title: beer-00153: LN73

source_name: normal

tag: organism

value: Homo Sapiens

tag: age (years)

value: normal lung

tag: tumor size (cm)

tag: nodal status

tag: followup time (months)

tag: death (1=dead,0=alive)

tag: differentiation

tag: p53 nucl.accum.

tag: k-ras mutation

tag: smoking (pack years)


title: beer-00153: LN74

status: Public on May 06 2015

type: RNA

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

country: USA

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: Sex

value: normal

tag: histology


title: beer-00153: LN71

scan_protocol: See mage-tab files linked to series entry for additional details


title: HeLa H2A overexpression, replicate 1

city: New York

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

description: HeLa H2A overexpression, replicate 1

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

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

data_processing: DNA microarray analyses were performed with R. RMA normalization and log2 transformation was used. Differentially expressed genes were called if FC ≥1.5 and p<0.05.

source_name: HeLa H2A overexpression

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

growth_protocol: HeLa and Namalwa cell lines (purchased from ATCC) were maintained in DMEM and RPMI respectively, containing 10% FBS,

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified with the RNAeasy kit from QIAGEN

treatment_protocol: Cells were infected with Sendai virus (+SV) for 6 and 12 hours. Double stranded shRNA sequences directed against macroH2A1 or a scramble sequence were cloned into the pLL3.7 vector harbouring GFP and recombinant lentiviral particles were produced and purified before transfection into the different cell lines.

tag: cell line

value: HeLa

tag: expression

value: H2A overexpression


title: WT ProB and PreB bone marrow cells, biological replicate 2

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

country: Spain

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description:
SAMPLE 16
Gene expression data from WT ProB and PreB bone marrow cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The RMA function provided by the package oligo from R/Bioconductor was applied to the raw expression data.

organism: Mus musculus

source_name: WT ProB and PreB bone marrow cells

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

growth_protocol: Animals were housed in conventional facility and they have been exposed to common pathogens.

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

treatment_protocol: Not applicable

tag: strain background

tag: genotype/variation

value: wild type

tag: tissue/cell type

value: Bone marrow ProB and PreB Cells


title: Namalwa shscr, replicate 1

description: Namalwa shscr, replicate 1

source_name: Namalwa shscr

value: Namalwa

tag: treatment

value: scramble sequence


title: Namalwa shmH2A1, replicate 2

source_name: Namalwa shmH2A2

value: shRNA sequences directed against macroH2A1


title: Namalwa shscr + SV 6 hours, replicate 2

source_name: Namalwa shscr + SV 6 hours

tag: infection

value: Sendai virus (+SV) for 6 hours


title: WT ProB and PreB bone marrow cells, biological replicate 1

description:
SAMPLE 15
Gene expression data from WT ProB and PreB bone marrow cells


title: Namalwa shmH2A1, replicate 3

source_name: Namalwa shmH2A3


title: beer-00153: LN72B

data_processing: See mage-tab files linked to series entry for additional details

tag: organism

tag: age (years)

tag: tumor size (cm)


title: B220+ bone marrow B cells, biological replicate 5

description:
SAMPLE 14
Gene expression data from B220+ bone marrow B cells

source_name: B220+ bone marrow B cells

value: Bone marrow B220 Cells


title: Namalwa shmH2A1, replicate 1

description: Namalwa shmH2A1, replicate 1

source_name: Namalwa shmH2A1


title: HeLa shscr + SV 6 hours, replicate 3

source_name: HeLa shscr + SV 6 hours


title: Namalwa shscr, replicate 2


title: B220+ bone marrow B cells, biological replicate 4

description:
SAMPLE 13
Gene expression data from B220+ bone marrow B cells


title: HeLa shscr + SV 6 hours, replicate 2


title: B220+ bone marrow B cells, biological replicate 3

description:
SAMPLE 12
Gene expression data from B220+ bone marrow B cells


title: HeLa shmH2A1 + SV 6 hours, replicate 3

source_name: HeLa shmH2A1 + SV 6 hours


title: beer-00153: LN69

label_protocol: See mage-tab files linked to series entry for additional details

tag: nodal status

tag: followup time (months)

tag: death (1=dead,0=alive)


title: beer-00153: LN70

extract_protocol: See mage-tab files linked to series entry for additional details

tag: differentiation

tag: p53 nucl.accum.

tag: k-ras mutation


title: beer-00153: LN67

tag: Sex

tag: histology

tag: smoking (pack years)


title: HeLa shmH2A1 + SV 6 hours, replicate 2

tag: cell line


title: HeLa shscr, replicate 3

source_name: HeLa shscr


title: beer-00153: L99

source_name: lung cancer

value: M

value: lung cancer

value: lung

value: lung adenocarcinoma

value: bronchial alveolar / mucinous

value: Well


title: HeLa shmH2A1 + SV 6 hours, replicate 1

description: HeLa shmH2A1 + SV 6 hours, replicate 1


title: HeLa shscr, replicate 2


title: B220+ bone marrow B cells, biological replicate 2

description:
SAMPLE 11
Gene expression data from B220+ bone marrow B cells

tag: strain background

tag: genotype/variation


title: beer-00153: LN64

value: Homo Sapiens

value: normal lung


title: beer-00153: LN66

value: normal


title: HeLa shscr + SV 6 hours, replicate 1

description: HeLa shscr + SV 6 hours, replicate 1

value: HeLa

tag: treatment


title: HeLa shmH2A1, replicate 2

source_name: HeLa shmH2A1


title: Namalwa SV 12 hours, replicate 3

source_name: Namalwa SV 12 hours

tag: infection

value: Sendai virus (+SV) for 12 hours


title: HeLa shmH2A1, replicate 1

description: HeLa shmH2A1, replicate 1


title: HeLa shscr, replicate 1

description: HeLa shscr, replicate 1


title: Pax5 +/- bone marrow cells, biological replicate 5

description:
SAMPLE 8
Gene expression data from Pax5 +/- bone marrow cells

source_name: Pax5 +/- bone marrow cells

tag: tissue/cell type

value: Bone marrow


title: beer-00153: L97

tag: organism

value: F

tag: age (years)

value: bronchial alveolar


title: beer-00153: L96

value: bronchial derived

tag: tumor size (cm)

tag: nodal status

value: Moderate


title: HeLa shmH2A1, replicate 3

value: shRNA sequences directed against macroH2A1


title: B220+ bone marrow B cells, biological replicate 1

description:
SAMPLE 10
Gene expression data from B220+ bone marrow B cells

value: wild type

value: Bone marrow B220 Cells


title: beer-00153: L95

value: lung cancer

value: lung

tag: followup time (months)

tag: death (1=dead,0=alive)

value: Poor


title: Namalwa SV 12 hours, replicate 1

description: Namalwa SV 12 hours, replicate 1

value: Namalwa


title: Pax5 +/- bone marrow cells, biological replicate 6

description:
SAMPLE 9
Gene expression data from Pax5 +/- bone marrow cells


title: Namalwa shmH2A1 + SV 6 hours, replicate 1

source_name: Namalwa shmH2A1 + SV 6 hours

value: Sendai virus (+SV) for 6 hours


title: Namalwa SV 6 hours, replicate 3

source_name: Namalwa SV 6 hours


title: Namalwa SV 12 hours, replicate 2


title: Pax5 +/- bone marrow cells, biological replicate 3

description:
SAMPLE 6
Gene expression data from Pax5 +/- bone marrow cells


title: Namalwa SV 6 hours, replicate 2


title: Pax5 +/- bone marrow cells, biological replicate 2

description:
SAMPLE 5
Gene expression data from Pax5 +/- bone marrow cells


title: Pax5 +/- bone marrow cells, biological replicate 1

description:
SAMPLE 4
Gene expression data from Pax5 +/- bone marrow cells


title: beer-00153: L94

value: Homo Sapiens

value: M

value: lung adenocarcinoma

value: bronchial derived/mucinous

tag: differentiation

tag: p53 nucl.accum.


title: Namalwa SV 6 hours, replicate 1

description: Namalwa SV 6 hours, replicate 1


title: beer-00153: L92

tag: Sex

tag: k-ras mutation


title: Pax5 +/- bone marrow cells, biological replicate 4

description:
SAMPLE 7
Gene expression data from Pax5 +/- bone marrow cells

value: Bone marrow


title: Namalwa no infection, replicate 3

source_name: Namalwa no infection

value: no infection


title: Namalwa no infection, replicate 2


title: Pax5 ProB and PreB bone marrow cells, biological replicate 3

description:
SAMPLE 3
Gene expression data from Pax5 ProB and PreB bone marrow cells

source_name: Pax5 ProB and PreB bone marrow cells

value: Bone marrow ProB and PreB Cells


title: Namalwa no infection, replicate 1

description: Namalwa no infection, replicate 1


title: Pax5 ProB and PreB bone marrow cells, biological replicate 2

description:
SAMPLE 2
Gene expression data from Pax5 ProB and PreB bone marrow cells


title: beer-00153: L91

tag: histology

tag: smoking (pack years)


title: beer-00153: L90

value: F

value: bronchial derived/papillary


title: HeLa SV 12 hours, replicate 3

source_name: HeLa SV 12 hours

tag: cell line

value: HeLa

value: Sendai virus (+SV) for 12 hours


title: HeLa SV 12 hours, replicate 2


title: beer-00153: L89

value: bronchial derived

value: Moderate


title: beer-00153: L88

value: lung cancer

value: lung


title: HeLa SV 6 hours, replicate 1

description: HeLa SV 6 hours, replicate 1

source_name: HeLa SV 6 hours


title: brown-00173: BC305A-BE

source_name: common “reference” mRNA pool

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

tag: tissue

value: Breast

tag: cell type

value: Primary tumor


title: HeLa SV 6 hours, replicate 3

tag: infection

value: Sendai virus (+SV) for 6 hours


title: EPCs, DHT-treated 3

city: shanghai

first: Li

middle: xi

last: zhe

address: xinsongjianglu 650

department: cadiovascular surgery

country: China

institute: Shanghai general hospital

description: Gene expression data from DHT-treated mice endothelial progenitor cells

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix Expression Console default analysis settings and global scaling as normalization method. Normalized signal intensities were transformed to the log base 2 scale.

source_name: 10nmol/L DHT-treated-EPCs

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

growth_protocol: mononuclear cells were separated from the spine, gladiolus, humerus, tibia and femur using Ficoll density gradient centrifugation and cultured on Endothelial Cell Basal Medium-2 (Lonza, Switzerland), supplemented with EGM-2 MV SingleQuots (Lonza, Switzerland) and 10% fetal bovine serum. Following two days of culture in a 5% CO2 incubator, non-adherent cells were removed by washing with phosphate-buffered saline (PBS) and adherent cells were incubated in fresh medium for a further five days for characterization.

extract_protocol: All samples were prepared using Trizol. Total RNA was isolated using the RNeasy Mini Kit (QIAGEN), cDNA synthesis and amplification was performed using the WT cDNA synthesis and amplification kit (Affymetrix).

treatment_protocol: For microarray analysis and qPCR, the cells were grown in culture medium supplemented with 10nmol/L DHT, which was changed on day 2. On day 7, cells was collected for RNA extraction and subsequent experiments.

value: bone marrow

tag: strain

tag: age

value: 8 weeks

value: endothelial progenitor cells (EPCs)


title: beer-00153: LN75

source_name: normal

tag: organism

value: Homo Sapiens

tag: age (years)

value: normal

value: normal lung


title: beer-00153: L84

value: F

value: lung adenocarcinoma

tag: tumor size (cm)

tag: nodal status

value: Poor


title: beer-00153: L83

value: bronchial alveolar/mucinous

tag: followup time (months)

tag: death (1=dead,0=alive)

value: Well


title: beer-00153: L87

value: M

value: lung cancer

value: bronchial derived

tag: differentiation

value: Moderate

tag: p53 nucl.accum.


title: EPCs, DHT-treated 2


title: HeLa SV 12 hours, replicate 1

description: HeLa SV 12 hours, replicate 1

value: HeLa

value: Sendai virus (+SV) for 12 hours


title: HeLa SV 6 hours, replicate 2

value: Sendai virus (+SV) for 6 hours


title: EPCs, blank control 2

description: Gene expression data from untreated mice endothelial progenitor cells

source_name: blank control EPCs

value: bone marrow

value: 8 weeks


title: Pax5 ProB and PreB bone marrow cells, biological replicate 1

description:
SAMPLE 1
Gene expression data from Pax5 ProB and PreB bone marrow cells

tag: strain background

tag: genotype/variation

tag: tissue/cell type

value: Bone marrow ProB and PreB Cells


title: HeLa no infection, replicate 3

source_name: HeLa no infection

tag: cell line

value: no infection


title: EPCs, blank control 1

tag: tissue

value: endothelial progenitor cells (EPCs)


title: HeLa no infection, replicate 1

description: HeLa no infection, replicate 1


title: HeLa no infection, replicate 2


title: brown-00173: 184B5

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

value: Breast

tag: cell type

value: Cell-line


title: brown-00173: NB4+ATRA


title: beer-00153: L86

value: Homo Sapiens

tag: Sex

value: F

value: lung

value: lung adenocarcinoma

tag: histology

value: bronchial alveolar

tag: k-ras mutation

tag: smoking (pack years)


title: beer-00153: L85

tag: organism

value: M

tag: age (years)

value: lung cancer

value: bronchial derived/mucinous

value: Moderate


title: beer-00153: L82

value: bronchial alveolar/bronchial derived

tag: tumor size (cm)

tag: nodal status

value: Well


title: brown-00173: 184Aa


title: beer-00153: L81

tag: followup time (months)

tag: death (1=dead,0=alive)


title: brown-00173: HUVEC

source_name: HUVEC


title: EPCs, DHT-treated 1

value: bone marrow

tag: strain

tag: age

value: 8 weeks


title: beer-00153: L79

value: bronchial derived

tag: differentiation

value: Poor

tag: p53 nucl.accum.


title: brown-00173: HMVEC

tag: cell line

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

source_name: HMVEC

value: Breast


title: beer-00153: L80

source_name: lung cancer

value: Homo Sapiens


title: EPCs, blank control 3

tag: tissue

value: endothelial progenitor cells (EPCs)


title: brown-00173: 184A1-LATE

tag: cell type

value: Cell-line


title: brown-00173: SW872


title: brown-00173: MOLT4


title: brown-00173: BC790

value: Primary tumor


title: beer-00153: L65

tag: Sex

value: lung

value: lung adenocarcinoma


title: beer-00153: L76

value: M

value: lung cancer

tag: histology


title: brown-00173: BC23


title: beer-00153: L62

value: F

value: Moderate

tag: k-ras mutation


title: GR Injected, biological rep5

first: Jean-Pierre

last: Saint-Jeannet

state: NY

address: 345 East 24th Street

department: Basic Science and Craniofacial Biology

institute: New York University

hyb_protocol: 3ug of labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Xenopus laevis 2.0  GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A GeneChip 3000 7G scanner was used to collect fluorescence signal

data_processing: Cel files were imported into Partek Genomics Suite (Partek Inc., St. Louis, MO) where GCRMA normalization was applied

label: Biotin

organism: Xenopus laevis

source_name: Animal cap explant dissected from embryo injected with GR mRNA

label_protocol: Microarray services were provided by the UPENN Molecular Profiling Facility, including quality control tests of the total RNA samples by Agilent Bioanalyzer and Nanodrop spectrophotometry. All protocols were conducted as described in the NuGEN Ovation User Guide and the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, 100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly(T) and random oligomers that incorporated an RNA priming region.  Second-strand cDNA synthesis was followed by ribo-SPIA linear amplification of each transcript using an isothermal reaction with RNase, RNA primer and DNA polymerase. The resulting cDNA was fragmented, assessed by Bioanalyzer, and biotinylated by terminal transferase end labeling.

extract_protocol: Individual animal cap explants were homogenized and total RNA extracted using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: Xenopus laevis embryos were injected at the 2-cell stage with mRNA encoding Pax3GR and Zic1GR , the hormone-inducible version of Pax3 and Zic1, alone or in combination. At the blastula stage (stage9), animal cap explants were dissected and cultured for 8 hours in the presence of dexamethasone. A glucocorticoid receptor (GR) mRNA was also injected as negative control.

value: Blastula stage animal cap explant

tag: treatment

value: Animal cap explant treated with dexamethasone for 8 hours

tag: injection

value: GR


title: beer-00153: L64

tag: organism

tag: age (years)

value: bronchial derived

tag: smoking (pack years)


title: beer-00153: L57

value: bronchial derived/papillary

tag: tumor size (cm)

tag: nodal status

tag: followup time (months)


title: beer-00153: L61

tag: death (1=dead,0=alive)


title: beer-00153: L78

tag: differentiation


title: brown-00173: BC308B-BE

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: beer-00153: L59

tag: p53 nucl.accum.


title: beer-00153: L56

value: bronchial derived/clear cell


title: GR Injected, biological rep4


title: GR Injected, biological rep2


title: Pax3GR/Zic1GR Injected, biological rep5

source_name: Animal cap explant dissected from embryo injected with Pax3GR and Zic1GR mRNA


title: GR Injected, biological rep1


title: beer-00153: L54

value: Homo Sapiens

value: Poor


title: brown-00173: BC708A-AF

tag: cell line

source_name: BC708A-AF weak in middle, redo?

value: Breast


title: beer-00153: L53


title: Pax3GR/Zic1GR Injected, biological rep4

tag: tissue


title: GR Injected, biological rep3


title: Pax3GR/Zic1GR Injected, biological rep3


title: beer-00153: L52

value: bronchial alveolar

value: Well


title: Pax3GR/Zic1GR Injected, biological rep1


title: Pax3GR/Zic1GR Injected, biological rep2


title: brown-00173: BC808A-BE

tag: cell type

value: Primary tumor


title: brown-00173: BC208B-AF


title: Zic1GR Injected, biological rep5

source_name: Animal cap explant dissected from embryo injected with Zic1GR mRNA


title: beer-00153: L50

tag: Sex

value: M

value: lung

value: lung adenocarcinoma


title: brown-00173: BC117A-BE


title: Zic1GR Injected, biological rep4


title: brown-00173: BC711B-BE


title: Zic1GR Injected, biological rep3


title: brown-00173: BC808A-AF


title: brown-00173: BC807A-BE


title: beer-00153: L49

value: F

value: lung cancer

tag: histology

value: Moderate


title: brown-00173: RPMI-8226

value: Cell-line


title: brown-00173: BC123A-AF


title: brown-00173: Normal Breast2

source_name: Normal Breast2 (pooled NB2)


title: Zic1GR Injected, biological rep2

value: Blastula stage animal cap explant

value: Animal cap explant treated with dexamethasone for 8 hours


title: brown-00173: BC112B-BE

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: brown-00173: BC214B-BE


title: beer-00153: L45

value: bronchial derived

tag: k-ras mutation


title: beer-00153: L48

value: Homo Sapiens


title: beer-00153: L43


title: brown-00173: Normal Breast-Norway1


title: beer-00153: L41

value: bronchial derived/clear cell

value: Poor


title: brown-00173: BC112A-AF

value: Breast


title: beer-00153: L42

value: Well


title: Pax3GR Injected, biological rep3

source_name: Animal cap explant dissected from embryo injected with Pax3GR mRNA

tag: treatment


title: beer-00153: L46


title: beer-00153: L47


title: Pax3GR Injected, biological rep4

tag: injection


title: Zic1GR Injected, biological rep1


title: brown-00173: BC38-LN38

value: Primary tumor


title: Pax3GR Injected, biological rep5


title: brown-00173: BC213B-BE


title: beer-00153: L38

tag: organism


title: beer-00153: L40

tag: age (years)


title: brown-00173: BC110A-AF


title: beer-00153: L37

value: M

tag: smoking (pack years)


title: brown-00173: BC37-FA


title: Pax3GR Injected, biological rep2


title: beer-00153: L36

value: lung

value: bronchial derived/papillary

tag: tumor size (cm)


title: brown-00173: BC110B-BE


title: beer-00153: L34

value: lung adenocarcinoma

tag: nodal status


title: clonal human induced pluripotent stem cell line E2 rep2

city: Kiel

first: Franz-Josef

last: Müller

address: Niemannsweg 147

department: Klinik für Psychiatrie und Psychotherapie

country: Germany

institute: Zentrum für Integrative Psychiatrie Kiel

hyb_protocol: standard protocol according to vendor guidlines (www.illumina.com)

data_processing: data was extracted with GenomeStudio 2010 with no background correction, VST transformation and RSN normalization (both as provided by the lumi R/Bioconductor package)

source_name: in vitro culture of hiPSC line Clone E2

extract_protocol: mRNA extraction kit (Quiagen)

tag: cell line/clone

value: hiPSC reprogrammed with an integrating vector


title: beer-00153: L35

value: lung cancer

tag: followup time (months)

tag: death (1=dead,0=alive)

value: Moderate


title: brown-00173: BC710B-AF


title: clonal human induced pluripotent stem cell line C1 rep2

scan_protocol: standard protocol according to vendor guidlines (www.illumina.com)

source_name: in vitro culture of hiPSC line Clone C1

value: episomally reprogrammed hiPSC


title: brown-00173: BC118A-AF


title: clonal human induced pluripotent stem cell line A1 rep2

source_name: in vitro culture of hiPSC line Clone A1

label_protocol: standard protocol according to vendor guidlines (www.illumina.com)


title: clonal human induced pluripotent stem cell line C1 rep1


title: clonal human induced pluripotent stem cell line E2 rep1


title: Pax3GR Injected, biological rep1

value: Blastula stage animal cap explant

value: Animal cap explant treated with dexamethasone for 8 hours


title: brown-00173: BC2-LN2

source_name: common “reference” mRNA pool

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: beer-00153: L31

value: Homo Sapiens

value: F

value: bronchial alveolar/mucinous

tag: differentiation

tag: p53 nucl.accum.


title: beer-00153: L27

value: bronchial derived

value: Poor


title: Epiblast_E6.5_rep2

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: E6.5 epiblast

hyb_protocol: After hybridization cocktails preparation, the Affymetrix GeneChip Primeview Gene Expression Arrays were hybridized with the fragmented labelled cRNA for 16 h at 45 °C as described in the Affymetrix Technical Analysis Manual.

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner 3000 7G.

data_processing: CEL files were analyzed using the oligo package in R/Bioconductor and normalized using RMA

source_name: In vivo epiblast tissue

label_protocol: The Affymetrix GeneChip microarrays was performed by the Functional Genomics Core Facility at The Salk Institute for Biological Studies following the manufacturer’s protocol (Affymetrix, Santa Clara, CA). Briefly, 100 ng of total RNA of each sample were processed using Affymetrix GeneChip 3’ IVT Expression Kit following the manufacturer’s protocol. For each sample, 12.5 μg fragmented and labeled aRNA were hybridized to the Affymetrix PrimeView Human Gene Expression Arrays.

growth_protocol: ESCs were grown on MEFs in N2B27 media supplimented with 2I (CHIR99021, 3uM; PD0325901, 1uM) and LIF(Millipore) 10ug/ml; EpiSCs were grown on MEFs in N2B27 media containing 12ng/ml FGF2 and 20ng/ml Activin-A  supllementated with 20% KSR; IS-EPIs were grown on MEFs in N2B27 media containing 20ng/ml and IWR1 2.5uM

extract_protocol: Total RNA of all samples was extracted using Rneasy Mini Kit (Qiagen) and subjected to amplification with MessageAmpII aRNA kit (Ambion) per manufacturer's instructions.

value: E6.5 epiblast

tag: passages

value: Embryonic day 6.5

tag: strain

value: OCT4-deltaPE-GFP x C57BL/14


title: brown-00173: BC38

tag: cell line

tag: tissue

value: Breast

tag: cell type

value: Primary tumor


title: brown-00173: HMEC-C Confluent

source_name: HMEC-C Confluent

value: Cell-line


title: human embryonic stem cells

source_name: in vitro culture of hESC line WA09

value: hESC


title: beer-00153: L26

tag: Sex

value: M

value: lung cancer

value: lung

value: lung adenocarcinoma

tag: histology

tag: k-ras mutation


title: Epiblast_E6.5_rep1

description: E6.5 epiblast

value: OCT4-deltaPE-GFP x C57BL/13


title: beer-00153: L33

tag: organism

value: Homo Sapiens

tag: age (years)

value: Moderate


title: clonal human induced pluripotent stem cell line A1 rep1

value: episomally reprogrammed hiPSC


title: brown-00173: BC805A-BE

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: Epiblast_E5.75_rep2

description: E5.75 epiblast

value: E5.75 epiblast

value: Embryonic day 5.75

value: OCT4-deltaPE-GFP x C57BL/12


title: beer-00153: L30

value: F

value: bronchial derived

tag: tumor size (cm)

tag: smoking (pack years)


title: rsEpiSCs_E6.5_rep1

description: E6.5 derived IS-EPIs

source_name: Intrinsic state epiblast stem cells

value: E6.5 derived IS-EPIs

value: OCT4-deltaPE-GFP x C57BL/9


title: brown-00173: BC115A-AF

value: Breast

value: Primary tumor


title: brown-00173: BC115B-BE


title: rsEpiSCs_E6.5_rep2

description: E6.5 derived IS-EPIs

value: OCT4-deltaPE-GFP x C57BL/10


title: brown-00173: BC710A-BE


title: Fibroblast

source_name: in vitro culture of fibroblast cell line

tag: cell line/clone

value: fibroblasts


title: Epiblast_E5.75_rep1

description: E5.75 epiblast

value: OCT4-deltaPE-GFP x C57BL/11


title: rsEpiSCs_E5.75_rep2

description: E5.75 derived IS-EPIs

value: E5.75 derived IS-EPIs

value: OCT4-deltaPE-GFP x C57BL/8


title: rsEpiSCs_E5.75_rep1

description: E5.75 derived IS-EPIs

value: OCT4-deltaPE-GFP x C57BL/7


title: brown-00173: Normal Breast1

source_name: Normal Breast 1 (6 pooled)


title: beer-00153: L23

source_name: lung cancer

value: Homo Sapiens

value: M

value: lung cancer

value: lung

value: lung adenocarcinoma

value: bronchial derived/papillary

tag: nodal status

tag: followup time (months)

value: Moderate


title: beer-00153: L25

value: F

value: bronchial derived

tag: death (1=dead,0=alive)

tag: differentiation

value: Well


title: brown-00173: T47D

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

value: Breast

value: Cell-line


title: beer-00153: L20

value: bronchial alveolar

tag: p53 nucl.accum.


title: brown-00173: BC214A-AF

value: Primary tumor


title: beer-00153: L24

value: Poor


title: Namalwa_Input_Replicate2

type: SRA

city: Athens

first: Dimitris

last: Thanos

address: 4 Soranou Ephessiou

department: Basic Research II

country: Greece

institute: BIOMEDICAL RESEARCH FOUNDATION ACADEMY OF ATHENS (BRFAA)

description:
Input-seq
Processed data file: Namalwa_Input_Replicate1+2.bed
This is an early experiment from which the sequencing facility provide not fastq but rather fasta format (Namalwa_Input_Replicate2.txt.bz2).

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
ChIP-seq reads were aligned to the hg18 genome assembly using ELAND or Bowtie
Data were filtered using FastQC.
RNA-seq RPKM data were calculated by counting the  number of reads inRefSeq annotated exons.
Genome_build: hg18
Supplementary_files_format_and_content: ChIP-seq: bed files were generated using in-house unix scripts.
Supplementary_files_format_and_content: RNA-seq: Tab-delimited .txt file reporting RPKM exons values.

molecule: genomic DNA

source_name: Namalwa B lymphoblasts

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for ChIP-seq. RNA was harvested using Trizol reagent and mRNA isolated with polydT dynabeads. Strand-specific protocol was used with 5 ug of mRNA for the construction of the library.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment  and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for a controlled (qPCR estimated) cycles and library fragments of ~220 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (GA), GAIIx, or Hiseq2000) following the manufacturer's protocols.

value: Namalwa B lymphoblasts

tag: chip antibody

value: none (input)


title: EpiSC_rep2

description: E5.75 derived EpiSCs

source_name: Epiblast stem cells

value: E5.75 derived EpiSCs

tag: passages

tag: strain

value: OCT4-deltaPE-GFP x C57BL/6


title: EpiSC_rep1

description: E5.75 derived EpiSCs

tag: cell type


title: brown-00173: HMEC-C+IFNalpha

tag: cell line

source_name: HMEC-C+IFNalpha 24hours

tag: tissue


title: ESC_rep2

description: E3.5 derived ESCs

source_name: Embryonic stem cells

value: E3.5 derived ESCs


title: beer-00153: L22

value: Homo Sapiens

tag: Sex

value: M

value: lung cancer

value: lung

value: lung adenocarcinoma

tag: histology

tag: k-ras mutation


title: beer-00153: L19

tag: organism

tag: age (years)

value: bronchial derived

tag: tumor size (cm)

value: Moderate


title: beer-00153: L18

value: F

tag: nodal status

value: Well

tag: smoking (pack years)


title: brown-00173: MDA-MB-231-NCI

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

value: Breast

value: Cell-line


title: beer-00153: L17

value: bronchial derived/papillary

tag: followup time (months)

tag: death (1=dead,0=alive)


title: brown-00173: BC708B-BE

value: Primary tumor


title: beer-00153: L13

tag: differentiation

tag: p53 nucl.accum.


title: ESC_rep1

description: E3.5 derived ESCs

tag: passages


title: beer-00153: L12


title: brown-00173: BC711A-AF


title: brown-00173: BC208A-BE


title: beer-00153: L111

value: bronchial alveolar


title: F+S+ D1

city: Montreal

first: Eva

last: d'Hennezel

state: Quebec

address: 1650 Cedar avenue

department: Microbiology and Immunology

country: Canada

institute: McGill University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: data were normalized using the robust-spline (RSN) method, without background correction and with base 2-logarithmic transformation, using the R software.

source_name: clone

label_protocol: Biotinylated cRNA were prepared with the NuGen ovation kit for Illumina arrays

growth_protocol: Individual CD4+CD25High or Cd4+CD25- T cells were isolated from human PBMCs and expanded in vitro by activation in the presence of anti-CD3 antibody and exogenous rhIL-2 and irradiated allogeneic feeders cells (PBMCs)

extract_protocol: RNA was extracted with RNeasy mini kit, including on-column DNAse I in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Wh

tag: culture

value: Clone

tag: activation

value: resting

tag: donor

tag: foxp3 expression

tag: function

value: suppressive


title: brown-00173: BC402B-AF

tag: cell line

tag: tissue

tag: cell type


title: beer-00153: L11

tag: organism

value: Homo Sapiens

tag: Sex

tag: age (years)

tag: histology

tag: k-ras mutation


title: beer-00153: L107

value: lung cancer

tag: tumor size (cm)

tag: nodal status

tag: followup time (months)

tag: death (1=dead,0=alive)

value: well/mod.

tag: smoking (pack years)


title: brown-00173: BC111B-BE


title: beer-00153: L108

value: lung

value: lung adenocarcinoma

tag: differentiation

tag: p53 nucl.accum.


title: FEEDER CTL4

description: this sample was produced by control wells where no T cell was seeded and only the irradiated feeders were maintained throughout the expansion protocol

source_name: irradiated feeder contribution

tag: culture

value: irradiated feeders

tag: activation

tag: donor

tag: foxp3 expression


title: F-S- D1

tag: function

value: not suppressive


title: FEEDER CTL1 ACT

value: activated


title: beer-00153: L106

tag: organism

value: F

value: Well


title: beer-00153: L105

tag: Sex

value: bronchial alveolar/papillary


title: brown-00173: BC116A-BE

tag: cell line

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

tag: tissue

value: Breast

tag: cell type


title: brown-00173: BC124B-AF

value: Primary tumor


title: EFF (F-S- ctl) fresh

source_name: freshly sorted control

value: fresh cells


title: EFF (F-S- ctl) fresh ACT


title: beer-00153: L104

tag: age (years)

tag: histology

value: bronchial alveolar

tag: tumor size (cm)

tag: k-ras mutation


title: brown-00173: BT-549

value: Cell-line


title: F+S- ACT D1

value: Clone


title: FEEDER CTL4 ACT


title: brown-00173: BC24


title: beer-00153: L103

value: Homo Sapiens

value: lung cancer

tag: nodal status

tag: followup time (months)

tag: death (1=dead,0=alive)

tag: smoking (pack years)


title: brown-00173: BC35-0


title: beer-00153: L102

value: lung

value: bronchial derived

tag: differentiation

value: Moderate

tag: p53 nucl.accum.


title: F+S+ ACT D1

tag: culture

tag: activation

tag: donor

tag: foxp3 expression

value: suppressive


title: brown-00173: BC1257

tag: cell line


title: F+S- D2

value: resting

tag: function

value: not suppressive


title: beer-00153: L100

tag: organism

tag: Sex

value: F

value: lung adenocarcinoma

value: Well


title: beer-00153: L101

tag: age (years)

tag: histology

value: bronchial alveola/mucinous


title: brown-00173: BC17

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

tag: tissue

value: Breast

tag: cell type

value: Primary tumor


title: F+S+ D2


title: beer-00153: L09

tag: tumor size (cm)

tag: nodal status

tag: followup time (months)

tag: k-ras mutation


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 86-103874_copy_number

type: genomic

city: Pamplona

first: Bruno

last: Paiva

address: Av. Pio XII, 55

institute: Clinica Universidad de Navarra

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: ChAS console from Affymetrix was used to assess genome wide copy number frequencies. Log2 Ratio copy number values with associated chromosome positions are available on the series record.

source_name: Bone marrow

label_protocol: Labelling and hybridizations were performed according to protocols from Affymetrix

extract_protocol: Genomic DNA was digested with Nsp I and Sty I restriction enzymes, ligated to adapters with T4 DNA ligase and amplified. PCR products were concentrated and fragmented (DNAsal), and then end-labeled with deoxynucleotidil transferase

value: Bone marrow

value: Clonal B-Lymphocytes


title: brown-00173: BC213A-AF


title: HI (F+S+ ctl) fresh

value: fresh cells


title: beer-00153: L08

value: Homo Sapiens

value: lung cancer

tag: death (1=dead,0=alive)

tag: differentiation

tag: p53 nucl.accum.

tag: smoking (pack years)


title: brown-00173: Hs578T-NCI

source_name: Hs578T reference sample

value: Cell-line


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 58-103420_copy_number


title: F-S- D2

tag: culture

value: Clone

tag: activation

tag: donor

tag: foxp3 expression


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 66-99532_copy_number


title: beer-00153: L06

tag: organism

tag: Sex

value: lung

value: bronchial derived

value: Poor


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 65-99702_copy_number


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 67-97054_copy_number


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 51-101201_copy_number


title: brown-00173: BC114A-BE

source_name: common “reference” mRNA pool

tag: cell line


title: beer-00153: L05

value: F

tag: age (years)

tag: histology

value: bronchial derived/clear cell

value: Moderate


title: brown-00173: BC124A-BE

tag: tissue

tag: cell type


title: FEEDER CTL1

value: irradiated feeders

value: resting

tag: function


title: HI (F+S+ ctl) fresh ACT

value: activated


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 72-103266_copy_number


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 78-97894_copy_number


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 46-97220_copy_number


title: brown-00173: BC206A-BE

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205

value: Breast

value: Primary tumor


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 112311_copy_number

value: Bone marrow

value: Clonal B-Lymphocytes


title: F+S-D1

value: not suppressive


title: beer-00153: L04

value: Homo Sapiens

value: M

value: lung cancer

value: lung adenocarcinoma

tag: tumor size (cm)

tag: nodal status

tag: followup time (months)

tag: k-ras mutation


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 111362_copy_number


title: beer-00153: L02

value: lung

value: bronchial derived

tag: death (1=dead,0=alive)

tag: differentiation

value: Poor

tag: p53 nucl.accum.

tag: smoking (pack years)


title: brown-00173: BT-474/ATCC

value: Cell-line


title: F-S- ACT D2

tag: culture

value: Clone

tag: activation

tag: donor

tag: foxp3 expression


title: FEEDER CTL2

value: irradiated feeders

value: resting


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 32-101918_copy_number


title: brown-00173: SK-BR-3

tag: cell line

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: beer-00153: L01

tag: organism

tag: Sex

tag: age (years)

tag: histology

value: bronchial derived/clear cell


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 53-102429_copy_number

tag: tissue

tag: cell type


title: beer-00153: AD8

tag: tumor size (cm)

tag: nodal status

tag: followup time (months)

value: Moderate


title: brown-00173: HMEC-C

source_name: HMEC-C

value: Breast


title: F+S+ ACT D2

value: activated

tag: function

value: suppressive


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 73-100996_copy_number

value: Bone marrow

value: Clonal B-Lymphocytes


title: Clonal B-Cells from IgM Waldenström's Macroglobulinemia 111450_copy_number


title: FEEDER CTL2 ACT


title: beer-00153: AD7

value: Homo Sapiens

value: M

value: lung cancer

tag: death (1=dead,0=alive)

tag: differentiation

tag: p53 nucl.accum.

tag: k-ras mutation


title: beer-00153: AD6

value: lung

value: lung adenocarcinoma

value: bronchial alveolar

value: Well

tag: smoking (pack years)


title: brown-00173: BC305B-AF

value: Primary tumor


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 52-101511_copy_number


title: brown-00173: BC309A-BE


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 59-97940_copy_number


title: beer-00153: AD5

value: F

value: positive


title: brown-00173: BC2

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: Primary human epidermis keratinocyte stem cells versus progenitors - n4

city: Evry

first: Nicolas

middle: O

last: FORTUNEL

address: 2 Rue Gaston Crémieux

department: Institute of Cellular and Molecular Radiobiology (iRCM)

country: France

institute: CEA - INSERM U967

description: Primary flow cytometry-sorted cell samples

hyb_protocol: Direct hybridization sample (Cy5 vs Cy3). Full experimental procedure described in: Franco N, Lamartine J, Frouin V, et al. Radiat Res 2005;163:623–35 ; Lamartine J, Franco N, Le Minter P, et al. J Cell Biochem 2005;95:620–31 ; Rachidi W, Harfouche G, Lemaitre G, et al. Radiother Oncol 2007;83:267–276.

scan_protocol: Genpix 4000B (Axon).

data_processing: Normalized ratio Cy5/Cy3 Bioconductor (method : prinTipLoess, span : 0,4)

molecule: polyA RNA

source_name: Sorted KSC = keratinocyte stem cells, [Itg-α6bright / Trf-Rdim] phenotype

label_protocol: Ambion / Amino Allyl MessageAmp II aRNA kit (Cy3 or 5). Full experimental procedure described in: Franco N, Lamartine J, Frouin V, et al. Radiat Res 2005;163:623–35 ; Lamartine J, Franco N, Le Minter P, et al. J Cell Biochem 2005;95:620–31 ; Rachidi W, Harfouche G, Lemaitre G, et al. Radiother Oncol 2007;83:267–276.

growth_protocol: Primary KSC and KP sub-populations were sorted from normal human skin samples by flow cytometry (full sorting procedure described in Rachidi W, Harfouche G, Lemaitre G, et al. Radiother Oncol 2007;83:267–276). Cells were not amplified in culture before transcriptome analysis, in order to maintain their initial characteristics.

extract_protocol: Qiagen / microRNAeasy kit. Full experimental procedure described in: Franco N, Lamartine J, Frouin V, et al. Radiat Res 2005;163:623–35 ; Lamartine J, Franco N, Le Minter P, et al. J Cell Biochem 2005;95:620–31 ; Rachidi W, Harfouche G, Lemaitre G, et al. Radiother Oncol 2007;83:267–276.

treatment_protocol: Sorted keratinocytes (MoFlo) were seeded in culture plates and maintained in culture medium (feeder-and serum-free condition, KGM medium) overnight (15 hours), and genome-wide transcriptome analysis of the two subpopulations (KSC and KP) was directly performed, in order to globally maintain the initial phenotypes.

tag: sorted cells

value: keratinocyte stem cells

value: Normal skin, neonatal foreskin

source_name: Sorted KP = keratinocyte progenitors, [Itg-α6bright / Trf-Rbright] phenotype

value: keratinocyte progenitors


title: F-S- ACT D1

tag: culture

value: Clone

tag: activation

value: activated

tag: donor

tag: foxp3 expression

value: not suppressive


title: beer-00153: AD3

tag: organism

value: Homo Sapiens

tag: Sex

tag: age (years)

tag: histology

value: bronchial derived

value: Moderate


title: brown-00173: BC114B-AF

tag: cell line

tag: tissue

value: Breast

tag: cell type


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 42-101534_copy_number

value: Bone marrow

value: Clonal B-Lymphocytes


title: F+S- ACT D2

tag: function


title: Primary human epidermis keratinocyte stem cells versus progenitors - n3


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 45-97150_copy_number


title: becic-00229: a7a_001021jd_ProNor670

source_name: Normal

value: Normal

value: Prostate

value: male


title: brown-00173: BC805B-AF

value: Primary tumor


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 44-105403_copy_number


title: beer-00153: AD2

value: F

value: lung cancer

value: lung

value: lung adenocarcinoma

tag: tumor size (cm)

tag: nodal status

tag: followup time (months)

tag: death (1=dead,0=alive)

tag: differentiation

value: Poor


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 71-97861_copy_number


title: brown-00173: BC118B-BE

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: Primary human epidermis keratinocyte stem cells versus progenitors - n2

tag: sorted cells

value: keratinocyte stem cells

value: Normal skin, neonatal foreskin

value: keratinocyte progenitors


title: becic-00229: a7a_001021jd_ProNor666


title: brown-00173: BC111A-BE


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 37-105404_copy_number


title: bonda-00136: Young Medium 71m

source_name: Young Medium 71m

value: macrophage


title: bonda-00136: Young LPS 77L

source_name: Young LPS 77L


title: becic-00229: a7a_001021jd_ProNor668


title: brown-00173: BC206B-AF

value: Breast


title: brown-00173: BC16


title: becic-00229: a7a_001021jd_ProNor662


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 122-106533_copy_number

value: Bone marrow


title: bonda-00136: Young LPS 76L

source_name: Young LPS 76L


title: brown-00173: BC406A-BE


title: becic-00229: a7a_001021jd_ProNor660


title: brown-00173: BC14


title: becic-00229: a7a_001021jd_ProNor642


title: bonda-00136: Aged Medium 82m

source_name: Aged Medium 82m


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 111847_copy_number

value: Clonal B-Lymphocytes


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 41-98776_copy_number


title: bonda-00136: Aged LPS 88L

source_name: Aged LPS 88L


title: brown-00173: BC107A-AF


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 83-99739_copy_number


title: becic-00229: a7a_001021jd_ProNor638

value: Normal


title: beer-00153: AD10

source_name: lung cancer

value: Homo Sapiens

value: M

value: bronchial derived

value: Moderate

tag: p53 nucl.accum.

tag: k-ras mutation

tag: smoking (pack years)


title: bonda-00136: Aged LPS 80L

source_name: Aged LPS 80L


title: brown-00173: BC1369

value: Primary tumor


title: brown-00173: BC123B-BE


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 80-97938_copy_number


title: becic-00229: a7a_001021jd_ProNor634

value: Prostate

value: male


title: becic-00229: a7a_001021jd_ProNor636


title: bonda-00136: Young LPS 75L

source_name: Young LPS 75L


title: bonda-00136: Aged LPS 86L

source_name: Aged LPS 86L


title: bonda-00136: Aged Medium 81m

source_name: Aged Medium 81m


title: brown-00173: MCF7-NCI

source_name: MCF7-NCI reference sample

value: Cell-line


title: brown-00173: BC107B-BE

value: MCF7, Hs578T, OVCAR3, HepG2, NTERA2, MOLT4, RPMI-8226, NB4+ATRA, UACC-62, SW872, Colo205


title: bonda-00136: Young Medium 73m

source_name: Young Medium 73m


title: becic-00229: a7a_001021jd_ProNor632


title: becic-00229: a7a_990615jd_ProNor1050


title: Primary human epidermis keratinocyte stem cells versus progenitors - n1

value: keratinocyte stem cells


title: brown-00173: BC709A-AF

source_name: common “reference” mRNA pool


title: becic-00229: a7a_990615jd_ProNor1009


title: bonda-00136: Young Medium 72m

source_name: Young Medium 72m


title: becic-00229: a7a_990615jd_ProNor1008


title: brown-00173: BC709B-BE


title: Clonal B-Cells from IgM Smoldering Waldenström's Macroglobulinemia 111431_copy_number

source_name: Bone marrow


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 50-104115_copy_number


title: brown-00173: BC402B-BE


title: becic-00229: a7a_990615jd_ProNor1007


title: becic-00229: a7a_990615jd_ProNor1006


title: bonda-00136: Aged Medium 84m

source_name: Aged Medium 84m


title: becic-00229: a7a_990615jd_ProCan966

source_name: Prostate Cancer


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 47-103284_copy_number


title: Ripmir_islets

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

country: Switzerland

institute: FGCZ Zuerich

hyb_protocol: 12.5 ug of labeled cDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to MOE430V2 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: Microarrays were scanned in a GeneChip® Scanner 3000 7G (Affymetrix) and quality control was evaluated by Affymetrix software (Expression ConsoleTM).

data_processing: The data where preprocessed (RMA) using the Expression Console TM from Affymetrix.

source_name: beta-cells

label_protocol: Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

growth_protocol: Mice were kept in standard conditions, i.e. 12h/12h dark/light cycle with ad libitum access to food and water.

treatment_protocol: After extraction, islets from transgenic and control mice were not further treated before RNA extraction.

tag: genotype/variation

tag: age

value: 6 weeks

value: islets


title: PA3Lysates_phage-80min_rep1

city: ChongQing

first: Xia

last: Zhao

address: Shapingba

institute: Third military medical school

description: Gene expression after phage infection of 80min

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression 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.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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings，Scan resolution=5μm, PMT100%，10%.

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Bruynoghevirus PaP3

source_name: PA3 lysates, 80min, replicate 1

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplification kit (Cat#5184-3523, Agilent technologies, Santa  Clara, CA, US), 5-(3-aminoallyl)-UTP (Cat#AM8436, Ambion, Austin, TX,US), Cy3 NHS ester (Cat#PA13105,GE healthcare Biosciences, Pittsburgh, PA,US) followed  the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: PA3 with or wihout phage infection was grown in Luria-Bertani (LB) broth medium aerobically.

extract_protocol: Total RNA was isolated using SV Total RNA Isolation System (Promega) according to the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set    (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Bacterial culture were infected with phage PaP3 at MOI of 10 for 0min, 5min, 10min, 20min, 30min and 80min.The uninfected samples (0 min) served as reference.

tag: bacteriophage

tag: time


title: Ad-ctrl infected Min6 cells

description: Ad-ctrl infected Min6 cells

source_name: Min6 beta-cell line

growth_protocol: Min6 cells were cultured in DMEM containing 25 mM glucose, 15%FBS, 55µM beta-Mercaptoethanol.

treatment_protocol: Cells were infected with viruses at 25MOI, medium was changed after 24hrs, and cells were harvested 48hrs later.

tag: cell line

value: Min6 beta

tag: infection

value: Adenovirus control


title: PA3Lysates_phage-30min_rep2

description: Gene expression after phage infection of 30min

source_name: PA3 lysates, 30min, replicate 2


title: becic-00229: a7a_990615jd_ProCan965

tag: Sex


title: becic-00235: PT39: HG_U95A

tag: diseasestate

tag: tumorgrading

tag: diseasestaging

value: pT T3a, pN N0, pM MX

tag: organismpart

tag: histology

value: ALI unknown, ECI focal, SVI no, SMI yes

tag: prostatetissue

value: tumor


title: becic-00229: a7a_990615jd_ProCan964


title: becic-00235: PT38: HG_U95A

value: pT T2b, pN N0, pM MX

value: ALI unknown, ECI no, SVI no, SMI no


title: PA3Lysates_phage-30min_rep3

source_name: PA3 lysates, 30min, replicate 3


title: Ad-141/200c infected Min6 cells

description: Ad-141/200c infected Min6 cells

value: Adenovirus overexpression miR-141/200c


title: C57Bl6_islets

tag: tissue


title: becic-00229: a7a_990615jd_ProCan963


title: PA3Lysates_phage-20min_rep3

description: Gene expression after phage infection of 20min

source_name: PA3 lysates, 20min, replicate 3


title: PA3Lysates_phage-30min_rep1

source_name: PA3 lysates, 30min, replicate 1


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 39-97713_copy_number

value: Bone marrow

tag: cell type

value: Clonal B-Lymphocytes


title: becic-00229: a7a_990615jd_ProCan1051

value: Prostate


title: becic-00229: a7a_001021jd_ProCan669

value: male


title: PA3Lysates_phage-20min_rep2

source_name: PA3 lysates, 20min, replicate 2


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 48-98644_copy_number


title: PA3Lysates_phage-20min_rep1

source_name: PA3 lysates, 20min, replicate 1


title: becic-00229: a7a_001021jd_ProCan667


title: becic-00229: a7a_001021jd_ProCan665


title: PA3Lysates_phage-10min_rep2

description: Gene expression after phage infection of 10min

source_name: PA3 lysates, 10min, replicate 2


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 40-99624_copy_number


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 33-99638_copy_number


title: Peripheral blood T-Cells. Unpaired control 77_copy_number

source_name: Peripheral blood

value: Peripheral blood

value: T-Lymphocytes


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 70-101677_copy_number


title: Peripheral blood T-Cells. Unpaired control 76_copy_number


title: becic-00229: a7a_001021jd_ProCan661


title: PA3Lysates_phage-10min_rep1

source_name: PA3 lysates, 10min, replicate 1


title: SK_hypoxia_8hr_rep3

city: Hangzhou

first: Chengli

last: Du

state: Zhejiang

address: NO.79 Qingchun Road

institute: The First Affiliated Hospital of Zhejiang University

description: Gene expression after 8hr under hypoxic condition

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)in hybridization Oven(Cat#G2545A, Agilent technologies, Santa Clara, CA, US)at 55°C, 20rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After 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).

scan_protocol: Slides were scanned by Agilent Microarray Scanner(Cat#G2565BA , Agilent technologies, Santa Clara, CA, US)and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US)with default settings. Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0(Agilent technologies, Santa Clara, CA, US)

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

label_protocol: miRNA molecules in total RNA was labeled by miRNA Complete Labeling and Hyb Kit(Cat#5190-0456, Agilent technologies, Santa Clara, CA, US)followed the manufacturer’s instructions, labeling section.

growth_protocol: SK-HEP-1 cells were cultured with MEM media supplemented with 10% FBS and incubated in the atmosphere of 5% CO2 and 37 ºC

extract_protocol: Total RNA was extracted and purified using mirVanaTM miRNA Isolation Kit (Cat#AM1560, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100(Agilent technologies, Santa Clara, CA, US)

treatment_protocol: SK-HEP-1 cells were applied to hypoxic conditions (1% oxygen) for 0hr or 8hr

value: SK-HEP-1 cells

tag: stress

value: hypoxia

value: 8 hr


title: PA3Lysates_phage-5min_rep3

description: Gene expression after phage infection of 5min

source_name: PA3 lysates, 5min, replicate 3


title: PA3Lysates_phage-10min_rep3

source_name: PA3 lysates, 10min, replicate 3


title: Peripheral blood T-Cells. Unpaired control 57_copy_number


title: becic-00229: a7a_001021jd_ProCan641


title: SK_hypoxia_8hr_rep2


title: SK_hypoxia_8hr_rep1


title: Peripheral blood T-Cells. Unpaired control 74_copy_number


title: Peripheral blood T-Cells. Paired control 145_copy_number


title: becic-00229: a7a_001021jd_ProCan635


title: PA3Lysates_phage-5min_rep1

source_name: PA3 lysates, 5min, replicate 1


title: Peripheral blood T-Cells. Unpaired control 64_copy_number


title: SK_hypoxia_0hr_rep3

description: Gene expression after 0hr under hypoxic condition

value: control

value: 0 hr


title: PA3Lysates_phage-5min_rep2

source_name: PA3 lysates, 5min, replicate 2


title: Peripheral blood T-Cells. Paired control 142_copy_number


title: PA3Lysates_phage-0min_rep3

description: Gene expression without phage infection control

source_name: PA3 lysates, 0min, replicate 3


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 133-106884_copy_number

source_name: Bone marrow


title: Peripheral blood T-Cells. Unpaired control 35_copy_number


title: SK_hypoxia_0hr_rep2


title: Peripheral blood T-Cells. Paired control 143_copy_number


title: Clonal B-Cells from IgM Monoclonal Gammopathy of Undetermined Significance 130-106878_copy_number


title: PA3Lysates_phage-0min_rep2

source_name: PA3 lysates, 0min, replicate 2


title: becic-00229: a7a_001021jd_ProCan633

source_name: Prostate Cancer


title: SK_hypoxia_0hr_rep1


title: becic-00229: a7a_001021jd_ProCan631


title: PA3Lysates_phage-0min_rep1

source_name: PA3 lysates, 0min, replicate 1


title: Peripheral blood T-Cells. Unpaired control 79_copy_number


title: becic-00229: a7a_001021jd_ProCan659


title: Peripheral blood T-Cells. Paired control 144_copy_number


title: becic-00229: a7a_001021jd_ProCan637


title: Red sector of red/white sectored colony 12 of FM1468

status: Public on May 05 2015

city: Durham

first: Thomas

middle: D

last: Petes

state: NC

address: 213 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

hyb_protocol: The hybridization reactions were prepared using an Agilent Oligo aCGH/ChIP-on-Chip Hybridization kit (5188-5220) following kit instructions. Arrays were incubated for 48 hours at 62°. Following hybridization, the arrays were washed for 5 minutes in Oligo aCGH/ChIP-on-Chip Wash Buffer 1 (Agilent 5188-5221) and 1 minute in Oligo aCGH/ChIP-on-Chip Wash Buffer 2 (Agilent 5188-5222) that was pre-warmed to 37°. The arrays were then scanned at wavelengths of 635 and 532 nm using the GenePix scanner and the GenePix Pro software using settings recommended by the manufacturer.Microarrays could be re-used approximately 4-6 times by removing the hybridized labeled DNA sequences from the oligonucleotides. Microarrays and gasket slides were stripped separately in 1x stripping buffer (10 mM potassium phosphate, pH6.6). The slides were slowly heated to the boiling point in the stripping buffer for 30-45 minutes. After stripping, they were transferred to deionized water, and then slowly removed and stored in a nitrogen cabinet. The gasket slides were centrifuged at 500 rpm to remove excess liquid. Labels on microarrays were removed prior to stripping.

scan_protocol: The data generated by GenePix Pro were exported to text files and analyzed with Microsoft Excel. Probes that were flagged by the software were deleted from the analysis.

data_processing: The ratio of the medians (635 nm/532 nm) for each probe was used for analysis, and replicate probe medians were averaged. The data was centered around one by dividing each probe median by the average of all of the probe medians in order to normalize for differences in the hybridization levels for the reference and experimental strain samples. The data were plotted separately for each haploid parental strain and, in plots showing whole chromosomes, the medians were “smoothed” by averaging over nine consecutive probes.

organism: Saccharomyces cerevisiae

source_name: FM1468 colony after 37 degree heat treatment

label_protocol: The description of the labeling and hybridization protocol are copied with minor modifications from the Supplementary Information of our previous publication: DNA from these colonies was labeled with Cy5, and mixed with control DNA (DNA from the strain FM1468 not incubated at 37C) labeled with Cy3. The two samples were mixed and competitively hybridized to the SNP microarrays.

growth_protocol: For our experiments, the strain FM1468 was incubated at 37C for three hours. The cells were then plated at the permissive temperature of 25C and allowed to form colonies.

extract_protocol: We purified single colonies derived from each sector, and prepared DNA by standard procedures (St. Charles et al., 2012).

treatment_protocol: We observed sectored colonies of a variety of types including red/white, red/pink, and pink/white; in addition, some tri-colored colonies (white/pink/red) were observed.

tag: growth condition

value: 6 hours at 37 degrees

source_name: FM1468 colonies untreated at 25 degrees

value: Grown at 25 degrees


title: Red sector of red/white sectored colony 13 of FM1468


title: Heart_at normal developmental age of 173d in control lamb_rep2

city: Adelaide

first: Janna

last: Morrison

state: SA

address: City East Campus, P5-50

department: School of Pharmacy and Medical Sciences

country: Australia

institute: University of South Australia

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org), sequences obtained from next-gen sequencing, or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

organism: Ovis aries

source_name: Left ventricle heart, at normal developmental age of 173d in control lamb

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 0.5 µg total RNA sample which were first subject to dephosphorylation reaction to remove 5’ phosphate groups of the miRNA molecules. Then an oligonucleotide adapter was added to the 3’ end of the samples (3’OH containing) RNA sequences using T4 RNA ligase. The adapter sequence contained a tag segment for capturing fluorescent Cy3 dye during a later dye staining process.

growth_protocol: Frozen heart samples from three biological replicates from each of the four normal developmental ages in sheep were used for RNA extraction

extract_protocol: Total RNA from the left ventricle (~50 mg) was extracted using the miRNeasy Mini Kit (QIAGEN Pty Ltd, Doncaster, Australia)

tag: species

value: Merino sheep

tag: gender

value: Female

tag: fetal number

value: Singleton

value: Heart

tag: developmental stage

value: 173d (postnatal)


title: Peripheral blood T-Cells. Unpaired control 62_copy_number


title: Heart_at normal developmental age of 173d in control lamb_rep3


title: Red sector of pink/red/white sectored colony 11 of FM1468


title: Peripheral blood T-Cells. Paired control 131_copy_number


title: Pink sector of pink/red/white sectored colony 11 of FM1468


title: Heart_at normal developmental age of 5d in control lamb_rep3

source_name: Left ventricle heart, at normal developmental age of 5d in control lamb

value: Twin

value: 5d (postnatal)


title: White sector of red/white sectored colony 12 of FM1468


title: White sector of pink/red/white sectored colony 11 of FM1468


title: Red sector of pink/red/white sectored colony 10 of FM1468


title: White sector of pink/red/white sectored colony 10 of FM1468


title: Pink sector of pink/red/white sectored colony 10 of FM1468


title: Peripheral blood T-Cells. Unpaired control 36_copy_number


title: Pink sector of pink/white sectored colony 9 of FM1468


title: Peripheral blood T-Cells. Paired control 141_copy_number


title: White sector of pink/white sectored colony 9 of FM1468


title: Peripheral blood T-Cells. Unpaired control 129_copy_number


title: Peripheral blood T-Cells. Paired control 111847_copy_number


title: Heart_at normal developmental age of 5d in control lamb_rep2


title: Heart_at normal developmental age of 5d in control lamb_rep1


title: Heart_at normal developmental age of 91d in control fetus_rep3

source_name: Left ventricle heart, at normal developmental age of 91d in control fetus

value: Male

value: 90d (fetal)


title: Heart_at normal developmental age of 141d in control fetus_rep1

source_name: Left ventricle heart, at normal developmental age of 141d in control fetus

value: 141d (fetal)


title: Heart_at normal developmental age of 91d in control fetus_rep2


title: Heart_at normal developmental age of 141d in control fetus_rep2


title: Pituitary_YC

city: Guangzhou

first: Ruisong

last: Ye

state: Guangdong

address: 483 Wushan Tianhe

institute: South China Agricultural University

description:
Custom-designed µParaflo microfluidic chips (LC Sciences, Houston, TX) were used for miRNA expression analysis. In this study, we used all porcine miRNAs deposited in miRBase 18.0 and designed sequences as miRNA microarray probes. In detail, miRBase 18.0 collected a total of 257 porcine miRNAs (255 miRNAs according to its sequence). We added 100 probes (probes labelled with prefix 'Y-') according to our previous reports
miRNA profiling

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies, Houston, TX).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device, Silicon Valley, CA) and digitized using Array-Pro image analysis software (Media Cybernetics, Bethesda, MD).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (locally weighted regression).

organism: Sus scrofa

source_name: anterior pituitary

label_protocol: Cy5.In brief, 2–5 µg total RNA samples were used for small RNAs (<300 nt) enrichment by a YM-100 Microcon centrifugal filter (Millipore, Billerica, MA); the collected small RNAs were then 3′-extended with a poly (A) tail using poly (A) polymerase and an oligonucleotide tag was ligated to the poly (A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted from the anterior pituitary tissue using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions.

value: 20-day after birth

tag: breed

value: Landrace pigs

value: anterior pituitary


title: Pink sector of pink/red sectored colony 8 of FM1468


title: Heart_at normal developmental age of 173d in control lamb_rep1


title: Pink sector of pink/red sectored colony 7 of FM1468


title: Pituitary_YB

description:
Custom-designed µParaflo microfluidic chips (LC Sciences, Houston, TX) were used for miRNA expression analysis. In this study, we used all porcine miRNAs deposited in miRBase 18.0 and designed sequences as miRNA microarray probes. In detail, miRBase 18.0 collected a total of 257 porcine miRNAs (255 miRNAs according to its sequence). We added 100 probes (probes labelled with prefix ‘Y-’) according to our previous reports
miRNA profiling

value: Bama minipigs


title: Peripheral blood T-Cells. Unpaired control 54_copy_number

source_name: Peripheral blood

value: Peripheral blood

value: T-Lymphocytes


title: Red sector of pink/red sectored colony 8 of FM1468

value: 6 hours at 37 degrees

value: Grown at 25 degrees


title: White sector of pink/white sectored colony 7 of FM1468


title: Heart_at normal developmental age of 91d in control fetus_rep1

value: Merino sheep

value: Female


title: Pink sector of pink/white sectored colony 6 of FM1468


title: White sector of pink/white sectored colony 4 of FM1468


title: Red sector of red/white sectored colony 5 of FM1468


title: White sector of pink/white sectored colony 6 of FM1468


title: Pink sector of pink/white sectored colony 4 of FM1468


title: White sector of red/white sectored colony 5 of FM1468


title: White sector of pink/white sectored colony 3 of FM1468


title: Pink sector of pink/white sectored colony 3 of FM1468


title: Heart_at normal developmental age of 141d in control fetus_rep3

value: Singleton

value: Heart


title: Serum starved MDA-MB-231 cells, Rep2

city: Lyon

first: Olivier

last: Peyruchaud

state: Rhone Alpes

address: UFR de medicine Lyon Est (Domaine Laennec), 7-11 Rue Guillaume Paradin

institute: INSERM U1033

hyb_protocol: Array hybridized for 20h using miRNA complete labeling and hybridization kit (Agilent).

scan_protocol: The arrays were washed with gene expression wash buffer kit (Agilent) and read with High-resolution microarray scanner (Agilent).

data_processing:
The data was extracted using Agilent feature extraction software (Agilent v11.5.1.1). The data was internally normalized by spike labelling. 3 samples from platform GPL13264 and 3 samples from platform GPL19263 were averaged together. So in total we have 6 samples.
The mean fluorescent intensities were obtained after subtracting background.
The mean of different probesets for each miRNA was calculated
All the samples with negative values (Negative values -  the miRNA's expression value after subtracting the background was negative) were eliminated as a quality check.
The remaining 182 miRNAs were overall median normalized.

source_name: Serum starved MDA-MB-231 cells

label_protocol: Total RNA including miRNA (100 ng) was directly labeled with Cyanine-3-labeled

growth_protocol: The MDA-MB-231 cells were cultured in DMEM Medium, suplemented with 10% FBS and 1% Penicillin/streptomycin at 37°C in a 5% CO2 incubator

extract_protocol: Total RNA including miRNA was extracted using the miRNeasy kit (QIAGEN) as per manufacturer's protocol

treatment_protocol: The cells were serum starved for 24h and then stimulated with LPA (1µM) for 45min.

tag: cell line

value: human breast cancer cell line

tag: stimulated with

value: none (control)


title: Red sector of pink/red sectored colony 2 of FM1468


title: Pink sector of pink/red sectored colony 2 of FM1468


title: MDA-MB-231 cells stimulated with LPA, Rep1

source_name: MDA-MB-231 cells stimulated with LPA

value: LPA (1µM) for 45min


title: White sector of red/white sectored colony 13 of FM1468


title: Peripheral blood T-Cells. Paired control 111362_copy_number


title: Pink sector of pink/white sectored colony 1 of FM1468


title: Peripheral blood T-Cells. Unpaired control 120_copy_number


title: White sector of pink/white sectored colony 1 of FM1468


title: Peripheral blood T-Cells. Unpaired control 84_copy_number


title: Serum starved MDA-MB-231 cells, Rep1


title: Peripheral blood T-Cells. Unpaired control 38_copy_number


title: HeLa_Reversed_rep1

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

hyb_protocol: Affymetrix Human Transcriptome Array 2.0 ST arrays were hybridized according to Affymetrix recommendations using the Affymetrix WT Plus kit.  Affymetrix GeneChip® Human Transcriptome 2.0 ST microarrays (HTA2) were hybridized with 5.5 ug of labeled DNA.

scan_protocol: HTA 2.0 ST arrays were scanned using the Affymetrix 3000 7G scanner and the Command Console software version 4.1.2.

data_processing: CEL files were first processed using the Affymetrix® Expression Console Software (build 1.3.1.187) to produce CHP files for each of the eight samples.  The Gene Level - Default: RMA-Sketch normalization was used.  The eight CHP files were then imported into the Affymetrix® Transcriptome Analysis Console (TAC) 2.0 (build 2.0.0.9) using the Gene Level Differential Analysis option.  Within TAC, the genome assembly hg19 was used with the annotation file HTA-2_0.na34.hg19.transcript.csv.  Intensity values reported for each transcript cluster ID are calculated as log2 of Tukey's bi-weight average.

source_name: HeLa_1 uM arsenite for 26 days_removal of arsenite for 10 days (iAs-Rev)

label_protocol: Total RNA (100ng) was processed in parallel with an external MAQC A RNA to control robustness of data.  Labeled DNA mean yield was min: 13.6 ug; max: 16.7 ug).

growth_protocol: Cell cultures were incubated at 37o C with humidified air and 5% CO2.  Cells were harvested after each culture ensuring that the cells had ~95% cell viability.  Harvested cells were centrifuged for five minutes at 200 x g.  Samples were taken each day for counting.  Cell viability was determined by trypan blue dye exclusion using a hemacytometer and calculated as percent viability times total cells/ml.

extract_protocol: Total RNA was isolated from cells using an miRNeasy mini kit (Qiagen) and quality assessment was conducted using RNA 6000 Nano-labchip (Bioanalyzer, Agilent) and by a Nanodrop spectrophotometer (Thermo).  Total RNA RIN values were between 7.7 and 9 (average 8.65).

treatment_protocol: HeLa cells were continuously exposed to Vehicle Control (deionized water) or 1 uM of arsenite (Na3AsO3, Sigma-Aldrich), respectively.  When reaching about 80-90% confluence, cells were subcultured and Na3AsO3 was then added to cells after overnight attachment.  These procedures were repeated every 3 or 4 days for 16 weeks.  During the exposure period, cell morphology changes were monitored.  Cell malignant transformation was assessed by changes in cell morphology and EMT markers protein levels.

value: HeLa

tag: treated with

value: 1 uM sodium arsenite for 26 days followed by removal of sodium arsenite for 10 days (measured at day 36)


title: Sacrum Chordoma Cell Line U-CH11_1

city: Ulm

first: Adrian

last: von Witzleben

address: Albert-Einstein-Allee 23

institute: Institute of Pathology

hyb_protocol: The hybridization was done by using the "One-color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) with Tecan HS Pro Hybridization" protocol.

scan_protocol: The slides were scanned with the Agilent SureScan Microarray Scanner

data_processing: The scanned images were analyzed with Feature Extraction (Agilent) using default parameters.

source_name: Os sacrum region

label_protocol: The labeling was done by using the "One-color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) with Tecan HS Pro Hybridization" protocol.

growth_protocol: Fresh tumor tissue was used for establishment of a stable cell line according to standard protocols.(Scheil S, Bruderlein S;Genome-wide analysis of sixteen chordomas by comparative genomic hybridization and cytogenetics of the first human chordoma cell line, U-CH1)

extract_protocol: mRNA was extracted and prepared with the Qiagen RNeasy Plus Mini Kit.

value: male

tag: age at diagnosis

value: Chordoma Cell Line


title: Sacrum Chordoma Cell Line U-CH2_2

value: female


title: Sacrum Chordoma Cell Line U-CH12_2


title: Sacrum Chordoma Cell Line U-CH6_1

value: Not known


title: HeLa_Treated_rep2

source_name: HeLa_1 uM arsenite (iAs-T) for 36 d

value: 1 uM of sodium arsenite (iAs-T) for 36 days


title: Sacrum Chordoma Cell Line U-CH2_1


title: Sacrum Chordoma Cell Line U-CH1_1


title: Sacrum Chordoma Cell Line U-CH3_2


title: Sacrum Chordoma Cell Line U-CH7_2


title: Sacrum Chordoma Cell Line U-CH10_1


title: Sacrum Chordoma Cell Line U-CH12_1


title: Sacrum Chordoma Cell Line U-CH7_1


title: HeLa_ReversedTreated_rep2

source_name: HeLa_1 uM arsenite for 26 days_removal of arsenite for 10 days_1uM arsenite for 10 days (iAs-Rev-T)

value: 1 uM sodium arsenite for 26 days,  followed by removal of sodium arsenite for 10 days, followed by 1uM sodium arsenite treatment for 10 days  (measured at day 46)


title: HeLa_ReversedTreated_rep1


title: HeLa_WildType_rep2

source_name: HeLa_no-treatment (NT)

value: deionized H2O for 36 days (NT)


title: HeLa_WildType_rep1


title: HeLa_Treated_rep1


title: Sacrum Chordoma Cell Line U-CH1_2


title: Sacrum Chordoma Cell Line U-CH3_1


title: Sacrum Chordoma Cell Line U-CH11_2


title: FE1, D3 (100 µg) sample 6

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

institute: Health Canada

hyb_protocol: Equal amounts of Cy5-labeled experimental cRNA and Cy3-labeled reference RNA (300ng) were co-hybridized to Agilent Sureprint G3 Mouse GE 8x60K microarray slides, according to the instructions outlined in the Agilent Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol.  Samples were hybridized for 17 hours at 65oC and 10 rpm.

scan_protocol: Microarray slides were scanned using an Agilent DNA Microarray Scanner (G2505B) according to manufacturer's recommendations.  Data was extracted from the scanned images using Feature Extraction Version 10.7.3.1.

data_processing: The log2 of the ratio (sample(Cy5)/reference(Cy3)), using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R.

source_name: FE1 Muta(TM)Mouse lung epithelial cell line, D3 (100 µg)

label_protocol: Total RNA (200ng per sample) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: The FE1 epithelial cells were cultivated in DMEM/F-12 + GlutaMaxTM-1 supplemented with 2% fetal bovine serum, 1% penicillin/streptomycin solution and 100 ng/μl murine epidermal growth factor. Cells were maintained in T150 bottle at 37.0°C with 5% CO2 and 90% humidity. Media was replaced every 2-3 days, to ensure proper growth conditions.

extract_protocol: Following the incubation, cells were trypsinized and centrifuged to collect cell pellets.  The cell pellets were stored at -80°C until further use. Three individual exposures were conducted per dose per experiment-day. Total RNA was extracted (n=6 per group) using Trizol reagent and further purified using the RNeasy Mini Kit with an on-column DNase I digestion according to the manufacturer's instructions.  Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios between 2.0 and 2.15 and RINs above 7.0.

treatment_protocol: Immediately before the treatment, Mitsui7 suspensions were prepared as follows. A total of 8.9 mg of Mitsui7 was suspended in 2.6 ml of cell culture media containing to a total stock concentration of 3.4 mg/ml. Particle suspensions were prepared by sonication of Mitsui7 stock concetrations on ice using a Branson S-450D sonifier equipped with a disruptor horn at 10% amplitude for a total of 4 minutes at amplitude of 10%, with alternating 10 s pulses and pauses. FE1 cells were seeded in a density  of 1,000,000 cells/ml to a total of 6.81 ml/well in 4-well plates and incubated at 37°C for 24 hours. The next day cells were examined for overall natural appearance and growth.  Cells were incubated with 0, 12.5, 25, 50 and 100 µg Mitsui7/ml for 24 h.

value: lung epithelial

source_name: Universal Mouse Reference RNA

tag: source

value: 11 mouse cell lines


title: FE1, D3 (100 µg) sample 5


title: FE1, D3 (100 µg) sample 4


title: FE1, D3 (100 µg) sample 3


title: Sacrum Chordoma Cell Line U-CH6_2


title: Sacrum Chordoma Cell Line U-CH10_2


title: FE1, D3 (100 µg) sample 2


title: HeLa_Reversed_rep2


title: FE1, D2 (25 µg) sample 5

source_name: FE1 Muta(TM)Mouse lung epithelial cell line, D2 (25 µg)


title: FE1, D2 (25 µg) sample 4


title: FE1, D2 (25 µg) sample 1


title: FE1, D1 (12.5 µg) sample 5

source_name: FE1 Muta(TM)Mouse lung epithelial cell line, D1 (12.5 µg)


title: FE1, D2 (25 µg) sample 3


title: FE1, D1 (12.5 µg) sample 1


title: FE1, D3 (100 µg) sample 1


title: Lung tissue, D3 (162 µg) sample 4

source_name: Right lung, D3 (162 µg)

label_protocol: Total RNA (200ng per array) was labeled using the Agilent Quick Amp Labeling Kit, Two-Color (Agilent Cat #: 5190-0444), according to the manufacturer's instructions.  Control and experimental samples were labeled with Cyanine 5-CTP; whereas universal mouse reference RNA was labeled with Cyanine 3-CTP.

growth_protocol: Female C57BL/6 mice aged 5-7 weeks were obtained from Taconic (Ry, Denmark). The mice were allowed to acclimatize for 1-3 weeks before the experiment. All mice were given food and water ad libitum during the whole experiment. Mice were group housed in polypropylene cages with sawdust bedding at controlled temperature 21±1ºC and humidity 50±10% with a 12-h light:12-h dark cycle. Experiments were initiated at 8 weeks of age. All procedure complied with EC Directive 86/609/EEC and Danish laws regulating experiments on animals (permit 2010/561-1779). Mice did not display any signs of respiratory distress, lethargy or any other physical symptoms following exposure.

extract_protocol: For tissue collection, mice were anaesthetized with Hypnorm/Dormicum as described above and killed by exsanguination via intracardiac puncture. The right lung lobes were snap frozen in cryotubes in liquid N2 and stored at –80°C. Total RNA was extracted (n=6 per group) using Trizol reagent and further purified using the RNeasy Mini Kit with an on-column DNase I digestion according to the manufacturer's instructions. Total RNA concentration and quality was determined using a Nanodrop 1000 Spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.  RNA samples used for gene expression microarray had A260/280 ratios between 2.0 and 2.15 and RINs above 7.0.

treatment_protocol: Mice were anesthetized by subcutaneous injection of 0.2 ml of Hypnorm® (fentanyl citrate 0.315 mg/ml and fluanisone 10 mg/ml ) and Dormicum® in sterile water.  The mice were kept on their back at a 40 degree angle on a hot plate (37 ºC) during the entire procedure. Mice were exposed to 18, 54 and 162 µg of Mitsui7 via a single intratracheal instillation. A 40 µl suspension was instilled followed by 150 μl air with a 250 µl SGE glass syringe. Control animals were instilled with the vehicle (0.9% NaCl with 10% BAL). After the intubation instillation catheter was removed, breathing was observed in order to assure that the delivered material did not block the airways.  Mice were allowed to recover for 24 hours before sacrifice.

tag: strain

value: Female

value: Right lung


title: Lung tissue, D3 (162 µg) sample 5


title: FE1, Control sample 2

source_name: FE1 Muta(TM)Mouse lung epithelial cell line, Control


title: FE1, D1 (12.5 µg) sample 2


title: FE1, D1 (12.5 µg) sample 4


title: FE1, Control sample 4


title: Lung tissue, D3 (162 µg) sample 1


title: Lung tissue, D1 (18 µg) sample 6

source_name: Right lung, D1 (18 µg)


title: FE1, Control sample 5


title: Lung tissue, D3 (162 µg) sample 6


title: Lung tissue, D3 (162 µg) sample 2


title: Lung tissue, D3 (162 µg) sample 3


title: FE1, Control sample 1


title: Lung tissue, D2 (54 µg) sample 2

source_name: Right lung, D2 (54 µg)


title: Lung tissue, D2 (54 µg) sample 5


title: Lung tissue, D2 (54 µg) sample 3


title: FE1, D1 (12.5 µg) sample 3


title: Lung tissue, D1 (18 µg) sample 5


title: Lung tissue, D2 (54 µg) sample 1


title: Lung tissue, D2 (54 µg) sample 4


title: FE1, D2 (25 µg) sample 2


title: FE1, D1 (12.5 µg) sample 6


title: CcO IVi1 silenced 1

city: Philadelphia

first: Dawei

middle: W

last: Dong

state: Pennsylvania

address: 3620 Hamilton Walk

department: Biomedical Sciences

institute: University of Pennsylvania

description: RNA samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.6

hyb_protocol: labeled cDNA (3.25ug) hybridized for 17hrs at 45C to Affymetrix GeneChip Mouse Gene 2.0ST Arrays (PN:  902118)

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were processed by Affymetrix Expression Console using Probeset-Summarize-Engine with default setting of RMA method to calculate the expression level for each probeset of the array

source_name: C2C12 cells_CcO_IVi1_silenced

label_protocol: 5.5ug single-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (PN: 900671)

growth_protocol: Cells were grown in Dulbecco's Modified Eagle medium supplemented with 10% fetal bovine serum and 0.1% penicillin/streptomycin. In case of CcOIVi1 silenced cells, the medium was further supplemented with 1mM Pyruvate and 50micrograms/ml Uridine

extract_protocol: RNA was prepared using Qiagen Rneasy kit following manufacturer's instructions

treatment_protocol: No additional treatment was done on the samples before extraction

tag: growth status

value: Cells growing at 70% confluence


title: Lung tissue, D1 (18 µg) sample 4


title: Lung tissue, D1 (18 µg) sample 3


title: Lung tissue, Control sample 5

source_name: Right lung, Control


title: Control 3

description: RNA samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.11

source_name: C2C12 cells_control


title: Lung tissue, Control sample 3


title: Lung tissue, D1 (18 µg) sample 2


title: Non-CAD 2

city: chongqing

first: yujia

last: yang

address: Daping, Yuzhong District, the 10th branch of the Yangtze River

institute: Daping Hospital, Third Military Medical University, Cardiovascular Hospital, Chongqing Institute of Cardiovascular Disease

description: lncRNA  expression of human plasma

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

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization was performed using Expander6 and subsequent data processing was performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After low intensity filtering, LncRNAs and mRNAs that at least 2 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for quantile normalization and further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: plasma

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104), following the manufacturer's recommendations.  The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Blood samples collected from radial artery, after insertion of the arterial catheter and before the administration of any anticoagulants, were put into test tube containing EDTA. Freshly drawn plasma was then carefully collected, aliquoted, and stored at -80℃ prior to use.

tag: diagnosis

value: Non-Coronary Artery Disease (non-CAD)

value: plasma

tag: age


title: CAD Patient 1

description: lncRNA  expression of human plasma

value: Coronary Artery Disease (CAD)

tag: tissue


title: Lung tissue, Control sample 1


title: 202 Area4 17 05 13

city: Quebec

first: Remi

last: Labrecque

state: QC

address: 2440, boulevard Hochelaga

department: Animal Science

institute: Laval University

hyb_protocol: 825 ng of each labeled sample were incubated in a solution containing 2x blocking agent and 5x fragmentation buffer in a volume of 55 µl at 65°C for 15 minutes and were then put on ice. 55 µl of 2x GEx Hybridization Buffer HI-RPM was added for a final volume of 110 µl. The hybridization mix (100 µl) was added onto the array and hybridization was performed at 65°C for 17 h using an Agilent Hybridization chamber in a rotating oven. After the hybridization step, slides were washed with gene expression wash buffer 1 containing 0.005% triton X-102 for 3 minutes at room temperature and then transferred to gene expression wash buffer 2 containing 0.005% triton X-102 for 3 minutes at 42°C. Final washes with acetonitrile for 10 sec at room temperature and with drying and stabilisation solution for 30 sec at room temperature were performed before air-drying the slides.

scan_protocol: Scanned on an Tecan Power scanner (Tecan group ltd.)

data_processing: Images were quantified using ArrayPro 6.4 software (Media Cybernetics). Background subtracted, LOESS normalized, data obtained from log2 of processed Red signal/processed Green signal.

organism: Bos taurus

label_protocol: Samples were labeled using the ULS Fluorescent Labeling Kit for Agilent arrays (with Cy3 and Cy5) (Kreatech Diagnostics, Amsterdam, The Netherlands). The labeled product was then purified using the picopure RNA extraction kit (Applied Biosystems, Carlsbad, CA, USA) to remove uncoupled dyes.

growth_protocol: Oocytes were collected from slaughterhouse-derived ovaries and grouped according to the chromatin configuration as described by Lodde et al. 2007.

extract_protocol:
Total RNA extraction was performed using the PicoPure RNA isolation kit (Applied Biosystems, Carlsbad, CA, USA), with DNase treatment on the purification column according to the manufacturer instructions. RNA was eluted in 11 µl of elution buffer. Quantity and quality of each pool of RNA was verified on a 2100 Bioanalyzer (Agilent Technologies, Mississauga, On, Canada). Samples were stored at -80°C.
RNA_amplication: Anti-sense RNA was produced using the RiboAmp HS RNA amplification kit (Applied Biosystems, Carlsbad, CA, USA). Quantity of aRNA was determined using a Nanodrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Cumulus-oocyte complexes (COC’s) were collected byaspiration with a 16G needle mount on an aspiration pump. The COC’s were denuded by vortexing, washed and stained with Hoechst 33342. Chromatin organization was evaluated under a inverted fluorescence microscope and classified according to the degree of chromatin condensation within the nuclear enveloppe. Oocytes were then washed, collected in small volumes of PBS, snap-frozen in liquid nitrogen and stored at -80°C until RNA extraction.

value: oocyte

tag: chromatin condensation stage


title: Control 1

description: RNA samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.9


title: Lung tissue, D1 (18 µg) sample 1


title: Normal bone marrow CD25+ B-cells from healthy donor 125

hyb_protocol: Labeled RNA was hybridized to Human Gene 1.0 ST Array

scan_protocol: Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

data_processing:
Expression value for each probe set was calculated using Affymetrix Expression Console that uses RMA (Robust Multi-Array Average) algorithm.
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps

label_protocol: The integrity of extracted RNA was assessed using Agilent 2100 Bioanalyzer. Afterwards, RNA was amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix), and then hybridized to Human Gene 1.0 ST Array (Affymetrix)

extract_protocol: RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s instructions

tag: subject status

value: healthy donor

tag: donor id

value: donor 125

value: Bone marrow

tag: cell type

value: CD25+ B-cells


title: Normal bone marrow CD25+ B-cells from healthy donor 122

value: donor 122


title: CAD Patient 2

description: lncRNA  expression of human plasma

tag: gender

value: male


title: Lung tissue, Control sample 2


title: CAD Patient 3

description: lncRNA  expression of human plasma


title: FE1, Control sample 3


title: CcO IVi1 silenced 2

description: RNA samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.7


title: Normal bone marrow CD25+ B-cells from healthy donor 123

value: donor 123


title: CcO IVi1 silenced 3

description: RNA samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.8


title: Non-CAD 3

description: lncRNA  expression of human plasma


title: Lung tissue, Control sample 4


title: Normal bone marrow CD25+ B-cells from healthy donor 121

value: donor 121


title: 202 Area3 17 05 13


title: Non-CAD 1

description: lncRNA  expression of human plasma


title: Control 2

description: RNA samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.10


title: 202 Area2 17 05 13


title: Normal bone marrow CD25- B-cells from healthy donor 123

value: CD25- B-cells


title: 201 Area4 9 04 13