scanned on Agilent scanner

data_processing: Images were quantified using Feature Extraction

source_name: Human Tissue Biopsy

label_protocol: 50g of total RNA was reversed transcribed using Agilent Quick-Amp Labeling Kit and labeled with Perkin Elmer Cy3

extract_protocol: Total RNA extracted using RNeasy Fibrous Tissue Mini kit following manufacturers protocol

treatment_protocol: Storage of human tissue in RNAlater

tag: disease state

value: systemic sclerosis

tag: treatment

value: placebo

tag: mrss score

source_name: Universal Human Reference

tag: sample type

value: reference


title: Flow-v-Static D9 60 min Rep 3

description:
Biological replicate 3 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-60min-S3-v-F5-rep3


title: Flow-v-Static D9 60 min Rep 2

description:
Biological replicate 2 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-60min-S3-v-F5-rep2


title: 433_Plb2

description: Placebo


title: 443_NonImp1

description: SSc

value: abatacept


title: Flow-v-Static D9 30 min Rep 2

description:
Biological replicate 2 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-30min-S3-v-F5-rep2


title: 843_Imp5

description: SSc


title: Flow-v-Static D9 60 min Rep 2 dye-swap

description:
Biological replicate 2 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-60min-F3-v-S5-rep2


title: MBS130

tag: tissue

tag: sample collection time

value: January 2014

tag: sample collection site

tag: sample source

value: community mass blood survey (ACD)


title: 688_Imp4

description: SSc


title: Flow-v-Static D9 60 min Rep 1 dye-swap

description:
Biological replicate 1 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-60min-F3-v-S5-rep1

value: megakaryocyte


title: MBS129

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: exposed


title: MBS128

tag: symptomatic or asymptomatic at sample collection

value: asymptomatic

value: positive

value: P. vivax


title: 257_Imp1

description: SSc


title: Flow-v-Static D9 30 min Rep 1 dye-swap

description:
Biological replicate 1 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-30min-F3-v-S5-rep1

value: 30 min

value: Flow

value: Static


title: Flow-v-Static D9 60 min Rep 1

description:
Biological replicate 1 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-60min-S3-v-F5-rep1


title: 378_NonImp1

description: SSc


title: 778_Imp5

description: SSc


title: Flow-v-Static D9 30 min Rep 1

description:
Biological replicate 1 of 3. mRNA from static control or shear-treated d9 stem cell-derived megakaryocytes.
d9-mk-30min-S3-v-F5-rep1


title: 277_Imp2

description: SSc


title: MBS125

value: plasma

value: March 2013

value: healthy

tag: age (years)

value: negative


title: 362_Plb2

description: Placebo

value: systemic sclerosis

value: placebo


title: MBS161

value: Mae Salid Noi, Tak, Thailand

tag: qpcr screening for plasmodium genus


title: 198_Imp2

description: SSc

value: abatacept

value: reference


title: Liver_Maternal_Separation_5

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

institute: INRAE

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray 4x44K v3 (design 028282) enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on an Agilent High Resolution C Scanner (G2565CA)

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 028282_D_F_20110906). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot):  myfunw<-function(x)  {okType<-x$ControlType==0  okFoundGreen<-x$gIsFound==1  okPos=x$gIsPosAndSignif==1  okWellAbove<- x$gIsWellAboveBG==1  as.numeric(okType & okFoundGreen & okPos & okWellAbove)}  We selected the spots with a weight of 1 for at least 8 out of 9 microarrays or with a weight of 1 in 4 microarrays from at least one experimental group. The filtered data were then stored as an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 17604 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Rattus norvegicus

source_name: Liver, Maternal Separation, replicate 5

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-color Low Input Quick Amp Labeling kit (Agilent Technologies) according to the manufacturer's instructions,  followed by RNeasy column purification (QIAGEN, Courtaboeuf, France).  Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Litters of Wistar rats and their mothers were housed at 23+/-1°C on a 12 hour light/dark cycle. The in vivo study was conducted under the European Union Guidelines for the use and care of laboratory animals and were approved by an independent ethics committee.

extract_protocol: Immediately following euthanasia, liver was removed and an approx. 100mg fragment was snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Total RNA was extracted from frozen liver samples with TRIzol reagent (Invitrogen) following  manufacturer's instructions. Total RNA samples were controlled for integrity on an Agilent 2100 Bioanalyzer (Agilent Technologies) and assayed at 260nm on a Nanodrop ND-1000 spectrophotometer (Thermo Scientific).

treatment_protocol: At 10 days post-partum female Wistar rats from at least 3 different litters were separated from their mothers for 4 hours (MS=maternal separation) or not (CT=controls). The animals were put back with their mothers for 24h prior to microarray analysis of their livers.

tag: gender

value: female

value: Wistar

tag: age

value: 10 days

value: liver

value: maternal separation


title: MBS126

value: community mass blood survey (ACD)

value: exposed

tag: qpcr plasmodium species


title: MCF7+hASC_1

city: Sendai

first: Minako

last: Sakurai

state: Miyagi

address: 2-1 Seiryo-Machi, Aoba-ku

department: School of Medicine

institute: Tohoku University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 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 Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (Protocol: GE1_107_Sep09 and Grid: 028004_D_F_20101102) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCF-7 co-cultured with primary human adipocytes

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

growth_protocol: DMEM media

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

treatment_protocol: co-culture

tag: cell line

value: co-culture with hASC


title: MCF7+hASC_2


title: 483_Imp3

description: SSc


title: MCF7+prehASC_2

source_name: MCF-7 co-cultured with primary human preadipocytes

value: co-culture with prehASC


title: MBS124

value: plasma

value: January 2014


title: Liver_Maternal_Separation_2

source_name: Liver, Maternal Separation, replicate 2

tag: strain


title: MCF7+prehASC_1


title: MBS123

value: healthy

value: negative


title: MBS133

value: March 2013


title: Liver_Maternal_Separation_3

source_name: Liver, Maternal Separation, replicate 3


title: 425_Imp3

description: SSc

tag: disease state

value: systemic sclerosis


title: Liver_Maternal_Separation_1

source_name: Liver, Maternal Separation, replicate 1

tag: treatment


title: MCF7 mono_2

source_name: MCF-7 mono-cultured cells

value: mono-culture


title: MBS122

value: Mae Salid Noi, Tak, Thailand

value: asymptomatic

value: positive

value: P. vivax


title: MBS118


title: MCF7 mono_1


title: MBS116


title: MBS117

value: P. falciparum, P. vivax


title: MBS114


title: MBS115


title: Patient 62

city: Madrid

first: Juan Ángel

last: Fresno Vara

address: Paseo de la castellana 261

department: INGEMM

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

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

value: FFPE tumor sample

tag: histology

value: invasive ductal carcinoma

tag: Sex

value: female

tag: size

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: Patient 64

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

tag: tissue

tag: age (years)


title: Patient 63

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


title: Patient 65


title: Liver_Control_4

source_name: Liver, Control, replicate 4

tag: gender

value: Wistar

tag: age

value: 10 days

value: liver

value: control


title: MBS121

source_name: plasma, exposed, healthy

value: plasma

tag: sample collection time

value: August 2013

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

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Patient 61

tag: histology

tag: Sex

tag: size

tag: number of nodes

tag: grade

value: negative


title: 235_Plb1

description: Placebo

tag: disease state

value: systemic sclerosis

tag: treatment

value: placebo

tag: mrss score

tag: sample type

value: reference


title: Patient 59

tag: tissue

tag: age (years)

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: Patient 58

value: positive


title: Patient 60

value: FFPE tumor sample


title: MBS111

tag: sample collection time

value: January 2014

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: MBS113


title: MBS112

source_name: plasma, exposed, fever at 2mo

value: fever at 2mo

value: P. falciparum


title: MBS119


title: Liver_Control_1

source_name: Liver, Control, replicate 1

tag: gender

value: female

tag: strain

value: Wistar

tag: age

value: 10 days

value: liver

tag: treatment


title: Liver_Control_2

source_name: Liver, Control, replicate 2

tag: tissue

value: control


title: MBS110

value: plasma

value: community mass blood survey (ACD)

value: exposed

tag: age (years)


title: Liver_Control_3

source_name: Liver, Control, replicate 3


title: Patient 57

tag: histology

value: invasive ductal carcinoma

tag: Sex

tag: size

tag: number of nodes

tag: grade

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

value: negative

tag: disease metastasis-free survival (months)


title: MBS109

tag: sample collection time

tag: sample collection site

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: healthy


title: Patient 56

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 55


title: Patient 54

value: positive


title: MBS108

source_name: plasma, exposed, asymptomatic

tag: symptomatic or asymptomatic at sample collection

value: asymptomatic

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species

value: P. vivax


title: MBS104

tag: tissue

value: March 2013

value: Mae Salid Noi, Tak, Thailand

tag: age (years)

value: P. falciparum, P. ovale


title: MBS107

value: August 2013


title: MBS106


title: MBS105


title: Patient 53

value: FFPE tumor sample

tag: histology

tag: Sex

value: female

tag: size


title: Patient 51

tag: number of nodes

tag: grade

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

value: not assessable


title: Patient 50

tag: disease metastasis-free survival (months)


title: Patient 52


title: MBS101

tag: sample collection time

tag: sample collection site

tag: sample source


title: MBS103

tag: naturally exposed or unexposed to plasmodium sp. parasites


title: Patient 48

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: MBS100

value: January 2014

tag: symptomatic or asymptomatic at sample collection

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: Patient 47

tag: tissue

tag: histology

tag: age (years)


title: FRI;flc-3 fully-expanded leaf 11, day 32

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description: small RNA

library_source: transcriptomic

data_processing:
Adapter sequences were trimmed from raw sequence reads. Only trimmed reads were used in further processing
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: TAIR9
Supplementary_files_format_and_content: text file with sequences and read count

organism: Arabidopsis thaliana

source_name: fully-expanded leaf 11 (cauline leaf)

growth_protocol: Plants were sown in MetroMix 360 soil (Sun Gro Horticulture, Vancouver, British Columbia, Canada) in 12-well (for the shoot apex and primordia collections) or 96-well flats (for the fully-expanded leaf collections). Flats were elevated on supports above a water reservoir, with wicks made from strips of batting extending from each pot into the reservoir to ensure a constant moisture level.  Flats were kept at 4oC for five days, and then grown at 23oC under long day conditions (16 hr light :8 hr dark) at a light intensity of 100-125 µ-mol m-2 s-1, provided by a one-to-one ratio of T8 Sylvania Octron (4100K Ecologic), and GroLite WS fluorescent lamps (Interlectric). Flats were covered with a clear dome for the first 3-5 days to aid germination.  Plants were fertilized twice—at planting and at 20 days—with Peters 15-16-17.  Plant age was measured from the date flats were transferred to the growth chamber.

extract_protocol:
Samples were collected in tubes submerged in liquid nitrogen, so that the tissues were instantly flash frozen. RNA was extracted by Trizol (Life Technologies), followed by a chloroform phase separation according to the manufacturer's protocol. We then performed a second extraction using a 5:1 mix of acid phenol:chlorform, pH 4.5, and precipitated with 2 volumes of isopropanol.
Libraries were made by a home assembled and modified version of Illumina's 2007 small RNA sequencing kit protocol. For each library, 20-30 nt small RNAs were selected by running 10 ug of total RNA on a 15% polyacrylamide/urea gel, using a 10 bp DNA ladder to identify the correct size range. The RNA was eluted from the gel slice by crushing the gel and adding 2-3 gel volumes of 0.3 M NaCl and shaking overnight. Following filtering out the gel, the RNA was precipitated with 3 volumes of 100% ethanol and 20 ug glycogen. The 5' adapter (a modified Illumina Genome Analyzer II adapter of sequence listed above) was ligated using T4 RNA ligase 1 (Ambion) at room temperature for 6 hours. Free 5' adapters and non-adapter-ligated small RNAs were removed by running the product on a second 15% polyacrylamide/urea gel and cutting and saving the 49-65 nt portion of the gel. The RNA was eluted and precipitated as before. The 3' adapter (the same sequence as the Illumina Genome Analyzer II 3' adapter) was then ligated, again using T4 RNA ligase 1 at room temperature for 6 hours. Free 3' adapter and RNAs lacking a 3' adapter were removed by running the samples on a 7.5% polyacrylamide/urea gel and cutting and saving the 68-88 nt portion of the gel. The RNA was eluted and precipitated as before. RT-PCR and PCR were performed using the Illumina Genome Analyzer II primers. RT-PCR was performed using Superscript II (Life Technologies) and PCR using Phusion (New England Biolabs). The final product was run on a 10% non-denaturing polyacrylamide gel, and the band around 92 bp was cut, and eluted and precipitated as before. sRNA-seq, with 36 nt reads for all apex libraries and 35 nt reads for the leaf and cotyledon libraries.

tag: genetic background

value: Col-0 with FRI introgressed from Sf-2

tag: genotype

value: fully-expanded leaf 11 (cauline leaf)

tag: days after plants put in the growth chamber

tag: day length

value: 16 hours (long day conditions)

tag: 5'-adapter with index base followed by an asterisk

value: 5' GUUCAGAGUUCUACAGUCCGACGAUCA*UC 3'


title: MBS127

value: plasma

tag: sample collection time

tag: sample collection site

value: community mass blood survey (ACD)

value: exposed

value: negative


title: FRI;flc-3 fully-expanded leaf 7, day 29

description: small RNA

source_name: fully-expanded leaf 7 (rosette leaf)

value: fully-expanded leaf 7 (rosette leaf)


title: MBS99

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

value: healthy


title: Liver_Maternal_Separation_4

source_name: Liver, Maternal Separation, replicate 4

tag: gender

tag: strain

value: Wistar

tag: age

value: 10 days

value: liver

tag: treatment

value: maternal separation


title: Patient 46

value: FFPE tumor sample

value: invasive ductal carcinoma

tag: Sex

value: female

tag: size

tag: number of nodes

tag: grade

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

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: FRI;flc-3 fully-expanded leaf 5, day 26

description: small RNA

source_name: fully-expanded leaf 5 (rosette leaf)

tag: genetic background

value: Col-0 with FRI introgressed from Sf-2

tag: genotype

tag: tissue

value: fully-expanded leaf 5 (rosette leaf)

tag: days after plants put in the growth chamber

tag: day length

tag: 5'-adapter with index base followed by an asterisk


title: 625_Imp4

description: SSc

source_name: Human Tissue Biopsy

tag: disease state

value: systemic sclerosis

value: abatacept

tag: mrss score

source_name: Universal Human Reference

tag: sample type

value: reference


title: Patient 49

tag: histology

tag: age (years)

tag: Sex

tag: size


title: MBS102

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

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: FRI;flc-3 fully-expanded leaves 1+2, day 14

description: small RNA

source_name: fully-expanded leaves 1+2 (rosette leaf)

tag: genetic background

tag: genotype

tag: tissue

tag: days after plants put in the growth chamber

value: 16 hours (long day conditions)

value: 5' GUUCAGAGUUCUACAGUCCGACGAUCA*UC 3'


title: FRI;flc-3 fully-expanded leaf 3, day 23

description: small RNA

source_name: fully-expanded leaf 3 (rosette leaf)

value: fully-expanded leaf 3 (rosette leaf)

tag: day length

tag: 5'-adapter with index base followed by an asterisk


title: FRI;flc-3 cotyledons, day 6

description: small RNA

source_name: cotyledons

value: cotyledons


title: FRI;FLC fully-expanded leaf 11, day 33

description: small RNA

source_name: fully-expanded leaf 11 (rosette leaf)

value: FRI;FLC

value: fully-expanded leaf 11 (rosette leaf)


title: Patient 45

source_name: primary breast cancer

value: FFPE tumor sample

tag: histology

value: invasive ductal carcinoma

value: female

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 44

tag: age (years)

tag: Sex

tag: size

value: unknown


title: FRI;FLC fully-expanded leaf 7, day 29

description: small RNA

tag: genetic background

value: Col-0 with FRI introgressed from Sf-2

value: fully-expanded leaf 7 (rosette leaf)


title: MBS98

source_name: plasma, exposed, healthy

value: plasma

tag: sample collection time

value: August 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

value: healthy

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: 190_Imp1

description: SSc

tag: disease state

value: systemic sclerosis

tag: treatment

value: abatacept

tag: mrss score

tag: sample type

value: reference


title: MBS97

tag: tissue

value: community mass blood survey (ACD)

value: exposed


title: FRI;FLC fully-expanded leaf 9, day 33

description: small RNA

source_name: fully-expanded leaf 9 (rosette leaf)

tag: genotype

value: FRI;FLC

value: fully-expanded leaf 9 (rosette leaf)

tag: days after plants put in the growth chamber

tag: day length

value: 16 hours (long day conditions)

tag: 5'-adapter with index base followed by an asterisk

value: 5' GUUCAGAGUUCUACAGUCCGACGAUCA*UC 3'


title: FRI;flc-3 fully-expanded leaf 9, day 32

description: small RNA

tag: genetic background


title: MBS96

tag: sample collection time

tag: age (years)

value: negative


title: MBS95

tag: sample collection site

tag: sample source


title: FRI;FLC fully-expanded leaf 3, day 23

description: small RNA

value: fully-expanded leaf 3 (rosette leaf)


title: FRI;FLC fully-expanded leaves 1+2, day 14

description: small RNA

value: Col-0 with FRI introgressed from Sf-2

value: fully-expanded leaves 1+2 (rosette leaf)


title: Patient 43

value: FFPE tumor sample

tag: histology

value: invasive ductal carcinoma

tag: Sex

value: female

tag: size

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: Patient 42

tag: tissue


title: MBS94

value: plasma

value: March 2013

value: Mae Salid Noi, Tak, Thailand

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

value: healthy

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: FRI;FLC cotyledons, day 6, rep 1

description: small RNA

tag: genetic background

tag: genotype

value: cotyledons

tag: days after plants put in the growth chamber

tag: day length

tag: 5'-adapter with index base followed by an asterisk


title: FRI;flc-3 shoot apices, day 11, rep 2

description: small RNA

source_name: shoot apices plus leaf primordia ≤ 1 mm

value: shoot apices plus leaf primordia ≤ 1 mm

value: 5' GUUCAGAGUUCUACAGUCCGACGAUCG*UC 3'


title: Patient 41

tag: histology

tag: age (years)

tag: Sex

tag: size

tag: number of nodes


title: MBS93

tag: sample collection time

tag: sample collection site

tag: sample source

value: community mass blood survey (ACD)

value: exposed


title: Patient 40

tag: tissue

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: FRI;flc-3 shoot apices, day 11, rep 1

description: small RNA

tag: genetic background

tag: genotype

tag: days after plants put in the growth chamber

tag: day length

value: 16 hours (long day conditions)

value: 5' GUUCAGAGUUCUACAGUCCGACGAUCA*UC 3'


title: FRI;flc-3 shoot apices, day 9, rep 2

description: small RNA

tag: 5'-adapter with index base followed by an asterisk


title: FRI;flc-3 shoot apices, day 9, rep 1

description: small RNA


title: FRI;flc-3 shoot apices, day 6, rep 2

description: small RNA


title: MBS92

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

value: negative

tag: qpcr plasmodium species


title: FRI;FLC shoot apices, day 21, rep 2

description: small RNA

value: Col-0 with FRI introgressed from Sf-2

value: FRI;FLC

tag: tissue


title: FRI;FLC fully-expanded leaf 5, day 26

description: small RNA

value: fully-expanded leaf 5 (rosette leaf)


title: Patient 39

value: FFPE tumor sample

tag: histology

value: invasive ductal carcinoma

tag: Sex

tag: size

tag: number of nodes

tag: grade

value: positive


title: Patient 38

value: female

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: Patient 37


title: FRI;FLC shoot apices, day 11, rep 1

description: small RNA

tag: genetic background

tag: genotype

tag: days after plants put in the growth chamber

tag: day length

tag: 5'-adapter with index base followed by an asterisk


title: MBS90

value: plasma

tag: sample collection time

value: March 2013

tag: sample collection site

value: Mae Salid Noi, Tak, Thailand

tag: sample source

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: FRI;FLC shoot apices, day 11, rep 2

description: small RNA

tag: tissue

value: shoot apices plus leaf primordia ≤ 1 mm


title: Patient 36

tag: histology

tag: Sex

tag: size

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: FRI;FLC shoot apices, day 9, rep 1

description: small RNA

tag: genetic background

tag: genotype

tag: days after plants put in the growth chamber

tag: day length

tag: 5'-adapter with index base followed by an asterisk


title: FRI;flc-3 shoot apices, day 6, rep 1

description: small RNA


title: MBS89

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: healthy

tag: age (years)


title: FRI;FLC shoot apices, day 6, rep 2

description: small RNA

tag: tissue

value: 5' GUUCAGAGUUCUACAGUCCGACGAUCG*UC 3'


title: FRI;FLC shoot apices, day 21, rep 1

description: small RNA


title: Patient 35

tag: histology

tag: Sex

tag: size

tag: number of nodes

tag: overall survival (months)

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


title: FRI;FLC shoot apices, day 9, rep 2

description: small RNA

tag: genetic background

tag: genotype


title: MBS87

value: community mass blood survey (ACD)

value: exposed

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species


title: MBS88

tag: sample collection time


title: MBS86

tag: sample collection site


title: Patient 33

tag: grade

value: unknown

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

tag: disease metastasis-free survival (months)

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


title: FRI;FLC shoot apices, day 6, rep 1

description: small RNA

tag: tissue

tag: days after plants put in the growth chamber

tag: day length

value: 16 hours (long day conditions)

tag: 5'-adapter with index base followed by an asterisk

value: 5' GUUCAGAGUUCUACAGUCCGACGAUCA*UC 3'


title: MBS91

tag: sample source

tag: naturally exposed or unexposed to plasmodium sp. parasites

tag: symptomatic or asymptomatic at sample collection

tag: age (years)

value: negative


title: MBS85


title: Patient 32

tag: histology

tag: Sex

tag: size

tag: number of nodes

tag: overall survival (months)

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


title: MBS84

tag: sample collection time

tag: sample collection site

value: asymptomatic

tag: qpcr screening for plasmodium genus

tag: qpcr plasmodium species

value: P. vivax


title: Patient 31

tag: tissue

value: FFPE tumor sample

value: invasive ductal carcinoma

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)