title: ALLSIL_JQ1_12h_2

status: Public on Aug 05 2015

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

description: Gene expression after 12h JQ1 treatment of ALLSIL cell line replicate 2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x GEx Hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to the array for 17 hours at 65°C in a rotating  hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner with SureScan High-Resolution Technology using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting at least a two-fold higher expression than the negative control probes of the array design in at least 60% of either treatment groups.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low Input Quick Amp Labling kit (Agilent) according to the manufacturer's instructions, followed by miRNeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin

extract_protocol: Total RNA was harvested with the miRNeasy mini kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: Cells were seeded at 1*10^6 cells/ml and treated with either DMSO or 1 µM of JQ1 compound. Cells were harvested 12 h after treatment.

value: ALL-SIL

value: T-cell acute lymphoblastic leukemia (T-ALL) cell line

tag: treated with

tag: time


title: ALLSIL_DMSO_12h_2

type: RNA

description: Gene expression after 12h DMSO treatment of ALLSIL cell line replicate 2

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: DMSO


title: ALLSIL_DMSO_12h_1

description: Gene expression after 12h DMSO treatment of ALLSIL cell line replicate 1


title: Bone marrow 4 from HCC patient 12

status: Public on Aug 06 2015

city: Beppu

first: Shotaro

last: Sakimura

address: 4546 Tsurumihara Tsurumi

department: Department of surgeryy

country: Japan

institute: Kyushu University Beppu Hospital

description: microRNA

hyb_protocol: Labeled RNAs were hybridized onto 3D-Gene Human microRNA Oligo chips containing 837 anti-sense probes printed in duplicate spots (Toray, Kamakura, Japan).

scan_protocol: After stringent washes, fluorescent signals were scanned with the 3D-Gene Scanner (Toray).

data_processing:
The scanned images were analyzed using GenePix Pro version 5.0 (Molecular Devices, Sunnyvale, CA, USA).
We filtered out star-miR and miR that are not annotated as hsa-miR. Raw data were quantile-normalized after log2 scaling. If the Agilent Probe Names are not unique, we chose the most variable probe.

source_name: Macrophage fraction of BM cells (CD14+ cell fraction)

label_protocol: Extracted total RNA was labeled with Cy3 using the miRCURY LNA Array miR labelling kit (Exiqon, Vedbaek, Denmark).

extract_protocol: Aspiration of BM was conducted under general anesthesia immediately before surgery. BM cells were separated into 3 fractions using a 3-step automagnetic-activated cell separation system (MACS) by MACS Cell Separators (Miltenyi Biotec, Bergisch Gladbach, Germany). CD45+, CD14+, and CD45−/EpCAM+ cell fractions were collected using CD45, CD14, and EpCAM (CD326) microbeads according to the manufacturer's instructions (Miltenyi Biotec). RNA was extracted from each BM fraction separated by the Auto MACS system using the miRNeasy Mini Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol.

tag: age

tag: Sex

value: male

tag: Stage

value: stage 2

tag: recurrence

value: yes

tag: number of tumors

value: multiple


title: ALLSIL_JQ1_12h_1

description: Gene expression after 12h JQ1 treatment of ALLSIL cell line replicate 1


title: ALLSIL_DMSO_12h_3

description: Gene expression after 12h DMSO treatment of ALLSIL cell line replicate 3


title: ALLSIL_GSI_48h_3

description: Gene expression after 48h GSI treatment of ALL-SIL cell line replicate 3

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting a 10 % higher expression than the negative control probes of the array design in at least one treatment.

treatment_protocol: Cells were seeded at 1*10^6 cells/ml and treated with either DMSO or 1 µM of Compound E. Cells were harvested 48h after treatment.

tag: treatment

value: 1 µM of Compound E (γ-Secretase Inhibitor, GSI)


title: ALLSIL_JQ1_12h_3

description: Gene expression after 12h JQ1 treatment of ALLSIL cell line replicate 3


title: Progenitors from patient with predisposition JAK2V617F and TET2 mutation

type: genomic

city: VILLEJUIF

first: Bastien

last: Job

address: 39 rue Camille Desmoulins

country: France

institute: Institut Gustave Roussy

description: Sample name in figure S3a : P3 (F2, III-2) (CD34+)

hyb_protocol: Pooled test and reference labeled DNA samples were hybridized for 40 hours at 65°C on Agilent 244K high density oligo microarrays (G4411B, AMADID 014693), and washed with Agilent Wash Buffers 1 & 2 and acetonitril.

scan_protocol: Washed arrays were dried using a nitrogen pulse gun and scanned on an Agilent G2565CA scanner (Agilent, Palo Alto, CA) using a resolution of 3µm per pixel and 100% of the photomultiplicator for both signals.

data_processing: Intensity aquisition and data normalization and transformation were performed using Feature Extraction v10.7.3.1 (Agilent Sotware) using default protocol.

molecule: genomic DNA

source_name: Blood

label_protocol: DNA was digested with AluI and RsaI restriction enzymes. Sample DNA was labeled with Cy5-dUTP, whereas sex-matched normal reference DNA from Promega was labeled with Cy3-dUTP). Samples with unknown gender where hybridized with labeled male reference DNA.

growth_protocol: IPSC (passage between P15 and P33) were cultured on MEF layers in the presence of FGF2

extract_protocol: DNA extraction was performed using the DNEasy Mini Kit (Qiagen). DNA was purified using the ChargeSwitch Forensic DNA Purification Kit (Invitrogen, Carlsberg, CA). Concentration and purity of DNA was determined using a Qubit dsDNA BR kit (Life Technologies).

tag: gender

value: F

tag: pathology

value: Essential thrombocythemia

tag: cell status

value: Primary cells (CD34+)

tag: biosource

value: hematopoieitc progenitors amplified 7 days  with a cocktail of cytokines

source_name: Commercial DNA (Promega)


title: IPSC JAK2V617F clone a

description: Sample name in figure S3a : P2-VF a

source_name: IPS

value: Polycythemia vera

value: iPS

value: undifferentiated


title: ALLSIL_GSI_48h_2

description: Gene expression after 48h GSI treatment of ALL-SIL cell line replicate 2


title: ALLSIL_DMSO_48h_2

description: Gene expression after 48h DMSO treatment of ALL-SIL cell line replicate 2

value: DMSO (vehicle)


title: thymus_CD34+_TLX1_vector_72h_2

description: Gene expression of human thymus CD34+ T-cell progenitors transduced with TLX1 vector and cultured for 72h on OP9-DLL1

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities. Normalization was performed using the VSN-package (Bioconductor).

source_name: thymus CD34+, TLX1 vector, 72h, 2

extract_protocol: Total RNA was harvested with the miRNeasy micro kit (Qiagen) with Dnase treatment on-column.

treatment_protocol: Pediatric thymus samples were obtained and used according to the guidelines of the Medical Ethical Commission of the Ghent University Hospital (Belgium). CD34+ thymocytes were purified using magnetic activated cell sorting (MACS, Miltenyi Biotec) and cultured for 24h in complete IMDM, supplemented with penicillin (100 U/ml), streptomycin (100 µg/ml), L-glutamine (2 mM) (all from Invitrogen) and 10% heat-inactivated FCS (Biochrom) in the presence of 10 ng/ml IL-7 and SCF. After 24h, cells were retrovirally transduced with either LZRS-IRES-EGFP (LIE) or LZRS-TLX1-IRES-EGFP (TLX1) as described previously (Van de Walle et al. 2013). 24h later, transduced cells were seeded onto confluent OP9-GFP or OP9-DLL1 plates in α-MEM media supplemented with 20% heat-inactivated FCS plus 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM L-glutamine and the T-lineage supporting cytokines SCF, Flt3-L and IL-7 at 5 ng/ml each. Following 72h of OP9 co-culture, cells were harvested by forceful pipetting and stained with CD45-PE (Miltenyi) to purify CD45+EGFP+ human transduced leukocytes through sorting to remove contaminating OP9 stromal cells. After sorting, part of the cells were lysed in 700 µl QIAzol (Qiagen) and stored at -70°C prior to RNA isolation

value: human thymic CD34+

value: TLX1 vector


title: ALLSIL_GSI_48h_1

description: Gene expression after 48h GSI treatment of ALL-SIL cell line replicate 1

value: ALL-SIL

value: T-cell acute lymphoblastic leukemia (T-ALL) cell line


title: ALLSIL_DMSO_48h_1

description: Gene expression after 48h DMSO treatment of ALL-SIL cell line replicate 1


title: IPSC predisposition +JAK2V617F clone a

description: Sample name in figure S3a : P3-CNV-VF  a


title: ALLSIL_DMSO_48h_3

description: Gene expression after 48h DMSO treatment of ALL-SIL cell line replicate 3


title: IPSC predisposition only clone b

description: Sample name in figure S3a : P4-CNV b


title: IPSC JAK2V617F clone b

description: Sample name in figure S3a : P2-VF b


title: Squamous carcinoma (TE7) cell line Replicate 1

city: Baltimore

first: James

middle: M

last: Donahue

address: 10 North Greene

department: Surgery

country: USA

institute: University of Maryland

description:
Biological replicate 1 of 2. Esophageal squamous cancer cells, harvested at passage 5.
PP3

hyb_protocol: The Hy3 labeled samples and a Hy5-labeled reference RNA samples were  mixed pair-wise and hybridized to the miRCURY LNA microRNA Array (7th Gen) , which contains capture probes targeting all microRNAs for human registered in the miRBASE 18.0.  The hybridization was performed according to the miRCURY LNA microRNA Array Instruction manual using a Tecan HS4800 hybridization station (Tecan, Austria).  http://www.exiqon.com/ls/documents/scientific/mircury-lna-microrna-array-7th-gen-hsa-mmu-rno-manual.pdf

scan_protocol: miRCURY LNA microRNA Array slides were scanned using the Agilent G2565BA Microarray scanner system Agilent Technologies Inc.,USA). The Image analysis was carried out using the Exiqon-tailored ImaGene9 data analysis software (www.exiqon.com/mirna-array-software)

data_processing: The quantified signals were background corrected (Noemexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.n the norm.xlxs a 'G' sheet contains the signals from the samples (Hy3) and a 'R' sheet which is the signals from the common reference (Hy5).

source_name: squamous cancer cell line

label_protocol: 750 ng total RNA from both sample and reference was labeled  with Hy3 and Hy5 fluorescent label, respectively, using the EXIQON miRCURY LNA microRNA Hi-Power Labeling Kit, HY3/Hy5 (Exiqon,Denmark) following the procedure described by the manufacture.  http://www.exiqon.com/ls/documents/scientific/mircury-lna-microrna-array-7th-gen-hsa-mmu-rno-manual.pdf

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% heat inactivated Fetal Bovine Serum.

extract_protocol: Total RNA including miRNA was extracted using QIAGEN miRNeasy kit,  following manufacturer's instructions. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

value: TE7:Human esophageal squamous cells

tag: passage

value: Human cells derived from an esophageal squamous cell carcinoma


title: Progenitors from patient with predisposition only

description: Sample name in figure S3a : P4 (F2,IV-2) (CD34+)


title: Progenitors from JAK2V617F sporadic patient

description: Sample name in figure S3a : P2(CD34+)

value: Myelofibrosis (post-polycythemia vera)


title: Control IPSC clone a

description: Sample name in figure S3a : control a

value: unknown

value: M


title: thymus_CD34+_empty_vector_72h_2

description: Gene expression of human thymus CD34+ T-cell progenitors transduced with empty vector and cultured for 72h on OP9-DLL1

source_name: thymus CD34+, empty vector, 72h, 2

value: empty vector


title: IPSC predisposition only clone a

description: Sample name in figure S3a : P4-CNV a

value: F

value: Essential thrombocythemia


title: thymus_CD34+_TLX1_vector_72h_1

source_name: thymus CD34+, TLX1 vector, 72h, 1


title: IPSC predisposition +JAK2V617F clone b

description: Sample name in figure S3a : P3-CNV-VF b


title: thymus_CD34+_empty_vector_72h_1

source_name: thymus CD34+, empty vector, 72h, 1


title: Control progenitors

description: Sample name in figure S3a : Control (CD34+)

value: Primary cells (CD34+)

value: hematopoieitc progenitors amplified 7 days  with a cocktail of cytokines


title: Control IPSC clone b

description: Sample name in figure S3a : control b

value: iPS


title: IPSC predisposition +JAK2V617F+TET2 mutation clone b

description: Sample name in figure S3a : P3-CNV-VF-TET2 b

value: undifferentiated


title: ALLSIL_TLX1_siRNA1_24h_2

description: Gene expression 24h post-electroporation of TLX1 targeting siRNA1 in the ALL-SIL cell line replicate 2

source_name: ALLSIL, TLX1 siRNA1, 24h, 2

treatment_protocol: Cells were seeded at 1,6*10^6 cells/ml and electroporated with 400 nM final concentration of either scrambled siRNA or TLX1 targeting siRNAs. Cells were harvested 24 h after treatment.

value: ALLSIL

value: TLX1 siRNA1


title: ALLSIL_TLX1_siRNA1_24h_3

description: Gene expression 24h post-electroporation of TLX1 targeting siRNA1 in the ALL-SIL cell line replicate 3

source_name: ALLSIL, TLX1 siRNA1, 24h, 3


title: ALLSIL_scrambled_siRNA_24h_3 [TLX1 knockdown experiment]

description: Gene expression 24h post-electroporation of scrambled siRNA in the ALL-SIL cell line replicate 3

source_name: ALLSIL, scrambled siRNA, 24h, 3

value: scrambled siRNA


title: IPSC predisposition +JAK2V617F+TET2 mutation clone a

description: Sample name in figure S3a : P3-CNV-VF-TET2 a


title: ALLSIL_TLX1_siRNA2_24h_1

description: Gene expression 24h post-electroporation of TLX1 targeting siRNA2 in the ALL-SIL cell line replicate 1

source_name: ALLSIL, TLX1 siRNA2, 24h, 1

value: TLX1 siRNA2


title: ALLSIL_TLX1_siRNA1_24h_1

description: Gene expression 24h post-electroporation of TLX1 targeting siRNA1 in the ALL-SIL cell line replicate 1

source_name: ALLSIL, TLX1 siRNA1, 24h, 1


title: ALLSIL_scrambled_siRNA_24h_2 [TLX1 knockdown experiment]

description: Gene expression 24h post-electroporation of scrambled siRNA in the ALL-SIL cell line replicate 2

source_name: ALLSIL, scrambled siRNA, 24h, 2


title: Bone marrow 4 from HCC patient 6

description: microRNA

value: Macrophage fraction of BM cells (CD14+ cell fraction)

value: male

value: stage 1

value: yes

value: single


title: ALLSIL_scrambled_siRNA_24h_1 [TLX1 knockdown experiment]

description: Gene expression 24h post-electroporation of scrambled siRNA in the ALL-SIL cell line replicate 1

source_name: ALLSIL, scrambled siRNA, 24h, 1


title: ALLSIL_RUNX1_siRNA2_24h_2

description: Gene expression 24h post-electroporation of RUNX1 targeting siRNA2 in the ALL-SIL cell line replicate 2

source_name: ALLSIL, RUNX1 siRNA2, 24h, 2

treatment_protocol: Cells were seeded at 1,6*10^6 cells/ml and electroporated with 400 nM final concentration of either scrambled siRNA or RUNX1 targeting siRNAs. Cells were harvested 24 h after treatment.

value: RUNX1 siRNA2


title: ALLSIL_RUNX1_siRNA1_24h_3

description: Gene expression 24h post-electroporation of RUNX1 targeting siRNA1 in the ALL-SIL cell line replicate 3

source_name: ALLSIL, RUNX1 siRNA1, 24h, 3

value: RUNX1 siRNA1


title: ALLSIL_RUNX1_siRNA2_24h_3

description: Gene expression 24h post-electroporation of RUNX1 targeting siRNA2 in the ALL-SIL cell line replicate 3

source_name: ALLSIL, RUNX1 siRNA2, 24h, 3


title: ALLSIL_RUNX1_siRNA1_24h_2

description: Gene expression 24h post-electroporation of RUNX1 targeting siRNA1 in the ALL-SIL cell line replicate 2

source_name: ALLSIL, RUNX1 siRNA1, 24h, 2


title: ALLSIL_RUNX1_siRNA1_24h_1

description: Gene expression 24h post-electroporation of RUNX1 targeting siRNA1 in the ALL-SIL cell line replicate 1

source_name: ALLSIL, RUNX1 siRNA1, 24h, 1


title: ALLSIL_scrambled_siRNA_24h_3

treatment_protocol: Cells were seeded at 1,6*10^6 cells/ml and electroporated with 400 nM final concentration of either scrambled siRNA or ETS1 targeting siRNAs. Cells were harvested 24 h after treatment.

tag: time point


title: ALLSIL_scrambled_siRNA_24h_3  [RUNX1 experiment]


title: ALLSIL_ETS1_siRNA2_24h_1

description: Gene expression 24h post-electroporation of ETS1 targeting siRNA2 in the ALL-SIL cell line replicate 1

source_name: ALLSIL, ETS1 siRNA2, 24h, 1

value: ETS1 siRNA2


title: ALLSIL_RUNX1_siRNA2_24h_1

description: Gene expression 24h post-electroporation of RUNX1 targeting siRNA2 in the ALL-SIL cell line replicate 1

source_name: ALLSIL, RUNX1 siRNA2, 24h, 1


title: ALLSIL_ETS1_siRNA2_24h_2

description: Gene expression 24h post-electroporation of ETS1 targeting siRNA2 in the ALL-SIL cell line replicate 2

source_name: ALLSIL, ETS1 siRNA2, 24h, 2


title: ALLSIL_scrambled_siRNA_24h_1 [RUNX1 experiment]


title: ALLSIL_ETS1_siRNA1_24h_2

description: Gene expression 24h post-electroporation of ETS1 targeting siRNA1 in the ALL-SIL cell line replicate 2

source_name: ALLSIL, ETS1 siRNA1, 24h, 2

value: ETS1 siRNA1


title: ALLSIL_ETS1_siRNA2_24h_3

description: Gene expression 24h post-electroporation of ETS1 targeting siRNA2 in the ALL-SIL cell line replicate 3

source_name: ALLSIL, ETS1 siRNA2, 24h, 3


title: ALLSIL_ETS1_siRNA1_24h_3

description: Gene expression 24h post-electroporation of ETS1 targeting siRNA1 in the ALL-SIL cell line replicate 3

source_name: ALLSIL, ETS1 siRNA1, 24h, 3


title: ALLSIL_scrambled_siRNA_24h_1


title: ALLSIL_ETS1_siRNA1_24h_1

description: Gene expression 24h post-electroporation of ETS1 targeting siRNA1 in the ALL-SIL cell line replicate 1

source_name: ALLSIL, ETS1 siRNA1, 24h, 1


title: ALLSIL_scrambled_siRNA_24h_2


title: ALLSIL_scrambled_siRNA_24h_2  [RUNX1 experiment]


title: TALL_JS_63

description: Gene expression of T-ALL patient bone marrow sample

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-105_Dec08 and Grid: 041648_D_F_20120615) to obtain background subtracted and spatially detrended Processed Signal intensities.Normalization was performed using the VSN-package (Bioconductor) and background correction was performed during the normalization process, selecting those probes detecting at least a two-fold higher expression than the negative control probes of the array design in at least 60% of either T-ALL subgroup types.

source_name: bone marrow

tag: subgroup

value: other subgroup


title: TALL_JS_64

description: Gene expression of T-ALL patient blood sample

source_name: blood


title: TALL_JS_61


title: TALL_JS_62

value: TLX3 subgroup


title: TALL_JS_57


title: TALL_JS_59


title: TALL_JS_58


title: TALL_JS_60

value: TLX1 subgroup


title: TALL_JS_54


title: TALL_JS_55


title: TALL_JS_56


title: TALL_JS_53

description: Gene expression of T-ALL patient EM sample

source_name: EM


title: ALLSIL_TLX1_siRNA2_24h_3

description: Gene expression 24h post-electroporation of TLX1 targeting siRNA2 in the ALL-SIL cell line replicate 3

source_name: ALLSIL, TLX1 siRNA2, 24h, 3


title: TALL_JS_50


title: TALL_JS_52


title: TALL_JS_41


title: TALL_JS_49


title: TALL_JS_43


title: ALLSIL_TLX1_siRNA2_24h_2

description: Gene expression 24h post-electroporation of TLX1 targeting siRNA2 in the ALL-SIL cell line replicate 2

source_name: ALLSIL, TLX1 siRNA2, 24h, 2


title: TALL_JS_36


title: TALL_JS_44


title: TALL_JS_45


title: TALL_JS_47


title: TALL_JS_33


title: TALL_JS_37


title: TALL_JS_42


title: TALL_JS_32


title: TALL_JS_40


title: TALL_JS_46


title: TALL_JS_31


title: TALL_JS_30


title: TALL_JS_28


title: TALL_JS_39


title: TALL_JS_29


title: TALL_JS_35


title: TALL_JS_25


title: TALL_JS_34


title: TALL_JS_38


title: TALL_JS_23


title: TALL_JS_48


title: TALL_JS_20


title: TALL_JS_19


title: TALL_JS_16


title: TALL_JS_13


title: TALL_JS_11


title: TALL_JS_10


title: TALL_JS_8


title: TALL_JS_18


title: TALL_JS_7


title: TALL_JS_22


title: TALL_JS_9


title: TALL_JS_17


title: TALL_JS_15


title: TALL_JS_12


title: TALL_JS_24


title: TALL_JS_6


title: TALL_JS_14


title: TALL_JS_3


title: TALL_JS_5


title: S. clavuligerus ΔclaR::aac_46.5h_rep2

type: mixed

city: León

first: Paloma

last: Liras

state: León, Spain

address: Facultad de Biología. Campus de Vegazana

department: Molecular Biology

country: Spain

institute: Universidad de León

description: Biological replicate 2 of 2. ΔclaR::aac_46.5h-rep2

hyb_protocol: Cy3-cDNA (300 ng) and Cy5-labeled gDNA (2,5 pmol) were mixed, resuspended in 32 μl of hybridization solution (Agilent) and applied on the microarray surface. Hybridizations were carried out at 55°C and extended to 60 h to improve the quality of the results.

scan_protocol: Scanned on an Agilent DNA Microarray Scanner G2565BA. Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: Microarrays data were processed with the Bioconductor package limma (Smyth and Speed 2003; Smyth 2004). Background corrected signals (the median background signal was substracted from the mean foreground signal) were log2-transformed and normalized with the global median procedure (within arrays), and with the cyclic loess procedure (between arrays). The Mg value is the normalized log2 of Cy3/Cy5 intensities, which is proportional to the abundance of the transcript for a particular gene.

organism: Streptomyces clavuligerus

source_name: ΔclaR::aac_46.5h _totalRNA

label_protocol: Labelling reactions were performed according to the recommendations described by BioPrime® Array CGH Genomic Labeling Systems (Life Technologies). Total RNA was labelled with Cy3-dCTP (Amersham) using random primers and SuperScript™ II reverse transcriptase (Invitrogen). gDNA was labelled with Cy5-dCTP (Amersham) from random primers extended with the Klenow fragment of DNA polymerase (Roche). The final products were purified with MinElute columns (Qiagen) and labelling efficiencies were quantified spectrophotometrically.

growth_protocol: Culture conditions were optimized using SA medium (Starch-Asparagine, Aido et al., 1994) and the samples to extract RNA were collected at 22.5 h, 46.5 h and 60 h of the cultures.

extract_protocol: lisozime 30 mg/ml in TE was added to stabilized culture samples. After 10 min, 600 µl RLT-β-mercaptoethanol was added to samples, mixed with vortex and, samples within microtubes containing silica beads were processed in FastPrep equipment with the following program: 30 s 6.5 m/s, 1 min at 0 °C, 30 s 6.5 m/s, 1 min at 0 °C. The preparation was extracted with one volume of phenol/chloroform-isoamilic alcohol and the aqueous-phase was applied to RNeasy Mini Kit Columns (Qiagen) according to the manufacturer’s instructions. RNA preparations were incubated with DNaseI (Qiagen) to eliminate DNA contamination. Sample quantification was done with a NanoDrop ND-1000 UV-Vis Spectrophotometer and the integrity of the RNA was determined in a Bioanalyzer 2100 (Agilent Technologies). Only RNAs with an RNA integrity value above 7.0 were used.

treatment_protocol: Samples from the Streptomyces cultures were stabilized with two volumes of RNA Protect Bacteria Reagent (Qiagen) for 5 min

tag: strain/genotype

source_name: ATCC 27064_ Stationary growth phase _genomicDNA [reference]

extract_protocol: Genomic DNA from a stationary phase culture was purified by the salting out procedure (Pospiech, and Neumann, 1995).

value: Stationary growth phase


title: TALL_JS_1


title: S. clavuligerus ΔclaR::aac_60 h_rep2

description: Biological replicate 2 of 2. ΔclaR::aac_60h-rep2

source_name: ΔclaR::aac_60h _totalRNA

tag: time


title: TALL_JS_4


title: S. clavuligerus ΔclaR::aac_22.5h_rep2

description: Biological replicate 2 of 2. ΔclaR::aac_22.5h-rep2

source_name: ΔclaR::aac_22.5h _totalRNA


title: TALL_JS_26


title: Burkitt Lymphoma 18

city: Bologna

first: Fabio

last: Fuligni

address: Via Massarenti 9

department: Department of Experimental, Diagnostic, and Specialty Medicine Bologna University Medical School

country: Italy

institute: University of Bologna

description: MYC-translocation negative Burkitt Lymphoma

hyb_protocol: miRCURY™ LNA Array (5th Generation arrays, hsa, mmu and rno, Exiqon)

data_processing: Data normalized using global Lowess (Locally weighted scatterplot smoothing) regression algorithm

label_protocol: miRCURY™ Hy3/Hy5 Power labelling kit

tag: diagnosis

value: Burkitt Lymphoma

tag: cell population

value: MYC negative


title: Burkitt Lymphoma 17

scan_protocol: miRCURY™ LNA Array (5th Generation arrays, hsa, mmu and rno, Exiqon)

source_name: MYC-translocation negative Burkitt Lymphoma


title: Burkitt Lymphoma 16

extract_protocol: miRCURY™ LNA Array (5th Generation arrays, hsa, mmu and rno, Exiqon)


title: Burkitt Lymphoma 20


title: Burkitt Lymphoma 15


title: Burkitt Lymphoma 12


title: Burkitt Lymphoma 14


title: Burkitt Lymphoma 10

description: MYC-translocation positive Burkitt Lymphoma

value: MYC positive


title: Burkitt Lymphoma 13


title: Burkitt Lymphoma 11


title: S. clavuligerus ΔclaR::aac_22.5h_rep1

description: Biological replicate 1 of 2.  ΔclaR::aac_22.5h-rep1


title: Burkitt Lymphoma 8

source_name: MYC-translocation positive Burkitt Lymphoma


title: Burkitt Lymphoma 9


title: Burkitt Lymphoma 7


title: S. clavuligerus ATCC 27064_60h_rep2

description: Biological replicate 2 of 2. Control strain. Wt_60h-rep2

source_name: ATCC 27064_60h _totalRNA


title: S. clavuligerus ATCC 27064_22.5h_rep2

description: Biological replicate 2 of 2. Control strain. Wt_22.5h-rep2

source_name: ATCC 27064_22.5h _totalRNA


title: Burkitt Lymphoma 5


title: S. clavuligerus ATCC 27064_46.5h_rep1

description: Biological replicate 1 of 2. Control strain. Wt_46.5h-rep1

source_name: ATCC 27064_46.5h _totalRNA


title: S. clavuligerus ATCC 27064_46.5h_rep2

description: Biological replicate 2 of 2. Control strain. Wt_46.5h-rep2


title: S. clavuligerus ATCC 27064_60h_rep1

description: Biological replicate 1 of 2. Control strain. Wt_60h-rep1


title: S. clavuligerus ATCC 27064_22.5h_rep1

description: Biological replicate 1 of 2. Control strain. Wt_22.5h-rep1


title: Burkitt Lymphoma 6


title: Burkitt Lymphoma 4


title: Burkitt Lymphoma 19


title: S. clavuligerus ΔclaR::aac_46.5h_rep1

description: Biological replicate 1 of 2. ΔclaR::aac_46.5h-rep1


title: Burkitt Lymphoma 3


title: Burkitt Lymphoma 2


title: Burkitt Lymphoma 1


title: TALL_JS_2

description: Gene expression of T-ALL patient blood sample


title: TALL_JS_21


title: TALL_JS_27


title: TALL_JS_51


title: 11170

city: Perth

first: Eric

middle: K

last: Moses

state: Western Australia

address: Level 5, Medical Research Foundation (MRF) Building, 50 Murray Street

department: Centre for Genetic Origins of Health and Disease

country: Australia

institute: The University of Western Australia

description:
wg6v3
Singleton pregnancy

scan_protocol: Scanned using Illumina iScan System with iScan Control Software (v3.2.45)

data_processing: Background noise subtracted using GenomeStudio (v2010.2), Gene Expression Module (v1.7.0), Data then log2-transformed and quantile normalised with lumi R package (Bioconductor) on R.

label_protocol: Illumina's Whole-Genome Gene Expression Direct Hybridisation assay protocol (includes labelling method)

extract_protocol: Total RNA was extracted from decidual samples using Rneasy Midi kits (Qiagen) following manufacturer's protocol. Complementary RNA was then synthesised, amplified and purified as described in PMID:20934677, Am J Obstet Gynecol. 2011 Jan;204(1):84.e1-27. doi: 10.1016/j.ajog.2010.08.043

treatment_protocol: Harvested decidual tissue was placed in RNA-later for at least 24 hours at 4C. Decidual tissue was then removed from RNA-later and stored at -80OC.

tag: subject status

value: pre-eclamptic patient

tag: maternal age (yrs)

tag: gestational age (wks)

tag: gravidity

tag: parity

tag: infant sex

value: F

tag: infant weight (g)

tag: tissue

value: Decidua basalis


title: 10564

description:
wg6v3
Singleton pregnancy

hyb_protocol: Illumina's Whole-Genome Gene Expression Direct Hybridisation assay protocol

value: M


title: 11032

description:
wg6v3
Singleton pregnancy


title: 11323

description:
wg6v3
Singleton pregnancy


title: Control Kidney Papilla FACS-Separated Cells rep5

city: New York

first: Qais

last: Al-Awqati

state: NY

department: Medicine

institute: Columbia University

description: Biological replicate 5 of 5. GFP- vs. GFP+ cell populations.

hyb_protocol: The corresponding Cy3- and Cy5- labeled cDNAs were combined and hybridized overnight (17 hours, 65 degrees C) to an Agilent While Mouse Genome Oligo Micrarray 4x44K using Agilent's recommended hybridization chamber and oven.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (v. 9.1).

data_processing: For determination of differential gene expression, Feature Extraction Software-derived output data files were further anlyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware).

organism: Mus musculus

source_name: Kidney papilla cells; GFP+

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 and Cy5 labeling according to Miltenyi Biotec's protocol.

growth_protocol: H2B-GFP mice were pulsed with doxycycline during embryonic life and chased to ~2-3 months. Kidney papillae were isolated and cells were dispersed with collagenase digestion. Live cells were sorted into GFP positive and GFP negative cell populations directly into lysis buffer.

extract_protocol: Isolated cells were sent to Miltenyi Biotec on dry ice. Total RNA was extracted was performed by miltenyi Biotec. SuperAmp RNA amplification was performed according to Miltenyi Biotec's procedure based on a global PCR protocol using mRNA-derived cDNA.

tag: population

value: GFP+

value: Kidney papilla

tag: age

value: 2-3 months

tag: strain

source_name: Kidney papilla cells; GFP-

value: GFP-


title: 10556

description:
wg6v3
Singleton pregnancy


title: Control Kidney Papilla FACS-Separated Cells rep2

description: Biological replicate 2 of 5. GFP- vs. GFP+ cell populations.


title: Control Kidney Papilla FACS-Separated Cells rep1

description: Biological replicate 1 of 5. GFP- vs. GFP+ cell populations.


title: 11444

description:
wg6v3
Singleton pregnancy


title: 11272

description:
wg6v3
Singleton pregnancy


title: 10550

description:
wg6v3
Singleton pregnancy


title: 11219

description:
wg6v3
Singleton pregnancy


title: Control Kidney Papilla FACS-Separated Cells rep4

description: Biological replicate 4 of 5. GFP- vs. GFP+ cell populations.


title: 10615

description:
wg6v3
Singleton pregnancy


title: 11375

description:
wg6v3
Singleton pregnancy


title: 10545

description:
wg6v3
Singleton pregnancy


title: HepG2 [MeDIP-chip]

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

country: China

institute: Tongji Hospital

description: MeDIP-chip for cancerous hepatocytes HepG2

hyb_protocol: The labeled DNA was hybridized to Human miRNA Tiling Microarray, which is a NimbleGen custom-designed 385k array.

scan_protocol: The array scanning was performed by the Axon GenePix 4000B microarray scanner.

data_processing: Raw data containing signal intensity was extracted from array images as pair files by NimbleGen DEVA software. Then a scaled log2 ratio data for individual probe was generated by bi-weight mean algorithm while the ratio is MeDIP/Input.

source_name: 5-methylcytidine ChIP DNA from HepG2

label_protocol: The Input and IP DNA were labeled with Cy3- and Cy5-labeled random 9-mers, respectively.

growth_protocol: HepG2 was cultured and maintained in Dulbecco’s modified Eagle medium supplemented with 100 ml/l fetal bovine serum,100 IU/ml penicillin and 100 mg/ml streptomycin at 37 0C with 5% CO2.

extract_protocol: Genomic DNA from tissues and cells were extracted and sonicated to random fragments in size about 500bp. Immunoprecipitation of methylated DNA was performed using mouse monoclonal antibody against 5-methylcytidine and BiomagTM magnetic beads coupled anti-mouse IgG. Immunoprecipitated DNA was eluted and purified by phenol chloroform extraction and ethanol precipitation.

tag: cell line

tag: cell type

value: cancerous hepatocytes

tag: antibody

value: Anti-5-methylcytosine antibody

source_name: Input DNA from HepG2

growth_protocol: HepG2 was cultured and maintained in Dulbecco’s modified Eagle medium supplemented with 100 ml/l fetal bovine serum,100 IU/ml penicillin and 100 mg/ml streptomycin at 37 ℃ with 5% CO2.

tag: sample type

value: input DNA


title: 11811

description:
wg6v3
Singleton pregnancy


title: 10513

description:
wg6v3
Singleton pregnancy


title: 11707

description:
wg6v3
Singleton pregnancy


title: PHHC-4-1 [MeDIP-chip]

description: MeDIP-chip for normal hepatocytes PHHC-4-1

source_name: 5-methylcytidine ChIP DNA from PHHC-4

growth_protocol: PHHC-4-1(one technical repeat of PHHC-4) was isolated from normal liver tissues adjacent to hepatic hemangioma under sterile conditions using a modified four-step retrograde perfusion technique as reported elsewhere.

value: normal hepatocytes

source_name: Input DNA from PHHC-4


title: PHHC-4-2 [MeDIP-chip]

description: MeDIP-chip for normal hepatocytes PHHC-4-2

growth_protocol: PHHC-4-2(one technical repeat of PHHC-4) was isolated from normal liver tissues adjacent to hepatic hemangioma under sterile conditions using a modified four-step retrograde perfusion technique as reported elsewhere.


title: 11684

description:
wg6v3
Singleton pregnancy


title: 11459

description:
wg6v3
Singleton pregnancy


title: 11465

description:
wg6v3
Singleton pregnancy


title: 10526

description:
wg6v3
Singleton pregnancy


title: Control Kidney Papilla FACS-Separated Cells rep3

description: Biological replicate 3 of 5. GFP- vs. GFP+ cell populations.


title: S. clavuligerus ΔclaR::aac_60 h_rep1

description: Biological replicate 1 of 2. ΔclaR::aac_60h-rep1

tag: strain/genotype

tag: time


title: PHHC-4-3 [MeDIP-chip]

description: MeDIP-chip for normal hepatocytes PHHC-4-3

growth_protocol: PHHC-4-3(one technical repeat of PHHC-4) was isolated from normal liver tissues adjacent to hepatic hemangioma under sterile conditions using a modified four-step retrograde perfusion technique as reported elsewhere.


title: 10281

description:
wg6v3
Singleton pregnancy

tag: subject status


title: 11360

description:
wg6v3
Singleton pregnancy

source_name: normotensive control_decidua

value: normotensive control patient

tag: maternal age (yrs)


title: 11665

description:
wg6v3
Singleton pregnancy

tag: gestational age (wks)


title: 9142

description:
wg6v3
Singleton pregnancy

tag: gravidity


title: 11347

description:
wg6v3
Singleton pregnancy

tag: parity


title: MHCC97-H [MeDIP-chip]

description: MeDIP-chip for cancerous hepatocytes MHCC97-H

source_name: 5-methylcytidine ChIP DNA from MHCC97-H

growth_protocol: MHCC97-H was cultured and maintained in Dulbecco’s modified Eagle medium supplemented with 100 ml/l fetal bovine serum,100 IU/ml penicillin and 100 mg/ml streptomycin at 37 0C with 5% CO2.

source_name: Input DNA from MHCC97-H

growth_protocol: MHCC97-H was cultured and maintained in Dulbecco’s modified Eagle medium supplemented with 100 ml/l fetal bovine serum,100 IU/ml penicillin and 100 mg/ml streptomycin at 37 ℃ with 5% CO2.


title: 10837

description:
wg6v3
Singleton pregnancy

tag: infant sex


title: 10948

description:
wg6v3
Singleton pregnancy

tag: infant weight (g)


title: 7447

description:
wg6v3
Singleton pregnancy

tag: tissue


title: 11055

description:
wg6v3
Singleton pregnancy


title: 11469

description:
wg6v3
Singleton pregnancy


title: 11670

description:
wg6v3
Singleton pregnancy


title: 8954

description:
wg6v3
Singleton pregnancy


title: 10884

description:
wg6v3
Singleton pregnancy


title: 7397

description:
wg6v3
Singleton pregnancy


title: 9109

description:
wg6v3
Singleton pregnancy


title: 11600

description:
wg6v3
Singleton pregnancy


title: 11603

description:
wg6v3
Singleton pregnancy


title: 11747

description:
wg6v3
Singleton pregnancy


title: 11420

description:
wg6v3
Singleton pregnancy


title: 11697

description:
wg6v3
Singleton pregnancy


title: SK-HEP-1 [MeDIP-chip]

description: MeDIP-chip for cancerous hepatocytes SK-HEP-1

source_name: 5-methylcytidine ChIP DNA from SK-HEP-1

growth_protocol: SK-HEP-1 was cultured and maintained in Dulbecco’s modified Eagle medium supplemented with 100 ml/l fetal bovine serum,100 IU/ml penicillin and 100 mg/ml streptomycin at 37 0C with 5% CO2.

source_name: Input DNA from SK-HEP-1

growth_protocol: SK-HEP-1 was cultured and maintained in Dulbecco’s modified Eagle medium supplemented with 100 ml/l fetal bovine serum,100 IU/ml penicillin and 100 mg/ml streptomycin at 37 ℃ with 5% CO2.


title: 11668

description:
wg6v3
Singleton pregnancy


title: 11440

description:
wg6v3
Singleton pregnancy


title: 11714

description:
wg6v3
Singleton pregnancy


title: 11303

description:
wg6v3
Singleton pregnancy


title: 11792

description:
wg6v3
Singleton pregnancy


title: 11826

description:
wg6v3
Singleton pregnancy


title: 11761

description:
wg6v3
Singleton pregnancy


title: 9 days after wound closure, high regeneration

first: Luis

middle: Andres

last: Garza

state: MD

address: 1550 Orleans St. Suite 204 CRBII Koch

department: Dermatology

institute: Johns Hopkins School of Medicine

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip® Expression Wash, Stain and Scan User Manual (www.affymetrix.com).

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Image analysis used the Affymetrix Command Console version 3 (AGCC v3.0) software, processed with the Expression Console PLIER algorithm and the manufacturer’s specifications.
probe group file: MoEx-1_0-st-v1.r2.pgf

label: biotin

source_name: skin scar

label_protocol: One round amplification protocol for total RNA following Affymetrix’ specifications using T7 promoter engineered random primers for cDNA synthesis, and Ambion® WT Expression Kit (www.affymetrix.com).

growth_protocol: after biopsy, samples were stored in RNAlater prior to RNA extraction. No growth.

extract_protocol: Qiangen Fibrous RNA kit

tag: day post wound closure

tag: regeneration level

value: High


title: 6 days after wound closure, high regeneration


title: 9 days after wound closure, low regeneration

value: Low


title: 4 days after wound closure, low regeneration


title: High regeneraiton 3


title: High regeneraiton 4


title: High regeneraiton 2


title: Low regeneration 4


title: 11769

description:
wg6v3
Singleton pregnancy


title: 6 days after wound closure, low regeneration


title: High regeneraiton 1


title: 4 days after wound closure, high regeneration


title: 15557

description:
ht12v4
Singleton pregnancy


title: 15664

description:
ht12v4
Singleton pregnancy


title: 15145

description:
ht12v4
Singleton pregnancy


title: Low regeneration 1


title: 11838

description:
wg6v3
Singleton pregnancy


title: 15143

description:
ht12v4
Singleton pregnancy


title: 15210

description:
ht12v4
Singleton pregnancy


title: 15541

description:
ht12v4
Singleton pregnancy


title: 15215

description:
ht12v4
Singleton pregnancy


title: Low regeneration 3


title: 15889

description:
ht12v4
Singleton pregnancy


title: 15111

description:
ht12v4
Singleton pregnancy


title: Low regeneration 2


title: 14963

description:
ht12v4
Singleton pregnancy


title: 15052

description:
ht12v4
Singleton pregnancy


title: 15102

description:
ht12v4
Singleton pregnancy


title: 14951

description:
ht12v4
Singleton pregnancy


title: 14628

description:
ht12v4
Singleton pregnancy


title: 12844

description:
ht12v4
Singleton pregnancy


title: 15085

description:
ht12v4
Singleton pregnancy


title: 13134

description:
ht12v4
Singleton pregnancy


title: 13801

description:
ht12v4
Singleton pregnancy


title: 13941

description:
ht12v4
Singleton pregnancy


title: 14016

description:
ht12v4
Singleton pregnancy


title: 14030

description:
ht12v4
Singleton pregnancy


title: 12665

description:
ht12v4
Twin pregnancy

value: F+F


title: 14037

description:
ht12v4
Singleton pregnancy


title: 14508

description:
ht12v4
Singleton pregnancy


title: 13013

description:
ht12v4
Singleton pregnancy


title: 14711

description:
ht12v4
Singleton pregnancy


title: 13581

description:
ht12v4
Singleton pregnancy


title: 14705

description:
ht12v4
Singleton pregnancy


title: 14347

description:
ht12v4
Singleton pregnancy


title: 14320

description:
ht12v4
Singleton pregnancy


title: 13463

description:
ht12v4
Singleton pregnancy


title: 14218

description:
ht12v4
Singleton pregnancy


title: 14199

description:
ht12v4
Singleton pregnancy


title: 14458

description:
ht12v4
Singleton pregnancy


title: 14603

description:
ht12v4
Singleton pregnancy


title: 14836

description:
ht12v4
Singleton pregnancy


title: 12664

description:
ht12v4
Singleton pregnancy


title: 14370

description:
ht12v4
Singleton pregnancy


title: 14384

description:
ht12v4
Singleton pregnancy


title: 14379

description:
ht12v4
Singleton pregnancy


title: 14829

description:
ht12v4
Singleton pregnancy


title: 14293

description:
ht12v4
Singleton pregnancy


title: 14954

description:
ht12v4
Singleton pregnancy


title: 14275

description:
ht12v4
Singleton pregnancy


title: 14082

description:
ht12v4
Singleton pregnancy


title: 14115

description:
ht12v4
Singleton pregnancy


title: 13933

description:
ht12v4
Singleton pregnancy


title: 14154

description:
ht12v4
Singleton pregnancy


title: 14129

description:
ht12v4
Singleton pregnancy


title: 14086

description:
ht12v4
Singleton pregnancy


title: 13664

description:
ht12v4
Singleton pregnancy


title: 14019

description:
ht12v4
Singleton pregnancy


title: 14258

description:
ht12v4
Singleton pregnancy


title: 13547

description:
ht12v4
Singleton pregnancy


title: 13694

description:
ht12v4
Singleton pregnancy


title: 13701

description:
ht12v4
Singleton pregnancy


title: 13839

description:
ht12v4
Singleton pregnancy


title: P0720 38years F

city: Milwaukee

first: Yi

last: Zhang

state: WI

address: 8701 W Watertown Plank Rd

department: Department of Medicine

institute: Medical College of Wisconsin

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

scan_protocol: Arrays were imaged using Iscan Reader using standard recommended Illumina scanner settings

data_processing:
Lumi:QN + BMIQ pipeline. Raw signal intensities and detection p-values of 22 autosomal chromosomes were extracted from GenomeStudio and loaded into Lumi. After data filtering, Lumi was used to generate Beta and M Values
Series supplementary file signals.txt reports unmethylated and methylated signal intensities.

label: Cy3 and Cy5

source_name: peripheral blood

label_protocol: Standard Illumina Protocol

growth_protocol: Genomic DNA was isolated from peripheral blood after an overnight fast on the same day when each subject was assayed for obesity and MetS phenotypes

extract_protocol: Genomic DNA was extracted and prepared from whole blood using commercial kits (Puregene, Minneapolis, MN).

treatment_protocol: One microgram of human genomic DNA was sodium bisulfite–treated for cytosine (C) to thymine (T) conversion using the EZ DNA Methylation kit (Zymo Research) according to the manufacturer’s guidelines

tag: ancestry

value: Northern European

tag: age

tag: gender

value: peripheral blood


title: 14085

description:
ht12v4
Singleton pregnancy

value: F


title: 13803

description:
ht12v4
Singleton pregnancy

value: Decidua basalis


title: 13399

description:
ht12v4
Singleton pregnancy


title: 13497

description:
ht12v4
Singleton pregnancy

value: M


title: 13521

description:
ht12v4
Singleton pregnancy


title: 13519

description:
ht12v4
Singleton pregnancy


title: 13319

description:
ht12v4
Singleton pregnancy


title: 13398

description:
ht12v4
Singleton pregnancy


title: 13281

description:
ht12v4
Singleton pregnancy


title: 13303

description:
ht12v4
Singleton pregnancy


title: P0384 43years M


title: P0719 43years M


title: P0380 34years F


title: P0362 41years F


title: 13243

description:
ht12v4
Singleton pregnancy


title: P0357 40years F


title: P0385 52years F


title: P0361 43years M


title: P0376 64years M


title: 13035

description:
ht12v4
Singleton pregnancy


title: 13231

description:
ht12v4
Singleton pregnancy


title: 13190

description:
ht12v4
Singleton pregnancy


title: P0716 58years M


title: 12907

description:
ht12v4
Singleton pregnancy


title: 13256

description:
ht12v4
Singleton pregnancy


title: P0379 36years M


title: P0358 47years M


title: NP36 51years M


title: P0717 41years F


title: NP113 50years F


title: P0378 41years M


title: NP96 46years F


title: NP95 44years M


title: NP35 51years F


title: 11924

description:
ht12v4
Singleton pregnancy


title: 12868

description:
ht12v4
Singleton pregnancy


title: NP117 42years F


title: NP111 41years F


title: LS174T_mATF6aOE_rep2

city: Tokushima

first: Seiichi

last: Oyadomari

state: Tokushima

address: 3-18-15 Kuramoto

department: Division of Molecular Biology

institute: Institute for Genome Research

description: Gene expression of LS175T cells overexpressed active ATF6a

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent Fragmentation buffer and 1x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17.5 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 air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 014868_D_F_20080627) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LS174T, mATF6aOE, rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the Low Input Quick Amp Labeling Kit (One-Color) (Agilent) according to the manufacturer's instructions, followed by RNeasy mini column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer.

growth_protocol: LS174T cells were cultured in Eagle's minimal essential medium supplemented with 10% FCS and 1% non-essential amino acids.

extract_protocol: After washing the cells with PBS, total RNA was extranted using the conventional acid guanidinium thiocyanate phenol-chloroform (AGPC) procedure immediately and cleaned up using the Rneasy MinElute Cleanup Kit according to manufactuer's instructions (QIAGEN Valencia, CA).

treatment_protocol: LS174T cells were treated with 2 mM sodium butyrate, which induces LS174T cells to differentiate to mature goblet cells.

tag: cell line

tag: treatment


title: 11882

description:
ht12v4
Singleton pregnancy


title: LS174T_Tx-_rep2

description: Gene expression of LS175T cells

source_name: LS174T, Tx-, rep2

value: non transfection


title: LS174T_mATF6bOE_rep2

description: Gene expression of LS175T cells overexpressed active ATF6b

source_name: LS174T, mATF6bOE, rep2


title: NP44 44years M


title: 12780

description:
ht12v4
Singleton pregnancy


title: NP43 39years F


title: P0377 40years F


title: NK55 12years M


title: LS174T_mATF6bOE_rep1

source_name: LS174T, mATF6bOE, rep1


title: LS174T_Tx-_rep1

description: Gene expression of LS175T cells

source_name: LS174T, Tx-, rep1


title: LS174T_mATF6aOE_rep1

source_name: LS174T, mATF6aOE, rep1


title: NK36 10years M


title: NK56 9years M


title: NK35 12years M


title: NP101 45years M


title: NK23 11years M


title: NK37 9years M


title: NK22 15years M


title: NK195 12years M


title: NK54 13years M


title: NK20 17years M


title: NK194 10years F


title: NK17 12years M


title: NK193 12years F


title: NK191 17years F


title: NK18 10years M


title: NK114 15years M


title: NK192 15years F


title: K0379 13years F


title: NK15 17years M


title: NK19 10years M


title: NK132 10years F


title: NK16 15years M


title: NK133 17years F


title: K0368 10years M


title: K1131 6years M


title: K0377 8years F


title: K0375 11years F


title: K0367 15years F


title: K0378 12years F


title: K0374 14years F


title: NK135 16years M


title: K0376 11years M


title: K0364 10years F


title: K0156 14years F


title: K0363 12years M


title: K0366 7years M


title: K0155 16years M


title: K0158 10years F


title: K0153 18years M


title: D0522 46years M


title: EN-01 3, biological rep3

city: Beijing

first: yongliang

last: yan

address: zhongguancun south 12th

institute: CAAS

description: RNA extracted from cells of E. coli K-12 DH10B with NFI cultured for 20 h under nitrogen fixation conditions.

hyb_protocol: The biotin-labeled target was hybridized to the Affymetrix GeneChip E. coli 2.0 array at 45ºC for 16 hour at 60 rpm using the Hybridization Oven 640 (Affymetrix), then a three-step fluorescent staining was conducted using the Fluidics Station 450 (Affymetrix) during the washing and staining procedure.

scan_protocol: The data were collected by using Affymetrix GeneChip Scanner 3000.

data_processing:
Affymetrix GeneChip Operating Software (GCOS) Version 1.4.
Details: Intra-chip normalizations were performed using Affymetrix GeneChip Operating Software (GCOS). Default statistical parameters were used to normalize each chip to the same target intensity (1500) as described in the Affymetrix GeneChip Expression Analysis manual. All nine possible inter-chip comparisons were performed in GCOS. The data were subsequently exported to a Microsoft Excel spreadsheet for manipulation. Consensus “detection p-value”, “change p-value”, and “signal log ratios” were calculated, and the default E. coli array p-value cutoff parameters were applied to these consensus values to estimate the transcript change between two conditions and the transcript presence under each condition. Background-subtracted data sets were used to calculate up-regulated and down-regulated genes based on fold changes of greater than 2.

organism: Escherichia coli str. K-12 substr. DH10B

source_name: E. coli K12 strain DH10B harboring NFI, nitrogen fixation

label_protocol: Affymetrix Technical Manual, Prokaryotic Sample and Array Processing.

growth_protocol:
E. coli cells with A1501 NFI were cultured overnight (OD600=2), and added (0.2 ml) to NFDM (5 ml) in a bijou bottle (vol. capacity of 9 ml). Cultures were incubated at 30 ℃. After 16 to 20 h, when visible growth had occurred, 0.5 ml acetylene was injected. After 20 h at 30℃, the cells were harvested to extract RNA.
LB medium recipe is as follow: 10g tryptone, 5g yeast extract, 10g NaCl per 1 liter. Nitrogen-free minimal medium with glucose (NFDM) was made as follows: Solution I consisted of 20 g glucose, 0.7 g MgSO4•7H2O, 25 mg Na2MoO4•2H2O, and 1,000 ml distilled water; Solution II consisted of 68 g KH2PO4, 241 g K2HPO4, and 1,000 ml distilled water (final pH 7.4); Solution III consisted of 3.6 g Fe (III) citrate and 1,000 ml distilled water. The solutions were prepared and sterilized separately. Before use, 950 ml solution I, 50 ml of solution II, and 10 ml of solution III were mixed.

extract_protocol: Total RNA was extracted using the commercial product TRIzol Reagent (Invitrogen, Carlsbad, CA). Disrupt about 10^7cells with a homogenizer with 1ml TRIzol Reafent on ice. Store the homogenate for 5 minutes at room temperature to permit the complete dissociation of nucleoprotein complexes. Next, supplement the homogenate with 0.2 ml chloroform per 1 ml of TRI Reagent, cover the samples tightly and shake vigorously for 15 seconds. Store the resulting mixture at room temperature for 2-15 minutes and centrifuge at 12,000 g for 15 minutes at 4 C. Following centrifugation, the mixture separates into a lower red phenol-chloroform phase, interphase and the colorless upper aqueous phase. Transfer the aqueous phase to a fresh tube. Precipitate RNA from the aqueous phase by mixing with isopropanol. Use 0.5 ml of isopropanol per 1 ml of TRI Reagent used for the initial homogenization. Store samples at room temperature for 5-10 minutes and centrifuge at 12,000 g for 8 minutes at 4-25 C. Remove the supernatant and wash the RNA pellet (by vortexing) with 75% ethanol and subsequent centrifugation at 7,500 g for 5 minutes at 4-25 C. Add at least 1 ml of 75% ethanol per 1 ml TRI Reagent used for the initial homogenization. Remove the ethanol wash and briefly air-dry the RNA pellet for 3-5 min. Dissolve RNA in DEPC-treated water by passing solution a few times through a pipette tip. Use an on-column DNase digestion with RNase-free DNase I (Qiagen) to purify the total RNA.

treatment_protocol: E. coli K-12 DH10B cells with NFI were cultured 20 h in NFDM medium under nitrogen fixation conditions (30℃, anaerobic, no ammonium) or nitrogen excess conditions (30℃, anaerobic, 20 mmol ammonium).

tag: strain

tag: substrain

tag: genotype/variation

value: harboring nitrogen fixation island (NFI) from Pseudomonas stutzeri A1501

value: nitrogen fixation


title: K0159 8years M


title: D0457 48years M


title: K0365 7years M


title: K0154 17years M


title: D0521 41years F


title: EN-01 2, biological rep2


title: EN-01 ammonium 3, biological rep3

description: RNA extracted from cells of E. coli K-12 DH10B with NFI cultured for 20 h under nitrogen excess conditions.

source_name: E. coli K12 strain DH10B harboring NFI, nitrogen excess

value: nitrogen excess


title: EN-01 1, biological rep1


title: D0520 43years M


title: D0496 43years M


title: D0405 45years M


title: D0440 18years F


title: D0456 74years F


title: Dnmt1chip/c, Apcmin/+ No.1

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

institute: University of Tokyo

description: 13.889T1 Min C_(MoGene-1_0-st-v1).CEL

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 TG

data_processing: Data were processed using Genespring GX software.

label: Biotin

source_name: colon tumor

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

extract_protocol: RNeasy Plus Mini kit

tag: strain background

value: mixed; C57BL/6 and 129Sv4

value: Dnmt1chip/c; ApcMin/+

value: 20 wks

value: colon tumor

tag: tissue subtype

value: DNA hypomethylated tumors


title: Dnmt1chip/c, Apcmin/+ No.3

description: 15.889T3 Min C_(MoGene-1_0-st-v1).CEL


title: Dnmt1chip/+, Apcmin/+ No.2

description: 887T2 Min

value: Dnmt1chip/+; ApcMin/+

value: control tumor


title: Dnmt1chip/c, Apcmin/+ No.2

description: 14.889T2 Min C_(MoGene-1_0-st-v1).CEL


title: Dnmt1chip/+, Apcmin/+ No.3

description: 997T3 Min _(MoGene-1_0-st-v1).CEL


title: D0493 21years F


title: D0399 18years M


title: D0398 21years F


title: D0403 25years F


title: EN-01 ammonium 2, biological rep2


title: D0401 53years M


title: D0400 39years M


title: Dnmt1chip/+, Apcmin/+ No.1

description: 887T1 Min


title: D0455 75years M


title: SW900 Cisplatin treated, biological replicate 2

city: Singapore

first: Chong-Lei

last: Bi

address: #12-02, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive

country: Singapore

institute: Cancer Science Institute Singapore

description: 46.SW900 cisplatin.CEL

hyb_protocol: Following fragmentation, 12.5 ug of cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip HG1.0ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix scanner 3000 7G

data_processing: The data were analyzed with Genespring GX 11(Agilent Technologies)

source_name: SW900 Cisplatin treated

label_protocol: Biotinylated cDNA were prepared using Nugen Applause WT kit and Encore biotin module (Nugen, USA) according to the manufecturer's instructions from 100ng total RNA.

growth_protocol: All cell lines were cultured in humidified incubator supplemented with 5% CO2.

extract_protocol: Total RNA from cell lines were harvested with RNeasy Mini Kit (Qiagen) 8 hours post-cisplatin treatment to capture cisplatin-induced transcriptional changes before activation of apoptosis.

treatment_protocol: SCC cell lines were treated at their respective cisplatin IC50 doses for 8 hours.

tag: cell type

value: Squamous Cell Carcinoma (SCC)

tag: cisplatin phenotype

value: resistant

tag: treated with

value: cisplatin IC50 doses for 8 hrs


title: K0360 16years M

value: Northern European

value: peripheral blood


title: D0397 20years F

value: F


title: SW900 Cisplatin treated, biological replicate 1

description: 45.SW900 cisplatin.CEL


title: D0494 42years F


title: SW900 Control, biological replicate 2

description: 44.SW900 control.CEL

source_name: SW900 Control

value: none (control)


title: calu-1 Control, biological replicate 2

description: 38.calu-1 control.CEL

source_name: calu-1 Control


title: D0388 50years F


title: calu-1 Cisplatin treated, biological replicate 2

description: 40.calu-1 cisplatin.CEL

source_name: calu-1 Cisplatin treated


title: SW900 Control, biological replicate 1

description: 43.SW900 control.CEL


title: H2066 Cisplatin treated, biological replicate 2

description: 34.H2066 cisplatin.CEL

source_name: H2066 Cisplatin treated


title: H2066 Cisplatin treated, biological replicate 1

description: 33.H2066 cisplatin.CEL


title: calu-1 Cisplatin treated, biological replicate 1

description: 39.calu-1 cisplatin.CEL


title: D0356 48years M

value: M


title: D0519 41years F


title: H2066 Control, biological replicate 2

description: 32.H2066 control.CEL

source_name: H2066 Control


title: EN-01 ammonium 1, biological rep1

value: harboring nitrogen fixation island (NFI) from Pseudomonas stutzeri A1501


title: D0374 41years F


title: D0389 25years F


title: D0373 39years F


title: H1869 Cisplatin treated, biological replicate 2

description: 28.H1869 cisplatin.CEL

source_name: H1869 Cisplatin treated

value: sensitive


title: D0357 20years F

source_name: peripheral blood


title: H2066 Control, biological replicate 1

description: 31.H2066 control.CEL


title: H1869 Cisplatin treated, biological replicate 1

description: 27.H1869 cisplatin.CEL


title: D0328 27years M


title: H1869 Control, biological replicate 1

description: 25.H1869 control.CEL

source_name: H1869 Control


title: calu-1 Control, biological replicate 1

description: 37.calu-1 control.CEL


title: H1869 Control, biological replicate 2

description: 26.H1869 control.CEL


title: D0327 27years M


title: D0331 45years F


title: D0329 48years F


title: D0173 19years F


title: H596 Cisplatin treated, biological replicate 1

description: 21.H596 cisplatin.CEL

source_name: H596 Cisplatin treated


title: D0326 21years F


title: D0325 49years M


title: D0330 22years F


title: H596 Control, biological replicate 2

description: 20.H596 control.CEL

source_name: H596 Control


title: D0171 40years F


title: D0402 53years F


title: NK137 11years M


title: D0172 41years M


title: D0165 52years F


title: H226 Cisplatin treated, biological replicate 1

description: 15.H226 cisplatin.CEL

source_name: H226 Cisplatin treated


title: H226 Control, biological replicate 1

description: 13.H226 control.CEL

source_name: H226 Control


title: CHAG0 Cisplatin treated, biological replicate 1

description: 09.CHAG0 Cis.CEL

source_name: CHAG0 Cisplatin treated


title: H226 Control, biological replicate 2

description: 14.H226 control.CEL


title: CHAG0 Cisplatin treated, biological replicate 2

description: 10.CHAG0 Cis.CEL


title: H226 Cisplatin treated, biological replicate 2

description: 16.H226 cisplatin.CEL


title: D0174 18years M


title: H596 Cisplatin treated, biological replicate 2

description: 22.H596 cisplatin.CEL


title: H596 Control, biological replicate 1

description: 19.H596 control.CEL


title: D0164 50years M


title: D0458 48years F


title: D0155 18years F


title: D0163 21years M


title: D0126 41years F


title: CHAG0 Control, biological replicate 2

description: 08.CHAG0 Ctrl.CEL

source_name: CHAG0 Control


title: D0154 21years F


title: D0161 46years M


title: H2170 Control, biological replicate 2

description: 02.H2170 Ctrl.CEL

source_name: H2170 Control


title: H2170 Control, biological replicate 1

description: 01.H2170 Ctrl.CEL


title: H2170 Cisplatin treated, biological replicate 2

description: 04.H2170 Cis.CEL

source_name: H2170 Cisplatin treated


title: H2170 Cisplatin treated, biological replicate 1

description: 03.H2170 Cis.CEL


title: D0166 22years F


title: CHAG0 Control, biological replicate 1

description: 07.CHAG0 Ctrl.CEL


title: D0017 62years M


title: Eyed_5000F_Rep-6

city: Oslo

first: You

last: Song

address: Økernveien 94

department: Ecotoxicology and Risk Assessment

country: Norway

institute: Norwegian Institute for Water Research (NIVA)

description: Gene expression of exposed egg to salt after 24 h

hyb_protocol: Totally 600 ng of Cy3-labeled, linearly amplified cRNA was fragmented and hybridized to 8x60k microarrays and rotationally (10 rpm) incubated at 65 ºC for 17 h.

scan_protocol: Microarray slides were scanned immediately after washing on the Agilent DNA Microarray C Scanner (Dye channel: G (green), scan region: Agilent HD (61 × 21.6 mm), Scan resolution: 3 µm, Tiff file dynamic range: 20 bit, Green PMI gain: 100%).

data_processing: The microarray scan images (raw signal intensity) were extracted using Agilent Feature Extraction software v10.7. Raw data were normalization (quantile) and statistical analyses were performed using GeneSpring GX v11.0 (Agilent Technologies). Non-uniform outliers were excluded.

organism: Salmo salar

label_protocol: Cyanine 3-CTP (Cy3) labeled cRNA was made from 100 ng total RNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies, Santa Clara, California, USA). The cRNA dye incorporation and yiled were checked using Agilent Bioanalyzer (Agilent Technologies).

extract_protocol: Total RNA was extracted from each individual egg using Direct-zol™ RNA MiniPrep kit (Zymo Research Corp., Irvine, CA, USA) according to the manufacturer’s instructions.The RNA quality (purity and yield) was controlled by photometric analyses (260/280>1.8, yield >150 ng/μL) using Nanodrop® spectrophotometer (ND-1000, Nanodrop Technologies, Wilminton, Delaware, USA) and RNA integrity (RIN>7.0) inspected by Bioanalyzer gelelectrophoresis with RNA 6000 Nano chips (Agilent technologies, Santa Clara, California, USA) according to the manufacturer’s instructions.

treatment_protocol: Atlantic salmon eggs were exposed from fertilization to 24h post fertilization to Lake Maridalsvannet water (Oslo, Norway) as control and 5000 mg/L road salt.

value: Embryo


title: D0152 44years M


title: D0128 33years F


title: Eyed_5000F_Rep-5


title: D0127 46years M


title: A0946WI 52years M


title: Eyed_5000F_Rep-1


title: Eyed_5000F_Rep-3


title: Eyed_Ctrl_Ref-4

description: Gene expression of unexposed egg after 24 h

source_name: Eyed Ref-4


title: A0562WI 68years F


title: Eyed_Ctrl_Ref-3

source_name: Eyed Ref-3


title: D0035 32years F


title: A0614WI 66years F


title: D0162 18years F


title: A0572WI 62years F


title: A0615WI 70years F


title: A0568WI 77years F


title: A0565WI 42years F


title: Eyed_Ctrl_Ref-2

source_name: Eyed Ref-2


title: A0566WI 51years F


title: A0564WI 42years F


title: Cow6_CONT+LPS

city: Hatfield

first: Zhangrui

last: Cheng

state: Hertfordshire

address: Hawkshead Lane

department: Production and Population Health

country: United Kingdom

institute: Royal Veterinary College

hyb_protocol: Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).

scan_protocol: The stained chips were scanned with the GeneChip Scanner 3000 based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).

data_processing:
The raw data cel files were summarized and normalized using RMA16 built in Genespring GX software version 12.5 (Agilent Technologies) with the annotation files provided by the company.
BovGene-1_1-st.pgf
BovGene-1_1-st-v1.na34.umd3.probeset.csv

organism: Bos taurus

source_name: CONT+LPS

growth_protocol: Fresh and apparently healthy bovine reproductive tracts (BVDV free) in the early luteal phase of the estrous cycle were collected at slaughter from the local abattoir and preserved temporarily in ice. Primary mixed endometrial epithelial and stromal cell cultures were isolated and cultured for 4 days in the culture medium containing 10 fetal bovine serum (BVDV free) before BVDV infection.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy Mini kit following the supplied protocol.

treatment_protocol: The cells were infected with  ncpBVDV for 4 days followed by treatment with CONT, CONT+LPS, BVDV or ncpBVDV+LPS for 6 h.

value: Cow

tag: cells

value: uterine endometrium

tag: treatment group

value: CONT+LPS


title: Cow6, ncpBVDV+LPS

source_name: ncpBVDV+LPS

label_protocol: Based on the established ARK-Genomics protocols (http://www.ark-genomics.org/protocols).

value: ncpBVDV+LPS


title: Cow5, ncpBVDV

source_name: ncpBVDV

value: ncpBVDV


title: Eyed_Ctrl_Ref-5

source_name: Eyed Ref-5

tag: tissue


title: A0200WI 58years F

source_name: peripheral blood


title: A0198WI 39years F


title: Cow6, CONT

source_name: CONT

value: CONT


title: A0201WI 85years M


title: Cow5, CONT


title: Cow5, ncpBVDV+LPS


title: Cow5, CONT+LPS


title: Cow4, ncpBVDV+LPS


title: A0197WI 56years F


title: Cow6, ncpBVDV


title: Cow4, CONT


title: Cow4, CONT+LPS


title: A0199WI 54years F


title: Cow4, ncpBVDV


title: Cow3, ncpBVDV


title: Cow3, ncpBVDV+LPS


title: A0030WI 47years F


title: A0031WI 67years F


title: A0563WI 75years F


title: Cow3, CONT


title: A0046IL 72years F


title: A0117WI 31years F


title: A0486WI 33years M


title: Cow2, ncpBVDV+LPS


title: A0032WI 62years F


title: A0028WI 46years F


title: Cow3, CONT+LPS


title: Cow2, CONT+LPS


title: A0029WI 57years F


title: Cow2, ncpBVDV


title: A0196WI 32years F


title: Cow2, CONT


title: Cow1, ncpBVDV+LPS


title: A0026WI 44years F


title: 2798 35years F


title: Cow1, ncpBVDV


title: Slc6a14-KnockOut/Polyoma Mammary Tumor-2 (Slc6a14-KO/PyMT-2)

city: Augusta

first: Pachiappan

last: Arjunan

state: Georgia

address: 1120 15th ST, Laney walker Blvd,

department: Anatomy, Unit on Retinal Vascular Neurobiology, BMB

institute: NUS, NIH, GRU

description:
Slc6a14-KO/PyMT-2
Gene expression data from Slc6a14-KO/PyMT mammary tumor tissue.

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

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Intensities of arrays have been quantile-normalized using Partek Genomic Suite (v6.6). Differential expressions were calculated using ANOVA of Partek package.

source_name: Mammary tumor excised from Slc6a14-/-/PyMT

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen, Life Technologies, NY).

treatment_protocol: Sample was collected from mammary tumor excised from WT/PyMT and Slc6a14-/-/PyMT mice for total RNA isolation.

tag: strain/background

value: mammary tumor tissue

value: 16 weeks


title: Slc6a14-KnockOut/Polyoma Mammary Tumor-3 (Slc6a14-KO/PyMT-3)

description:
Slc6a14-KO/PyMT-3
Gene expression data from Slc6a14-KO/PyMT mammary tumor tissue.


title: A0025WI 74years F

tag: ancestry


title: A0027WI 65years F

tag: age


title: Cow1, CONT+LPS

tag: gender


title: A0025IL 42years F


title: A0023IL 45years F


title: Cow1, CONT


title: 2794 40years F


title: Wild Type/Polyoma Mammary Tumor-3 (WT/PyMT-3)

description:
WT/PyMT-3
Gene expression data from WT/PyMT mammary tumor tissue.

source_name: Mammary tumor excised from WT/PyMT

value: WT/PyMT


title: A0024IL 49years F

value: Northern European


title: 2_2

city: shanghai

first: wenbang

last: yu

address: meilong road 130, east china university of science and technology, shanghai, china

description: Biological replicate 2 of sample with addition of Fe3+ (20min) vs sample without addition of Fe3+ (0min)

hyb_protocol: Each Slide was hybridized with 300ng Cy3-labeled cRNA and 300ng Cy-5 labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US)in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), Stabilization and Drying Solution (Cat#5185-5979, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Red&Green, Scan resolution=5μm, PMT 100%, 10% , 16bit. and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)

data_processing: Raw data were normalized by Lowess(locally weighted scatter plot smoothing) algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Bacillus subtilis

source_name: Sample with adition of Fe3+ (4 mM) (20min)

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, Two-Color (Cat#5190-2306, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Strains were grown in liquid LB medium with or without addition of Fe3+, and total RNA were extracted from the bacteria samples harvested at 0min, 20min respectively.

extract_protocol: RNA was extracted from samples derived from two independent culture samples collected at each time point  using the RNeasy Mini Kit (Qiagen, Valencia, CA) following manufacturer's instructions.

treatment_protocol: Four B.subtilis cultures were grown, of which two were treated with 4mM Fe3+ and the other two remain untreated.

tag: growth condition

value: With addition of Fe3+ (4 mM)

tag: time

value: 20 min

value: mycelia

source_name: Sample mixture without addition of Fe3+ (0min)

value: Without addition of Fe3+


title: Slc6a14-KnockOut/Polyoma Mammary Tumor-1 (Slc6a14-KO/PyMT-1)

description:
Slc6a14-KO/PyMT-1
Gene expression data from Slc6a14-KO/PyMT mammary tumor tissue.


title: A0047IL 50years M

value: M

value: peripheral blood


title: 2793 34years F

value: F


title: Wild Type/Polyoma Mammary Tumor-2 (WT/PyMT-2)

description:
WT/PyMT-2
Gene expression data from WT/PyMT mammary tumor tissue.


title: 2789 20years M


title: 2783 33years M


title: 2788 44years F


title: 2_1

institute: east china university of science and technology

description: Biological replicate 2 of sample without addition of Fe3+ (20min) vs sample without addition of Fe3+ (0min)

source_name: Sample without addition of Fe3+ (20min)


title: 1_2

description: Biological replicate 1 of sample with addition of Fe3+ (20min) vs sample without addition of Fe3+ (0min)


title: 1_1

description: Biological replicate 1 of sample without addition of Fe3+ (20min) vs sample without addition of Fe3+ (0min)


title: 2782 34years F


title: Wild Type/Polyoma Mammary Tumor-1 (WT/PyMT-1)

description:
WT/PyMT-1
Gene expression data from WT/PyMT mammary tumor tissue.


title: 2796 41years M


title: 2780 29years M


title: Mouse_TG_BAT_AP_rep1

description: Gene expression of mouse (Fv2E-PERK) BAT after 12 hour treatment of AP

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent Fragmentation buffer and 1x Agilent Blocking Agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17.5 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 air-dried immediately.

scan_protocol: Slides were scanned immediately after washing and drying on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%, NoXDR setting).

source_name: Mouse Fv2E-PERK, BAT

growth_protocol: All the mouse protocols were approved by the Animal Experimentation Committee of the University of Tokushima. The mice were maintained under SPF conditions.

extract_protocol: Both WAT and BAT were snap frozen in liquid nitrogen. Total RNA was extracted using the conventional acid guanidinium thiocyanate phenol-chloroform (AGPC) procedure and cleaned up using the RNeasy MinElute Cleanup Kit according to manufacturer's instructions (QIAGEN Valencia, CA).

treatment_protocol: In mice, AP20187 (100 ng/g) or vehicle (4% ethanol, 10% PEG-400, 1.75% Tween-20 in water) was intraperitoneally injected and muscles were collected after 12 h.

tag: strain

value: male

value: BAT

tag: genotype

tag: treatment

value: AP for 12h


title: Mouse_TG_BAT_Vehicle_rep1

description: Gene expression of mouse (Fv2E-PERK) Vehicle BAT

source_name: Mouse Fv2E-PERK, WAT

value: Vehicle


title: Mouse_TG_BAT_AP_rep2


title: 2787 44years M


title: Mouse_TG_BAT_Vehicle_rep2


title: Mouse_TG_WAT_AP_rep3

description: Gene expression of mouse (Fv2E-PERK) WAT after 12 hour treatment of AP

value: WAT


title: 2779 18years F


title: Mouse_TG_WAT_AP_rep2


title: 2791 25years F


title: Mouse_TG_WAT_AP_rep1


title: 2776 32years M


title: Mouse_WT_WAT_UT_rep3

description: Gene expression of mouse (WT) untreated WAT

source_name: Mouse WT

value: WT

value: untreated


title: Mouse_WT_WAT_UT_rep1


title: Furin_cKO_CD4+CD25+FoxP3+_regulatoryTcells

city: Tampere

first: Ilkka

last: Junttila

state: Tampere

address: Arvo Ylpön katu 34

department: Institute of Medical and Life Science

country: Finland

institute: University of Tampere

description: fresh isolated by flow cytometric sorting

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip MOE430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station.

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

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

source_name: CD4+CD25+FoxP3+ regulatory T cells, Furin cKO

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

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

value: 10 - 11 weeks

value: CD4 cre Fur flox/flox

tag: cell markers

value: fresh isolated


title: Mouse_TG_WAT_Vehicle_rep2

description: Gene expression of mouse (Fv2E-PERK) Vehicle WAT


title: WT_CD4+CD25+FoxP3+_regulatoryTcells

source_name: CD4+CD25+FoxP3+ regulatory T cells, WT

value: Fur flox/flox


title: Mouse_TG_WAT_Vehicle_rep1


title: Furin_cKO_CD4+CD62L-CD44+_memoryTcells

source_name: CD4+CD62L-CD44+ memory T cells, Furin cKO


title: Mouse_WT_WAT_UT_rep2


title: 2792 38years M

value: Northern European


title: 2769 61years F


title: Furin_cKO_CD4+CD62L+CD44-Tcells_activated

description: Naive T cells were isolated and activated with plate-bound anti-CD3/CD28 (5/5 µg/ml) fo two days.

source_name: in vitro activated  CD4+CD62L+CD44- naive T cells, Furin cKO

value: in vitro activated


title: 2775 31years M


title: WT_CD4+CD62L-CD44+_memoryTcells

source_name: CD4+CD62L-CD44+ memory T cells, WT


title: H2A_R78A_rep3

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

hyb_protocol: Labeled cRNA was hybridized for 12-14 hours at 45˚C. GeneChips were washed and stained on a GeneChip Fluidics Station 450

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 7G following default scanning protocol

data_processing: Data was processed using the MAS 5.0 analysis method implemented in the bioconductor package in R. Differentially expressed genes were analyzed using limma

organism: Saccharomyces cerevisiae

source_name: H2A R78A mutant yeast

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol

growth_protocol: Yeast cells were grown in Yeast Extract Peptone Dextrose (YPD) media at 30˚C to mid-log phase (OD600 ~ 0.5 to 0.7)

extract_protocol: Total RNA was extracted using hot acid phenol chloroform, and total RNA was cleaned up using an RNeasy minikit

tag: h2a genotype


title: 2773 54years F


title: 2778 35years F


title: 2768 64years M


title: 2772 33years M


title: WT_CD4+CD62L+CD44-Tcells_activated

source_name: in vitro activated CD4+CD62L+CD44- naive T cells, WT


title: H2A_R78A_rep2


title: 2766 17years M

source_name: peripheral blood


title: 2765 55years M


title: 2762 58years M


title: wtH2A_rep1

source_name: wild-type yeast

value: wt


title: wtH2A_rep2


title: wtH2A_rep3


title: H2A_R78A_rep1


title: Viremic Controller_15R

status: Public on Aug 04 2015

city: Barcelona

first: Mireia

last: Arnedo

state: Other

address: Casanovas, 143. CELLEX, A41

department: AIDS Unit

institute: Institut Investigacions Biomediques Agusti Pi i Sunyer (IDIBAPS)

description: non-coding small RNAs

hyb_protocol: Labeled samples were hybridized to the miRNA array at 48°C for 16 h and then washed and stained with a Streptavidin-PE solution prior to imaging.

scan_protocol: Chips were scanned with a GeneChip scanner 3000 G7 (Affimetrix, Santa Clara, CA, USA).

data_processing: All microarray statistical analyses were performed using Bioconductor (http://www.bioconductor.org). After background correction, quantile normalization and median polish summarization the normalized data were fit to a linear model as implemented in bioconductor’s affy package.

source_name: CD8+ T-cells

label_protocol: All procedures were carried out according to the manufacturer's protocols. Briefly, 1 µg of each total RNA sample was poly-A tailed and the proprietary biotin-labeled dendramer molecule was joined to the 3´-end using the FlashTag Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were either isolated from fresh blood by Ficoll-Hypaque gradient centrifugation or used after thawing. PBMCs were cultured in RPMI medium containing 10% FBS and 2% gentamycin. CD8+ T-lymphocytes were isolated for RNA extraction after a positive selection with monoclonal antibodies.conjugated to microbeads AutoMACS (Miltenyi Biotec, Bergisch Gladbach, Germany).

extract_protocol: Total RNA (enriched for small non-coding RNAs) was isolated according to manufacturer’s instructions using the ReliaPrep RNA Cell miniprep system kit (Promega, Fitchburg, WI, USA).

treatment_protocol: The isolated CD8+ population was used to generate resting and stimulated/activated pellets. CD8+ cell-subset was stimulated/activated using 10 ng/ml of CD3-OKT3 (ORTHO biotech Products, L.P., Raritan, NJ, USA) and 400 μg/ml of CD28 (kindly provided by Dr. R. Vilella (Laboratory of Immunology, Hospital Clinic, Barcelona, Spain) during three days.

tag: cell type

value: CD8+ T-cells

tag: patient type

value: Viremic Controller

tag: resting/stimuli

value: R


title: Viremic Controller_15S

description: non-coding small RNAs


title: Viremic Controller_14S

description: non-coding small RNAs


title: 2761 55years F

value: F

value: peripheral blood


title: Mouse_TG_BAT_Vehicle_rep3

value: male

value: BAT


title: 2764 52years F


title: 2760 27years M

value: M


title: 2758 48years M


title: 2763 29years M


title: Viremic Controller_14R

description: non-coding small RNAs


title: 2767 15years F


title: Viremic Progressor_13S

description: non-coding small RNAs

value: Viremic Progressor


title: Treated Patient_14S

description: non-coding small RNAs

value: Treated Patient


title: Treated Patient_14R

description: non-coding small RNAs


title: 2756 35years M


title: Viremic Progressor_12S

description: non-coding small RNAs


title: Viremic Progressor_13R

description: non-coding small RNAs


title: 2757 45years F


title: 2752 38years F


title: 2774 55years M


title: 2781 32years F


title: Elite Controller_15R

description: non-coding small RNAs

value: Elite Controller


title: 2759 27years F


title: Elite Controller_15S

description: non-coding small RNAs


title: Treated Patient_13S

description: non-coding small RNAs


title: Treated Patient_13R

description: non-coding small RNAs


title: 2746 43years F


title: Elite Controller_14S

description: non-coding small RNAs


title: Uninfected Donor_11R

description: non-coding small RNAs

value: Uninfected Donor


title: Viremic Progressor_11R

description: non-coding small RNAs


title: Viremic Progressor_11S

description: non-coding small RNAs


title: Uninfected Donor_11S

description: non-coding small RNAs


title: 2744 67years M


title: Viremic Progressor_10R

description: non-coding small RNAs


title: Viremic Progressor_10S

description: non-coding small RNAs


title: Treated Patient_12S

description: non-coding small RNAs


title: Treated Patient_12R

description: non-coding small RNAs


title: 2658 74years F


title: Treated Patient_11S

description: non-coding small RNAs


title: Elite Controller_13S

description: non-coding small RNAs


title: Viremic Progressor_12R

description: non-coding small RNAs


title: Elite Controller_13R

description: non-coding small RNAs


title: Uninfected Donor_10S

description: non-coding small RNAs


title: Elite Controller_12S

description: non-coding small RNAs


title: Viremic Progressor_09S

description: non-coding small RNAs


title: Uninfected Donor_09R

description: non-coding small RNAs


title: 2745 66years F


title: Elite Controller_12R

description: non-coding small RNAs


title: 2653 71years M


title: Uninfected Donor_09S

description: non-coding small RNAs


title: Viremic Progressor_09R

description: non-coding small RNAs


title: Uninfected Donor_10R

description: non-coding small RNAs


title: Treated Patient_10S

description: non-coding small RNAs


title: Treated Patient_11R

description: non-coding small RNAs


title: Treated Patient_09S

description: non-coding small RNAs


title: Treated Patient_09R

description: non-coding small RNAs


title: Treated Patient_10R

description: non-coding small RNAs


title: Treated Patient_08R

description: non-coding small RNAs


title: Uninfected Donor_08S

description: non-coding small RNAs


title: Treated Patient_08S

description: non-coding small RNAs


title: Uninfected Donor_08R

description: non-coding small RNAs


title: 2755 18years F


title: Elite Controller_14R

description: non-coding small RNAs


title: Elite Controller_11S

description: non-coding small RNAs


title: Elite Controller_10S

description: non-coding small RNAs


title: Elite Controller_11R

description: non-coding small RNAs


title: Elite Controller_09S

description: non-coding small RNAs


title: Viremic Controller_13S

description: non-coding small RNAs


title: Treated Patient_06S

description: non-coding small RNAs


title: Uninfected Donor_07R

description: non-coding small RNAs


title: Uninfected Donor_07S

description: non-coding small RNAs


title: Viremic Controller_11R

description: non-coding small RNAs


title: Viremic Progressor_08R

description: non-coding small RNAs


title: Uninfected Donor_06R

description: non-coding small RNAs


title: Treated Patient_06R

description: non-coding small RNAs


title: Uninfected Donor_06S

description: non-coding small RNAs


title: Viremic Controller_12S

description: non-coding small RNAs


title: Treated Patient_07R

description: non-coding small RNAs


title: Viremic Controller_11S

description: non-coding small RNAs


title: Elite Controller_08R

description: non-coding small RNAs


title: Viremic Controller_13R

description: non-coding small RNAs


title: Elite Controller_09R

description: non-coding small RNAs


title: Elite Controller_08S

description: non-coding small RNAs


title: Elite Controller_10R

description: non-coding small RNAs


title: Treated Patient_07S

description: non-coding small RNAs


title: Viremic Controller_12R

description: non-coding small RNAs


title: Viremic Controller_10S

description: non-coding small RNAs


title: Viremic Progressor_08S

description: non-coding small RNAs


title: Viremic Controller_10R

description: non-coding small RNAs


title: Treated Patient_05S

description: non-coding small RNAs


title: Uninfected Donor_05R

description: non-coding small RNAs


title: Treated Patient_05R

description: non-coding small RNAs


title: Viremic Progressor_06S

description: non-coding small RNAs


title: Viremic Progressor_07S

description: non-coding small RNAs


title: Uninfected Donor_04R

description: non-coding small RNAs


title: Uninfected Donor_05S

description: non-coding small RNAs


title: Viremic Progressor_06R

description: non-coding small RNAs


title: Viremic Controller_09S

description: non-coding small RNAs


title: Uninfected Donor_04S

description: non-coding small RNAs


title: Viremic Progressor_07R

description: non-coding small RNAs


title: Elite Controller_07R

description: non-coding small RNAs


title: Viremic Progressor_05R

description: non-coding small RNAs


title: Elite Controller_05R

description: non-coding small RNAs


title: Treated Patient_04S

description: non-coding small RNAs


title: Elite Controller_04R

description: non-coding small RNAs


title: Elite Controller_04S

description: non-coding small RNAs


title: Elite Controller_05S

description: non-coding small RNAs


title: Viremic Controller_08S

description: non-coding small RNAs


title: Elite Controller_06R

description: non-coding small RNAs


title: Elite Controller_06S

description: non-coding small RNAs


title: Treated Patient_03S

description: non-coding small RNAs


title: Viremic Controller_09R

description: non-coding small RNAs


title: Treated Patient_04R

description: non-coding small RNAs


title: Viremic Progressor_05S

description: non-coding small RNAs


title: Viremic Controller_07S

description: non-coding small RNAs


title: Viremic Controller_08R

description: non-coding small RNAs


title: Elite Controller_07S

description: non-coding small RNAs


title: Viremic Controller_07R

description: non-coding small RNAs


title: Viremic Progressor_04S

description: non-coding small RNAs


title: Treated Patient_03R

description: non-coding small RNAs


title: Viremic Progressor_04R

description: non-coding small RNAs


title: Viremic Progressor_03S

description: non-coding small RNAs


title: Viremic Controller_05S

description: non-coding small RNAs


title: 863b, biological replicate 3

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: Gene expression data from DDLPS, 863b

hyb_protocol: Following fragmentation, 10 ug of fragmented cRNA were hybridized for 16 hr at 45C on Affymetrix U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: Robust multi-array average (RMA) method was used with default options (with background correction, quantile normalization, and log transformation) to normalize raw data from batches using R/Bioconductor‘s affy package (12925520). For genes, which have represented by multiple probes on the array, maximum expression value was retained for further analyses. A gene is called as differentially expressed if FDR corrected p-value is less than 0.05, which is calculated with empirical Bayes method by eBayes function in Bioconductor’s limma package

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Plus reagent kit user manual (P/N 703210 Rev. 1) from 1 ug total RNA [Expression Analysis Technical Manual, 2009, Affymetrix (P/N 702232 Rev. 3)].

growth_protocol: LPS cell lines were cultures in DMEM containing 10% fetal bovine serum and maintained in standard tissue culture conditions (5% CO2, 37 degrees Celsius).

extract_protocol: Extraction of total RNA was performed using Qiagen RNaccording to the manufacturer's instructions.

treatment_protocol: Prior to extraction of total RNA, cells were treated with 0.25% trypsin and washed with PBS.

tag: cell line

value: DDLPS


title: Viremic Progressor_03R

description: non-coding small RNAs


title: Viremic Controller_06R

description: non-coding small RNAs


title: Viremic Controller_05R

description: non-coding small RNAs


title: Elite Controller_03S

description: non-coding small RNAs


title: Viremic Controller_06S

description: non-coding small RNAs


title: 863b, biological replicate 2

description: Gene expression data from DDLPS, 863b


title: Elite Controller_03R

description: non-coding small RNAs


title: Treated Patient_02R

description: non-coding small RNAs


title: Treated Patient_02S

description: non-coding small RNAs


title: Uninfected Donor_03R

description: non-coding small RNAs


title: Uninfected Donor_03S

description: non-coding small RNAs


title: 247b, biological replicate 3

description: Gene expression data from WDLPS, 247b

value: WDLPS


title: 029b, biological replicate 1

description: Gene expression data from WDLPS, 029b


title: 863b, biological replicate 1

description: Gene expression data from DDLPS, 863b


title: 029b, biological replicate 2

description: Gene expression data from WDLPS, 029b


title: 247b, biological replicate 1

description: Gene expression data from WDLPS, 247b


title: 247b, biological replicate 2

description: Gene expression data from WDLPS, 247b


title: Elite Controller_02S

description: non-coding small RNAs


title: 029b, biological replicate 3

description: Gene expression data from WDLPS, 029b


title: 224b, biological replicate 2

description: Gene expression data from DDLPS, 224b


title: 224a, biological replicate 3

description: Gene expression data from DDLPS, 224a


title: 224b, biological replicate 1

description: Gene expression data from DDLPS, 224b


title: 246a, biological replicate 3

description: Gene expression data from DDLPS, 248


title: 246a, biological replicate 2

description: Gene expression data from DDLPS, 247


title: 246a, biological replicate 1

description: Gene expression data from DDLPS, 246


title: 224b, biological replicate 3

description: Gene expression data from DDLPS, 224b


title: Primary open-angle glaucoma group C

city: Shanghai，China

first: Xiangmei

last: Kong

address: 83 Fenyang Road, Xuhui District

department: Department of Ophthalmology

institute: Eye & ENT Hospital of Fudan University

description:
Total RNAs were isolated using TRIzolLS (Invitrogen, Grand Island, NY, USA) and a miRNeasy mini kit (Qiagen, Shenzhen, China), which efficiently obtained all RNA species, including miRNAs. RNA was measured using the NanoDrop 1000 (ND-1000, Nanodrop Technologies), and then labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform containing 3100 capture probes.
PC

hyb_protocol: The samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform.

scan_protocol: Following the washing steps the slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA) and imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.

data_processing: Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expression data were normalized using the median normalization.

source_name: Primary open-angle glaucoma group

label_protocol: Total RNAs (100 ng) were hy3-labeled using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions.

extract_protocol: At the beginning of the surgery the aqueous humor was collected as previously reported. After a corneal paracentesis, a 30-gauge needle on a tuberculin microsyringe was used to aspirate aqueous humor from the anterior chamber, not contacting any iris or lens tissue during the whole sample collection. Approximately 0.1-0.2ml of aqueous humor was collected from each patient, transferred to 1.5ml tubes, and immediately placed on dry ice. Then the samples were subsequently stored at −80°C until analysis.

tag: subject group

value: ocular hypertensive POAG patient group

tag: mean age

value: 65.8 years

tag: gender (male

value: female) ratio in the group:3:2

value: Aqueous humor


title: Viremic Controller_04S

description: non-coding small RNAs

value: CD8+ T-cells

value: Viremic Controller


title: Viremic Controller_03S

description: non-coding small RNAs


title: Primary open-angle glaucoma group A

description:
Total RNAs were isolated using TRIzolLS (Invitrogen, Grand Island, NY, USA) and a miRNeasy mini kit (Qiagen, Shenzhen, China), which efficiently obtained all RNA species, including miRNAs. RNA was measured using the NanoDrop 1000 (ND-1000, Nanodrop Technologies), and then labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform containing 3100 capture probes.
PA

value: 65.6 years

tag: tissue


title: Normal group C

description:
Total RNAs were isolated using TRIzolLS (Invitrogen, Grand Island, NY, USA) and a miRNeasy mini kit (Qiagen, Shenzhen, China), which efficiently obtained all RNA species, including miRNAs. RNA was measured using the NanoDrop 1000 (ND-1000, Nanodrop Technologies), and then labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) and hybridized on the specific miRCURY ™ LNA Array (v.18.0, Exiqon, Denmark) platform containing 3100 capture probes.
NC

source_name: normal group

value: patients with cataract undergoing cataract surgery

value: 68.0 years


title: Treated Patient_01S

description: non-coding small RNAs


title: Uninfected Donor_02R

description: non-coding small RNAs

value: R


title: Viremic Controller_04R

description: non-coding small RNAs


title: Elite Controller_01S

description: non-coding small RNAs


title: Treated Patient_01R

description: non-coding small RNAs


title: Viremic Controller_03R

description: non-coding small RNAs


title: Elite Controller_02R

description: non-coding small RNAs