title: CKCS_Saliva_Affected_42

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: cj

tag: fh

tag: l5 (aeb)


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 5, technical rep. left

status: Public on Mar 01 2018

type: RNA

city: Freising

first: Stefanie

last: Müller-Herbst

address: Weihenstephaner Berg 3

department: ZIEL and Chair for Microbial Ecology

country: Germany

institute: Technical University Munich

hyb_protocol: Differently labeled samples derived from one RNA set were combined. The volume was reduced to 30 μl in a SpeedVac Concentrater 5301 (Eppendorf). Then, 6 μl 20 x SSC and 4 μl 1 % SDS were added. Reaction mix was incubated 1 min at 94 °C and subsequently put on ice. Then, the reaction mix was applied to the microarray slide and the slide was covered with a cover slip. Hybridization was performed over night at 64 °C.

scan_protocol: Slides were scanned with the GenePix 4000B scanner (MDS Analytical Technologies) and data were analyzed via the GenePix 6.0 software (MDS Analytical Technologies).

data_processing: For normalization, the arithmetic mean of the ratios was set to one (GenePix Pro 6.0 software). In general, only spots with a fluorescence signal higher than the local background plus one standard deviation were included in the final analysis. Spots with irregular morphology were in general excluded from the interpretation when the ratio of medians, the ratio of means and the regression ratio differed by more than 30 %. To minimize the possibility of incorrect exclusion of spots due to automated interpretation, raw data of spots with a log2 ratio of median ≥ 1.0 or ≤ -1.0 were further analyzed. If either the Cy5 or the Cy3 fluorescence intensity reached at least 50 % of the average intensity of all spots of the respective array, the spot was included in the final analysis. Genes were treated as significantly up or down regulated if (i) at least for nine valid spots the log2 ratio of medians (pH 6.0 - 200 mg/l NaNO2/pH 6.0 - 0 mg/l NaNO2) was ≥ 1.0 or ≤ -1.0 and (ii) the arithmetic mean of the log2 ratio of medians of valid spots was ≥ 1.0 or ≤ -1.0. log2 RTL (relative transcription level) indicates the arithmetic mean of the log2 ratio of medians of all valid spots.

molecule: total RNA

organism: Listeria monocytogenes EGD-e

source_name: cells were exposed to pH 6.0 - 200 mg/l NaNO2 for one hour

label_protocol: 30 μg of bacterial RNA were used for each labelling reaction and 3 µl random nonamers with the reverse transcription reaction mix (GE Healthcare) were added for priming. The samples were added up to 18 µl with DEPC-dH2O. To elimate secondary structures, RNA preparation was inczbated at 70 °C for 5 min. A 10 min incubation period a RT allowed hybridization of the oligonucleotdies to the RNA. Subsequently, the reverse transcription mix  (1 μl Superscript III Reverse Transcriptase (200 U/μl), 8 μl 5 x reaction buffer, 4 μl DTT (0.1 M) (Invitrogen), and 1 μl dNTP mix (20 mM dATP, 20 mM dGTP, 20 mM dTTP, and 16 mM dCTP (Fermentas)) was added. Volume was adjusted to 38 μl with DEPC treated water, and 2 μl of a Cy3- or Cy5-labelled dCTP analogue were used for fluorescent labeling of the cDNA. Samples were incubated at 42 °C for 2 h. Then, 2 μl DNase-free RNase (> 30 U/mg, Roche Diagnostics) were added and the sample was incubated for 45 min at 37 °C and cDNA was purified using the QIAquick® PCR-Purification Kit (Qiagen) and eluted in 40 μl dH2O.

growth_protocol: 2.5 – 3.0 ml of a Listeria monocytogenes EGDe overnight culture were used to inoculate 150 ml BHI medium (500 ml conical flask). Cells were grown at 24 °C under constant shaking (150 rpm) to an OD600 of 0.825 – 0.850. Then, two 50 ml aliquots were centrifuged (6000 rpm, 8 min, RT). The pellets were resuspended either in BHI pH 6.0 (pH adjusted with lactic acid prior to autoclaving) without NaNO2 (0 mg/l) or in BHI pH 6.0 to which NaNO2 was added in a concentration of 200 mg/l and cells were further incubated for one hour.

extract_protocol: The cell pellet was resuspendet in 1 ml TRIzol/TRI Reagent (Invitrogen/Sigma) and transferred into a 2 ml shredder-tube (Sarstedt) containing silica beads (diameter 0.1 mm). Solution was incubated at room temperature for 1 min, before cell walls were disrupted mechanically in a FastPrep cell disrupter. Silica beads were removed by centrifugation, RNA was extracted with chloroforme extraction, precipitated with isopropanol and the pellet was washed with 70 % EtOH. Residual DNA was removed by DNaseI digestion (Promega) according to manufacturer´s instructions. RNA was purified again follwoing the RNA clean-up protocol from the RNeasy Mini Kit (Quiagen), and an additional on column DNA digest was performed.

treatment_protocol: After exposure to pH 6.0 - 200 mg/l NaNO2 or pH 6.0 - 0 mg/l  NaNO2 for one hour, cells were again collected by centrifugation (6000 rpm, 10 min, RT). Finally, the cell pellet was snap frozen in liquid nitrogen and stored at - 80 °C until further processing. The transcriptome of the two conditions was compared.

tag: od600 before exposure

tag: treatment

value: 200 mg/l NaNO2 for one hour

source_name: cells were exposed to pH 6.0 - 0 mg/l NaNO2 for one hour

value: 0 mg/l NaNO2 for one hour


title: CKCS_Saliva_Affected_49

type: genomic

city: Montreal

first: Philippe

last: Lemay

state: Quebec

address: 3175 Chemin de la Côte-Sainte-Catherine

country: Canada

institute: Université de Montréal

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a iScan Autoloader 2X (Illumina).

data_processing:
Genomic DNA extracted from saliva was genotyped using Infinium CanineHD Genotyping BeadChips (Illumina).
GenomeStudio 2.0 was used to generate processed data using the final report function.

label: CY3 and CY5

molecule: genomic DNA

organism: Canis lupus familiaris

source_name: Saliva

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-MA1, WG-MA2) and primer/neutralization mix (WG-MSM). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FMS), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: DNA was extracted from blood or saliva using the ORAGENE Animal kit (DNAgenotek)

value: Cavalier King Charles Spaniel

value: case

tag: vd

tag: ae

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 6, technical rep. right

tag: od600 before exposure

tag: treatment


title: CKCS_Saliva_Unaffected_51

tag: breed

tag: disease state

value: control

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: cj

tag: fh

tag: l5 (aeb)


title: 19Asbestos

city: morgantown

first: Anna

middle: A

last: Shvedova

state: WV

address: 1095 willowdale Rd

department: HELD

country: USA

institute: CDC/NIOSH

description: mrna expression after 7d post exposure to Crocidolite Asbestos

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA).

scan_protocol: After being washed in an ozone-free environment, the slides were scanned using the Axon GenePix 4000B microarray scanner. Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis.

organism: Mus musculus

source_name: Exposure to 120µg/mouse of Crocidolite

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Total RNA was isolated from left lung tissues of control and erionite, tremolite, crocidolite or wollastonite exposed female mice 7 days post exposure (n=3 for each group). The RNA was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified using RNeasy MiniKits (Qiagen, Mississauga, ON, Canada) as described by the manufacturer. On-column DNase treatment was applied (Qiagen, Mississauga, ON, Canada). Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. All RNA samples showed a A260/280 ratio greater than 2.0.

tag: strain

tag: gender

value: Female

tag: tissue

value: left lung


title: BP165_5418_W16_D1_B_CTRL

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: gene expression week 16, day 1 , control group

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Agilent Rhesus (8x60K) oligonucleotide microarrays  were used. Dry slides were scanned on an Agilent Technologies Scanner G2505C US93503719 using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 10.7.3.1) and the GE1-v5_95_Feb07 extraction protocol.

organism: Macaca mulatta

source_name: gene expression week 16, day 1

growth_protocol: 22 Indian-orgin Rhesus Macaques were used. 10 vaccinated animals that acquired SIV infection with two challenges (early SIV acquirers) and 12 vaccinated animals that acquired SIV infection after 6 challenges (late SIV acquirers).

extract_protocol: Microarray analysis was performed on whole blood samples on 22 vaccined animals. (10 early acquires and 12 late acquirers).  For both set of animals at multiple days after the 1st DNA vaccine (Wk0), 1st MVA boost (Wk16), 2nd MVA boost (Wk32) and 1st rectal challenge

treatment_protocol: Total RNA was isolated from Paxgene tubes by use of Paxgene Blood RNeasy minikits (Qiagen) following the manufacturer's protocol.

value: whole blood

tag: vaccine treatment

value: control group

tag: siv acquirers

value: Early acquisition


title: CKCS_Saliva_Affected_44

tag: breed

tag: disease state

tag: sm

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: CKCS_Saliva_Affected_39

tag: breed

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: cj

tag: fh

tag: l5 (aeb)


title: CKCS_Saliva_Affected_40

tag: disease state

tag: sm

tag: ID

tag: ac

tag: ai

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l8 (ebd)


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 4, technical rep. right

tag: od600 before exposure

tag: treatment


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 6, technical rep. left


title: CKCS_Saliva_Affected_41

tag: breed

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: cj

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: 18Asbestos

tag: strain

tag: gender

tag: tissue


title: 20Asbestos


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 4, technical rep. left

tag: od600 before exposure

tag: treatment


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 3, technical rep. right


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 3, technical rep. left


title: CKCS_Saliva_Affected_37

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: ID

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: 17Wollastonite

description: mrna expression after 7d post exposure to Wollastonite Fibers

source_name: Exposure to 120µg/mouse of Wollastonite

tag: strain

tag: gender

tag: tissue


title: 16Wollastonite


title: CKCS_Saliva_Affected_38

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: cj

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 5, technical rep. right

tag: od600 before exposure

tag: treatment


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 1, technical rep. right


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 2, technical rep. left


title: CKCS_Saliva_Affected_35

tag: breed

tag: vd

tag: ID

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: CKCS_Saliva_Affected_31

tag: disease state

tag: sm

tag: ccd size

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: cj

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: CKCS_Saliva_Affected_36

tag: breed

tag: vd

tag: ID

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 1, technical rep. left

tag: od600 before exposure

tag: treatment


title: CKCS_Saliva_Affected_32

tag: disease state

tag: sm

tag: ccd size

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: cj

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: CKCS_Saliva_Affected_33

tag: breed

tag: vd

tag: ID

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd

tag: f-d/bc


title: 15Wollastonite

tag: strain

tag: gender

tag: tissue


title: 13Tremolite

description: mrna expression after 7d post exposure to Tremolite Asbestos

source_name: Exposure to 120µg/mouse of Tremolite


title: 6Erionite

description: mrna expression after 7d post exposure to Erionite

source_name: Exposure to 120µg/mouse of Erionite


title: CKCS_Saliva_Affected_34

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: cj

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: 11Tremolite

tag: strain

tag: gender


title: CKCS_Saliva_Affected_30

tag: breed

tag: vd

tag: ID

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd

tag: f-d/bc


title: 7Erionite

tag: tissue


title: 3control

description: mrna expression in unexposed C57BL6 Female mice

source_name: Unexposed C57BL6 Female mice

tag: strain


title: RCC DMSO repeat 1

type: SRA

city: Shanghai

first: Cheng

last: Luo

state: Shanghai

address: No. 555 Zuchongzhi Road

country: China

institute: Shanghai Institute of Materia Medica

description:
gene_exp.diff
786-O cells treated with DMSO repeat 1, R1

library_source: transcriptomic

data_processing:
tophat2 with default parameters
samtools to sort and convert the file format
cufflinks with default parameters
cuffmerge with default parameters
cuffdiff with default parameters
Genome_build: ensembl GRch38
Supplementary_files_format_and_content: gene_exp.diff, generated by Cuffdiff, normalized values for each sample

organism: Homo sapiens

source_name: renal clear carcinoma

growth_protocol: density 1e7 786-O cells in 15cm dish, 24 hours, to 70% confluentence

extract_protocol:
2100 Bioanalyzer for quality check, DNaseI (Takara, Japan) for digestion at 37 C and 30 mins
100ng purified RNA, NEBNext® UltraTM RNA Library Prep Kit for Illumina (NEB, USA)

treatment_protocol: treatment with compounds or DMSO, after 24 hours

tag: cell line

value: 786-O cells

tag: treatment

value: DMSO


title: RCC DMSO repeat 3

description:
gene_exp.diff
786-O cells treated with DMSO repeat 3, R1


title: RCC DMSO repeat 2

description:
gene_exp.diff
786-O cells treated with DMSO repeat 2, R1


title: 2control

tag: gender


title: CKCS_Saliva_Affected_29

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: RCC inhibitor 30uM repeat 3

description:
gene_exp.diff
786-O cells treated with inhibitor 30uM repeat 3, R1

tag: cell line

tag: treatment

value: BRD4 inhibitor BDF-1253


title: RCC inhibitor 30uM repeat 2

description:
gene_exp.diff
786-O cells treated with inhibitor 30uM repeat 2, R1


title: 5Erionite

tag: strain

tag: gender

tag: tissue


title: CKCS_Saliva_Affected_27

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd

tag: f-d/bc


title: CKCS_Saliva_Affected_28

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)


title: 1control

tag: strain

tag: gender

tag: tissue


title: CKCS_Saliva_Unaffected_23

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: f-d/cd


title: CKCS_Saliva_Affected_25

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/bc


title: NV25_LH2

city: Tartu

first: Kaarel

last: Krjutskov

state: Tartumaa

address: Teaduspargi tänav 13

country: Estonia

institute: The Competence Centre on Health Technologies

description: small RNA

data_processing:
Quality control and adapter trimming of raw sequences was performed using Trimmomatic version 0.36. All sequences were scanned with 4 base long sliding window and reads were dropped if the average quality of base pair was below 30 according to Phred +33 quality score system or if total read length was less than 17.
Identification of miRNAs from sequencing reads was performed by miRDeep2 algorithm according to miRBase version 21. Standard settings were used.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: raw counts

source_name: endometrium

extract_protocol:
Endometrial tissue was processed by using miRNeasy Mini and RNeasy MinElute kits (Qiagen), following the manufacturer’s protocol for isolating the small RNA fraction (< 200 nucleotides). DNase I treatment was performed on column with RNase-Free DNase Set (Qiagen). Purified RNA quantity was determined on Bioanalyzer 2100 with Small RNA kit (Agilent Technologies, USA).
Libraries were constructed according to the TruSeq Small RNA Library Preparation Guide (Illumina, USA) and Illumina index sequences were used for the option of  12-plexing the libraries on a single sequencing lane. 1 µg of small RNA fraction was used as input. Final purification step was performed by manually selecting libraries corresponding to the length of inserted miRNAs (area between 145-160 bp) using gel electrophoresis (6% Novex TBE gels). Libraries were quantified and validated with Agilent 2100 Bioanalyzer (Agilent Technologies), normalized, pooled, used for cluster generation on the cbot and sequenced on HiSeq 2000/2500 with a configuration of 50 cycles Single Reads following manufacturer’s instructions (Illumina).

tag: lh day


title: NV25_LH8

description: small RNA


title: CKCS_Saliva_Affected_26

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)


title: NV16_LH8

description: small RNA


title: CKCS_Saliva_Unaffected_22

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: f-d/cd


title: 12Tremolite

tag: strain

tag: gender

tag: tissue


title: CKCS_Saliva_Unaffected_19

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l10 (afg)

tag: f-d/bc


title: CKCS_Saliva_Unaffected_21

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: f-d/cd


title: CKCS_Saliva_Affected_20

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l2 (fac)


title: CKCS_Saliva_Unaffected_24

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l3 (dib)

tag: l4 (fae)

tag: l10 (afg)

tag: f-d/bc


title: NV16_LH2

description: small RNA

tag: lh day


title: NV13_LH2

description: small RNA


title: L. monocytogenes EGDe, pH 6.0 - 200 mg/l NaNO2 vs. pH 6.0 - 0 mg/l NaNO2, biological rep. 2, technical rep. right

tag: od600 before exposure

tag: treatment


title: CKCS_Saliva_Unaffected_14

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l5 (aeb)

tag: l8 (ebd)

tag: l9 (jcb)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_17

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l10 (afg)

tag: f-d/bc


title: NV12_LH8

description: small RNA

tag: lh day


title: CKCS_Saliva_Unaffected_15

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l5 (aeb)

tag: l8 (ebd)


title: CKCS_Saliva_Unaffected_16

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l9 (jcb)

tag: f-d/cd


title: NV06_LH8

description: small RNA

tag: lh day


title: CKCS_Saliva_Unaffected_18

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l1 (hae)

tag: l10 (afg)

tag: f-d/bc


title: NV12_LH2

description: small RNA


title: NV06_LH2

description: small RNA


title: CKCS_Saliva_Unaffected_13

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: CKCS_Saliva_Unaffected_12

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: bk

tag: l9 (jcb)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_11

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: l1 (hae)

tag: l2 (fac)

tag: l10 (afg)

tag: f-d/bc


title: 12013_LH8

description: small RNA

tag: lh day


title: 12013_LH2

description: small RNA


title: CKCS_Saliva_Unaffected_9

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: CKCS_Saliva_Unaffected_7

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l9 (jcb)

tag: f-d/cd


title: CKCS_Saliva_Unaffected_8

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ac

tag: ai

tag: fh

tag: fg

tag: l3 (dib)

tag: l10 (afg)

tag: f-d/bc


title: CKCS_Saliva_Unaffected_6

tag: breed

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: cj

tag: bk

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: BM CD34+ cells from Healthy Donor 9 (GEP)_reanalyzed

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

hyb_protocol: Regarding GEP, fragmented cRNA was hybridized for 16 hr at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were finally scanned using GeneAtlas Scanner.

data_processing: Gene and miRNA expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

label: biotin

source_name: Bone marrow CD34+ Cells

label_protocol: Gene expression profiling (GEP) and miRNA expression profiling (miEP) were performed on the same RNA preparation. As regards GEP, biotinylated cRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the cRNA sample concentration.

growth_protocol: Bone marrow (BM) CD34+ cells were obtained from PV (n=26), and ET (n=24) patients. CD34+ cells were collected from 5 ml of BM aspirates, all obtained in preservative free heparin. Mononuclear cells were separated over a Ficoll-Paque gradient (Lympholyte; Cederlane Labs) and processed through two sequential steps of immunomagnetic CD34  selection (Miltenyi Biotec, Bergisch Gladbach,Germany,http://www.miltenyibiotec.com). Purity of the isolated CD34+ cell population was evaluated by flow cytometry after labeling with PE-HPCA2 anti-CD34 monoclonal antibody (BD Biosciences) and was always > 95%.

extract_protocol: CD34+ cells were purified from BM aspirates and immediately  lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA). Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations for Purification of Total RNA, Including Small RNAs, from Animal Cells. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

tag: supplier

value: Vannucchi

tag: Sex

value: not provided

tag: condition

value: Control (CTR)

tag: disease

value: healthy control

value: neg

tag: tissue

value: Bone marrow

tag: cell marker


title: CKCS_Saliva_Unaffected_5

tag: breed

value: Cavalier King Charles Spaniel

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: ac

tag: ai

tag: fh

tag: fg

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: BM CD34+ cells from Healthy Donor 7 (GEP)_reanalyzed

tag: supplier

tag: Sex

tag: condition

tag: disease

tag: tissue

tag: cell marker


title: NV13_LH8

description: small RNA

tag: lh day


title: RCC inhibitor 30uM repeat 1

description:
gene_exp.diff
786-O cells treated with inhibitor 30uM repeat 1, R1

tag: cell line

tag: treatment


title: BM CD34+ cells from Healthy Donor 8 (GEP)_reanalyzed


title: CKCS_Saliva_Unaffected_1

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg

tag: bk

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: CKCS_Saliva_Unaffected_3

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: CKCS_Saliva_Unaffected_4

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: ai

tag: cj

tag: fh

tag: fg


title: CKCS_Saliva_Unaffected_10

tag: breed

tag: disease state

tag: sm

tag: ccd size

tag: vd

tag: bk

tag: l1 (hae)

tag: l2 (fac)

tag: l3 (dib)

tag: l4 (fae)

tag: l5 (aeb)

tag: l8 (ebd)


title: CKCS_Saliva_Unaffected_2

tag: f-diam

tag: ab

tag: bc

tag: cd

tag: bd

tag: ae

tag: ID

tag: ac

tag: l9 (jcb)

tag: l10 (afg)

tag: f-d/cd

tag: f-d/bc


title: BM CD34+ cells from Healthy Donor 4 (GEP)_reanalyzed

tag: supplier

tag: Sex

tag: condition

tag: disease

tag: tissue

tag: cell marker


title: BM CD34+ cells from Healthy Donor 3 (GEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 2 (GEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 5 (GEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 15 (GEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 14 (GEP)_reanalyzed


title: Adrenocortical carcinoma Sample 48

city: Copenhagen

first: Wiktor

last: Majewski

address: Blegdamsvej 9

department: Center for Genomic Medicine

country: Denmark

institute: Copenhagen University Hospital

description: Hybridized to CytoScanHD

hyb_protocol: affymetrix manufactures procedure

scan_protocol: affymetrix manufactures procedure

data_processing:
BioDiscovery software NEXUS 8.0
data represent the CNAs calls based on CytoScanHD arrays from Affymetrix

label: Biotin

source_name: tumor biopsy

label_protocol: affymetrix manufactures procedure

extract_protocol: Qiagen manufactures procedure automatized on QiaCube; specifically Rneasy MIniPrep. DNA quality and quantity was controled by BioAnalyzer and Nanodrop.

value: Adrenocortical carcinoma


title: BM CD34+ cells from Healthy Donor 13 (GEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 6 (GEP)_reanalyzed


title: Enchodroms Sample 40

description: Hybridized to CytoScanHD

value: Enchodroms


title: Anaplastic ependymoma Sample 50

description: Hybridized to CytoScanHD

value: Anaplastic ependymoma


title: Rhabdomyosarcoma Sample 51

description: Hybridized to CytoScanHD

value: Rhabdomyosarcoma


title: Ependymom Sample 52

description: Hybridized to CytoScanHD

value: Ependymom


title: BM CD34+ cells from Healthy Donor 11 (GEP)_reanalyzed


title: Neuroblastoma Sample 37

description: Hybridized to CytoScanHD

value: Neuroblastoma


title: BM CD34+ cells from Healthy Donor 12 (GEP)_reanalyzed


title: BM CD34+ cells from Healthy Donor 1 (GEP)_reanalyzed


title: BM CD34+ cells from patient 5764 (GEP)

value: M

value: myeloproliferative neoplasm (MPN)

value: PV

value: pos

tag: mpl-mutated

tag: calr-mutated

tag: gene mutation


title: Ewing sarcoma Sample 47

description: Hybridized to CytoScanHD

value: Ewing sarcoma


title: BM CD34+ cells from Healthy Donor 10 (GEP)_reanalyzed

value: Vannucchi

value: not provided


title: BM CD34+ cells from patient 11_46 (GEP)

value: Cazzola

value: ND


title: Anaplastic ependymoma Sample 38

description: Hybridized to CytoScanHD


title: BM CD34+ cells from patient 11_202 (GEP)

value: neg

value: Bone marrow


title: Atypical neurocytoma Sample 34

description: Hybridized to CytoScanHD

value: Atypical neurocytoma


title: BM CD34+ cells from patient 10_591 (GEP)


title: BM CD34+ cells from patient 11_122 (GEP)

value: F


title: Alveolar rhabdomyosarcoma Sample 33

description: Hybridized to CytoScanHD

value: Alveolar rhabdomyosarcoma


title: Ganglioneuroblastoma Sample 30

description: Hybridized to CytoScanHD

value: Ganglioneuroblastoma


title: Astrocytoma Sample 36

description: Hybridized to CytoScanHD

value: Astrocytoma


title: Anaplastic ependymoma Sample 31

description: Hybridized to CytoScanHD

value: Anaplastic ependymoma


title: BM CD34+ cells from patient 7164 (GEP)


title: Chondroblastic osteosarcoma Sample 35

description: Hybridized to CytoScanHD

value: Chondroblastic osteosarcoma


title: BM CD34+ cells from patient 7201 (GEP)

value: M

value: myeloproliferative neoplasm (MPN)


title: Choroid plexus carcinoma / Malignant peripheral nerve sheeth tumor Sample 28

description: Hybridized to CytoScanHD


title: BM CD34+ cells from patient 7144 (GEP)

value: PV

value: pos


title: BM CD34+ cells from patient 7153 (GEP)

value: Vannucchi


title: Malignant peripheral nerve sheeth tumor Sample 46

description: Hybridized to CytoScanHD

value: Malignant peripheral nerve sheeth tumor


title: Pilocytic astrocytoma Sample 24

description: Hybridized to CytoScanHD

value: Pilocytic astrocytoma


title: Malignant peripheral nerve sheeth tumor Sample 23

description: Hybridized to CytoScanHD


title: BM CD34+ cells from patient 7124 (GEP)

value: ND


title: Gastrointestinal neuroectodermal tumour Sample 32

description: Hybridized to CytoScanHD

value: Gastrointestinal neuroectodermal tumour


title: BM CD34+ cells from patient 7028 (GEP)

value: Bone marrow


title: BM CD34+ cells from patient 7025 (GEP)


title: S16

data_processing:
Library strategy: TAC-seq (targeted allele counting by sequencing)
Reads were converted to FASTA format, trimmed to 62 bp, shorter than 62 bp reads were removed using FASTX-Toolkit
UMI subsequences were joined using AWK
Reads were demultiplexed by target sequence using FASTX-Toolkit with 2 mismatches
Target sequence (54 bp) were trimmed, reads with N nucleotide were removed using FASTX-Toolkit
Merge sequences by UMI using FASTX-Toolkit
Read and molecule counts were calculated per sample and target (UMI threshold = 1)
Supplementary_files_format_and_content: tab-delimited text file containing targeted read, molecule counts and redundancy of each sample.

molecule: polyA RNA

source_name: Endometrium

extract_protocol:
Total RNA was extracted from up to 30 mg of endometrial tissue. The biopsy was homogenized in the presence of QIAzol reagent (Qiagen, Venlo, Netherlands) and processed using miRNeasy Mini kit following the manufacturer's protocol (Qiagen).
Non-skirted low profile PCR Strip Tube Plate (Thermo Fisher) was used with domed cap strips (Thermo Fisher). 1 ul of total-RNA sample was used. The RIN values 7.7 -9.6 were quantified by Qubit (Invitrogen) and diluted to concentration 90 ng/ul. RT master mix contained 1 ul of 1:50,000 of ERCC RNA Spike-In Mix 1 (Life Technologies) dilution for technical normalization. TAC-seq detector set contained 57 biomarker genes, five ERCC spike-ins (00131; 00108; 00092; 00019 and 00004) and eight housekeeping genes (ACTB, GAPDH, YWHAZ, PPIA, CYC1, HMBS, TBP and SDHA). Altogether 70 TAC-seq detector pairs targeting biomarkers, ERCC spike-in molecules and housekeepers were previously mixed together from 100 uM stock solutions, creating a 100uMoligo pool. The mixture was diluted to 5 uM by water and stored at -20°C. 1 ul of total-RNA template for each individual library was added to 2 ul denaturation buffer, containing 5 mM Tris-HCl (pH 7.0) (Sigma-Aldrich), 1 mM dNTP mixture (Thermo Fisher), 400 nM Oligo-T30 primer and 0.05% Triton X-100 (Sigma-Aldrich). Reaction was mixed by pipetting and centrifuged briefly. RNA was denatured by 1 min at 80°C and placed on ice. After that, reverse transcriptase (RT) master mix containing 100 mM Tris-HCl (pH 8.5) (Sigma-Aldrich), 2.5 M betaine (Sigma-Aldrich), 150 mM KCl (Sigma-Aldrich), 10 mM DTT (Sigma-Aldrich), 15 mM MgCl (Sigma-Aldrich), 4 U RiboLock RNase inhibitor (Thermo Fisher) and 20 U Maxima H Minus Reverse Transcriptase (Thermo Fisher) was prepared. The content was mixed on vortex and centrifuged briefly. 2 ul of RT master mix was added to previously denatured RNA (3 ul). All RT pipetting steps were performed on ice. cDNA synthesis was performed by 30 min at 42°C, following 5 min at 85°C for RT inactivation. Once cDNA synthesis was completed, 1 ul of 5 uM TAC-seq detector mixture was added to RT mixture. The content was mixed on vortex and centrifuged briefly. Strip tubes were placed on thermocycler, denatured 1 min at 98°C and following 1 h at 60°C to enable specific cDNA and TAC-seq probe hybridization. After hybridization, thermostable ligase reaction mixture was added on thermocycler, keeping a constant (60°C) hybridization temperature. The cycler lid was opened and strip caps were removed. 5 ul of Taq DNA ligase master mix, containing 2 Taq DNA ligation buffer (New England Biolabs, NEB) and 1 U Taq DNA ligase (NEB, cat no M0208) were added to each individual reaction tube and mixed by pipetting. The strip tubes were not removed from 60°C thermocycler to avoid self- and mispairing of TAC-seq probes. Ligation reaction was stopped after 20 min incubation by placing reaction plate on ice. 15 ul of previously combined Dynabeads MyOne Carboxylic Acid beads (2 ul) (Thermo Fisher) and 13 ul of capture buffer (30% PEG-6000 (Sigma-Aldrich), 2 M NaCl (Sigma-Aldrich), 5 mM Tris-HCl (pH 7.5) (Sigma-Aldrich), 10 mM EDTA (Sigma-Aldrich) and 0.02% Tween-20 (Sigma-Aldrich)) was added to ice-cooled ligated sample. The content was mixed by vortex. The capture was carried out for 10 min at RT, and after that the samples were placed on DynaMag-96 Side Magnet (Thermo Fisher) holding 8-well strip tubes on VersiPlate Frame (Thermo Fisher). The clean supernatant was removed. The beads on magnet were washed once with 50 ul fresh 80% ethanol. Ethanol was removed by pipetting, and the clean pellet, without ethanol drops, was dried for 2 min. Once beads were dry, strip tubes were removed from the magnet and 18 ul of PCR master mix was added directly to beads. The master mix contained 1 proofreading HOT FIREPol Blend Master Mix (SolisBiodyne, Tartu, Estonia) and 250 nM TAC-seq Left primer. In addition to universal TAC-seq Left, different TAC-seq barcode oligonucleotides were used to introduce a six-nucleotide barcode to each studied sample. For that, 2 ul of 5 uM TAC-seq Barcoded primers were added individually to each PCR reaction. Strip tubes were closed with clean domed caps, mixed on vortex until all beads were suspended. The ERCC spike-in reaction was incubated at 95°C for 12 min, followed by two cycles of 95°C for 20 s, 57°C for 60 s and 72°C for 20 s. In addition, 10 cycles of 95°C for 20 s, 65°C for 20 s and 72°C for 20 s with a final extension at 72°C for 1 min using the default ramp speed of the T100 cycler (Bio-Rad) were performed. PCR products were pooled together into 1.5 ml tube. The pooled tube was placed on magnet to remove carboxylated beads before the following column purification. Clear supernatant was purified with DNA Clean & Concentrator-5 column (Zymo Research) and eluted with 50 ul EB. The library was size-selected using AMPure XP beads (Beckman Coulter) in a single-step selection to reduce 81 bp linear PCR double-stranded by-product. 50 ul beads were added to 50 ul of the purified PCR product, incubated for 5 min at room temperature and captured by a magnet for 3 min. After incubation on magnet, the supernatant was discarded and the remaining beads were centrifuged at 500g for 10 s. After centrifugation, the beads were placed again on the magnet and all remaining supernatant was removed. The beads were eluted directly without ethanol washing in 25 ul of EB and incubated for 1 min at RT. Finally, the eluted library was transferred to a clean tube after 1 min incubation on the magnet. The library (single 180 bp product) was visualized on a TapeStation High Sensitivity D1000 ScreenTape (Agilent Technologies) and quantified using KAPA Library Quantification Kit (Roche).

value: Endometrium

tag: origin

value: Estonia


title: S15


title: Glioblastoma Sample 21

description: Hybridized to CytoScanHD

value: Glioblastoma


title: Diffuse midline glioma H3K27M-mutated Sample 18

description: Hybridized to CytoScanHD

value: Diffuse midline glioma H3K27M-mutated


title: BM CD34+ cells from patient 5995 (GEP)

value: neg


title: BM CD34+ cells from patient 7083 (GEP)


title: Ganglioglioma / Diffuse astrocytoma Sample 22

description: Hybridized to CytoScanHD

value: Ganglioglioma / Diffuse astrocytoma


title: Neuroblastoma Sample 29

description: Hybridized to CytoScanHD

value: Neuroblastoma


title: S14


title: S13


title: Precursor T-lymphoblastic lymphoma Sample 20

description: Hybridized to CytoScanHD

value: Precursor T-lymphoblastic lymphoma


title: S11


title: BM CD34+ cells from patient 5983 (GEP)

value: M

value: myeloproliferative neoplasm (MPN)


title: Alveolar rhabdomyosarcoma Sample 19

description: Hybridized to CytoScanHD

value: Alveolar rhabdomyosarcoma


title: S12


title: BM CD34+ cells from patient 5907 (GEP)

value: Vannucchi

value: PV

value: pos


title: S9


title: BM CD34+ cells from patient 5933 (GEP)

value: F

value: ND


title: S8


title: BM CD34+ cells from patient 5883 (GEP)

value: Bone marrow


title: BM CD34+ cells from patient 5884 (GEP)


title: Nephroblastoma Sample 27

description: Hybridized to CytoScanHD

value: Nephroblastoma


title: S7

value: Endometrium

value: Estonia


title: BM CD34+ cells from patient 5903 (GEP)


title: S6


title: S5


title: Anaplastisc pleomorfic xanthoastrocytoma / Glioblastoma Sample 16

description: Hybridized to CytoScanHD


title: BM CD34+ cells from patient 5827 (GEP)


title: BM CD34+ cells from patient 5772 (GEP)


title: S4


title: S10


title: BM CD34+ cells from patient 5811 (GEP)


title: S3


title: S2


title: BM CD34+ cells from patient 4765 (GEP)


title: BM CD34+ cells from patient 4764 (GEP)


title: S1


title: Ganglioglioma / Diffuse astrocytoma Sample 17

description: Hybridized to CytoScanHD


title: BM CD34+ cells from patient 4763 (GEP)


title: Chordoma, dedefferentiated/anaplatic type (INI1-loss) Sample 10

description: Hybridized to CytoScanHD


title: Chondrosarkoma Sample 9

description: Hybridized to CytoScanHD

value: Chondrosarkoma


title: BM CD34+ cells from patient 7169 (GEP)

value: ET

value: neg


title: BM CD34+ cells from patient 7200 (GEP)


title: Anaplastisc ependymoma Sample 15

description: Hybridized to CytoScanHD

value: Anaplastisc ependymoma


title: BM CD34+ cells from patient 7092 (GEP)


title: adriamycin sensitive K562 cell rep2

city: Shenyang

first: Huihan

last: Wang

address: No. 36 Sanhao Street

institute: China Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on HuGene-1_0-st Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with rma using Affymetrix default analysis settings and global scaling as normalization method.

source_name: adriamycin sensitive K562 cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: All the cells were maintained in RPMI 1640 medium supplemented with 10% fetal calf serum in a 5% CO2 atmosphere at 37°C. The resistant subline was maintained in the presence of 50 nM adriamycin

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

treatment_protocol: Both KS and KA cells were treated with decitabine(5nM,72 hours) .

tag: cell line

value: KS

tag: agent

value: untreated


title: Diffuse midline glioma H3K27M-mutated Sample 12

description: Hybridized to CytoScanHD

value: Diffuse midline glioma H3K27M-mutated


title: adriamycin sensitive K562 cell treated with decitabine rep2

description: KS DAC2

value: DAC


title: BM CD34+ cells from patient 7009 (GEP)

value: Vannucchi

value: myeloproliferative neoplasm (MPN)


title: adriamycin sensitive K562 cell rep1


title: BM CD34+ cells from patient 5946 (GEP)

value: pos


title: BM CD34+ cells from patient 7018 (GEP)

value: F


title: BM CD34+ cells from patient 5927 (GEP)

value: M

value: ND


title: adriamycin sensitive K562 cell treated with decitabine rep1

description: KS DAC1


title: Juvenile xanthogranuloma Sample 14

description: Hybridized to CytoScanHD

value: Juvenile xanthogranuloma


title: Glioblastoma Sample 4

description: Hybridized to CytoScanHD

value: Glioblastoma


title: BM CD34+ cells from patient 7015 (GEP)

value: Bone marrow


title: BM CD34+ cells from patient 5908 (GEP)


title: Anaplastisc ependymoma Sample 13

description: Hybridized to CytoScanHD


title: Signetringcell carcinoma Sample 7

description: Hybridized to CytoScanHD

value: Signetringcell carcinoma


title: adriamycin resistant K562/ADR cell rep3

source_name: adriamycin resistant K562/ADR cell

value: KA


title: Mesoblastisc nephroma Sample 6

description: Hybridized to CytoScanHD

value: Mesoblastisc nephroma


title: adriamycin resistant K562/ADR cell rep2


title: Pilocytisc/pilomyxoid astrocytoma Sample 3

description: Hybridized to CytoScanHD

value: Pilocytisc/pilomyxoid astrocytoma


title: BM CD34+ cells from patient 5886 (GEP)

value: ET


title: BM CD34+ cells from patient 5890 (GEP)

value: neg


title: adriamycin resistant K562/ADR cell treated with decitabine rep3

description: KA DAC3


title: BM CD34+ cells from patient 5862 (GEP)


title: BM CD34+ cells from patient 5864 (GEP)


title: adriamycin resistant K562/ADR cell treated with decitabine rep1

description: KA DAC1


title: BM CD34+ cells from patient 5882 (GEP)


title: adriamycin sensitive K562 cell rep3

value: KS

value: untreated


title: BM CD34+ cells from patient 5947 (GEP)

value: Vannucchi

tag: calr mutation

value: L367FS52 (tipo I)

value: CALR


title: BmL3 vs. BmL3-Molting

city: Bethesda

first: Sasisekhar

last: Bennuru

state: MD

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

description: BmL3 vs BmL3-Molting (Day 8/Day9)

hyb_protocol: Each sample pair (~18ul) is resuspended in Formamide-based hybridization buffer (vial 7-Genisphere) (26ul), Array 50dT blocker (Genisphere) (2ul), and RNase/DNase-free water (6ul). Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 48ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity. Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 43C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the complimentary capture reagents provided in the 3DNA Array 900MPX kit (Genisphere). For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere) (26ul), and Rnase/Dnase-free water (21ul). The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min. Hybridization is performed by adding 48ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 4 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. To prevent fluorophore degradation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence. Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low pmt setting scan is also performed to recover signal from saturated elements. Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

data_processing:
Data analyzed using MADB - a Microarray analyses portal of NIAID.
Signal calculation: Median Intensity minus Median Background. Any Features designated Control were excluded.
Normalization method: 50th Percentile (Median) using all spot filtered Genes.
Spot Filter Options: Include Spots not flagged BAD or Not Found AND Both Chan A and Chan B Signal >= 2 SD above Background. Override other Chan A & B criteria and Include if Chan A Signal >= 100 OR Chan B Signal >= 100. Signal Values were floored at 50 (ChanA and ChanB). Data was extracted and aligned by the Inventory Well ID. Within array multiple occurrences of Well ID were reduced to a single instance by selecting the one with the strongest signal (Chan A + Chan B).
Note: For all GenePix results from Axon scanned arrays, Chan A is CY3 and Chan B is CY5.

organism: Brugia malayi

source_name: B. malayi L3 larvae

label_protocol: First strand cDNA is generated by random primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 900MPX kit (Genisphere). For cDNA synthesis, 2x mass of random primer (4ul) is added to 2ug of total RNA, and the solution is incubated at 80C for 10 minutes, then cooled on ice for 2 minutes. To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul). Reverse transcription is carried out at 42C for 2 hours. The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul). The cDNA is cleaned using MinElute PCR Purification columns (Qiagen). Water is added (6.5ul) to the eluted cDNA (10ul), heated to 80C for 10 minutes, then cooled on ice for 2 minutes. The cDNA is poly-T tailed by adding 10x Tailing buffer (2.5ul), 10mM dTTP (4ul), and Terminal Deoxynucleotidyl Transferase (2ul). The reaction is incubated at 37C for 30 minutes. The reaction is terminated by heating to 95C for 10minutes, then cooled on ice for 2 minutes. Fluorophore/dendrimer specific oligos are then ligated to the appropriate cDNAs by adding 6X Ligation Mix (cy3 or cy5 specific) (5ul) and T4 DNA Ligase (2ul). The reactions are incubated at room temperature for 30 minutes. The ligation reaction is terminated by adding 0.5M EDTA and then vortexing for 10 seconds. The cDNA is again cleaned using MinElute PCR Purification columns (Qiagen). The cDNAs are quantitated via spectrophotometry to confirm recovery. Samples are paired and balanced by mass.

growth_protocol: B. malayi L3 larvae were cultured in MEM-a medium supplemented with ribonucleosides and deoxyribonucleosides (Cat # 32571036, Life Technologies), for 10 days. Ascorbic acid (final concentration of 75mM) was added on day 5 of culture to induce molting. Successful molting to L4 larvae observed by day 8/9.

extract_protocol: Total RNA was extracted from ~1000 BmL3 larvae using Trizol following manufacturer's instructions. The quality of total RNA was determined by Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: strain/background

tag: developmental stage

value: L3 larvae

value: whole body

source_name: B. malayi L3 larvae-Molting

value: L3 larvae (molting)

tag: time point

value: day 8/day 9


title: BmL3 vs. BmL3-48hrsAsc

description: BmL3 vs BmL3-48hrsAsc (Day 7)

source_name: B. malayi L3 larvae-48hrsAsc

tag: treatment

value: 48 hrs ascorbic acid

value: day 7


title: BmL3 vs. BmL4

description: BmL3 vs BmL4 (Day 10)

source_name: B. malayi L3 larvae-L4

value: L4 larvae

value: day 10


title: BM CD34+ cells from patient 9198 (GEP)

tag: supplier

value: M

value: myeloproliferative neoplasm (MPN)

value: pos

value: del52 (tipo I)

value: Bone marrow


title: Atypical meningioma Sample 1

description: Hybridized to CytoScanHD

value: Atypical meningioma


title: BmL3 vs. BmL3-24hrsAsc

description: BmL3 vs BmL3-24hrsAsc (Day 6)

source_name: B. malayi L3 larvae-24hrsAsc

value: 24 hrs ascorbic acid

value: day 6


title: adriamycin resistant K562/ADR cell rep1

value: KA

value: untreated


title: BmL3 vs. BmL3-3hrsAsc

description: BmL3 vs BmL3-3hrsAsc (Day 5-Time point 2)

value: L3 larvae

value: whole body

source_name: B. malayi L3 larvae-3hrsAsc

value: 3 hrs ascorbic acid

value: day 5


title: adriamycin resistant K562/ADR cell treated with decitabine rep2

description: KA DAC2

value: DAC


title: BmL3 vs. BmL3-37C-5Days

description: BmL3 vs BmL3-37C-5Days (Day 5)

source_name: B. malayi L3 larvae-5Days 37C

value: 5 days 37C


title: WT vs. Zmynd17/Mss51 KO

city: Tsukuba

first: Ryo

last: Fujita

state: Ibaraki

department: Transborder Medical Research Center

country: Japan

institute: University of Tsukuba

hyb_protocol: 3D-Gene Mouse Oligo chip 24k (Toray)

scan_protocol: 3D-Gene scanner (Toray)

data_processing: global normalization

source_name: ZKO-PLA

label_protocol: Cy5 (KO), Cy3 (WT)

extract_protocol: Total RNA extracted using Isogen (Nippongene) following manufacturer's instructions

treatment_protocol: No treatment

value: plantaris muscle

tag: genotype/variation

value: Zmynd17/Mss51 KO

source_name: WT-PLA

value: WT


title: BmL3 vs. BmL3-37C-24hrs

description: BmL3 vs BmL3-37C-24hrs (Day 1)

source_name: B. malayi L3 larvae-24hrs 37C

value: 24 hrs 37C

value: day 1


title: BM CD34+ cells from patient 5928 (GEP)

value: Vannucchi

tag: Sex

value: M

tag: condition

value: myeloproliferative neoplasm (MPN)

value: ET

value: neg

value: pos

value: K391fs51 (tipo II)

value: CALR

value: Bone marrow


title: BM CD34+ cells from patient 5838 (GEP)

value: F

tag: disease

value: ND

tag: tissue


title: BM CD34+ cells from patient 3840 (GEP)

tag: mpl-mutated

value: E386del AGGA

tag: cell marker


title: BM CD34+ cells from patient 2766 (GEP)

tag: calr-mutated

value: 385insTTGTC (tipo II)

tag: gene mutation


title: BM CD34+ cells from patient 2485 (GEP)

value: L367FS52 (tipo I)


title: adriamycin sensitive K562 cell treated with decitabine rep3

description: KS DAC3

tag: cell line

value: KS

value: DAC


title: BM CD34+ cells from patient 5815 (GEP)


title: BM CD34+ cells from patient 3057 (GEP)


title: Pleomorphic xanthoastrocytoma Sample 5

description: Hybridized to CytoScanHD

value: Pleomorphic xanthoastrocytoma


title: Mock_RLM_rep3

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

hyb_protocol: Labeled cDNA were hybridized for 16 hr at 45C on GeneChip ATH1 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Each microarray was scanned at 2.5 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: Analysis was performed using the affylmaGUI R package (Wettenhall et al, 2006). Robust Muti-array Analysis (RMA) algorithm was used for background correction, normalization and expression levels summarization (Irizarry et al., 2003).

organism: Arabidopsis thaliana

source_name: Mock treatment, RLM

label_protocol: Decapped mRNA was isolated from poly(A)+ RNA using a modified RLM-RACE protocol as previously described (Franco-Zorrilla et al. (2009), Plant J 59,840; doi: 10.1111/j.1365-313X.2009.03904.x). In brief, poly(A)+ RNAs were ligated at 5' ends with an RNA adapter, first strand cDNA were synthesized using a poly(T) and second strand with an adapter-T7 promoter sequence (RLM samples). In parallel, poly(A)+ RNA from the same sources were not 5'-end ligated to the RNA adapter but first and second strand cDNA synthesized as above (non-ligated samples). Then, in vitro transcription was performed using MessageAmp aRNA kit (Ambion). Purified cRNA was then used as template for single stranded cDNA synthesis, according to Affymetrix instructions for prokaryotic target preparation. Briefly, cRNA was reverse transcribed with oligo(dT) as primer, cDNA fragmented and 3´ends were biotin-ddUTP labeled with terminal deoxynucleotidyl transferase (Promega)

growth_protocol: Arabidopsis thaliana (Col-0 ecotype) grown in growth chamber at 22ºC under a long day photoperiod (16 hours light) for a total period of 5 weeks after germination, corresponding to Boyes' developmental stage 6.7.

extract_protocol: Trizol extraction of total RNA and cleanup with RNeasy (Qiagen), according to the manufacturers's instructions. Poly A+-enriched RNA was obtained using Oligotex mRNA kit (Qiagen)

treatment_protocol: 23-24 days-old plants were inoculated with extracts of Tobacco rattle virus (TRV) infected Nicotiana benthamiana leaves (TRV samples) or with non-infected extracts (Mock samples). Plants were grown for 12 additional days (Boyes' 6.7 developmental stage, Boyes et al. Plant Cell, 2001), and inflorescences from infected and mock plants collected. Each replicate contains a pool of inflorescences from 25 different plants.

value: Inflorescences

tag: age

value: 5 weeks

tag: develpmental stage

value: Boyes 6.7


title: TRV_non_ligated_rep3

source_name: TRV infected, negative control


title: Mock_RLM_rep2


title: iPSC #2

city: Hannover

first: Adrian

last: Schwarzer

address: Carl-Neuberg-Str. 1

department: Experimental Hematology

institute: Hannover Medical School

description: Gene expression data from iPS Clone #2EX

hyb_protocol: amplified, fragmented, biotin labeled cDNA was hybridized for 18 hr at 45C on Mouse GeneChip1.0 ST Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 450 using protocol FS450_0007

scan_protocol: Affymetrix GeneChip Scanner 3000 7G

data_processing: RMA (Robust Multichip Average; Bioconductor)

source_name: iPS from reprogrammed fibroblasts

label_protocol: RNA was amplified by the Applause WT-Amp ST System (NuGEN Technologies, Bemmel, The Netherlands), amplified cDNA was fragmented and biotin labeled using the Encore Biotin Module (NuGEN Technologies)

growth_protocol: adult murine fibroblasts were isolated from ears of p14f/f (wt version of conditional loxP-flanked p14 knockout (KO); C57/Bl6) mice and grown in MEFmedium (low-glucose Dulbecco's modified Eagle's medium, 15% fetal bovine serum, 2 mmol/l l-glutamine, 100 units/ml penicillin/100 μg/ml streptomycin, 0.1 mmol/l nonessential amino acids and 100 μmol/l β-mercaptoethanol. iPSC were induced by transduction with lentiviral vectors carrying  c-Myc, Klf-4, Oct-4, Sox-2. iPSC were cultured in ES medium (KO Dulbecco's modified Eagle's medium, 15% ES-tested fetal bovine serum, 2 mmol/l l-glutamine, 100 units/ml penicillin/100 μg/ml streptomycin, 0.1 mmol/l nonessential amino acids, 100 μmol/l β-mercaptoethanol, and 10^3 units/ml leukemia inhibitory factor

extract_protocol: Qiagen Rneasy Micro Kit according to manufacturers instructions

treatment_protocol: no treatment

tag: background strain

tag: cell type

value: iPS


title: Ad fib I

description: Gene expression data from adult murine fibroblasts

source_name: adult murine fibroblasts from ear

value: fibroblast


title: Mock_non_ligated_rep1

source_name: Mock treatment, negative control


title: Ad fib II


title: BM CD34+ cells from patient 5909 (GEP)

source_name: Bone marrow CD34+ Cells

value: Vannucchi

value: M

value: myeloproliferative neoplasm (MPN)

value: ET

value: pos

value: neg


title: Mock_non_ligated_rep2


title: TRV_RLM_rep3

source_name: TRV infected, RLM


title: iPSC #2EX

description: Gene expression data from iPS Clone #3


title: TRV_non_ligated_rep2


title: Mock_non_ligated_rep3


title: Sequential Design timecourse t10_t11.1

city: Ikoma

first: Naotake

last: Ogasawara

state: Nara

institute: Nara Institute of Science and Technology

description: RNA was isolated from W3110 cells, grown in LB media.

hyb_protocol: Prehybridization of the array slides was performed for 4h in filtered prehybridization solution [25% formamide, 5x SSC, 10mg l-1 BSA (fraction V), 0.1% SDS] at 42℃. Slides were briefly washed in ethanol and dried by centrifugation at 1000g for 5 min. Hybridization of the probe was performed using hybridization solution (25% formamide, 5x SSC, 0.1% SDS, 0.1µg poly(A) ml-1, 1x Denhardt's solution and 80pmol Cy3 and Cy5 combined probe). The hybridization solution containing the Cy-Dye-labelled cDNA was heated to 95℃ for 3 min, Hybridization is performed by dvalytix hybridaization macine.

scan_protocol: After hybridization, slides were washed in wash buffer I (2x SSC/0.1% SDS) for 2min at 42℃, in wash buffer II (0.2x SSC) for 2min at room temperature and then twice in wash buffer III (0.05x SSC) for 2min at room temperature. All washes were done with vigorous shaking of the microarray slides. The slides were dried by centrifugation at 1000g for 5min, and then analysed using an Fuji FLA-8000 scanner and Array gauge ver.2.0 software (Fuji film)

data_processing: Normalization is performed by TREBAX, using MA-plots. MA-plots can reveal the spot artifacts globally and show the intensity-dependent logarithmic ratio of raw microarray data. In MA-plots, we calculate two parameters, average of logarithmic transferred intensity As=(log(Ts)+log(Rs))/2 and logarithmic ratio of intensity Ms=log(Ts/Rs) Here, Ts and Rs are the intensity of target and control experiments for sth spot, respectively.By plotting values of As on the abscissa and Ms on the ordinate of a coordinate system, it is possible to evaluate the bias error with respects to the average logarithmic intensities. Normalized log ratio M’’s is estimated as the difference between Ms and baseline M’s. Here, using a relation between Ms and As, (Ms=f(As)+es, es is the difference between Ms and f(As) for gene s) by MA plot; the baseline for sth spot is estimated by M’=f(A). The genes whose signal intensity is regarded as zero are eliminated in the present analysis. With this methodology, it is assumed that there is no large error due to expression intensity in the majority of the spots and that expression change does not occur on the majority of the spots.

organism: Escherichia coli

label_protocol: Cyscribe Kit

extract_protocol: Qiagen RNeasy mini Kit

tag: Strain

tag: Strain :W3110


title: Sequential Design timecourse t8_t9.2


title: Sequential Design timecourse t10_t11.2


title: TRV_non_ligated_rep1


title: Sequential Design timecourse t9_t10.2


title: Sequential Design timecourse t9_t10.1

tag: Strian :W3110


title: Choroid plexus carcinoma / Malignant peripheral nerve sheeth tumor Sample 2

description: Hybridized to CytoScanHD

source_name: tumor biopsy


title: PatientA_2007_5.7N

city: Basel

first: Joël

middle: Roman

last: Federer-Gsponer

address: Tangentenweg 34

department: Department of Pathology

country: Switzerland

institute: University Hospital Basel

hyb_protocol: Labeled DNAs were hybridized in an ozone free environment in a rotisserie oven at 20 rpm for 40 hours then washed according to array supplier's (Agilent)protocol

scan_protocol: All microarray slides were scanned using an Agilent G2505C DNA scanner and default settings for CGH.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.5. The data quality was assessed using the QC Report output in F.E. 10.5. All arrays that passed the experimental Q.C. were then analysed using the Limma package in the R environment. With minimum background correction and printtiploess normalization.

source_name: Prostate

label_protocol: A 1 microgram aliquot of each sample and reference DNA was digested with DNAse 1 then labeled with a fluorescent nucleotide (Cy5 for tumor and Cy3 for normal reference) using the BioPrime labeling kit (Invitrogen)according to manufacturer's protocol.

growth_protocol: Tumor samples from patients with prostate carcinoma were flash-frozen and maintaned at -80 degrees C until processed for flow sorting

extract_protocol: 25-100 mg of tumor was thawed then minced in the presence of NST and DAPI. Each sample was then mechanically sheared then filtered through a 30 micron mesh filter prior to sorting. All sorting was done with an Influx Flow Cytometer equiped with a UV laser. DNA was extracted from each sorted fraction using Qiagen DNA micro kits. All phi29 amplifications were done with a 100ng aliquot of either sample or reference genomic DNA using the GenomiPhi kit (G.E Health Care)

tag: amplification

tag: year

tag: ploidy

source_name: pooled 46, XX DNA (Promega, Madison, WI)

tag: sample type

value: reference


title: Sequential Design timecourse t7_t8.1


title: Sequential Design timecourse t7_t8.2


title: TRV_RLM_rep2

tag: tissue


title: TRV_RLM_rep1


title: genomic DNA from blood 9980102107_R05C01

city: Barcelona

first: Carolina

last: Soriano-Tarraga

state: Barcelona

address: Calle Doctor Aiguader 88

department: Department of Neurology

institute: Institut Hospital del Mar d’Investigacions Mèdiques (IMIM).Hospital del Mar

description: stroke blood sample

hyb_protocol: The bisulfite converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina, Inc.), according to the manufacturer's instructions.

scan_protocol: The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.

data_processing:
GenomeStudio 2011.1 software and R version 3.1.2. Processed data: raw Average Beta obtained from GenomeStudio, quality controls were done by MINFI Bioconductor package and probe type correction by SWAN bioconductor package.
Average Beta, normalized provided in
betas_normalized_meneas_185.txt
pval_detection_meneas_185.txt
Raw unmethylated and methylated signal intensities data is provided in
meth_raw_meneas_185.txt
unmeth_raw_meneas_185.txt

label: Cy5 and Cy3

source_name: stroke blood sample

label_protocol: Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research)

extract_protocol: DNA samples were extracted from whole peripheral blood collected in 10 mL EDTA tubes. The Chemagic Magnetic Separation Module I system (Chemagen)

tag: gender

value: Male

tag: stroke subtype

value: cardioembolic

value: blood

tag: disease state

value: stroke


title: genomic DNA from blood 9980102107_R04C02

description: stroke blood sample

value: Female


title: genomic DNA from blood 9980102107_R05C02

description: stroke blood sample

value: atherotrombotic


title: Sequential Design timecourse t5_t6.2


title: genomic DNA from blood 9980102107_R04C01

description: stroke blood sample


title: Sequential Design timecourse t6_t7.1


title: Sequential Design timecourse t5_t6.1


title: Sequential Design timecourse t8_t9.1


title: Sequential Design timecourse t4_t5.2


title: genomic DNA from blood 9980102107_R03C02

description: stroke blood sample


title: Sequential Design timecourse t6_t7.2


title: genomic DNA from blood 9980102107_R06C02

description: stroke blood sample


title: BmL3 vs. BmL3-37C-3hrs

description: BmL3 vs BmL3-37C-3hrs (Day 0)

source_name: B. malayi L3 larvae

tag: strain/background

tag: developmental stage

value: L3 larvae

value: whole body

source_name: B. malayi L3 larvae-3hrs 37C

tag: treatment

value: 3 hrs 37C

tag: time point

value: day 0


title: PatientA_2007_2N


title: Sequential Design timecourse t3_t4.2


title: Sequential Design timecourse t1_t2.2

tag: Strain W3110


title: Sequential Design timecourse t2_t3.2


title: genomic DNA from blood 9980102107_R02C02

description: stroke blood sample

tag: age


title: Mock_RLM_rep1

value: Inflorescences

value: 5 weeks

tag: develpmental stage

value: Boyes 6.7


title: Sequential Design timecourse t3_t4.1

tag: Strain

tag: Strain :W3110

tag: OD


title: genomic DNA from blood 9980102107_R01C02

description: stroke blood sample

value: small-vessel disease


title: Sequential Design timecourse t2_t3.1


title: Sequential Design timecourse t4_t5.1


title: Sequential Design timecourse t1_t2.1

tag: OD :OD 0.1


title: genomic DNA from blood 9980102075_R04C02

description: stroke blood sample


title: genomic DNA from blood 9980102075_R02C02

description: stroke blood sample


title: genomic DNA from blood 9980102075_R03C02

description: stroke blood sample


title: genomic DNA from blood 9980102075_R01C02

description: stroke blood sample


title: genomic DNA from blood 9980102075_R06C01

description: stroke blood sample


title: genomic DNA from blood 9980102044_R06C02

description: stroke blood sample


title: genomic DNA from blood 9980102044_R05C02

description: stroke blood sample


title: genomic DNA from blood 9980102044_R03C02

description: stroke blood sample


title: genomic DNA from blood 9980102044_R04C01

description: stroke blood sample


title: genomic DNA from blood 9980102044_R03C01

description: stroke blood sample


title: Col, biological rep3

city: Beijing

first: xi

last: chen

address: No.2 Yuanmingyuan West Road

institute: China Agricultural University

description: Gene expression data from wild-type Col seedlings

hyb_protocol: Performed at 45C with rotation for 16h (Affymetrix GeneChip Hybridization Oven 640)

scan_protocol: Using Affymetrix GeneChip Scanner 3000

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

source_name: 12-day-old Col whole seedlings

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

growth_protocol: Arabidopsis seedlings were grown in MS media at 22C in continuous white light.

extract_protocol: Total RNA from the was extracted using the Qiagen Plant RNeasy kit according to the manufacturer's instruction.

tag: ecotype

tag: genotype/variation

value: wild-type

value: seedling


title: hub2-3, biological rep2

description: Gene expression data from hub2-3 mutant seedlings

source_name: 12-day-old hub2-3 mutant whole seedlings

value: hub2-3 mutant

tag: tissue


title: genomic DNA from blood 9980102044_R02C02

description: stroke blood sample

tag: gender

tag: sample type


title: 35S:STOP1vs Col-0 NaCl, replicate-1

city: GIFU

first: AYAN

last: SADHUKHAN

state: GIFU

address: 1-1 YANAGIDO

department: APPLIED BIOLOGICAL SCIENCES

institute: GIFU UNIVERSITY

description: biological replicate 1 of 3: 35S:STOP1vs Col-0 NaCl

hyb_protocol: 0.825 μg of Cy3- and Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5 per μg cRNA) were fragmented with Gene Expression Hybridization Kit (5188-5242, Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 4 Oligo Microarray (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: scanned with a G2505C scanner (software version 6.5) Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature extraction software (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA were prepared from 200 ng of total RNA using the Low Input Quick Amp Labeling kit (5190-2306, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: Ten days old Arabidopsis thaliana seedlings in 1/2 MS solid media were treated with 200 mM NaCl for 24 h in 1/2 MS solid media

extract_protocol: Total RNA extracted using Sepasol following manufacturer's instructions

tag: strain

value: 10 days

value: whole seedlings


title: stop1 knockout vs Col-0 control, replicate-3

description: biological replicate 3 of 3: STOP1 knockout vs Col-0 control

source_name: stop1 knockout

value: stop1 knockout


title: hub2-3, biological rep1


title: hub2-3, biological rep3


title: stop1 knockout vs Col-0 control, replicate-2

description: biological replicate 2 of 3: STOP1 knockout vs Col-0 control


title: Col, biological rep2


title: 35S:STOP1vs Col-0 NaCl, replicate-2

description: biological replicate 2 of 3: 35S:STOP1vs Col-0 NaCl


title: stop1 knockout vs Col-0 NaCl, replicate-3

description: biological replicate 3 of 3: STOP1 knockout vs Col-0 NaCl

source_name: stop1 knockout_NaCl


title: Col, biological rep1


title: stop1 knockout vs Col-0 NaCl, replicate-2

description: biological replicate 2 of 3: STOP1 knockout vs Col-0 NaCl


title: 35S:STOP1vs Col-0 NaCl, replicate-3

description: biological replicate 3 of 3: 35S:STOP1vs Col-0 NaCl


title: genomic DNA from blood 9980102044_R01C02

description: stroke blood sample

value: Male

tag: stroke subtype

value: blood

tag: disease state

value: stroke


title: stop1 knockout vs Col-0 NaCl, replicate-1

description: biological replicate 1 of 3: STOP1 knockout vs Col-0 NaCl


title: stop1 knockout vs Col-0 control, replicate-1

description: biological replicate 1 of 3: STOP1 knockout vs Col-0 control


title: genomic DNA from blood 9980102020_R06C01

description: stroke blood sample

value: cardioembolic


title: 35S:STOP1vs Col-0 control, replicate-2

description: biological replicate 2 of 3: 35S:STOP1vs Col-0 control


title: genomic DNA from blood 9980102020_R05C01

description: stroke blood sample

value: Female


title: 35S:STOP1vs Col-0 control, replicate-3

description: biological replicate 3 of 3: 35S:STOP1vs Col-0 control


title: genomic DNA from blood 9980102020_R04C02

description: stroke blood sample


title: genomic DNA from blood 9980102020_R04C01

description: stroke blood sample


title: genomic DNA from blood 9980102020_R01C01

description: stroke blood sample


title: genomic DNA from blood 9980102002_R05C01

description: stroke blood sample


title: iPSC #3

description: Gene expression data from iPS Clone #2

tag: background strain

tag: cell type

value: iPS


title: genomic DNA from blood 9980102002_R06C02

description: stroke blood sample


title: genomic DNA from blood 9980102020_R02C02

description: stroke blood sample


title: genomic DNA from blood 9980102002_R06C01

description: stroke blood sample


title: genomic DNA from blood 9980102002_R04C02

description: stroke blood sample


title: genomic DNA from blood 9980102002_R05C02

description: stroke blood sample


title: genomic DNA from blood 9980102002_R04C01

description: stroke blood sample


title: genomic DNA from blood 9980102002_R03C02

description: stroke blood sample


title: genomic DNA from blood 9980102002_R03C01

description: stroke blood sample

value: atherotrombotic


title: 35S:STOP1vs Col-0 control, replicate-1

description: biological replicate 1 of 3: 35S:STOP1vs Col-0 control


title: genomic DNA from blood 9980102002_R02C02

description: stroke blood sample


title: PatientG_2009_AN

tag: amplification

tag: year

tag: ploidy

value: AN

value: reference


title: genomic DNA from blood 9980102002_R01C02

description: stroke blood sample

tag: age


title: genomic DNA from blood 9980092137_R06C02

description: stroke blood sample


title: genomic DNA from blood 9980092137_R04C01

description: stroke blood sample


title: genomic DNA from blood 9980092137_R05C02

description: stroke blood sample


title: PatientG_2012_AN


title: PatientE_2000_2N


title: PatientG_2009_2N


title: PatientE_2000_AN


title: genomic DNA from blood 9980092137_R01C02

description: stroke blood sample


title: genomic DNA from blood 9980092137_R03C01

description: stroke blood sample


title: genomic DNA from blood 9980092137_R03C02

description: stroke blood sample


title: genomic DNA from blood 9980102020_R03C02

description: stroke blood sample


title: genomic DNA from blood 9969489161_R06C02

description: stroke blood sample


title: genomic DNA from blood 9969489161_R06C01

description: stroke blood sample


title: PatientE_1999_AN


title: MCF7-HER2 Chronic Hypoxia, rep1

city: Edinburgh

first: Edward

middle: Joseph

last: Jarman

address: Crewe Road south

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using quantile normalisation with lumi in R.

source_name: HER2-overexpressing MCF7 cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit for Illumina arrays.

growth_protocol: Cells were grown in DMEM supplemented with 10% heat-inactivated FCS and 100IU/ml penicillin/streptomycin.

extract_protocol: RNA was extracted from flash-frozen pellets of approximately 3 million cells with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were either grown in ambient normoxic conditions (20%) or grown in 0.5% oxygen conditions using a Don Whitley H35 Hypoxystation for 24 hrs or continually passaged at 0.5% oxygen for 10 weeks.

tag: cell line

tag: origin

value: Genetically modified MCF7 line

tag: treatment

value: 0.5% Oxygen 10 weeks


title: genomic DNA from blood 9969489161_R05C02

description: stroke blood sample


title: PatientD_2005_2N


title: MCF7-HER2 Acute Hypoxia, rep2

value: 0.5% Oxygen 24 hrs


title: MCF7-HER2 Chronic Hypoxia, rep2


title: MCF7-HER2 Chronic Hypoxia, rep3


title: genomic DNA from blood 9969489161_R04C02

description: stroke blood sample


title: MCF7-HER2 Acute Hypoxia, rep1


title: MCF7-HER2 Normoxia, rep3

value: 20% Oxygen


title: PatientE_1999_2N


title: genomic DNA from blood 9969489161_R05C01

description: stroke blood sample


title: PatientD_2005_3.6N


title: MCF7-HER2 Normoxia, rep1


title: MCF7-HER2 Acute Hypoxia, rep3


title: MCF7-HER2 Normoxia, rep2


title: MCF7 Chronic Hypoxia, rep2

source_name: MCF7 breast cancer cell line

value: Human breast epithelial adenocarcinoma cells


title: genomic DNA from blood 9969489161_R03C02

description: stroke blood sample


title: genomic DNA from blood 9969489161_R03C01

description: stroke blood sample


title: PatientD_2010_3.6N


title: PatientC_2011_Neuroendocrine

value: Neuroendocrine aneuploid


title: PatientD_2010_6N


title: PatientC_2011_Adenocarcinoma

value: Adenocarcinoma aneuploid


title: genomic DNA from blood 9969489161_R02C02

description: stroke blood sample

value: small-vessel disease


title: genomic DNA from blood 9969489161_R04C01

description: stroke blood sample

value: Male


title: genomic DNA from blood 9969489161_R01C02

description: stroke blood sample

value: blood


title: MCF7 Chronic Hypoxia, rep3


title: genomic DNA from blood 9969489158_R06C02

description: stroke blood sample

value: stroke


title: genomic DNA from blood 9969489158_R05C02

description: stroke blood sample


title: genomic DNA from blood 9969489158_R05C01

description: stroke blood sample


title: MCF7 Chronic Hypoxia, rep1


title: genomic DNA from blood 9969489158_R02C01

description: stroke blood sample


title: genomic DNA from blood 9969489158_R04C02

description: stroke blood sample

value: cardioembolic


title: genomic DNA from blood 9969489158_R03C01

description: stroke blood sample


title: genomic DNA from blood 9969489156_R06C02

description: stroke blood sample

value: Female


title: genomic DNA from blood 9969489158_R01C01

description: stroke blood sample


title: MCF7 Acute Hypoxia, rep3


title: genomic DNA from blood 9969489158_R01C02

description: stroke blood sample


title: IMX-104, CON, Rep 2

city: Vicksburg

first: Kurt

last: Gust

state: MS

address: 3909 Halls Ferry Rd.

department: Environmental Laboratory

institute: US Army ERDC

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  Four exposure replicates for each treatment (IMX-104: Control (0 mg/L), 24.5, and 47.8 mg/L)  were hybridized to microarrays in a completely randomized design using a random number generator.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: An Agilent Surescan Microarray Scanner (G2505 C, Agilent Technologies Inc.) was used to scan microarrays at 2 μm resolution.

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct differential transcript expression analysis.  One-way ANOVA with Benjamini-Hochberg multiple-test corrected p = 0.05 was used to identify transcripts having significant differential expression.  Post-hoc tests for all chemical exposure experiments were conducted using a moderated t-test (p = 0.05) and log2 fold change cutoff of ≥ 1.5 to discern statistically significant differences in transcript expression for each chemical exposure concentration relative to the control.

organism: Pimephales promelas

source_name: whole animal

growth_protocol: Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment. Fish were fed <24-h old Artemia nauplii prior to test initiation.

extract_protocol: All samples were flash frozen in liquid nitrogen to preserve RNA.  A total of 4 larval fish were sampled per exposure replicate.  Samples were homogenized in lysis buffer with a FAST Prep-24 instrument (MP Biomedicals, Santa Ana, CA) before RNA isolation with RNeasy kits (Qiagen, Valencia, CA). Total RNA concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop technologies, Wilmington, DE, USA). The integrity of total RNA was assessed on an Agilent 2100 Bioanalyzer (Palo Alto, CA).  Criteria for acceptable RNA integrity included a RNA integrity number > 8.0 from the Agilent 2100 Bioanalyzer and a 260/280 spectrophotometric reading > 2.0

treatment_protocol: Fathead minnow larvae were exposed to IMX-104 at 0 (control), 24.5, 47.8, 97.3, 194.5 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment.

tag: agent

tag: dose

value: 0 (control)

tag: replicate

value: larvae


title: MCF7 Control, rep3


title: IMX-104, CON, Rep 4

label_protocol: The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.

tag: tissue


title: MCF7 Control, rep1


title: IMX-104, CON, Rep 1


title: IMX-104, 47.8, Rep 2


title: genomic DNA from blood 9969489156_R06C01

description: stroke blood sample

tag: gender

tag: sample type


title: IMX-104, CON, Rep 3


title: IMX-104, 47.8, Rep 1


title: IMX-104, 47.8, Rep 4


title: Control

city: Seoul

first: Jae-sung

last: Kim

address: 75, Nowon-ro

country: South Korea

institute: Korea Institute of Radiological and Medical Sciences

description:
control miRNA
SAMPLE 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0))
Statistical significance of the expression data was determined using independent LPE and Fold change in which the null hypothesis was that no difference exists among 2 groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: control miRNA

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

growth_protocol: HCT116 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin at 37 ℃ in a humidified 5 ℃ CO2 incubator.

extract_protocol: Total RNAs were isolated with Trizol reagent.

treatment_protocol: HCT116 cells were transfected with 20 nM control miRNA or 20 nM miR-550a-3-5p for 48 h.

value: colon cancer cell line


title: MCF7 Acute Hypoxia, rep1


title: IMX-104, 24.5, Rep 1


title: IMX-104, 47.8, Rep 3


title: MCF7 Control, rep2


title: genomic DNA from blood 9969489156_R03C02

description: stroke blood sample

tag: stroke subtype


title: genomic DNA from blood 9969489156_R04C02

description: stroke blood sample

tag: disease state


title: genomic DNA from blood 9969489155_R06C02

description: stroke blood sample


title: genomic DNA from blood 9969489156_R01C02

description: stroke blood sample


title: genomic DNA from blood 9969489155_R06C01

description: stroke blood sample


title: genomic DNA from blood 9969489155_R05C02

description: stroke blood sample

value: atherotrombotic


title: genomic DNA from blood 9969489155_R05C01

description: stroke blood sample


title: IMX-104, 24.5, Rep 3


title: IMX-104, 24.5, Rep 4


title: genomic DNA from blood 9980092137_R02C02

description: stroke blood sample


title: IMX-104, 24.5, Rep 2


title: genomic DNA from blood 9969489155_R04C02

description: stroke blood sample


title: miR-550a-3-5p

description:
mature miR-550a-3-5p
SAMPLE 2

source_name: mature miR-550a-3-5p


title: genomic DNA from blood 9969489155_R04C01

description: stroke blood sample


title: CON, Rep 4

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  Four exposure replicates for each treatment (IMX-101: Control (0 mg/L), 2.0 and 61.7 mg/L)  were hybridized to microarrays in a completely randomized design using a random number generator.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

treatment_protocol: Fathead minnow larvae were exposed to IMX-101 at 0 (control),1.9, 3.8, 7.6, 15.2, 30.2, 85.2, and 121.9 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment.


title: CON, Rep 1


title: 61.7, Rep 4


title: CON, Rep 2


title: 61.7, Rep 3


title: genomic DNA from blood 9969489155_R02C02

description: stroke blood sample


title: genomic DNA from blood 9969489155_R03C01

description: stroke blood sample


title: 61.7, Rep 2


title: genomic DNA from blood 9969489155_R02C01

description: stroke blood sample


title: 61.7, Rep 1


title: genomic DNA from blood 9969489155_R03C02

description: stroke blood sample


title: genomic DNA from blood 9969489155_R01C02

description: stroke blood sample


title: genomic DNA from blood 9969489155_R01C01

description: stroke blood sample


title: genomic DNA from blood 9969489154_R06C01

description: stroke blood sample


title: 2.0, Rep 4


title: genomic DNA from blood 9969489154_R06C02

description: stroke blood sample


title: DMSO vs. 1-HP, 8 h Timepoint, Replicate 2

city: Berlin

first: Philip

middle: Adrian

last: Huegli

state: Berlin

address: Charitéplatz 1

department: Vector Biology

institute: Max Planck Institute for Infection Biology

description: 1-HP vs. DMSO, 8 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control. Color-swap dye-reversal.

hyb_protocol: Microarray experiments were performed as dual-color hybridizations with color-swap dye-reversal.

scan_protocol: Scanning of microarrays was performed at 5 μm resolution using a G2565CA high-resolution laser microarray scanner (Agilent Technologies) with XDR extended range.

data_processing: Microarray image data were analyzed and extracted with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings.

organism: Anopheles coluzzii

source_name: Pooled A. coluzzii Ngousso third instar larvae

label_protocol: RNA was labeled with a two-color Low Input Quick Amp Labeling Kit according the supplier’s recommendations (Agilent Technologies). In brief, mRNA was reverse transcribed and amplified using an oligo-dT-T7 primer, and labeled with Cyanine 3-CTP or Cyanine 5-CTP. After precipitation, purification, and quantification, 1.25 μg of each labeled cRNA was fragmented and hybridized to A. gambiae whole genome 4x44K multipack microarrays (Design ID 020449) according to the manufacturer’s protocol (Agilent Technologies).

growth_protocol: Anopheles coluzzii Ngousso strain was maintained at 28 ± 2°C, 85 ± 5% humidity and 12 h day/night cycle. Larvae were reared in 0.1% NaCl/ddH2O and fed with generic cat food pellets.

extract_protocol: Total RNA was isolated with TRIzol (Life Technologies) according the supplier’s protocol using Glycogen RNA carrier. Quality control and quantification of total RNA was assessed using an Agilent 2100 Bioanalyzer with a RNA Nano 6000 microfluidics kit (Agilent Technologies).

treatment_protocol: Fifteen third instar larvae (ca. 6 days old) were incubated with 1-HP, Pyo (50 µM) or an equivalent volume of DMSO in single wells of 6-well tissue culture plates for 4 h or 8 h.

value: mixed

tag: strain

value: Ngousso

value: whole-body

tag: developmental stage

value: third instar larvae

tag: exposure time

value: 8 h

tag: exposure compound

value: DMSO

tag: exposure compound concentration

value: 50 µM 1-HP equivalent volume

value: 50 µM


title: 2.0, Rep 2


description: 1-HP vs. DMSO, 8 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control.


title: DMSO vs. 1-HP, 4 h Timepoint, Replicate 2

description: 1-HP vs. DMSO, 4 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control. Color-swap dye-reversal.

value: 4 h


description: 1-HP vs. DMSO, 4 h Timepoint, Replicate 2. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control.


title: 2.0, Rep 3


title: NQ, CON, Rep 4

hyb_protocol: The Agilent 8 x 60K, 2µm feature size microarray platform (Custom Array G4102A, AMADID 365741) was used for transcript expression assays (Agilent Technologies).  The Agilent Low Input One-Color Microarray Hybridization protocol (Agilent Technologies) was utilized for microarray hybridizations following manufacturer’s recommendations where 200 ng of total RNA was used as the starting material for each exposure replicate.  Four exposure replicates for each treatment (NQ: Control (0 mg/L), 20.7 and 2640 mg/L)  were hybridized to microarrays in a completely randomized design using a random number generator.  Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to the custom-designed Agilent test array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and with 37°C GE Wash buffer 2 (Agilent).

data_processing: Data were extracted from microarray images using Agilent Feature Extraction software (Agilent Technologies). Analysis of internal control spikes indicated that signal data was within the linear range of detection.  Microarray data were normalized to the 75th percentile within each array followed by median scaling among all exposures using GeneSpring Software version GX14.5 (Agilent Technologies). GeneSpring was additionally used to conduct differential transcript expression analysis.  Un-corrected one-way ANOVA with p = 0.005 was used to identify transcripts having significant differential expression.  Post-hoc tests for all chemical exposure experiments were conducted using a moderated t-test (p = 0.05) and log2 fold change cutoff of ≥ 1.5 to discern statistically significant differences in transcript expression for each chemical exposure concentration relative to the control.

treatment_protocol: Fathead minnow larvae were exposed to NQ at 0 (control), 20.7, 41.8, 82.7, 172, 367, 693. 1390, and 2640 mg/L (measured concentrations).   Exposure and control water was dechlorinated tap water (Vicksburg, MS USA municipal dechlorinated via activated carbon filtration) amended with artificial sea salts (Instant Ocean, Blacksburg, VA, USA) to a conductivity of 600 µS/cm.  Fathead minnow larvae were exposed in static nonrenewal acute 48-h bioassays.  Exposure chambers were 250 mL beakers with a test solution volume of 200 ml.  Ten larvae were exposed in each beaker, and 4 replicate beakers were tested per treatment.

value: NQ


title: 2.0, Rep 1


title: MCF7 Acute Hypoxia, rep2

value: Human breast epithelial adenocarcinoma cells

value: 0.5% Oxygen 24 hrs


title: genomic DNA from blood 9969489154_R05C01

description: stroke blood sample

tag: age

value: Female

value: cardioembolic

value: blood

value: stroke


title: genomic DNA from blood 9969489154_R04C02

description: stroke blood sample


title: genomic DNA from blood 9969489154_R04C01

description: stroke blood sample

value: small-vessel disease


title: DMSO vs. 1-HP, 8 h Timepoint, Replicate 1

description: 1-HP vs. DMSO, 8 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control. Color-swap dye-reversal.

value: mixed


title: DMSO vs. 1-HP, 4 h Timepoint, Replicate 1

description: 1-HP vs. DMSO, 4 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control. Color-swap dye-reversal.

value: Ngousso


title: NQ, CON, Rep 3

value: 0 (control)

value: larvae


title: NQ, CON, Rep 2


title: genomic DNA from blood 9969489154_R03C01

description: stroke blood sample

value: Male


title: NQ, CON, Rep 1


title: genomic DNA from blood 9969489154_R01C02

description: stroke blood sample


description: 1-HP vs. DMSO, 8 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control.

value: whole-body

value: third instar larvae

value: 8 h

value: DMSO


description: 1-HP vs. DMSO, 4 h Timepoint, Replicate 1. A. coluzzii Ngousso third instar larvae incubated with 50 µM 1-HP compared to DMSO control.

value: 4 h

value: 50 µM

value: 50 µM 1-HP equivalent volume


title: NQ, 2640, Rep 4

value: NQ